The command should be something like tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz Also, tksurfer is also obsolete (but should work). You should be using freeview (or tksurferfv, a freeview front end that takes the same command line args as tksurfer) Also, please remember to respond to the fs list
On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution
I got the mri_vol2surf output with .mgz:
my tksurfer command:
tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of mri_vol2surf was lh.inflated_MWI.mgz)
and the error i got:
*freadFloat: fread failed** No such file or directory*
To me, opening the surfer in tksurfer is only a way to get sure my vol2surf worked well. the main problem is i got this error for all mris_smooth, mris_inflate, mris_sphere ...
Do you think that means the output of mri_vol2surf is not correct, or otherwise i could proceed with that , even when tksurfer could not open it, for GLM in Qdec?
Thanks,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:01:15 PM *To:* Reza Rahmanzadeh *Subject:* Re: need for help what is your tksurfer command line? Also, the .w file is somewhat obsolete (it should still work); instead you can use .mgz file (and don't spec --paint)
On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Thanks Doug,
I used the one without --inflated also, again the tksurfer could not open it and i got the same error. Where is the problem with my cmd.?
In addition, i wanted to make the output of mri_vol2surf inflated using mris_inflate but i got the same error:
*freadFloat: fread failed No such file or directory*
*could you let me know what is the problem in registering my mwi volumes to surface that i getonly such errors.*
*Thanks,* *reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 5:37:17 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: need for help Don't use --inflated. The inflated surface is not a biological surface. The default is the white surface, which is the one you want (--projfrac 0.5 will project it to the middle between the white and pial)
On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Dear Freesurfer,
I have a batch of myelin water image (MWI) from patients and controls, and trying to have inflated cortex registered on standard surface for GLM (Qdec).
With the commandlines below i get my inflated surface of MWI map of my patients and controls.
1-using bbregister to put MWI into FS space and to calculate register.dat: bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg register.dat --o mwf_FS --t1
2-using mri_vol2surf to extract inflated surface of MWI: mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type paint--inflated (*or*--surf sphere)
However the tksurfer could not open the inflated surface and the error message is: *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface!*
I used the commandline below for #2: mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o mwf-lh.w --out_type paint and i got the error:
*ERROR: MRISread: file '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has many more faces than vertices!** Probably trying to use a scalar data file as a surface!*
As tksurfer could not open my surfaces with errors above, i think perhaps the vol2surf procedure is not done properly. Where is the problem? i need to get the inflated cortex and then putting ob sphere (using mris_sphere) and the registering to standard surface using mris_register for GLM in Qdec, right?
It is two weeks i am struggling with these commands, any helps highly appreciated. *
Best, Reza
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
External Email - Use Caution
(I assume now we are discussing in FS list, if no please let me how possible?)
Thanks Doug, now i could see the inflate surface, this means that my mri_vol2surf works well. As i would do GLM analysis over inflated cortex of patients and controls in Qdec,
1- should i input my surfaces to Qdec as inflated surface or just inputting the output_of_vol2surf.mgz to Qdec?
if inflated one is the input, then how could i get them? mris_inflate gives error.
2- should i input all patients and controls surfaces in standard surface before entering to Qdec?
3- I would like to resample whole cortex (whole cortical thickness, in other words: the average of all projfrac between 0 and 1), is it possible? or i am limited to resample one given depth of cortex into inflated surface only?
thanks a lot,
Reza
________________________________ From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Tuesday, July 16, 2019 6:22:56 PM To: Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu Subject: Re: need for help
The command should be something like tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz Also, tksurfer is also obsolete (but should work). You should be using freeview (or tksurferfv, a freeview front end that takes the same command line args as tksurfer) Also, please remember to respond to the fs list
On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionI got the mri_vol2surf output with .mgz:
my tksurfer command:
tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of mri_vol2surf was lh.inflated_MWI.mgz)
and the error i got:
*freadFloat: fread failed** No such file or directory*
To me, opening the surfer in tksurfer is only a way to get sure my vol2surf worked well. the main problem is i got this error for all mris_smooth, mris_inflate, mris_sphere ...
Do you think that means the output of mri_vol2surf is not correct, or otherwise i could proceed with that , even when tksurfer could not open it, for GLM in Qdec?
Thanks,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:01:15 PM *To:* Reza Rahmanzadeh *Subject:* Re: need for help what is your tksurfer command line? Also, the .w file is somewhat obsolete (it should still work); instead you can use .mgz file (and don't spec --paint)
On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks Doug,
I used the one without --inflated also, again the tksurfer could not open it and i got the same error. Where is the problem with my cmd.?
In addition, i wanted to make the output of mri_vol2surf inflated using mris_inflate but i got the same error:
*freadFloat: fread failed No such file or directory*
*could you let me know what is the problem in registering my mwi volumes to surface that i getonly such errors.*
*Thanks,* *reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 5:37:17 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: need for help Don't use --inflated. The inflated surface is not a biological surface. The default is the white surface, which is the one you want (--projfrac 0.5 will project it to the middle between the white and pial)
On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionDear Freesurfer,
I have a batch of myelin water image (MWI) from patients and controls, and trying to have inflated cortex registered on standard surface for GLM (Qdec).
With the commandlines below i get my inflated surface of MWI map of my patients and controls.
1-using bbregister to put MWI into FS space and to calculate register.dat: bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg register.dat --o mwf_FS --t1
2-using mri_vol2surf to extract inflated surface of MWI: mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type paint--inflated (*or*--surf sphere)
However the tksurfer could not open the inflated surface and the error message is: *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface!*
I used the commandline below for #2: mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o mwf-lh.w --out_type paint and i got the error:
*ERROR: MRISread: file '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has many more faces than vertices!** Probably trying to use a scalar data file as a surface!*
As tksurfer could not open my surfaces with errors above, i think perhaps the vol2surf procedure is not done properly. Where is the problem? i need to get the inflated cortex and then putting ob sphere (using mris_sphere) and the registering to standard surface using mris_register for GLM in Qdec, right?
It is two weeks i am struggling with these commands, any helps highly appreciated. *
Best, Reza
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution
(I assume now we are discussing in FS list, if no please let me how possible?)
Thanks Doug, now i could see the inflate surface, this means that my mri_vol2surf works well. As i would do GLM analysis over inflated cortex of patients and controls in Qdec,
1- should i input my surfaces to Qdec as inflated surface or just inputting the output_of_vol2surf.mgz to Qdec?
if inflated one is the input, then how could i get them? mris_inflate gives error.
QDEC is no longer being supported. Use the command line stream (mri_surf2surf, mri_glmfit, mri_glmfit-sim). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
2- should i input all patients and controls surfaces in standard surface before entering to Qdec?
3- I would like to resample whole cortex (whole cortical thickness, in other words: the average of all projfrac between 0 and 1), is it possible? or i am limited to resample one given depth of cortex into inflated surface only?
Run mri_vol2surf with --help and look for --projfrac-avg
thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:22:56 PM *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu *Subject:* Re: need for help The command should be something like tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz Also, tksurfer is also obsolete (but should work). You should be using freeview (or tksurferfv, a freeview front end that takes the same command line args as tksurfer) Also, please remember to respond to the fs list
On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution
I got the mri_vol2surf output with .mgz:
my tksurfer command:
tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of mri_vol2surf was lh.inflated_MWI.mgz)
and the error i got:
*freadFloat: fread failed** No such file or directory*
To me, opening the surfer in tksurfer is only a way to get sure my vol2surf worked well. the main problem is i got this error for all mris_smooth, mris_inflate, mris_sphere ...
Do you think that means the output of mri_vol2surf is not correct, or otherwise i could proceed with that , even when tksurfer could not open it, for GLM in Qdec?
Thanks,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:01:15 PM *To:* Reza Rahmanzadeh *Subject:* Re: need for help what is your tksurfer command line? Also, the .w file is somewhat obsolete (it should still work); instead you can use .mgz file (and don't spec --paint)
On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Thanks Doug,
I used the one without --inflated also, again the tksurfer could not open it and i got the same error. Where is the problem with my cmd.?
In addition, i wanted to make the output of mri_vol2surf inflated using mris_inflate but i got the same error:
*freadFloat: fread failed No such file or directory*
*could you let me know what is the problem in registering my mwi volumes to surface that i getonly such errors.*
*Thanks,* *reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 5:37:17 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: need for help Don't use --inflated. The inflated surface is not a biological surface. The default is the white surface, which is the one you want (--projfrac 0.5 will project it to the middle between the white and
pial)
On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Dear Freesurfer,
I have a batch of myelin water image (MWI) from patients and controls, and trying to have inflated cortex registered on standard surface for GLM (Qdec).
With the commandlines below i get my inflated surface of MWI map of my patients and controls.
1-using bbregister to put MWI into FS space and to calculate register.dat: bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg register.dat --o mwf_FS --t1
2-using mri_vol2surf to extract inflated surface of MWI: mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type paint--inflated (*or*--surf sphere)
However the tksurfer could not open the inflated surface and the error message is: *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface!*
I used the commandline below for #2: mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o mwf-lh.w --out_type paint and i got the error:
*ERROR: MRISread: file '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has many more faces than vertices!** Probably trying to use a scalar data file as a surface!*
As tksurfer could not open my surfaces with errors above, i think perhaps the vol2surf procedure is not done properly. Where is the problem? i need to get the inflated cortex and then putting ob sphere (using mris_sphere) and the registering to standard surface using mris_register for GLM in Qdec, right?
It is two weeks i am struggling with these commands, any helps highly appreciated. *
Best, Reza
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
External Email - Use Caution
Thanks a lot Doug,
I started to proceed with FS group analysis wiki you sent to me. Accordingly, i have to resample all my data (output of recon-all for a given subject for example) into fsaverage using mris_preproc. My commandline for a subject was:
mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out lh.FSP10.white.mgh --meas white
and i got the error:
Reading source surface reg /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory mri_surf2surf: could not read surface /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory
As there was no lh.fsaverage/.sphere.reg folder, i found one file in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder with the name lh.fsaverage and i copied/pasted the mentiomed file into this folder and i changed the file name to: ./sphere.reg. I got the error:
Reading curvature file /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere
What is the problem with my mris_preproc command-line?
Reza
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Tuesday, July 16, 2019 7:01:30 PM To: Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] need for help
On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution(I assume now we are discussing in FS list, if no please let me how possible?)
Thanks Doug, now i could see the inflate surface, this means that my mri_vol2surf works well. As i would do GLM analysis over inflated cortex of patients and controls in Qdec,
1- should i input my surfaces to Qdec as inflated surface or just inputting the output_of_vol2surf.mgz to Qdec?
if inflated one is the input, then how could i get them? mris_inflate gives error.
QDEC is no longer being supported. Use the command line stream (mri_surf2surf, mri_glmfit, mri_glmfit-sim). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
2- should i input all patients and controls surfaces in standard surface before entering to Qdec?
3- I would like to resample whole cortex (whole cortical thickness, in other words: the average of all projfrac between 0 and 1), is it possible? or i am limited to resample one given depth of cortex into inflated surface only?
Run mri_vol2surf with --help and look for --projfrac-avg
thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:22:56 PM *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu *Subject:* Re: need for help The command should be something like tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz Also, tksurfer is also obsolete (but should work). You should be using freeview (or tksurferfv, a freeview front end that takes the same command line args as tksurfer) Also, please remember to respond to the fs list
On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionI got the mri_vol2surf output with .mgz:
my tksurfer command:
tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of mri_vol2surf was lh.inflated_MWI.mgz)
and the error i got:
*freadFloat: fread failed** No such file or directory*
To me, opening the surfer in tksurfer is only a way to get sure my vol2surf worked well. the main problem is i got this error for all mris_smooth, mris_inflate, mris_sphere ...
Do you think that means the output of mri_vol2surf is not correct, or otherwise i could proceed with that , even when tksurfer could not open it, for GLM in Qdec?
Thanks,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:01:15 PM *To:* Reza Rahmanzadeh *Subject:* Re: need for help what is your tksurfer command line? Also, the .w file is somewhat obsolete (it should still work); instead you can use .mgz file (and don't spec --paint)
On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks Doug,
I used the one without --inflated also, again the tksurfer could not open it and i got the same error. Where is the problem with my cmd.?
In addition, i wanted to make the output of mri_vol2surf inflated using mris_inflate but i got the same error:
*freadFloat: fread failed No such file or directory*
*could you let me know what is the problem in registering my mwi volumes to surface that i getonly such errors.*
*Thanks,* *reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 5:37:17 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: need for help Don't use --inflated. The inflated surface is not a biological surface. The default is the white surface, which is the one you want (--projfrac 0.5 will project it to the middle between the white and
pial)
On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionDear Freesurfer,
I have a batch of myelin water image (MWI) from patients and controls, and trying to have inflated cortex registered on standard surface for GLM (Qdec).
With the commandlines below i get my inflated surface of MWI map of my patients and controls.
1-using bbregister to put MWI into FS space and to calculate register.dat: bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg register.dat --o mwf_FS --t1
2-using mri_vol2surf to extract inflated surface of MWI: mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type paint--inflated (*or*--surf sphere)
However the tksurfer could not open the inflated surface and the error message is: *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface!*
I used the commandline below for #2: mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o mwf-lh.w --out_type paint and i got the error:
*ERROR: MRISread: file '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has many more faces than vertices!** Probably trying to use a scalar data file as a surface!*
As tksurfer could not open my surfaces with errors above, i think perhaps the vol2surf procedure is not done properly. Where is the problem? i need to get the inflated cortex and then putting ob sphere (using mris_sphere) and the registering to standard surface using mris_register for GLM in Qdec, right?
It is two weeks i am struggling with these commands, any helps highly appreciated. *
Best, Reza
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
don't include the back slash (ie, fsaverage not fsaverage/ same for FSP010)
On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Thanks a lot Doug,
I started to proceed with FS group analysis wiki you sent to me. Accordingly, i have to resample all my data (output of recon-all for a given subject for example) into fsaverage using mris_preproc. My commandline for a subject was:
mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out lh.FSP10.white.mgh --meas white
and i got the error:
*Reading source surface reg /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory mri_surf2surf: could not read surface /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory*
As there was no**lh.fsaverage/.sphere.reg* *folder, i found one file in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder with the name lh.fsaverage and i copied/pasted the mentiomed file into this folder and i changed the file name to: ./sphere.reg. I got the error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere*
What is the problem with my mris_preproc command-line?
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 7:01:30 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution
(I assume now we are discussing in FS list, if no please let me how possible?)
Thanks Doug, now i could see the inflate surface, this means that my mri_vol2surf works well. As i would do GLM analysis over inflated cortex of patients and controls in Qdec,
1- should i input my surfaces to Qdec as inflated surface or just inputting the output_of_vol2surf.mgz to Qdec?
if inflated one is the input, then how could i get them? mris_inflate gives error.
QDEC is no longer being supported. Use the command line stream (mri_surf2surf, mri_glmfit, mri_glmfit-sim). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
2- should i input all patients and controls surfaces in standard surface before entering to Qdec?
3- I would like to resample whole cortex (whole cortical thickness, in other words: the average of all projfrac between 0 and 1), is it possible? or i am limited to resample one given depth of cortex into inflated surface only?
Run mri_vol2surf with --help and look for --projfrac-avg
thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:22:56 PM *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu *Subject:* Re: need for help The command should be something like tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz Also, tksurfer is also obsolete (but should work). You should be using freeview (or tksurferfv, a freeview front end that takes the same command line args as tksurfer) Also, please remember to respond to the fs list
On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution
I got the mri_vol2surf output with .mgz:
my tksurfer command:
tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of mri_vol2surf was lh.inflated_MWI.mgz)
and the error i got:
*freadFloat: fread failed** No such file or directory*
To me, opening the surfer in tksurfer is only a way to get sure my vol2surf worked well. the main problem is i got this error for all mris_smooth, mris_inflate, mris_sphere ...
Do you think that means the output of mri_vol2surf is not correct, or otherwise i could proceed with that , even when tksurfer could not open it, for GLM in Qdec?
Thanks,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:01:15 PM *To:* Reza Rahmanzadeh *Subject:* Re: need for help what is your tksurfer command line? Also, the .w file is somewhat obsolete (it should still work); instead you can use .mgz file (and don't spec --paint)
On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Thanks Doug,
I used the one without --inflated also, again the tksurfer could not open it and i got the same error. Where is the problem with my cmd.?
In addition, i wanted to make the output of mri_vol2surf inflated using mris_inflate but i got the same error:
*freadFloat: fread failed No such file or directory*
*could you let me know what is the problem in registering my mwi volumes to surface that i getonly such errors.*
*Thanks,* *reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 5:37:17 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: need for help Don't use --inflated. The inflated surface is not a biological surface. The default is the white surface, which is the one you want (--projfrac 0.5 will project it to the middle between the white and
pial)
On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Dear Freesurfer,
I have a batch of myelin water image (MWI) from patients and controls, and trying to have inflated cortex registered on standard surface for GLM (Qdec).
With the commandlines below i get my inflated surface of MWI map of my patients and controls.
1-using bbregister to put MWI into FS space and to calculate register.dat: bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg register.dat --o mwf_FS --t1
2-using mri_vol2surf to extract inflated surface of MWI: mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type paint--inflated (*or*--surf sphere)
However the tksurfer could not open the inflated surface and the error message is: *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface!*
I used the commandline below for #2: mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o mwf-lh.w --out_type paint and i got the error:
*ERROR: MRISread: file '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has many more faces than vertices!** Probably trying to use a scalar data file as a surface!*
As tksurfer could not open my surfaces with errors above, i think perhaps the vol2surf procedure is not done properly. Where is the problem? i need to get the inflated cortex and then putting ob sphere (using mris_sphere) and the registering to standard surface using mris_register for GLM in Qdec, right?
It is two weeks i am struggling with these commands, any helps highly appreciated. *
Best, Reza
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
I removed the back slash and the command line i executed is:
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got the error:
Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white ERROR: reading curvature file
I have added --srcfmt mgh as the last argument, but again i got the error: Reading source surface reg /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg Loading source data No such file or directory ERROR: could not read /usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3
What is wrong with my mris_prepoc command line?
Reza
________________________________ From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Tuesday, July 16, 2019 10:01:15 PM To: Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu Subject: Re: need for help
don't include the back slash (ie, fsaverage not fsaverage/ same for FSP010)
On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks a lot Doug,
I started to proceed with FS group analysis wiki you sent to me. Accordingly, i have to resample all my data (output of recon-all for a given subject for example) into fsaverage using mris_preproc. My commandline for a subject was:
mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out lh.FSP10.white.mgh --meas white
and i got the error:
*Reading source surface reg /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory mri_surf2surf: could not read surface /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory*
As there was no**lh.fsaverage/.sphere.reg* *folder, i found one file in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder with the name lh.fsaverage and i copied/pasted the mentiomed file into this folder and i changed the file name to: ./sphere.reg. I got the error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere*
What is the problem with my mris_preproc command-line?
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 7:01:30 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution(I assume now we are discussing in FS list, if no please let me how possible?)
Thanks Doug, now i could see the inflate surface, this means that my mri_vol2surf works well. As i would do GLM analysis over inflated cortex of patients and controls in Qdec,
1- should i input my surfaces to Qdec as inflated surface or just inputting the output_of_vol2surf.mgz to Qdec?
if inflated one is the input, then how could i get them? mris_inflate gives error.
QDEC is no longer being supported. Use the command line stream (mri_surf2surf, mri_glmfit, mri_glmfit-sim). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
2- should i input all patients and controls surfaces in standard surface before entering to Qdec?
3- I would like to resample whole cortex (whole cortical thickness, in other words: the average of all projfrac between 0 and 1), is it possible? or i am limited to resample one given depth of cortex into inflated surface only?
Run mri_vol2surf with --help and look for --projfrac-avg
thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:22:56 PM *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu *Subject:* Re: need for help The command should be something like tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz Also, tksurfer is also obsolete (but should work). You should be using freeview (or tksurferfv, a freeview front end that takes the same command line args as tksurfer) Also, please remember to respond to the fs list
On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionI got the mri_vol2surf output with .mgz:
my tksurfer command:
tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of mri_vol2surf was lh.inflated_MWI.mgz)
and the error i got:
*freadFloat: fread failed** No such file or directory*
To me, opening the surfer in tksurfer is only a way to get sure my vol2surf worked well. the main problem is i got this error for all mris_smooth, mris_inflate, mris_sphere ...
Do you think that means the output of mri_vol2surf is not correct, or otherwise i could proceed with that , even when tksurfer could not open it, for GLM in Qdec?
Thanks,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:01:15 PM *To:* Reza Rahmanzadeh *Subject:* Re: need for help what is your tksurfer command line? Also, the .w file is somewhat obsolete (it should still work); instead you can use .mgz file (and don't spec --paint)
On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks Doug,
I used the one without --inflated also, again the tksurfer could not open it and i got the same error. Where is the problem with my cmd.?
In addition, i wanted to make the output of mri_vol2surf inflated using mris_inflate but i got the same error:
*freadFloat: fread failed No such file or directory*
*could you let me know what is the problem in registering my mwi volumes to surface that i getonly such errors.*
*Thanks,* *reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 5:37:17 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: need for help Don't use --inflated. The inflated surface is not a biological surface. The default is the white surface, which is the one you want (--projfrac 0.5 will project it to the middle between the white and
pial)
On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionDear Freesurfer,
I have a batch of myelin water image (MWI) from patients and controls, and trying to have inflated cortex registered on standard surface for GLM (Qdec).
With the commandlines below i get my inflated surface of MWI map of my patients and controls.
1-using bbregister to put MWI into FS space and to calculate register.dat: bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg register.dat --o mwf_FS --t1
2-using mri_vol2surf to extract inflated surface of MWI: mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type paint--inflated (*or*--surf sphere)
However the tksurfer could not open the inflated surface and the error message is: *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface!*
I used the commandline below for #2: mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o mwf-lh.w --out_type paint and i got the error:
*ERROR: MRISread: file '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has many more faces than vertices!** Probably trying to use a scalar data file as a surface!*
As tksurfer could not open my surfaces with errors above, i think perhaps the vol2surf procedure is not done properly. Where is the problem? i need to get the inflated cortex and then putting ob sphere (using mris_sphere) and the registering to standard surface using mris_register for GLM in Qdec, right?
It is two weeks i am struggling with these commands, any helps highly appreciated. *
Best, Reza
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
I guess '-meas' expects a measure (like 'thickness' or 'area'), not a surface (like 'white').
Best,
Tim
On July 17, 2019 at 9:03 AM Reza Rahmanzadeh reza.rahmanzadeh@unibas.ch wrote:
External Email - Use CautionI removed the back slash and the command line i executed is:
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got the error:
Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white ERROR: reading curvature file
I have added --srcfmt mgh as the last argument, but again i got the error: Reading source surface reg /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg Loading source data No such file or directory ERROR: could not read /usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3
What is wrong with my mris_prepoc command line?
Reza
From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Tuesday, July 16, 2019 10:01:15 PM To: Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu Subject: Re: need for help
don't include the back slash (ie, fsaverage not fsaverage/ same for FSP010)
On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks a lot Doug,
I started to proceed with FS group analysis wiki you sent to me. Accordingly, i have to resample all my data (output of recon-all for a given subject for example) into fsaverage using mris_preproc. My commandline for a subject was:
mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out lh.FSP10.white.mgh --meas white
and i got the error:
*Reading source surface reg /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory mri_surf2surf: could not read surface /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory*
As there was no**lh.fsaverage/.sphere.reg* *folder, i found one file in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder with the name lh.fsaverage and i copied/pasted the mentiomed file into this folder and i changed the file name to: ./sphere.reg. I got the error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere*
What is the problem with my mris_preproc command-line?
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 7:01:30 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution(I assume now we are discussing in FS list, if no please let me how possible?)
Thanks Doug, now i could see the inflate surface, this means that my mri_vol2surf works well. As i would do GLM analysis over inflated cortex of patients and controls in Qdec,
1- should i input my surfaces to Qdec as inflated surface or just inputting the output_of_vol2surf.mgz to Qdec?
if inflated one is the input, then how could i get them? mris_inflate gives error.
QDEC is no longer being supported. Use the command line stream (mri_surf2surf, mri_glmfit, mri_glmfit-sim). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
2- should i input all patients and controls surfaces in standard surface before entering to Qdec?
3- I would like to resample whole cortex (whole cortical thickness, in other words: the average of all projfrac between 0 and 1), is it possible? or i am limited to resample one given depth of cortex into inflated surface only?
Run mri_vol2surf with --help and look for --projfrac-avg
thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:22:56 PM *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu *Subject:* Re: need for help The command should be something like tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz Also, tksurfer is also obsolete (but should work). You should be using freeview (or tksurferfv, a freeview front end that takes the same command line args as tksurfer) Also, please remember to respond to the fs list
On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionI got the mri_vol2surf output with .mgz:
my tksurfer command:
tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of mri_vol2surf was lh.inflated_MWI.mgz)
and the error i got:
*freadFloat: fread failed** No such file or directory*
To me, opening the surfer in tksurfer is only a way to get sure my vol2surf worked well. the main problem is i got this error for all mris_smooth, mris_inflate, mris_sphere ...
Do you think that means the output of mri_vol2surf is not correct, or otherwise i could proceed with that , even when tksurfer could not open it, for GLM in Qdec?
Thanks,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:01:15 PM *To:* Reza Rahmanzadeh *Subject:* Re: need for help what is your tksurfer command line? Also, the .w file is somewhat obsolete (it should still work); instead you can use .mgz file (and don't spec --paint)
On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks Doug,
I used the one without --inflated also, again the tksurfer could not open it and i got the same error. Where is the problem with my cmd.?
In addition, i wanted to make the output of mri_vol2surf inflated using mris_inflate but i got the same error:
*freadFloat: fread failed No such file or directory*
*could you let me know what is the problem in registering my mwi volumes to surface that i getonly such errors.*
*Thanks,* *reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 5:37:17 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: need for help Don't use --inflated. The inflated surface is not a biological surface. The default is the white surface, which is the one you want (--projfrac 0.5 will project it to the middle between the white and
pial)
On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionDear Freesurfer,
I have a batch of myelin water image (MWI) from patients and controls, and trying to have inflated cortex registered on standard surface for GLM (Qdec).
With the commandlines below i get my inflated surface of MWI map of my patients and controls.
1-using bbregister to put MWI into FS space and to calculate register.dat: bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg register.dat --o mwf_FS --t1
2-using mri_vol2surf to extract inflated surface of MWI: mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type paint--inflated (*or*--surf sphere)
However the tksurfer could not open the inflated surface and the error message is: *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface!*
I used the commandline below for #2: mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o mwf-lh.w --out_type paint and i got the error:
*ERROR: MRISread: file '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has many more faces than vertices!** Probably trying to use a scalar data file as a surface!*
As tksurfer could not open my surfaces with errors above, i think perhaps the vol2surf procedure is not done properly. Where is the problem? i need to get the inflated cortex and then putting ob sphere (using mris_sphere) and the registering to standard surface using mris_register for GLM in Qdec, right?
It is two weeks i am struggling with these commands, any helps highly appreciated. *
Best, Reza
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
External Email - Use Caution
Thanks Tim,
Then if i would resample my data to fsaverage and surfaces are of main importance to my work, what should i use for -meas ?
Reza
On 17 Jul 2019, at 09:39, Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use CautionI guess '-meas' expects a measure (like 'thickness' or 'area'), not a surface (like 'white').
Best,
Tim
On July 17, 2019 at 9:03 AM Reza Rahmanzadeh reza.rahmanzadeh@unibas.ch wrote:
External Email - Use CautionI removed the back slash and the command line i executed is:
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got the error:
Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white ERROR: reading curvature file
I have added --srcfmt mgh as the last argument, but again i got the error: Reading source surface reg /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg Loading source data No such file or directory ERROR: could not read /usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3
What is wrong with my mris_prepoc command line?
Reza
From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Tuesday, July 16, 2019 10:01:15 PM To: Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu Subject: Re: need for help
don't include the back slash (ie, fsaverage not fsaverage/ same for FSP010)
On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks a lot Doug,
I started to proceed with FS group analysis wiki you sent to me. Accordingly, i have to resample all my data (output of recon-all for a given subject for example) into fsaverage using mris_preproc. My commandline for a subject was:
mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out lh.FSP10.white.mgh --meas white
and i got the error:
*Reading source surface reg /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory mri_surf2surf: could not read surface /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory*
As there was no**lh.fsaverage/.sphere.reg* *folder, i found one file in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder with the name lh.fsaverage and i copied/pasted the mentiomed file into this folder and i changed the file name to: ./sphere.reg. I got the error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere*
What is the problem with my mris_preproc command-line?
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 7:01:30 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution(I assume now we are discussing in FS list, if no please let me how possible?)
Thanks Doug, now i could see the inflate surface, this means that my mri_vol2surf works well. As i would do GLM analysis over inflated cortex of patients and controls in Qdec,
1- should i input my surfaces to Qdec as inflated surface or just inputting the output_of_vol2surf.mgz to Qdec?
if inflated one is the input, then how could i get them? mris_inflate gives error.
QDEC is no longer being supported. Use the command line stream (mri_surf2surf, mri_glmfit, mri_glmfit-sim). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
2- should i input all patients and controls surfaces in standard surface before entering to Qdec?
3- I would like to resample whole cortex (whole cortical thickness, in other words: the average of all projfrac between 0 and 1), is it possible? or i am limited to resample one given depth of cortex into inflated surface only?
Run mri_vol2surf with --help and look for --projfrac-avg
thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:22:56 PM *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu *Subject:* Re: need for help The command should be something like tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz Also, tksurfer is also obsolete (but should work). You should be using freeview (or tksurferfv, a freeview front end that takes the same command line args as tksurfer) Also, please remember to respond to the fs list
On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionI got the mri_vol2surf output with .mgz:
my tksurfer command:
tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of mri_vol2surf was lh.inflated_MWI.mgz)
and the error i got:
*freadFloat: fread failed** No such file or directory*
To me, opening the surfer in tksurfer is only a way to get sure my vol2surf worked well. the main problem is i got this error for all mris_smooth, mris_inflate, mris_sphere ...
Do you think that means the output of mri_vol2surf is not correct, or otherwise i could proceed with that , even when tksurfer could not open it, for GLM in Qdec?
Thanks,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:01:15 PM *To:* Reza Rahmanzadeh *Subject:* Re: need for help what is your tksurfer command line? Also, the .w file is somewhat obsolete (it should still work); instead you can use .mgz file (and don't spec --paint)
On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks Doug,
I used the one without --inflated also, again the tksurfer could not open it and i got the same error. Where is the problem with my cmd.?
In addition, i wanted to make the output of mri_vol2surf inflated using mris_inflate but i got the same error:
*freadFloat: fread failed No such file or directory*
*could you let me know what is the problem in registering my mwi volumes to surface that i getonly such errors.*
*Thanks,* *reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 5:37:17 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: need for help Don't use --inflated. The inflated surface is not a biological surface. The default is the white surface, which is the one you want (--projfrac 0.5 will project it to the middle between the white and
pial)
> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > Dear Freesurfer, > > I have a batch of myelin water image (MWI) from patients and > controls, and trying to have inflated cortex registered on standard > surface for GLM (Qdec). > > With the commandlines below i get my inflated surface of MWI map of > my patients and controls. > > 1-using bbregister to put MWI into FS space and to calculate > register.dat: > bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg register.dat > --o mwf_FS --t1 > > 2-using mri_vol2surf to extract inflated surface of MWI: > mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 > --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type > paint--inflated (*or*--surf sphere) > > However the tksurfer could not open the inflated surface and the > error message is: > *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! > Probably trying to use a scalar data file as a surface!* > > I used the commandline below for #2: > mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o > mwf-lh.w --out_type paint > and i got the error: > > *ERROR: MRISread: file > '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has many > more faces than vertices!** > Probably trying to use a scalar data file as a surface!* > * > * > As tksurfer could not open my surfaces with errors above, i think > perhaps the vol2surf procedure is not done properly. Where is the > problem? i need to get the inflated cortex and then putting ob > sphere (using mris_sphere) and the registering to standard surface > using mris_register for GLM in Qdec, right? > > > It is two weeks i am struggling with these commands, any helps > highly appreciated. * > * > * > * > * > * > Best, > Reza >
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Dear Doug,
I took the back slash away and ran
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got error:
Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white ERROR: reading curvature file
Then i changed it to --meas : mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgz --meas area
Then, as i need to register my the inflated cortex of myelin water image (MWI) to the surface_registered_on_fsaverage (could it be the output of command-line above?), should i use this output "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling myelin water image to lh.white of my subject FSP10 before registration to fsaverage) for mri_surf2surf (to resample the latter to the former, to have MWI to surface_fsaverage)
Looking forward to answers
Thanks
Reza
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza Rahmanzadeh reza.rahmanzadeh@unibas.ch Sent: Wednesday, July 17, 2019 9:56:00 AM To: Freesurfer support list Cc: DGREVE@mgh.harvard.edu Subject: Re: [Freesurfer] need for help
External Email - Use Caution
Thanks Tim,
Then if i would resample my data to fsaverage and surfaces are of main importance to my work, what should i use for -meas ?
Reza
On 17 Jul 2019, at 09:39, Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use CautionI guess '-meas' expects a measure (like 'thickness' or 'area'), not a surface (like 'white').
Best,
Tim
On July 17, 2019 at 9:03 AM Reza Rahmanzadeh reza.rahmanzadeh@unibas.ch wrote:
External Email - Use CautionI removed the back slash and the command line i executed is:
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got the error:
Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white ERROR: reading curvature file
I have added --srcfmt mgh as the last argument, but again i got the error: Reading source surface reg /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg Loading source data No such file or directory ERROR: could not read /usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3
What is wrong with my mris_prepoc command line?
Reza
From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Tuesday, July 16, 2019 10:01:15 PM To: Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu Subject: Re: need for help
don't include the back slash (ie, fsaverage not fsaverage/ same for FSP010)
On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks a lot Doug,
I started to proceed with FS group analysis wiki you sent to me. Accordingly, i have to resample all my data (output of recon-all for a given subject for example) into fsaverage using mris_preproc. My commandline for a subject was:
mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out lh.FSP10.white.mgh --meas white
and i got the error:
*Reading source surface reg /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory mri_surf2surf: could not read surface /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory*
As there was no**lh.fsaverage/.sphere.reg* *folder, i found one file in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder with the name lh.fsaverage and i copied/pasted the mentiomed file into this folder and i changed the file name to: ./sphere.reg. I got the error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere*
What is the problem with my mris_preproc command-line?
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 7:01:30 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution(I assume now we are discussing in FS list, if no please let me how possible?)
Thanks Doug, now i could see the inflate surface, this means that my mri_vol2surf works well. As i would do GLM analysis over inflated cortex of patients and controls in Qdec,
1- should i input my surfaces to Qdec as inflated surface or just inputting the output_of_vol2surf.mgz to Qdec?
if inflated one is the input, then how could i get them? mris_inflate gives error.
QDEC is no longer being supported. Use the command line stream (mri_surf2surf, mri_glmfit, mri_glmfit-sim). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
2- should i input all patients and controls surfaces in standard surface before entering to Qdec?
3- I would like to resample whole cortex (whole cortical thickness, in other words: the average of all projfrac between 0 and 1), is it possible? or i am limited to resample one given depth of cortex into inflated surface only?
Run mri_vol2surf with --help and look for --projfrac-avg
thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:22:56 PM *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu *Subject:* Re: need for help The command should be something like tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz Also, tksurfer is also obsolete (but should work). You should be using freeview (or tksurferfv, a freeview front end that takes the same command line args as tksurfer) Also, please remember to respond to the fs list
On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionI got the mri_vol2surf output with .mgz:
my tksurfer command:
tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of mri_vol2surf was lh.inflated_MWI.mgz)
and the error i got:
*freadFloat: fread failed** No such file or directory*
To me, opening the surfer in tksurfer is only a way to get sure my vol2surf worked well. the main problem is i got this error for all mris_smooth, mris_inflate, mris_sphere ...
Do you think that means the output of mri_vol2surf is not correct, or otherwise i could proceed with that , even when tksurfer could not open it, for GLM in Qdec?
Thanks,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:01:15 PM *To:* Reza Rahmanzadeh *Subject:* Re: need for help what is your tksurfer command line? Also, the .w file is somewhat obsolete (it should still work); instead you can use .mgz file (and don't spec --paint)
On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks Doug,
I used the one without --inflated also, again the tksurfer could not open it and i got the same error. Where is the problem with my cmd.?
In addition, i wanted to make the output of mri_vol2surf inflated using mris_inflate but i got the same error:
*freadFloat: fread failed No such file or directory*
*could you let me know what is the problem in registering my mwi volumes to surface that i getonly such errors.*
*Thanks,* *reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 5:37:17 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: need for help Don't use --inflated. The inflated surface is not a biological surface. The default is the white surface, which is the one you want (--projfrac 0.5 will project it to the middle between the white and
pial)
> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > Dear Freesurfer, > > I have a batch of myelin water image (MWI) from patients and > controls, and trying to have inflated cortex registered on standard > surface for GLM (Qdec). > > With the commandlines below i get my inflated surface of MWI map of > my patients and controls. > > 1-using bbregister to put MWI into FS space and to calculate > register.dat: > bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg register.dat > --o mwf_FS --t1 > > 2-using mri_vol2surf to extract inflated surface of MWI: > mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 > --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type > paint--inflated (*or*--surf sphere) > > However the tksurfer could not open the inflated surface and the > error message is: > *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! > Probably trying to use a scalar data file as a surface!* > > I used the commandline below for #2: > mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o > mwf-lh.w --out_type paint > and i got the error: > > *ERROR: MRISread: file > '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has many > more faces than vertices!** > Probably trying to use a scalar data file as a surface!* > * > * > As tksurfer could not open my surfaces with errors above, i think > perhaps the vol2surf procedure is not done properly. Where is the > problem? i need to get the inflated cortex and then putting ob > sphere (using mris_sphere) and the registering to standard surface > using mris_register for GLM in Qdec, right? > > > It is two weeks i am struggling with these commands, any helps > highly appreciated. * > * > * > * > * > * > Best, > Reza >
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It is not clear to me what you are trying to do. Do you want to do a morphometry study (ie, comparing thickness, area, and/or volume across subjects)? Or do you want to compare MWI (sampled on the surface) across subjects?
On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Dear Doug,
I took the back slash away and ran
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got error:
Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white ERROR: reading curvature file
Then i changed it to --meas : mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgz --meas area
Then, as i need to register my the inflated cortex of myelin water image (MWI) to the surface_registered_on_fsaverage (could it be the output of command-line above?), should i use this output "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling myelin water image to lh.white of my subject FSP10 before registration to fsaverage) for mri_surf2surf (to resample the latter to the former, to have MWI to surface_fsaverage)
Looking forward to answers
Thanks
Reza
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza Rahmanzadeh reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch Sent: Wednesday, July 17, 2019 9:56:00 AM To: Freesurfer support list Cc: DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Subject: Re: [Freesurfer] need for help
External Email - Use Caution
Thanks Tim,
Then if i would resample my data to fsaverage and surfaces are of main importance to my work, what should i use for -meas ?
Reza
On 17 Jul 2019, at 09:39, Tim Schäfer ts+ml@rcmd.orgmailto:ts+ml@rcmd.org wrote:
External Email - Use CautionI guess '-meas' expects a measure (like 'thickness' or 'area'), not a surface (like 'white').
Best,
Tim
On July 17, 2019 at 9:03 AM Reza Rahmanzadeh reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch wrote:
External Email - Use CautionI removed the back slash and the command line i executed is:
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got the error:
Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white ERROR: reading curvature file
I have added --srcfmt mgh as the last argument, but again i got the error: Reading source surface reg /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg Loading source data No such file or directory ERROR: could not read /usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3
What is wrong with my mris_prepoc command line?
Reza
From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Tuesday, July 16, 2019 10:01:15 PM To: Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Subject: Re: need for help
don't include the back slash (ie, fsaverage not fsaverage/ same for FSP010)
On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks a lot Doug,
I started to proceed with FS group analysis wiki you sent to me. Accordingly, i have to resample all my data (output of recon-all for a given subject for example) into fsaverage using mris_preproc. My commandline for a subject was:
mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out lh.FSP10.white.mgh --meas white
and i got the error:
*Reading source surface reg /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory mri_surf2surf: could not read surface /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory*
As there was no**lh.fsaverage/.sphere.reg* *folder, i found one file in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder with the name lh.fsaverage and i copied/pasted the mentiomed file into this folder and i changed the file name to: ./sphere.reg. I got the error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere*
What is the problem with my mris_preproc command-line?
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 7:01:30 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution(I assume now we are discussing in FS list, if no please let me how possible?)
Thanks Doug, now i could see the inflate surface, this means that my mri_vol2surf works well. As i would do GLM analysis over inflated cortex of patients and controls in Qdec,
1- should i input my surfaces to Qdec as inflated surface or just inputting the output_of_vol2surf.mgz to Qdec?
if inflated one is the input, then how could i get them? mris_inflate gives error.
QDEC is no longer being supported. Use the command line stream (mri_surf2surf, mri_glmfit, mri_glmfit-sim). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
2- should i input all patients and controls surfaces in standard surface before entering to Qdec?
3- I would like to resample whole cortex (whole cortical thickness, in other words: the average of all projfrac between 0 and 1), is it possible? or i am limited to resample one given depth of cortex into inflated surface only?
Run mri_vol2surf with --help and look for --projfrac-avg
thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:22:56 PM *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: need for help The command should be something like tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz Also, tksurfer is also obsolete (but should work). You should be using freeview (or tksurferfv, a freeview front end that takes the same command line args as tksurfer) Also, please remember to respond to the fs list
On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionI got the mri_vol2surf output with .mgz:
my tksurfer command:
tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of mri_vol2surf was lh.inflated_MWI.mgz)
and the error i got:
*freadFloat: fread failed** No such file or directory*
To me, opening the surfer in tksurfer is only a way to get sure my vol2surf worked well. the main problem is i got this error for all mris_smooth, mris_inflate, mris_sphere ...
Do you think that means the output of mri_vol2surf is not correct, or otherwise i could proceed with that , even when tksurfer could not open it, for GLM in Qdec?
Thanks,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:01:15 PM *To:* Reza Rahmanzadeh *Subject:* Re: need for help what is your tksurfer command line? Also, the .w file is somewhat obsolete (it should still work); instead you can use .mgz file (and don't spec --paint)
On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks Doug,
I used the one without --inflated also, again the tksurfer could not open it and i got the same error. Where is the problem with my cmd.?
In addition, i wanted to make the output of mri_vol2surf inflated using mris_inflate but i got the same error:
*freadFloat: fread failed No such file or directory*
*could you let me know what is the problem in registering my mwi volumes to surface that i getonly such errors.*
*Thanks,* *reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 5:37:17 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu *Cc:* greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu *Subject:* Re: need for help Don't use --inflated. The inflated surface is not a biological surface. The default is the white surface, which is the one you want (--projfrac 0.5 will project it to the middle between the white and
pial)
> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > Dear Freesurfer, > > I have a batch of myelin water image (MWI) from patients and > controls, and trying to have inflated cortex registered on standard > surface for GLM (Qdec). > > With the commandlines below i get my inflated surface of MWI map of > my patients and controls. > > 1-using bbregister to put MWI into FS space and to calculate > register.dat: > bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg register.dat > --o mwf_FS --t1 > > 2-using mri_vol2surf to extract inflated surface of MWI: > mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 > --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type > paint--inflated (*or*--surf sphere) > > However the tksurfer could not open the inflated surface and the > error message is: > *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! > Probably trying to use a scalar data file as a surface!* > > I used the commandline below for #2: > mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o > mwf-lh.w --out_type paint > and i got the error: > > *ERROR: MRISread: file > '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has many > more faces than vertices!** > Probably trying to use a scalar data file as a surface!* > * > * > As tksurfer could not open my surfaces with errors above, i think > perhaps the vol2surf procedure is not done properly. Where is the > problem? i need to get the inflated cortex and then putting ob > sphere (using mris_sphere) and the registering to standard surface > using mris_register for GLM in Qdec, right? > > > It is two weeks i am struggling with these commands, any helps > highly appreciated. * > * > * > * > * > * > Best, > Reza >
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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I am trying to compare MWI(sampled on the surface) between couple patients and controls using group analysis, therefore i need to have all inflated surface_on_same space (according to the wiki of group analysis you sent me, i should use mris_preproc to put my data on fsaverage).
Could you now tell me whether my mris_prepoc is right? and one other question i have asked in last email?
Thanks a lot,
Reza
________________________________ From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Wednesday, July 17, 2019 4:14:41 PM To: Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] need for help
It is not clear to me what you are trying to do. Do you want to do a morphometry study (ie, comparing thickness, area, and/or volume across subjects)? Or do you want to compare MWI (sampled on the surface) across subjects?
On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Dear Doug,
I took the back slash away and ran
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got error:
Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white ERROR: reading curvature file
Then i changed it to --meas : mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgz --meas area
Then, as i need to register my the inflated cortex of myelin water image (MWI) to the surface_registered_on_fsaverage (could it be the output of command-line above?), should i use this output "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling myelin water image to lh.white of my subject FSP10 before registration to fsaverage) for mri_surf2surf (to resample the latter to the former, to have MWI to surface_fsaverage)
Looking forward to answers
Thanks
Reza
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza Rahmanzadeh reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch Sent: Wednesday, July 17, 2019 9:56:00 AM To: Freesurfer support list Cc: DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Subject: Re: [Freesurfer] need for help
External Email - Use Caution
Thanks Tim,
Then if i would resample my data to fsaverage and surfaces are of main importance to my work, what should i use for -meas ?
Reza
On 17 Jul 2019, at 09:39, Tim Schäfer ts+ml@rcmd.orgmailto:ts+ml@rcmd.org wrote:
External Email - Use CautionI guess '-meas' expects a measure (like 'thickness' or 'area'), not a surface (like 'white').
Best,
Tim
On July 17, 2019 at 9:03 AM Reza Rahmanzadeh reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch wrote:
External Email - Use CautionI removed the back slash and the command line i executed is:
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got the error:
Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white ERROR: reading curvature file
I have added --srcfmt mgh as the last argument, but again i got the error: Reading source surface reg /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg Loading source data No such file or directory ERROR: could not read /usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3
What is wrong with my mris_prepoc command line?
Reza
From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Tuesday, July 16, 2019 10:01:15 PM To: Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Subject: Re: need for help
don't include the back slash (ie, fsaverage not fsaverage/ same for FSP010)
On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks a lot Doug,
I started to proceed with FS group analysis wiki you sent to me. Accordingly, i have to resample all my data (output of recon-all for a given subject for example) into fsaverage using mris_preproc. My commandline for a subject was:
mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out lh.FSP10.white.mgh --meas white
and i got the error:
*Reading source surface reg /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory mri_surf2surf: could not read surface /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory*
As there was no**lh.fsaverage/.sphere.reg* *folder, i found one file in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder with the name lh.fsaverage and i copied/pasted the mentiomed file into this folder and i changed the file name to: ./sphere.reg. I got the error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere*
What is the problem with my mris_preproc command-line?
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 7:01:30 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution(I assume now we are discussing in FS list, if no please let me how possible?)
Thanks Doug, now i could see the inflate surface, this means that my mri_vol2surf works well. As i would do GLM analysis over inflated cortex of patients and controls in Qdec,
1- should i input my surfaces to Qdec as inflated surface or just inputting the output_of_vol2surf.mgz to Qdec?
if inflated one is the input, then how could i get them? mris_inflate gives error.
QDEC is no longer being supported. Use the command line stream (mri_surf2surf, mri_glmfit, mri_glmfit-sim). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
2- should i input all patients and controls surfaces in standard surface before entering to Qdec?
3- I would like to resample whole cortex (whole cortical thickness, in other words: the average of all projfrac between 0 and 1), is it possible? or i am limited to resample one given depth of cortex into inflated surface only?
Run mri_vol2surf with --help and look for --projfrac-avg
thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:22:56 PM *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: need for help The command should be something like tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz Also, tksurfer is also obsolete (but should work). You should be using freeview (or tksurferfv, a freeview front end that takes the same command line args as tksurfer) Also, please remember to respond to the fs list
On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionI got the mri_vol2surf output with .mgz:
my tksurfer command:
tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of mri_vol2surf was lh.inflated_MWI.mgz)
and the error i got:
*freadFloat: fread failed** No such file or directory*
To me, opening the surfer in tksurfer is only a way to get sure my vol2surf worked well. the main problem is i got this error for all mris_smooth, mris_inflate, mris_sphere ...
Do you think that means the output of mri_vol2surf is not correct, or otherwise i could proceed with that , even when tksurfer could not open it, for GLM in Qdec?
Thanks,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:01:15 PM *To:* Reza Rahmanzadeh *Subject:* Re: need for help what is your tksurfer command line? Also, the .w file is somewhat obsolete (it should still work); instead you can use .mgz file (and don't spec --paint)
On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks Doug,
I used the one without --inflated also, again the tksurfer could not open it and i got the same error. Where is the problem with my cmd.?
In addition, i wanted to make the output of mri_vol2surf inflated using mris_inflate but i got the same error:
*freadFloat: fread failed No such file or directory*
*could you let me know what is the problem in registering my mwi volumes to surface that i getonly such errors.*
*Thanks,* *reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 5:37:17 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu *Cc:* greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu *Subject:* Re: need for help Don't use --inflated. The inflated surface is not a biological surface. The default is the white surface, which is the one you want (--projfrac 0.5 will project it to the middle between the white and
pial)
> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > Dear Freesurfer, > > I have a batch of myelin water image (MWI) from patients and > controls, and trying to have inflated cortex registered on standard > surface for GLM (Qdec). > > With the commandlines below i get my inflated surface of MWI map of > my patients and controls. > > 1-using bbregister to put MWI into FS space and to calculate > register.dat: > bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg register.dat > --o mwf_FS --t1 > > 2-using mri_vol2surf to extract inflated surface of MWI: > mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 > --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type > paint--inflated (*or*--surf sphere) > > However the tksurfer could not open the inflated surface and the > error message is: > *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! > Probably trying to use a scalar data file as a surface!* > > I used the commandline below for #2: > mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o > mwf-lh.w --out_type paint > and i got the error: > > *ERROR: MRISread: file > '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has many > more faces than vertices!** > Probably trying to use a scalar data file as a surface!* > * > * > As tksurfer could not open my surfaces with errors above, i think > perhaps the vol2surf procedure is not done properly. Where is the > problem? i need to get the inflated cortex and then putting ob > sphere (using mris_sphere) and the registering to standard surface > using mris_register for GLM in Qdec, right? > > > It is two weeks i am struggling with these commands, any helps > highly appreciated. * > * > * > * > * > * > Best, > Reza >
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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to clarify better, i need to compare myelin water fraction in cortex of control and patients to find out the areas with reduced MWF in patients cortex compared with controls, that is the reason i want to have cortex in inflated format.
For this reason i used bbregister to have register.dat, and then mri_vol2surf to resample MWI cortex to surface. As i need to have all surfaces in fsaverage space for group analysis, i am using mri_preproc7mri_surf2surf (according to the group analysis wiki you sent me).
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza Rahmanzadeh reza.rahmanzadeh@unibas.ch Sent: Wednesday, July 17, 2019 4:26:21 PM To: Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] need for help
External Email - Use Caution
I am trying to compare MWI(sampled on the surface) between couple patients and controls using group analysis, therefore i need to have all inflated surface_on_same space (according to the wiki of group analysis you sent me, i should use mris_preproc to put my data on fsaverage).
Could you now tell me whether my mris_prepoc is right? and one other question i have asked in last email?
Thanks a lot,
Reza
________________________________ From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Wednesday, July 17, 2019 4:14:41 PM To: Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] need for help
It is not clear to me what you are trying to do. Do you want to do a morphometry study (ie, comparing thickness, area, and/or volume across subjects)? Or do you want to compare MWI (sampled on the surface) across subjects?
On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Dear Doug,
I took the back slash away and ran
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got error:
Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white ERROR: reading curvature file
Then i changed it to --meas : mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgz --meas area
Then, as i need to register my the inflated cortex of myelin water image (MWI) to the surface_registered_on_fsaverage (could it be the output of command-line above?), should i use this output "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling myelin water image to lh.white of my subject FSP10 before registration to fsaverage) for mri_surf2surf (to resample the latter to the former, to have MWI to surface_fsaverage)
Looking forward to answers
Thanks
Reza
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza Rahmanzadeh reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch Sent: Wednesday, July 17, 2019 9:56:00 AM To: Freesurfer support list Cc: DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Subject: Re: [Freesurfer] need for help
External Email - Use Caution
Thanks Tim,
Then if i would resample my data to fsaverage and surfaces are of main importance to my work, what should i use for -meas ?
Reza
On 17 Jul 2019, at 09:39, Tim Schäfer ts+ml@rcmd.orgmailto:ts+ml@rcmd.org wrote:
External Email - Use CautionI guess '-meas' expects a measure (like 'thickness' or 'area'), not a surface (like 'white').
Best,
Tim
On July 17, 2019 at 9:03 AM Reza Rahmanzadeh reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch wrote:
External Email - Use CautionI removed the back slash and the command line i executed is:
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got the error:
Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white ERROR: reading curvature file
I have added --srcfmt mgh as the last argument, but again i got the error: Reading source surface reg /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg Loading source data No such file or directory ERROR: could not read /usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3
What is wrong with my mris_prepoc command line?
Reza
From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Tuesday, July 16, 2019 10:01:15 PM To: Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Subject: Re: need for help
don't include the back slash (ie, fsaverage not fsaverage/ same for FSP010)
On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks a lot Doug,
I started to proceed with FS group analysis wiki you sent to me. Accordingly, i have to resample all my data (output of recon-all for a given subject for example) into fsaverage using mris_preproc. My commandline for a subject was:
mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out lh.FSP10.white.mgh --meas white
and i got the error:
*Reading source surface reg /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory mri_surf2surf: could not read surface /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory*
As there was no**lh.fsaverage/.sphere.reg* *folder, i found one file in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder with the name lh.fsaverage and i copied/pasted the mentiomed file into this folder and i changed the file name to: ./sphere.reg. I got the error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere*
What is the problem with my mris_preproc command-line?
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 7:01:30 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution(I assume now we are discussing in FS list, if no please let me how possible?)
Thanks Doug, now i could see the inflate surface, this means that my mri_vol2surf works well. As i would do GLM analysis over inflated cortex of patients and controls in Qdec,
1- should i input my surfaces to Qdec as inflated surface or just inputting the output_of_vol2surf.mgz to Qdec?
if inflated one is the input, then how could i get them? mris_inflate gives error.
QDEC is no longer being supported. Use the command line stream (mri_surf2surf, mri_glmfit, mri_glmfit-sim). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
2- should i input all patients and controls surfaces in standard surface before entering to Qdec?
3- I would like to resample whole cortex (whole cortical thickness, in other words: the average of all projfrac between 0 and 1), is it possible? or i am limited to resample one given depth of cortex into inflated surface only?
Run mri_vol2surf with --help and look for --projfrac-avg
thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:22:56 PM *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: need for help The command should be something like tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz Also, tksurfer is also obsolete (but should work). You should be using freeview (or tksurferfv, a freeview front end that takes the same command line args as tksurfer) Also, please remember to respond to the fs list
On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionI got the mri_vol2surf output with .mgz:
my tksurfer command:
tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of mri_vol2surf was lh.inflated_MWI.mgz)
and the error i got:
*freadFloat: fread failed** No such file or directory*
To me, opening the surfer in tksurfer is only a way to get sure my vol2surf worked well. the main problem is i got this error for all mris_smooth, mris_inflate, mris_sphere ...
Do you think that means the output of mri_vol2surf is not correct, or otherwise i could proceed with that , even when tksurfer could not open it, for GLM in Qdec?
Thanks,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:01:15 PM *To:* Reza Rahmanzadeh *Subject:* Re: need for help what is your tksurfer command line? Also, the .w file is somewhat obsolete (it should still work); instead you can use .mgz file (and don't spec --paint)
On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks Doug,
I used the one without --inflated also, again the tksurfer could not open it and i got the same error. Where is the problem with my cmd.?
In addition, i wanted to make the output of mri_vol2surf inflated using mris_inflate but i got the same error:
*freadFloat: fread failed No such file or directory*
*could you let me know what is the problem in registering my mwi volumes to surface that i getonly such errors.*
*Thanks,* *reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 5:37:17 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu *Cc:* greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu *Subject:* Re: need for help Don't use --inflated. The inflated surface is not a biological surface. The default is the white surface, which is the one you want (--projfrac 0.5 will project it to the middle between the white and
pial)
> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > Dear Freesurfer, > > I have a batch of myelin water image (MWI) from patients and > controls, and trying to have inflated cortex registered on standard > surface for GLM (Qdec). > > With the commandlines below i get my inflated surface of MWI map of > my patients and controls. > > 1-using bbregister to put MWI into FS space and to calculate > register.dat: > bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg register.dat > --o mwf_FS --t1 > > 2-using mri_vol2surf to extract inflated surface of MWI: > mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 > --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type > paint--inflated (*or*--surf sphere) > > However the tksurfer could not open the inflated surface and the > error message is: > *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! > Probably trying to use a scalar data file as a surface!* > > I used the commandline below for #2: > mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o > mwf-lh.w --out_type paint > and i got the error: > > *ERROR: MRISread: file > '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has many > more faces than vertices!** > Probably trying to use a scalar data file as a surface!* > * > * > As tksurfer could not open my surfaces with errors above, i think > perhaps the vol2surf procedure is not done properly. Where is the > problem? i need to get the inflated cortex and then putting ob > sphere (using mris_sphere) and the registering to standard surface > using mris_register for GLM in Qdec, right? > > > It is two weeks i am struggling with these commands, any helps > highly appreciated. * > * > * > * > * > * > Best, > Reza >
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Ah, I see. Try this tutorial. It is for fMRI, but it applies to any modality https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
to clarify better, i need to compare myelin water fraction in cortex of control and patients to find out the areas with reduced MWF in patients cortex compared with controls, that is the reason i want to have cortex in inflated format.
For this reason i used bbregister to have register.dat, and then mri_vol2surf to resample MWI cortex to surface. As i need to have all surfaces in fsaverage space for group analysis, i am using mri_preproc7mri_surf2surf (according to the group analysis wiki you sent me).
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza Rahmanzadeh reza.rahmanzadeh@unibas.ch *Sent:* Wednesday, July 17, 2019 4:26:21 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use Caution
I am trying to compare MWI(sampled on the surface) between couple patients and controls using group analysis, therefore i need to have all inflated surface_on_same space (according to the wiki of group analysis you sent me, i should use mris_preproc to put my data on fsaverage).
Could you now tell me whether my mris_prepoc is right? and one other question i have asked in last email?
Thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Wednesday, July 17, 2019 4:14:41 PM *To:* Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help It is not clear to me what you are trying to do. Do you want to do a morphometry study (ie, comparing thickness, area, and/or volume across subjects)? Or do you want to compare MWI (sampled on the surface) across subjects?
On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Dear Doug,
I took the back slash away and ran
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white** MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white** ERROR: reading curvature file*
Then i changed it to --meas : mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgz --meas area
Then, as i need to register my the inflated cortex of myelin water image (MWI) to the surface_registered_on_fsaverage (could it be the output of command-line above?), should i use this output "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling myelin water image to lh.white of my subject FSP10 before registration to fsaverage) for mri_surf2surf (to resample the latter to the former, to have MWI to surface_fsaverage)
Looking forward to answers
Thanks
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza Rahmanzadeh reza.rahmanzadeh@unibas.ch *Sent:* Wednesday, July 17, 2019 9:56:00 AM *To:* Freesurfer support list *Cc:* DGREVE@mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help External Email - Use Caution
Thanks Tim,
Then if i would resample my data to fsaverage and surfaces are of main importance to my work, what should i use for -meas ?
Reza
On 17 Jul 2019, at 09:39, Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use Caution
I guess '-meas' expects a measure (like 'thickness' or 'area'), not
a surface (like 'white').
Best,
Tim
On July 17, 2019 at 9:03 AM Reza Rahmanzadeh
reza.rahmanzadeh@unibas.ch wrote:
External Email - Use Caution
I removed the back slash and the command line i executed is:
mris_preproc --target fsaverage --hemi lh --s FSP010 --out
lh.FSP10.white.mgh --meas white
but i got the error:
Reading curvature file
/usr/local/freesurfer/subjects/FSP010/surf/lh.white
MRISreadBinaryCurvature: incompatible vertex number in file
/usr/local/freesurfer/subjects/FSP010/surf/lh.white
ERROR: reading curvature file
I have added --srcfmt mgh as the last argument, but again i got
the error:
Reading source surface reg
/usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg
Loading source data No such file or directory ERROR: could not read
/usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3
What is wrong with my mris_prepoc command line?
Reza
From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Tuesday, July 16, 2019 10:01:15 PM To: Reza Rahmanzadeh; Freesurfer support list;
greve@nmr.mgh.harvard.edu
Subject: Re: need for help
don't include the back slash (ie, fsaverage not fsaverage/ same
for FSP010)
On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Thanks a lot Doug,
I started to proceed with FS group analysis wiki you sent to me. Accordingly, i have to resample all my data (output of recon-all
for a
given subject for example) into fsaverage using mris_preproc. My commandline for a subject was:
mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out lh.FSP10.white.mgh --meas white
and i got the error:
*Reading source surface reg /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory mri_surf2surf: could not read surface /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory*
As there was no**lh.fsaverage/.sphere.reg* *folder, i found one file in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder with the name lh.fsaverage and i copied/pasted the mentiomed file
into
this folder and i changed the file name to: ./sphere.reg. I got the error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere*
What is the problem with my mris_preproc command-line?
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 7:01:30 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution
(I assume now we are discussing in FS list, if no please let me how possible?)
Thanks Doug, now i could see the inflate surface, this means that my mri_vol2surf works well. As i would do GLM analysis over inflated cortex of patients and controls in Qdec,
1- should i input my surfaces to Qdec as inflated surface or just inputting the output_of_vol2surf.mgz to Qdec?
if inflated one is the input, then how could i get them?
mris_inflate
gives error.
QDEC is no longer being supported. Use the command line stream (mri_surf2surf, mri_glmfit, mri_glmfit-sim). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
2- should i input all patients and controls surfaces in standard surface before entering to Qdec?
3- I would like to resample whole cortex (whole cortical
thickness, in
other words: the average of all projfrac between 0 and 1), is it possible? or i am limited to resample one given depth of cortex into inflated surface only?
Run mri_vol2surf with --help and look for --projfrac-avg
thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:22:56 PM *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu *Subject:* Re: need for help The command should be something like tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz Also, tksurfer is also obsolete (but should work). You should be
using
freeview (or tksurferfv, a freeview front end that takes the same command line args as tksurfer) Also, please remember to respond to the fs list
> On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > I got the mri_vol2surf output with .mgz: > > > my tksurfer command: > > tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of > mri_vol2surf was lh.inflated_MWI.mgz) > > > and the error i got: > > *freadFloat: fread failed** > No such file or directory* > > To me, opening the surfer in tksurfer is only a way to get sure my > vol2surf worked well. the main problem is i got this error for all > mris_smooth, mris_inflate, mris_sphere ... > > > Do you think that means the output of mri_vol2surf is not
correct, or
> otherwise i could proceed with that , even when tksurfer could not > open it, for GLM in Qdec? > > > Thanks, > > Reza > >
> *From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu > *Sent:* Tuesday, July 16, 2019 6:01:15 PM > *To:* Reza Rahmanzadeh > *Subject:* Re: need for help > what is your tksurfer command line? Also, the .w file is somewhat > obsolete (it should still work); instead you can use .mgz file (and > don't spec --paint) > >> On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote: >> >> External Email - Use Caution >> >> Thanks Doug, >> >> >> I used the one without --inflated also, again the tksurfer
could not
>> open it and i got the same error. Where is the problem with my
cmd.?
>> >> >> In addition, i wanted to make the output of mri_vol2surf inflated >> using mris_inflate but i got the same error: >> >> *freadFloat: fread failed >> No such file or directory* >> * >> * >> *could you let me know what is the problem in registering my mwi >> volumes to surface that i getonly such errors.* >> * >> * >> *Thanks,* >> *reza >> * >> >>
>> *From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu >> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >> *Cc:* greve@nmr.mgh.harvard.edu >> *Subject:* Re: need for help >> Don't use --inflated. The inflated surface is not a biological >> surface. The default is the white surface, which is the one
you want
>> (--projfrac 0.5 will project it to the middle between the
white and
pial) >> >>> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: >>> >>> External Email - Use Caution >>> >>> Dear Freesurfer, >>> >>> I have a batch of myelin water image (MWI) from patients and >>> controls, and trying to have inflated cortex registered on
standard
>>> surface for GLM (Qdec). >>> >>> With the commandlines below i get my inflated surface of MWI
map of
>>> my patients and controls. >>> >>> 1-using bbregister to put MWI into FS space and to calculate >>> register.dat: >>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg
register.dat
>>> --o mwf_FS --t1 >>> >>> 2-using mri_vol2surf to extract inflated surface of MWI: >>> mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 >>> --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type >>> paint--inflated (*or*--surf sphere) >>> >>> However the tksurfer could not open the inflated surface and the >>> error message is: >>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! >>> Probably trying to use a scalar data file as a surface!* >>> >>> I used the commandline below for #2: >>> mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o >>> mwf-lh.w --out_type paint >>> and i got the error: >>> >>> *ERROR: MRISread: file >>> '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has
many
>>> more faces than vertices!** >>> Probably trying to use a scalar data file as a surface!* >>> * >>> * >>> As tksurfer could not open my surfaces with errors above, i think >>> perhaps the vol2surf procedure is not done properly. Where is the >>> problem? i need to get the inflated cortex and then putting ob >>> sphere (using mris_sphere) and the registering to standard
surface
>>> using mris_register for GLM in Qdec, right? >>> >>> >>> It is two weeks i am struggling with these commands, any helps >>> highly appreciated. * >>> * >>> * >>> * >>> * >>> * >>> Best, >>> Reza >>> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners
Compliance
>> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the
sender
>> and properly >> dispose of the e-mail. >> >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and
Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main,
Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Dear Doug,
Thanks, the tutorial was super helpful. As i would compare the MWF value in cortex between control subjects and patients. Now my problem is how to make the contrast matrix for mris_preproc to do the comparison in both direction (in 1, the outcome should be voxels in which MWf value in control>patients & in 2, reversed).
The explanations in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre... is for one group analysis and in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is not clear about contrast.
I remember for -randomise command-line, there was possibility to make contrast and design matrix (something like FSGD) via design_ttest2. Can i use still design_ttest2 for producing contrast and design matrix?
Best,
Reza
________________________________ From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Wednesday, July 17, 2019 5:31:27 PM To: Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] need for help
Ah, I see. Try this tutorial. It is for fMRI, but it applies to any modality https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote:
External Email - Use Cautionto clarify better, i need to compare myelin water fraction in cortex of control and patients to find out the areas with reduced MWF in patients cortex compared with controls, that is the reason i want to have cortex in inflated format.
For this reason i used bbregister to have register.dat, and then mri_vol2surf to resample MWI cortex to surface. As i need to have all surfaces in fsaverage space for group analysis, i am using mri_preproc7mri_surf2surf (according to the group analysis wiki you sent me).
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza Rahmanzadeh reza.rahmanzadeh@unibas.ch *Sent:* Wednesday, July 17, 2019 4:26:21 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionI am trying to compare MWI(sampled on the surface) between couple patients and controls using group analysis, therefore i need to have all inflated surface_on_same space (according to the wiki of group analysis you sent me, i should use mris_preproc to put my data on fsaverage).
Could you now tell me whether my mris_prepoc is right? and one other question i have asked in last email?
Thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Wednesday, July 17, 2019 4:14:41 PM *To:* Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help It is not clear to me what you are trying to do. Do you want to do a morphometry study (ie, comparing thickness, area, and/or volume across subjects)? Or do you want to compare MWI (sampled on the surface) across subjects?
On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionDear Doug,
I took the back slash away and ran
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white** MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white** ERROR: reading curvature file*
Then i changed it to --meas : mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgz --meas area
Then, as i need to register my the inflated cortex of myelin water image (MWI) to the surface_registered_on_fsaverage (could it be the output of command-line above?), should i use this output "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling myelin water image to lh.white of my subject FSP10 before registration to fsaverage) for mri_surf2surf (to resample the latter to the former, to have MWI to surface_fsaverage)
Looking forward to answers
Thanks
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza Rahmanzadeh reza.rahmanzadeh@unibas.ch *Sent:* Wednesday, July 17, 2019 9:56:00 AM *To:* Freesurfer support list *Cc:* DGREVE@mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help External Email - Use Caution
Thanks Tim,
Then if i would resample my data to fsaverage and surfaces are of main importance to my work, what should i use for -meas ?
Reza
On 17 Jul 2019, at 09:39, Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use CautionI guess '-meas' expects a measure (like 'thickness' or 'area'), not
a surface (like 'white').
Best,
Tim
On July 17, 2019 at 9:03 AM Reza Rahmanzadeh
reza.rahmanzadeh@unibas.ch wrote:
External Email - Use CautionI removed the back slash and the command line i executed is:
mris_preproc --target fsaverage --hemi lh --s FSP010 --out
lh.FSP10.white.mgh --meas white
but i got the error:
Reading curvature file
/usr/local/freesurfer/subjects/FSP010/surf/lh.white
MRISreadBinaryCurvature: incompatible vertex number in file
/usr/local/freesurfer/subjects/FSP010/surf/lh.white
ERROR: reading curvature file
I have added --srcfmt mgh as the last argument, but again i got
the error:
Reading source surface reg
/usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg
Loading source data No such file or directory ERROR: could not read
/usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3
What is wrong with my mris_prepoc command line?
Reza
From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Tuesday, July 16, 2019 10:01:15 PM To: Reza Rahmanzadeh; Freesurfer support list;
greve@nmr.mgh.harvard.edu
Subject: Re: need for help
don't include the back slash (ie, fsaverage not fsaverage/ same
for FSP010)
On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks a lot Doug,
I started to proceed with FS group analysis wiki you sent to me. Accordingly, i have to resample all my data (output of recon-all
for a
given subject for example) into fsaverage using mris_preproc. My commandline for a subject was:
mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out lh.FSP10.white.mgh --meas white
and i got the error:
*Reading source surface reg /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory mri_surf2surf: could not read surface /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory*
As there was no**lh.fsaverage/.sphere.reg* *folder, i found one file in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder with the name lh.fsaverage and i copied/pasted the mentiomed file
into
this folder and i changed the file name to: ./sphere.reg. I got the error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere*
What is the problem with my mris_preproc command-line?
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 7:01:30 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution(I assume now we are discussing in FS list, if no please let me how possible?)
Thanks Doug, now i could see the inflate surface, this means that my mri_vol2surf works well. As i would do GLM analysis over inflated cortex of patients and controls in Qdec,
1- should i input my surfaces to Qdec as inflated surface or just inputting the output_of_vol2surf.mgz to Qdec?
if inflated one is the input, then how could i get them?
mris_inflate
gives error.
QDEC is no longer being supported. Use the command line stream (mri_surf2surf, mri_glmfit, mri_glmfit-sim). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
2- should i input all patients and controls surfaces in standard surface before entering to Qdec?
3- I would like to resample whole cortex (whole cortical
thickness, in
other words: the average of all projfrac between 0 and 1), is it possible? or i am limited to resample one given depth of cortex into inflated surface only?
Run mri_vol2surf with --help and look for --projfrac-avg
thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 6:22:56 PM *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu *Subject:* Re: need for help The command should be something like tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz Also, tksurfer is also obsolete (but should work). You should be
using
freeview (or tksurferfv, a freeview front end that takes the same command line args as tksurfer) Also, please remember to respond to the fs list
> On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > I got the mri_vol2surf output with .mgz: > > > my tksurfer command: > > tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of > mri_vol2surf was lh.inflated_MWI.mgz) > > > and the error i got: > > *freadFloat: fread failed** > No such file or directory* > > To me, opening the surfer in tksurfer is only a way to get sure my > vol2surf worked well. the main problem is i got this error for all > mris_smooth, mris_inflate, mris_sphere ... > > > Do you think that means the output of mri_vol2surf is not
correct, or
> otherwise i could proceed with that , even when tksurfer could not > open it, for GLM in Qdec? > > > Thanks, > > Reza > >
> *From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu > *Sent:* Tuesday, July 16, 2019 6:01:15 PM > *To:* Reza Rahmanzadeh > *Subject:* Re: need for help > what is your tksurfer command line? Also, the .w file is somewhat > obsolete (it should still work); instead you can use .mgz file (and > don't spec --paint) > >> On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote: >> >> External Email - Use Caution >> >> Thanks Doug, >> >> >> I used the one without --inflated also, again the tksurfer
could not
>> open it and i got the same error. Where is the problem with my
cmd.?
>> >> >> In addition, i wanted to make the output of mri_vol2surf inflated >> using mris_inflate but i got the same error: >> >> *freadFloat: fread failed >> No such file or directory* >> * >> * >> *could you let me know what is the problem in registering my mwi >> volumes to surface that i getonly such errors.* >> * >> * >> *Thanks,* >> *reza >> * >> >>
>> *From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu >> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >> *Cc:* greve@nmr.mgh.harvard.edu >> *Subject:* Re: need for help >> Don't use --inflated. The inflated surface is not a biological >> surface. The default is the white surface, which is the one
you want
>> (--projfrac 0.5 will project it to the middle between the
white and
pial) >> >>> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: >>> >>> External Email - Use Caution >>> >>> Dear Freesurfer, >>> >>> I have a batch of myelin water image (MWI) from patients and >>> controls, and trying to have inflated cortex registered on
standard
>>> surface for GLM (Qdec). >>> >>> With the commandlines below i get my inflated surface of MWI
map of
>>> my patients and controls. >>> >>> 1-using bbregister to put MWI into FS space and to calculate >>> register.dat: >>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg
register.dat
>>> --o mwf_FS --t1 >>> >>> 2-using mri_vol2surf to extract inflated surface of MWI: >>> mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 >>> --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type >>> paint--inflated (*or*--surf sphere) >>> >>> However the tksurfer could not open the inflated surface and the >>> error message is: >>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! >>> Probably trying to use a scalar data file as a surface!* >>> >>> I used the commandline below for #2: >>> mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o >>> mwf-lh.w --out_type paint >>> and i got the error: >>> >>> *ERROR: MRISread: file >>> '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has
many
>>> more faces than vertices!** >>> Probably trying to use a scalar data file as a surface!* >>> * >>> * >>> As tksurfer could not open my surfaces with errors above, i think >>> perhaps the vol2surf procedure is not done properly. Where is the >>> problem? i need to get the inflated cortex and then putting ob >>> sphere (using mris_sphere) and the registering to standard
surface
>>> using mris_register for GLM in Qdec, right? >>> >>> >>> It is two weeks i am struggling with these commands, any helps >>> highly appreciated. * >>> * >>> * >>> * >>> * >>> * >>> Best, >>> Reza >>> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners
Compliance
>> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the
sender
>> and properly >> dispose of the e-mail. >> >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and
Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main,
Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sort of. mri_glmfit will take a design matrix (--X) and contrast matrices (--C), but they need to be in the right format (simple text table). So, you'll have to convert the output of design_ttest2 into that format.
On 7/26/19 8:55 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Dear Doug,
Thanks, the tutorial was super helpful. As i would compare the MWF value in cortex between control subjects and patients. Now my problem is how to make the contrast matrix for mris_preproc to do the comparison in both direction (in 1, the outcome should be voxels in which MWf value in control>patients & in 2, reversed).
The explanations in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre... is for one group analysis and in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is not clear about contrast.
I remember for -randomise command-line, there was possibility to make contrast and design matrix (something like FSGD) via design_ttest2. Can i use still design_ttest2 for producing contrast and design matrix?
Best,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Wednesday, July 17, 2019 5:31:27 PM *To:* Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help Ah, I see. Try this tutorial. It is for fMRI, but it applies to any modality https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
to clarify better, i need to compare myelin water fraction in cortex of control and patients to find out the areas with reduced MWF in patients cortex compared with controls, that is the reason i want to have cortex in inflated format.
For this reason i used bbregister to have register.dat, and then mri_vol2surf to resample MWI cortex to surface. As i need to have all surfaces in fsaverage space for group analysis, i am using mri_preproc7mri_surf2surf (according to the group analysis wiki you sent me).
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza Rahmanzadeh reza.rahmanzadeh@unibas.ch *Sent:* Wednesday, July 17, 2019 4:26:21 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use Caution
I am trying to compare MWI(sampled on the surface) between couple patients and controls using group analysis, therefore i need to have all inflated surface_on_same space (according to the wiki of group analysis you sent me, i should use mris_preproc to put my data on fsaverage).
Could you now tell me whether my mris_prepoc is right? and one other question i have asked in last email?
Thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Wednesday, July 17, 2019 4:14:41 PM *To:* Reza Rahmanzadeh; Freesurfer support list;
greve@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] need for help It is not clear to me what you are trying to do. Do you want to do a morphometry study (ie, comparing thickness, area, and/or volume across subjects)? Or do you want to compare MWI (sampled on the surface) across subjects?
On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Dear Doug,
I took the back slash away and ran
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white** MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white** ERROR: reading curvature file*
Then i changed it to --meas : mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgz --meas area
Then, as i need to register my the inflated cortex of myelin water image (MWI) to the surface_registered_on_fsaverage (could it be the output of command-line above?), should i use this output "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling myelin water image to lh.white of my subject FSP10 before registration to fsaverage) for mri_surf2surf (to resample the latter to the former, to have MWI to surface_fsaverage)
Looking forward to answers
Thanks
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza Rahmanzadeh reza.rahmanzadeh@unibas.ch *Sent:* Wednesday, July 17, 2019 9:56:00 AM *To:* Freesurfer support list *Cc:* DGREVE@mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help External Email - Use Caution
Thanks Tim,
Then if i would resample my data to fsaverage and surfaces are of main importance to my work, what should i use for -meas ?
Reza
On 17 Jul 2019, at 09:39, Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use Caution
I guess '-meas' expects a measure (like 'thickness' or 'area'), not
a surface (like 'white').
Best,
Tim
On July 17, 2019 at 9:03 AM Reza Rahmanzadeh
reza.rahmanzadeh@unibas.ch wrote:
External Email - Use Caution
I removed the back slash and the command line i executed is:
mris_preproc --target fsaverage --hemi lh --s FSP010 --out
lh.FSP10.white.mgh --meas white
but i got the error:
Reading curvature file
/usr/local/freesurfer/subjects/FSP010/surf/lh.white
MRISreadBinaryCurvature: incompatible vertex number in file
/usr/local/freesurfer/subjects/FSP010/surf/lh.white
ERROR: reading curvature file
I have added --srcfmt mgh as the last argument, but again i got
the error:
Reading source surface reg
/usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg
Loading source data No such file or directory ERROR: could not read
/usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3
What is wrong with my mris_prepoc command line?
Reza
From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Tuesday, July 16, 2019 10:01:15 PM To: Reza Rahmanzadeh; Freesurfer support list;
greve@nmr.mgh.harvard.edu
Subject: Re: need for help
don't include the back slash (ie, fsaverage not fsaverage/ same
for FSP010)
On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Thanks a lot Doug,
I started to proceed with FS group analysis wiki you sent to me. Accordingly, i have to resample all my data (output of recon-all
for a
given subject for example) into fsaverage using mris_preproc. My commandline for a subject was:
mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out lh.FSP10.white.mgh --meas white
and i got the error:
*Reading source surface reg
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
No such file or directory mri_surf2surf: could not read surface
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
No such file or directory*
As there was no**lh.fsaverage/.sphere.reg* *folder, i found one
file
in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder with the name lh.fsaverage and i copied/pasted the mentiomed file
into
this folder and i changed the file name to: ./sphere.reg. I got the error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere*
What is the problem with my mris_preproc command-line?
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve,
Douglas
N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, July 16, 2019 7:01:30 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
> On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > (I assume now we are discussing in FS list, if no please let
me how
> possible?) > > > Thanks Doug, now i could see the inflate surface, this means
that my
> mri_vol2surf works well. As i would do GLM analysis over inflated > cortex of patients and controls in Qdec, > > > 1- should i input my surfaces to Qdec as inflated surface or just > inputting the output_of_vol2surf.mgz to Qdec? > > if inflated one is the input, then how could i get them?
mris_inflate
> gives error. > QDEC is no longer being supported. Use the command line stream (mri_surf2surf, mri_glmfit, mri_glmfit-sim). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > > > 2- should i input all patients and controls surfaces in standard > surface before entering to Qdec? > > > 3- I would like to resample whole cortex (whole cortical
thickness, in
> other words: the average of all projfrac between 0 and 1), is it > possible? or i am limited to resample one given depth of
cortex into
> inflated surface only? > Run mri_vol2surf with --help and look for --projfrac-avg > > > thanks a lot, > > Reza > > >
> *From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu > *Sent:* Tuesday, July 16, 2019 6:22:56 PM > *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: need for help > The command should be something like > tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz > Also, tksurfer is also obsolete (but should work). You should be
using
> freeview (or tksurferfv, a freeview front end that takes the same > command line args as tksurfer) > Also, please remember to respond to the fs list > >> On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote: >> >> External Email - Use Caution >> >> I got the mri_vol2surf output with .mgz: >> >> >> my tksurfer command: >> >> tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of >> mri_vol2surf was lh.inflated_MWI.mgz) >> >> >> and the error i got: >> >> *freadFloat: fread failed** >> No such file or directory* >> >> To me, opening the surfer in tksurfer is only a way to get
sure my
>> vol2surf worked well. the main problem is i got this error
for all
>> mris_smooth, mris_inflate, mris_sphere ... >> >> >> Do you think that means the output of mri_vol2surf is not
correct, or
>> otherwise i could proceed with that , even when tksurfer
could not
>> open it, for GLM in Qdec? >> >> >> Thanks, >> >> Reza >> >>
>> *From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu >> *Sent:* Tuesday, July 16, 2019 6:01:15 PM >> *To:* Reza Rahmanzadeh >> *Subject:* Re: need for help >> what is your tksurfer command line? Also, the .w file is somewhat >> obsolete (it should still work); instead you can use .mgz
file (and
>> don't spec --paint) >> >>> On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote: >>> >>> External Email - Use Caution >>> >>> Thanks Doug, >>> >>> >>> I used the one without --inflated also, again the tksurfer
could not
>>> open it and i got the same error. Where is the problem with my
cmd.?
>>> >>> >>> In addition, i wanted to make the output of mri_vol2surf
inflated
>>> using mris_inflate but i got the same error: >>> >>> *freadFloat: fread failed >>> No such file or directory* >>> * >>> * >>> *could you let me know what is the problem in registering my mwi >>> volumes to surface that i getonly such errors.* >>> * >>> * >>> *Thanks,* >>> *reza >>> * >>> >>> >
>>> *From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu >>> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >>> *Cc:* greve@nmr.mgh.harvard.edu >>> *Subject:* Re: need for help >>> Don't use --inflated. The inflated surface is not a biological >>> surface. The default is the white surface, which is the one
you want
>>> (--projfrac 0.5 will project it to the middle between the
white and
> pial) >>> >>>> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: >>>> >>>> External Email - Use Caution >>>> >>>> Dear Freesurfer, >>>> >>>> I have a batch of myelin water image (MWI) from patients and >>>> controls, and trying to have inflated cortex registered on
standard
>>>> surface for GLM (Qdec). >>>> >>>> With the commandlines below i get my inflated surface of MWI
map of
>>>> my patients and controls. >>>> >>>> 1-using bbregister to put MWI into FS space and to calculate >>>> register.dat: >>>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg
register.dat
>>>> --o mwf_FS --t1 >>>> >>>> 2-using mri_vol2surf to extract inflated surface of MWI: >>>> mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 >>>> --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type >>>> paint--inflated (*or*--surf sphere) >>>> >>>> However the tksurfer could not open the inflated surface
and the
>>>> error message is: >>>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! >>>> Probably trying to use a scalar data file as a surface!* >>>> >>>> I used the commandline below for #2: >>>> mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o >>>> mwf-lh.w --out_type paint >>>> and i got the error: >>>> >>>> *ERROR: MRISread: file >>>> '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has
many
>>>> more faces than vertices!** >>>> Probably trying to use a scalar data file as a surface!* >>>> * >>>> * >>>> As tksurfer could not open my surfaces with errors above, i
think
>>>> perhaps the vol2surf procedure is not done properly. Where
is the
>>>> problem? i need to get the inflated cortex and then putting ob >>>> sphere (using mris_sphere) and the registering to standard
surface
>>>> using mris_register for GLM in Qdec, right? >>>> >>>> >>>> It is two weeks i am struggling with these commands, any helps >>>> highly appreciated. * >>>> * >>>> * >>>> * >>>> * >>>> * >>>> Best, >>>> Reza >>>> >>> >>> The information in this e-mail is intended only for the
person to
>>> whom it is >>> addressed. If you believe this e-mail was sent to you in
error and
>>> the e-mail >>> contains patient information, please contact the Partners
Compliance
>>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was
sent to
>>> you in error >>> but does not contain patient information, please contact the
sender
>>> and properly >>> dispose of the e-mail. >>> >> >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and
Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main,
Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Dear Doug,
Thanks, the tutorial was super helpful. As i would compare the MWF value in cortex between control subjects and patients. Now my problem is how to make the contrast matrix for mris_preproc to do the comparison in both direction (in 1, the outcome should be voxels in which MWf value in control>patients & in 2, reversed).
The explanations in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre... is for one group analysis and in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is not clear about contrast.
I remember for -randomise command-line, there was possibility to make contrast and design matrix (something like FSGD) via design_ttest2. Can i use still design_ttest2 for producing contrast and design matrix?
Best,
Reza
________________________________ From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> Sent: Wednesday, July 17, 2019 5:31:27 PM To: Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] need for help
Ah, I see. Try this tutorial. It is for fMRI, but it applies to any modality https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote:
External Email - Use Cautionto clarify better, i need to compare myelin water fraction in cortex of control and patients to find out the areas with reduced MWF in patients cortex compared with controls, that is the reason i want to have cortex in inflated format.
For this reason i used bbregister to have register.dat, and then mri_vol2surf to resample MWI cortex to surface. As i need to have all surfaces in fsaverage space for group analysis, i am using mri_preproc7mri_surf2surf (according to the group analysis wiki you sent me).
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh <reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch> *Sent:* Wednesday, July 17, 2019 4:26:21 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionI am trying to compare MWI(sampled on the surface) between couple patients and controls using group analysis, therefore i need to have all inflated surface_on_same space (according to the wiki of group analysis you sent me, i should use mris_preproc to put my data on fsaverage).
Could you now tell me whether my mris_prepoc is right? and one other question i have asked in last email?
Thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> *Sent:* Wednesday, July 17, 2019 4:14:41 PM *To:* Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help It is not clear to me what you are trying to do. Do you want to do a morphometry study (ie, comparing thickness, area, and/or volume across subjects)? Or do you want to compare MWI (sampled on the surface) across subjects?
On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionDear Doug,
I took the back slash away and ran
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white** MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white** ERROR: reading curvature file*
Then i changed it to --meas : mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgz --meas area
Then, as i need to register my the inflated cortex of myelin water image (MWI) to the surface_registered_on_fsaverage (could it be the output of command-line above?), should i use this output "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling myelin water image to lh.white of my subject FSP10 before registration to fsaverage) for mri_surf2surf (to resample the latter to the former, to have MWI to surface_fsaverage)
Looking forward to answers
Thanks
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh <reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch> *Sent:* Wednesday, July 17, 2019 9:56:00 AM *To:* Freesurfer support list *Cc:* DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help External Email - Use Caution
Thanks Tim,
Then if i would resample my data to fsaverage and surfaces are of main importance to my work, what should i use for -meas ?
Reza
On 17 Jul 2019, at 09:39, Tim Schäfer <ts+ml@rcmd.orgmailto:ts+ml@rcmd.org> wrote:
External Email - Use CautionI guess '-meas' expects a measure (like 'thickness' or 'area'), not
a surface (like 'white').
Best,
Tim
On July 17, 2019 at 9:03 AM Reza Rahmanzadeh
<reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch> wrote:
External Email - Use CautionI removed the back slash and the command line i executed is:
mris_preproc --target fsaverage --hemi lh --s FSP010 --out
lh.FSP10.white.mgh --meas white
but i got the error:
Reading curvature file
/usr/local/freesurfer/subjects/FSP010/surf/lh.white
MRISreadBinaryCurvature: incompatible vertex number in file
/usr/local/freesurfer/subjects/FSP010/surf/lh.white
ERROR: reading curvature file
I have added --srcfmt mgh as the last argument, but again i got
the error:
Reading source surface reg
/usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg
Loading source data No such file or directory ERROR: could not read
/usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3
What is wrong with my mris_prepoc command line?
Reza
From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> Sent: Tuesday, July 16, 2019 10:01:15 PM To: Reza Rahmanzadeh; Freesurfer support list;
greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu
Subject: Re: need for help
don't include the back slash (ie, fsaverage not fsaverage/ same
for FSP010)
On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks a lot Doug,
I started to proceed with FS group analysis wiki you sent to me. Accordingly, i have to resample all my data (output of recon-all
for a
given subject for example) into fsaverage using mris_preproc. My commandline for a subject was:
mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out lh.FSP10.white.mgh --meas white
and i got the error:
*Reading source surface reg /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory mri_surf2surf: could not read surface /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory*
As there was no**lh.fsaverage/.sphere.reg* *folder, i found one file in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder with the name lh.fsaverage and i copied/pasted the mentiomed file
into
this folder and i changed the file name to: ./sphere.reg. I got the error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere*
What is the problem with my mris_preproc command-line?
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> *Sent:* Tuesday, July 16, 2019 7:01:30 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution(I assume now we are discussing in FS list, if no please let me how possible?)
Thanks Doug, now i could see the inflate surface, this means that my mri_vol2surf works well. As i would do GLM analysis over inflated cortex of patients and controls in Qdec,
1- should i input my surfaces to Qdec as inflated surface or just inputting the output_of_vol2surf.mgz to Qdec?
if inflated one is the input, then how could i get them?
mris_inflate
gives error.
QDEC is no longer being supported. Use the command line stream (mri_surf2surf, mri_glmfit, mri_glmfit-sim). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
2- should i input all patients and controls surfaces in standard surface before entering to Qdec?
3- I would like to resample whole cortex (whole cortical
thickness, in
other words: the average of all projfrac between 0 and 1), is it possible? or i am limited to resample one given depth of cortex into inflated surface only?
Run mri_vol2surf with --help and look for --projfrac-avg
thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> *Sent:* Tuesday, July 16, 2019 6:22:56 PM *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: need for help The command should be something like tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz Also, tksurfer is also obsolete (but should work). You should be
using
freeview (or tksurferfv, a freeview front end that takes the same command line args as tksurfer) Also, please remember to respond to the fs list
> On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > I got the mri_vol2surf output with .mgz: > > > my tksurfer command: > > tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of > mri_vol2surf was lh.inflated_MWI.mgz) > > > and the error i got: > > *freadFloat: fread failed** > No such file or directory* > > To me, opening the surfer in tksurfer is only a way to get sure my > vol2surf worked well. the main problem is i got this error for all > mris_smooth, mris_inflate, mris_sphere ... > > > Do you think that means the output of mri_vol2surf is not
correct, or
> otherwise i could proceed with that , even when tksurfer could not > open it, for GLM in Qdec? > > > Thanks, > > Reza > >
> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> > *Sent:* Tuesday, July 16, 2019 6:01:15 PM > *To:* Reza Rahmanzadeh > *Subject:* Re: need for help > what is your tksurfer command line? Also, the .w file is somewhat > obsolete (it should still work); instead you can use .mgz file (and > don't spec --paint) > >> On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote: >> >> External Email - Use Caution >> >> Thanks Doug, >> >> >> I used the one without --inflated also, again the tksurfer
could not
>> open it and i got the same error. Where is the problem with my
cmd.?
>> >> >> In addition, i wanted to make the output of mri_vol2surf inflated >> using mris_inflate but i got the same error: >> >> *freadFloat: fread failed >> No such file or directory* >> * >> * >> *could you let me know what is the problem in registering my mwi >> volumes to surface that i getonly such errors.* >> * >> * >> *Thanks,* >> *reza >> * >> >>
>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> >> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> *Cc:* greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >> *Subject:* Re: need for help >> Don't use --inflated. The inflated surface is not a biological >> surface. The default is the white surface, which is the one
you want
>> (--projfrac 0.5 will project it to the middle between the
white and
pial) >> >>> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: >>> >>> External Email - Use Caution >>> >>> Dear Freesurfer, >>> >>> I have a batch of myelin water image (MWI) from patients and >>> controls, and trying to have inflated cortex registered on
standard
>>> surface for GLM (Qdec). >>> >>> With the commandlines below i get my inflated surface of MWI
map of
>>> my patients and controls. >>> >>> 1-using bbregister to put MWI into FS space and to calculate >>> register.dat: >>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg
register.dat
>>> --o mwf_FS --t1 >>> >>> 2-using mri_vol2surf to extract inflated surface of MWI: >>> mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 >>> --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type >>> paint--inflated (*or*--surf sphere) >>> >>> However the tksurfer could not open the inflated surface and the >>> error message is: >>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! >>> Probably trying to use a scalar data file as a surface!* >>> >>> I used the commandline below for #2: >>> mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o >>> mwf-lh.w --out_type paint >>> and i got the error: >>> >>> *ERROR: MRISread: file >>> '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has
many
>>> more faces than vertices!** >>> Probably trying to use a scalar data file as a surface!* >>> * >>> * >>> As tksurfer could not open my surfaces with errors above, i think >>> perhaps the vol2surf procedure is not done properly. Where is the >>> problem? i need to get the inflated cortex and then putting ob >>> sphere (using mris_sphere) and the registering to standard
surface
>>> using mris_register for GLM in Qdec, right? >>> >>> >>> It is two weeks i am struggling with these commands, any helps >>> highly appreciated. * >>> * >>> * >>> * >>> * >>> * >>> Best, >>> Reza >>> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners
Compliance
>> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the
sender
>> and properly >> dispose of the e-mail. >> >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and
Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main,
Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Dear Doug,
I appreciat if you reply my question in the previous e-mail with this:
can not i use projfrac-avg in mris_preproc? Is --projfrac-max min max delta just the same?
Best,
Reza
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza Rahmanzadeh reza.rahmanzadeh@unibas.ch Sent: Monday, July 29, 2019 11:37:46 AM To: Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] need for help
External Email - Use Caution
Dear Doug,
Thanks, the tutorial was super helpful. As i would compare the MWF value in cortex between control subjects and patients. Now my problem is how to make the contrast matrix for mris_preproc to do the comparison in both direction (in 1, the outcome should be voxels in which MWf value in control>patients & in 2, reversed).
The explanations in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre... is for one group analysis and in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is not clear about contrast.
I remember for -randomise command-line, there was possibility to make contrast and design matrix (something like FSGD) via design_ttest2. Can i use still design_ttest2 for producing contrast and design matrix?
Best,
Reza
________________________________ From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> Sent: Wednesday, July 17, 2019 5:31:27 PM To: Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] need for help
Ah, I see. Try this tutorial. It is for fMRI, but it applies to any modality https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote:
External Email - Use Cautionto clarify better, i need to compare myelin water fraction in cortex of control and patients to find out the areas with reduced MWF in patients cortex compared with controls, that is the reason i want to have cortex in inflated format.
For this reason i used bbregister to have register.dat, and then mri_vol2surf to resample MWI cortex to surface. As i need to have all surfaces in fsaverage space for group analysis, i am using mri_preproc7mri_surf2surf (according to the group analysis wiki you sent me).
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh <reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch> *Sent:* Wednesday, July 17, 2019 4:26:21 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionI am trying to compare MWI(sampled on the surface) between couple patients and controls using group analysis, therefore i need to have all inflated surface_on_same space (according to the wiki of group analysis you sent me, i should use mris_preproc to put my data on fsaverage).
Could you now tell me whether my mris_prepoc is right? and one other question i have asked in last email?
Thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> *Sent:* Wednesday, July 17, 2019 4:14:41 PM *To:* Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help It is not clear to me what you are trying to do. Do you want to do a morphometry study (ie, comparing thickness, area, and/or volume across subjects)? Or do you want to compare MWI (sampled on the surface) across subjects?
On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionDear Doug,
I took the back slash away and ran
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white** MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white** ERROR: reading curvature file*
Then i changed it to --meas : mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgz --meas area
Then, as i need to register my the inflated cortex of myelin water image (MWI) to the surface_registered_on_fsaverage (could it be the output of command-line above?), should i use this output "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling myelin water image to lh.white of my subject FSP10 before registration to fsaverage) for mri_surf2surf (to resample the latter to the former, to have MWI to surface_fsaverage)
Looking forward to answers
Thanks
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh <reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch> *Sent:* Wednesday, July 17, 2019 9:56:00 AM *To:* Freesurfer support list *Cc:* DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help External Email - Use Caution
Thanks Tim,
Then if i would resample my data to fsaverage and surfaces are of main importance to my work, what should i use for -meas ?
Reza
On 17 Jul 2019, at 09:39, Tim Schäfer <ts+ml@rcmd.orgmailto:ts+ml@rcmd.org> wrote:
External Email - Use CautionI guess '-meas' expects a measure (like 'thickness' or 'area'), not
a surface (like 'white').
Best,
Tim
On July 17, 2019 at 9:03 AM Reza Rahmanzadeh
<reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch> wrote:
External Email - Use CautionI removed the back slash and the command line i executed is:
mris_preproc --target fsaverage --hemi lh --s FSP010 --out
lh.FSP10.white.mgh --meas white
but i got the error:
Reading curvature file
/usr/local/freesurfer/subjects/FSP010/surf/lh.white
MRISreadBinaryCurvature: incompatible vertex number in file
/usr/local/freesurfer/subjects/FSP010/surf/lh.white
ERROR: reading curvature file
I have added --srcfmt mgh as the last argument, but again i got
the error:
Reading source surface reg
/usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg
Loading source data No such file or directory ERROR: could not read
/usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3
What is wrong with my mris_prepoc command line?
Reza
From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> Sent: Tuesday, July 16, 2019 10:01:15 PM To: Reza Rahmanzadeh; Freesurfer support list;
greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu
Subject: Re: need for help
don't include the back slash (ie, fsaverage not fsaverage/ same
for FSP010)
On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks a lot Doug,
I started to proceed with FS group analysis wiki you sent to me. Accordingly, i have to resample all my data (output of recon-all
for a
given subject for example) into fsaverage using mris_preproc. My commandline for a subject was:
mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out lh.FSP10.white.mgh --meas white
and i got the error:
*Reading source surface reg /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory mri_surf2surf: could not read surface /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory*
As there was no**lh.fsaverage/.sphere.reg* *folder, i found one file in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder with the name lh.fsaverage and i copied/pasted the mentiomed file
into
this folder and i changed the file name to: ./sphere.reg. I got the error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere*
What is the problem with my mris_preproc command-line?
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> *Sent:* Tuesday, July 16, 2019 7:01:30 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution(I assume now we are discussing in FS list, if no please let me how possible?)
Thanks Doug, now i could see the inflate surface, this means that my mri_vol2surf works well. As i would do GLM analysis over inflated cortex of patients and controls in Qdec,
1- should i input my surfaces to Qdec as inflated surface or just inputting the output_of_vol2surf.mgz to Qdec?
if inflated one is the input, then how could i get them?
mris_inflate
gives error.
QDEC is no longer being supported. Use the command line stream (mri_surf2surf, mri_glmfit, mri_glmfit-sim). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
2- should i input all patients and controls surfaces in standard surface before entering to Qdec?
3- I would like to resample whole cortex (whole cortical
thickness, in
other words: the average of all projfrac between 0 and 1), is it possible? or i am limited to resample one given depth of cortex into inflated surface only?
Run mri_vol2surf with --help and look for --projfrac-avg
thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> *Sent:* Tuesday, July 16, 2019 6:22:56 PM *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: need for help The command should be something like tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz Also, tksurfer is also obsolete (but should work). You should be
using
freeview (or tksurferfv, a freeview front end that takes the same command line args as tksurfer) Also, please remember to respond to the fs list
> On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > I got the mri_vol2surf output with .mgz: > > > my tksurfer command: > > tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of > mri_vol2surf was lh.inflated_MWI.mgz) > > > and the error i got: > > *freadFloat: fread failed** > No such file or directory* > > To me, opening the surfer in tksurfer is only a way to get sure my > vol2surf worked well. the main problem is i got this error for all > mris_smooth, mris_inflate, mris_sphere ... > > > Do you think that means the output of mri_vol2surf is not
correct, or
> otherwise i could proceed with that , even when tksurfer could not > open it, for GLM in Qdec? > > > Thanks, > > Reza > >
> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> > *Sent:* Tuesday, July 16, 2019 6:01:15 PM > *To:* Reza Rahmanzadeh > *Subject:* Re: need for help > what is your tksurfer command line? Also, the .w file is somewhat > obsolete (it should still work); instead you can use .mgz file (and > don't spec --paint) > >> On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote: >> >> External Email - Use Caution >> >> Thanks Doug, >> >> >> I used the one without --inflated also, again the tksurfer
could not
>> open it and i got the same error. Where is the problem with my
cmd.?
>> >> >> In addition, i wanted to make the output of mri_vol2surf inflated >> using mris_inflate but i got the same error: >> >> *freadFloat: fread failed >> No such file or directory* >> * >> * >> *could you let me know what is the problem in registering my mwi >> volumes to surface that i getonly such errors.* >> * >> * >> *Thanks,* >> *reza >> * >> >>
>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> >> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> *Cc:* greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >> *Subject:* Re: need for help >> Don't use --inflated. The inflated surface is not a biological >> surface. The default is the white surface, which is the one
you want
>> (--projfrac 0.5 will project it to the middle between the
white and
pial) >> >>> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: >>> >>> External Email - Use Caution >>> >>> Dear Freesurfer, >>> >>> I have a batch of myelin water image (MWI) from patients and >>> controls, and trying to have inflated cortex registered on
standard
>>> surface for GLM (Qdec). >>> >>> With the commandlines below i get my inflated surface of MWI
map of
>>> my patients and controls. >>> >>> 1-using bbregister to put MWI into FS space and to calculate >>> register.dat: >>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg
register.dat
>>> --o mwf_FS --t1 >>> >>> 2-using mri_vol2surf to extract inflated surface of MWI: >>> mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 >>> --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type >>> paint--inflated (*or*--surf sphere) >>> >>> However the tksurfer could not open the inflated surface and the >>> error message is: >>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! >>> Probably trying to use a scalar data file as a surface!* >>> >>> I used the commandline below for #2: >>> mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o >>> mwf-lh.w --out_type paint >>> and i got the error: >>> >>> *ERROR: MRISread: file >>> '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has
many
>>> more faces than vertices!** >>> Probably trying to use a scalar data file as a surface!* >>> * >>> * >>> As tksurfer could not open my surfaces with errors above, i think >>> perhaps the vol2surf procedure is not done properly. Where is the >>> problem? i need to get the inflated cortex and then putting ob >>> sphere (using mris_sphere) and the registering to standard
surface
>>> using mris_register for GLM in Qdec, right? >>> >>> >>> It is two weeks i am struggling with these commands, any helps >>> highly appreciated. * >>> * >>> * >>> * >>> * >>> * >>> Best, >>> Reza >>> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners
Compliance
>> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the
sender
>> and properly >> dispose of the e-mail. >> >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and
Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main,
Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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one computes the average, the other computes the maximum
On 7/29/19 9:03 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Dear Doug,
I appreciat if you reply my question in the previous e-mail with this:
can not i use projfrac-avg in mris_preproc? Is --projfrac-max min max delta just the same?
Best,
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza Rahmanzadeh reza.rahmanzadeh@unibas.ch *Sent:* Monday, July 29, 2019 11:37:46 AM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use Caution
Dear Doug,
Thanks, the tutorial was super helpful. As i would compare the MWF value in cortex between control subjects and patients. Now my problem is how to make the contrast matrix for mris_preproc to do the comparison in both direction (in 1, the outcome should be voxels in which MWf value in control>patients & in 2, reversed).
The explanations in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre... is for one group analysis and in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is not clear about contrast.
I remember for -randomise command-line, there was possibility to make contrast and design matrix (something like FSGD) via design_ttest2. Can i use still design_ttest2 for producing contrast and design matrix?
Best,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> *Sent:* Wednesday, July 17, 2019 5:31:27 PM *To:* Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help Ah, I see. Try this tutorial. It is for fMRI, but it applies to any modality https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
to clarify better, i need to compare myelin water fraction in cortex of control and patients to find out the areas with reduced MWF in patients cortex compared with controls, that is the reason i want to have cortex in inflated format.
For this reason i used bbregister to have register.dat, and then mri_vol2surf to resample MWI cortex to surface. As i need to have all surfaces in fsaverage space for group analysis, i am using mri_preproc7mri_surf2surf (according to the group analysis wiki you sent me).
*From:* freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh
<reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Wednesday, July 17, 2019 4:26:21 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use Caution
I am trying to compare MWI(sampled on the surface) between couple patients and controls using group analysis, therefore i need to have all inflated surface_on_same space (according to the wiki of group analysis you sent me, i should use mris_preproc to put my data on fsaverage).
Could you now tell me whether my mris_prepoc is right? and one other question i have asked in last email?
Thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
*Sent:* Wednesday, July 17, 2019 4:14:41 PM *To:* Reza Rahmanzadeh; Freesurfer support list;
greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] need for help It is not clear to me what you are trying to do. Do you want to do a morphometry study (ie, comparing thickness, area, and/or volume across subjects)? Or do you want to compare MWI (sampled on the surface) across subjects?
On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Dear Doug,
I took the back slash away and ran
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white** MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white** ERROR: reading curvature file*
Then i changed it to --meas : mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgz --meas area
Then, as i need to register my the inflated cortex of myelin water image (MWI) to the surface_registered_on_fsaverage (could it be the output of command-line above?), should i use this output "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling myelin water image to lh.white of my subject FSP10 before registration to fsaverage) for mri_surf2surf (to resample the latter to the former, to have MWI to surface_fsaverage)
Looking forward to answers
Thanks
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza
Rahmanzadeh <reza.rahmanzadeh@unibas.ch
mailto:reza.rahmanzadeh@unibas.ch>
*Sent:* Wednesday, July 17, 2019 9:56:00 AM *To:* Freesurfer support list *Cc:* DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help External Email - Use Caution
Thanks Tim,
Then if i would resample my data to fsaverage and surfaces are of main importance to my work, what should i use for -meas ?
Reza
On 17 Jul 2019, at 09:39, Tim Schäfer <ts+ml@rcmd.org
mailto:ts+ml@rcmd.org> wrote:
External Email - Use Caution
I guess '-meas' expects a measure (like 'thickness' or 'area'), not
a surface (like 'white').
Best,
Tim
On July 17, 2019 at 9:03 AM Reza Rahmanzadeh
<reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> wrote:
External Email - Use Caution
I removed the back slash and the command line i executed is:
mris_preproc --target fsaverage --hemi lh --s FSP010 --out
lh.FSP10.white.mgh --meas white
but i got the error:
Reading curvature file
/usr/local/freesurfer/subjects/FSP010/surf/lh.white
MRISreadBinaryCurvature: incompatible vertex number in file
/usr/local/freesurfer/subjects/FSP010/surf/lh.white
ERROR: reading curvature file
I have added --srcfmt mgh as the last argument, but again i got
the error:
Reading source surface reg
/usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg
Loading source data No such file or directory ERROR: could not read
/usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3
What is wrong with my mris_prepoc command line?
Reza
From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
Sent: Tuesday, July 16, 2019 10:01:15 PM To: Reza Rahmanzadeh; Freesurfer support list;
greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
Subject: Re: need for help
don't include the back slash (ie, fsaverage not fsaverage/ same
for FSP010)
On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Thanks a lot Doug,
I started to proceed with FS group analysis wiki you sent to me. Accordingly, i have to resample all my data (output of recon-all
for a
given subject for example) into fsaverage using mris_preproc. My commandline for a subject was:
mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out lh.FSP10.white.mgh --meas white
and i got the error:
*Reading source surface reg
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
No such file or directory mri_surf2surf: could not read surface
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
No such file or directory*
As there was no**lh.fsaverage/.sphere.reg* *folder, i found one
file
in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder with the name lh.fsaverage and i copied/pasted the mentiomed file
into
this folder and i changed the file name to: ./sphere.reg. I got the error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere*
What is the problem with my mris_preproc command-line?
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> *Sent:* Tuesday, July 16, 2019 7:01:30 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] need for help
> On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > (I assume now we are discussing in FS list, if no please let
me how
> possible?) > > > Thanks Doug, now i could see the inflate surface, this means
that my
> mri_vol2surf works well. As i would do GLM analysis over inflated > cortex of patients and controls in Qdec, > > > 1- should i input my surfaces to Qdec as inflated surface or just > inputting the output_of_vol2surf.mgz to Qdec? > > if inflated one is the input, then how could i get them?
mris_inflate
> gives error. > QDEC is no longer being supported. Use the command line stream (mri_surf2surf, mri_glmfit, mri_glmfit-sim). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > > > 2- should i input all patients and controls surfaces in standard > surface before entering to Qdec? > > > 3- I would like to resample whole cortex (whole cortical
thickness, in
> other words: the average of all projfrac between 0 and 1), is it > possible? or i am limited to resample one given depth of
cortex into
> inflated surface only? > Run mri_vol2surf with --help and look for --projfrac-avg > > > thanks a lot, > > Reza > > >
> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
> *Sent:* Tuesday, July 16, 2019 6:22:56 PM > *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: need for help > The command should be something like > tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz > Also, tksurfer is also obsolete (but should work). You should be
using
> freeview (or tksurferfv, a freeview front end that takes the same > command line args as tksurfer) > Also, please remember to respond to the fs list > >> On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote: >> >> External Email - Use Caution >> >> I got the mri_vol2surf output with .mgz: >> >> >> my tksurfer command: >> >> tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of >> mri_vol2surf was lh.inflated_MWI.mgz) >> >> >> and the error i got: >> >> *freadFloat: fread failed** >> No such file or directory* >> >> To me, opening the surfer in tksurfer is only a way to get
sure my
>> vol2surf worked well. the main problem is i got this error
for all
>> mris_smooth, mris_inflate, mris_sphere ... >> >> >> Do you think that means the output of mri_vol2surf is not
correct, or
>> otherwise i could proceed with that , even when tksurfer
could not
>> open it, for GLM in Qdec? >> >> >> Thanks, >> >> Reza >> >>
>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>> *Sent:* Tuesday, July 16, 2019 6:01:15 PM >> *To:* Reza Rahmanzadeh >> *Subject:* Re: need for help >> what is your tksurfer command line? Also, the .w file is somewhat >> obsolete (it should still work); instead you can use .mgz
file (and
>> don't spec --paint) >> >>> On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote: >>> >>> External Email - Use Caution >>> >>> Thanks Doug, >>> >>> >>> I used the one without --inflated also, again the tksurfer
could not
>>> open it and i got the same error. Where is the problem with my
cmd.?
>>> >>> >>> In addition, i wanted to make the output of mri_vol2surf
inflated
>>> using mris_inflate but i got the same error: >>> >>> *freadFloat: fread failed >>> No such file or directory* >>> * >>> * >>> *could you let me know what is the problem in registering my mwi >>> volumes to surface that i getonly such errors.* >>> * >>> * >>> *Thanks,* >>> *reza >>> * >>> >>> >
>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>> *Cc:* greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu
>>> *Subject:* Re: need for help >>> Don't use --inflated. The inflated surface is not a biological >>> surface. The default is the white surface, which is the one
you want
>>> (--projfrac 0.5 will project it to the middle between the
white and
> pial) >>> >>>> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: >>>> >>>> External Email - Use Caution >>>> >>>> Dear Freesurfer, >>>> >>>> I have a batch of myelin water image (MWI) from patients and >>>> controls, and trying to have inflated cortex registered on
standard
>>>> surface for GLM (Qdec). >>>> >>>> With the commandlines below i get my inflated surface of MWI
map of
>>>> my patients and controls. >>>> >>>> 1-using bbregister to put MWI into FS space and to calculate >>>> register.dat: >>>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg
register.dat
>>>> --o mwf_FS --t1 >>>> >>>> 2-using mri_vol2surf to extract inflated surface of MWI: >>>> mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 >>>> --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type >>>> paint--inflated (*or*--surf sphere) >>>> >>>> However the tksurfer could not open the inflated surface
and the
>>>> error message is: >>>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! >>>> Probably trying to use a scalar data file as a surface!* >>>> >>>> I used the commandline below for #2: >>>> mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o >>>> mwf-lh.w --out_type paint >>>> and i got the error: >>>> >>>> *ERROR: MRISread: file >>>> '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has
many
>>>> more faces than vertices!** >>>> Probably trying to use a scalar data file as a surface!* >>>> * >>>> * >>>> As tksurfer could not open my surfaces with errors above, i
think
>>>> perhaps the vol2surf procedure is not done properly. Where
is the
>>>> problem? i need to get the inflated cortex and then putting ob >>>> sphere (using mris_sphere) and the registering to standard
surface
>>>> using mris_register for GLM in Qdec, right? >>>> >>>> >>>> It is two weeks i am struggling with these commands, any helps >>>> highly appreciated. * >>>> * >>>> * >>>> * >>>> * >>>> * >>>> Best, >>>> Reza >>>> >>> >>> The information in this e-mail is intended only for the
person to
>>> whom it is >>> addressed. If you believe this e-mail was sent to you in
error and
>>> the e-mail >>> contains patient information, please contact the Partners
Compliance
>>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was
sent to
>>> you in error >>> but does not contain patient information, please contact the
sender
>>> and properly >>> dispose of the e-mail. >>> >> >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and
Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main,
Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thanks
But mris_prepoc will not accept “projfrac-avg” and there’s an error: argument unrecognized!
Then how can i compute the average via mris_preproc? As based on tutorial, first i used tkregister/bbregister to compute the registration matrix and then i should put input images with transformation matrix in mris_preproc. I mean i shouldn’t use mri_vol2surf (that allows me to use projfrac-avg) in group analysis and that’s the reason i have problem with mris_proproc to compute the average.
What should i do?
Thanks, Reza
On 29 Jul 2019, at 23:03, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote:
one computes the average, the other computes the maximum
On 7/29/19 9:03 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Dear Doug,
I appreciat if you reply my question in the previous e-mail with this:
can not i use projfrac-avg in mris_preproc? Is --projfrac-max min max delta just the same?
Best,
Reza
------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh <reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch> *Sent:* Monday, July 29, 2019 11:37:46 AM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use Caution
Dear Doug,
Thanks, the tutorial was super helpful. As i would compare the MWF value in cortex between control subjects and patients. Now my problem is how to make the contrast matrix for mris_preproc to do the comparison in both direction (in 1, the outcome should be voxels in which MWf value in control>patients & in 2, reversed).
The explanations in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre... is for one group analysis and in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is not clear about contrast.
I remember for -randomise command-line, there was possibility to make contrast and design matrix (something like FSGD) via design_ttest2. Can i use still design_ttest2 for producing contrast and design matrix?
Best,
Reza
------------------------------------------------------------------------ *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> *Sent:* Wednesday, July 17, 2019 5:31:27 PM *To:* Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help Ah, I see. Try this tutorial. It is for fMRI, but it applies to any modality https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
to clarify better, i need to compare myelin water fraction in cortex of control and patients to find out the areas with reduced MWF in patients cortex compared with controls, that is the reason i want to have cortex in inflated format.
For this reason i used bbregister to have register.dat, and then mri_vol2surf to resample MWI cortex to surface. As i need to have all surfaces in fsaverage space for group analysis, i am using mri_preproc7mri_surf2surf (according to the group analysis wiki you sent me).
------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh <reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Wednesday, July 17, 2019 4:26:21 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
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I am trying to compare MWI(sampled on the surface) between couple patients and controls using group analysis, therefore i need to have all inflated surface_on_same space (according to the wiki of group analysis you sent me, i should use mris_preproc to put my data on fsaverage).
Could you now tell me whether my mris_prepoc is right? and one other question i have asked in last email?
Thanks a lot,
Reza
------------------------------------------------------------------------ *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> *Sent:* Wednesday, July 17, 2019 4:14:41 PM *To:* Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help It is not clear to me what you are trying to do. Do you want to do a morphometry study (ie, comparing thickness, area, and/or volume across subjects)? Or do you want to compare MWI (sampled on the surface) across subjects?
On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote:
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Dear Doug,
I took the back slash away and ran
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white** MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white** ERROR: reading curvature file*
Then i changed it to --meas : mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgz --meas area
Then, as i need to register my the inflated cortex of myelin water image (MWI) to the surface_registered_on_fsaverage (could it be the output of command-line above?), should i use this output "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling myelin water image to lh.white of my subject FSP10 before registration to fsaverage) for mri_surf2surf (to resample the latter to the former, to have MWI to surface_fsaverage)
Looking forward to answers
Thanks
Reza
------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh <reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Wednesday, July 17, 2019 9:56:00 AM *To:* Freesurfer support list *Cc:* DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help External Email - Use Caution
Thanks Tim,
Then if i would resample my data to fsaverage and surfaces are of main importance to my work, what should i use for -meas ?
Reza
On 17 Jul 2019, at 09:39, Tim Schäfer <ts+ml@rcmd.orgmailto:ts+ml@rcmd.org mailto:ts+ml@rcmd.org> wrote:
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I guess '-meas' expects a measure (like 'thickness' or 'area'), not a surface (like 'white').
Best,
Tim
On July 17, 2019 at 9:03 AM Reza Rahmanzadeh <reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> wrote:
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I removed the back slash and the command line i executed is:
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got the error:
Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white ERROR: reading curvature file
I have added --srcfmt mgh as the last argument, but again i got the error: Reading source surface reg /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg Loading source data No such file or directory ERROR: could not read /usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3
What is wrong with my mris_prepoc command line?
Reza
________________________________ From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> Sent: Tuesday, July 16, 2019 10:01:15 PM To: Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Subject: Re: need for help
don't include the back slash (ie, fsaverage not fsaverage/ same for FSP010)
On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote:
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Thanks a lot Doug,
I started to proceed with FS group analysis wiki you sent to me. Accordingly, i have to resample all my data (output of recon-all for a given subject for example) into fsaverage using mris_preproc. My commandline for a subject was:
mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out lh.FSP10.white.mgh --meas white
and i got the error:
* * *Reading source surface reg
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory mri_surf2surf: could not read surface
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg No such file or directory* * * As there was no**lh.fsaverage/.sphere.reg* *folder, i found one file in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder with the name lh.fsaverage and i copied/pasted the mentiomed file into this folder and i changed the file name to: ./sphere.reg. I got the error: * * *Reading curvature file /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere* * * * * What is the problem with my mris_preproc command-line?
Reza
------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> *Sent:* Tuesday, July 16, 2019 7:01:30 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote:
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(I assume now we are discussing in FS list, if no please let me how possible?)
Thanks Doug, now i could see the inflate surface, this means that my mri_vol2surf works well. As i would do GLM analysis over inflated cortex of patients and controls in Qdec,
1- should i input my surfaces to Qdec as inflated surface or just inputting the output_of_vol2surf.mgz to Qdec?
if inflated one is the input, then how could i get them? mris_inflate gives error.
QDEC is no longer being supported. Use the command line stream (mri_surf2surf, mri_glmfit, mri_glmfit-sim). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
2- should i input all patients and controls surfaces in standard surface before entering to Qdec?
3- I would like to resample whole cortex (whole cortical thickness, in other words: the average of all projfrac between 0 and 1), is it possible? or i am limited to resample one given depth of cortex into inflated surface only?
Run mri_vol2surf with --help and look for --projfrac-avg
thanks a lot,
Reza
------------------------------------------------------------------------ *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> *Sent:* Tuesday, July 16, 2019 6:22:56 PM *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: need for help The command should be something like tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz Also, tksurfer is also obsolete (but should work). You should be using freeview (or tksurferfv, a freeview front end that takes the same command line args as tksurfer) Also, please remember to respond to the fs list
On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote:
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I got the mri_vol2surf output with .mgz:
my tksurfer command:
tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of mri_vol2surf was lh.inflated_MWI.mgz)
and the error i got:
*freadFloat: fread failed** No such file or directory*
To me, opening the surfer in tksurfer is only a way to get sure my vol2surf worked well. the main problem is i got this error for all mris_smooth, mris_inflate, mris_sphere ...
Do you think that means the output of mri_vol2surf is not correct, or otherwise i could proceed with that , even when tksurfer could not open it, for GLM in Qdec?
Thanks,
Reza
------------------------------------------------------------------------ *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> *Sent:* Tuesday, July 16, 2019 6:01:15 PM *To:* Reza Rahmanzadeh *Subject:* Re: need for help what is your tksurfer command line? Also, the .w file is somewhat obsolete (it should still work); instead you can use .mgz file (and don't spec --paint)
On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote:
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Thanks Doug,
I used the one without --inflated also, again the tksurfer could not open it and i got the same error. Where is the problem with my cmd.?
In addition, i wanted to make the output of mri_vol2surf inflated using mris_inflate but i got the same error:
*freadFloat: fread failed No such file or directory* * * *could you let me know what is the problem in registering my mwi volumes to surface that i getonly such errors.* * * *Thanks,* *reza *
------------------------------------------------------------------------ *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> *Sent:* Tuesday, July 16, 2019 5:37:17 PM *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu *Cc:* greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: need for help Don't use --inflated. The inflated surface is not a biological surface. The default is the white surface, which is the one you want (--projfrac 0.5 will project it to the middle between the white and pial)
On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote:
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Dear Freesurfer,
I have a batch of myelin water image (MWI) from patients and controls, and trying to have inflated cortex registered on standard surface for GLM (Qdec).
With the commandlines below i get my inflated surface of MWI map of my patients and controls.
1-using bbregister to put MWI into FS space and to calculate register.dat: bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg register.dat --o mwf_FS --t1
2-using mri_vol2surf to extract inflated surface of MWI: mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type paint--inflated (*or*--surf sphere)
However the tksurfer could not open the inflated surface and the error message is: *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface!*
I used the commandline below for #2: mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o mwf-lh.w --out_type paint and i got the error:
*ERROR: MRISread: file '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has many more faces than vertices!** Probably trying to use a scalar data file as a surface!* * * As tksurfer could not open my surfaces with errors above, i think perhaps the vol2surf procedure is not done properly. Where is the problem? i need to get the inflated cortex and then putting ob sphere (using mris_sphere) and the registering to standard surface using mris_register for GLM in Qdec, right?
It is two weeks i am struggling with these commands, any helps highly appreciated. * * * * * * Best, Reza
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-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Oh, I guess that's a problem! I've created a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc See if that works. You should compare the output to using the max or -projfrac 0.5 to make sure they are at least similar since I have not run it even once:)
On 7/29/19 5:08 PM, Reza Rahmanzadeh wrote:
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Thanks
But mris_prepoc will not accept “projfrac-avg” and there’s an error: argument unrecognized!
Then how can i compute the average via mris_preproc? As based on tutorial, first i used tkregister/bbregister to compute the registration matrix and then i should put input images with transformation matrix in mris_preproc. I mean i shouldn’t use mri_vol2surf (that allows me to use projfrac-avg) in group analysis and that’s the reason i have problem with mris_proproc to compute the average.
What should i do?
Thanks, Reza
On 29 Jul 2019, at 23:03, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
one computes the average, the other computes the maximum
On 7/29/19 9:03 AM, Reza Rahmanzadeh wrote:
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Dear Doug,
I appreciat if you reply my question in the previous e-mail with this:
can not i use projfrac-avg in mris_preproc? Is --projfrac-max min max delta just the same?
Best,
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh <reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Monday, July 29, 2019 11:37:46 AM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
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Dear Doug,
Thanks, the tutorial was super helpful. As i would compare the MWF value in cortex between control subjects and patients. Now my problem is how to make the contrast matrix for mris_preproc to do the comparison in both direction (in 1, the outcome should be voxels in which MWf value in control>patients & in 2, reversed).
The explanations in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
is for one group analysis and in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is not clear about contrast.
I remember for -randomise command-line, there was possibility to make contrast and design matrix (something like FSGD) via design_ttest2. Can i use still design_ttest2 for producing contrast and design matrix?
Best,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> *Sent:* Wednesday, July 17, 2019 5:31:27 PM *To:* Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help Ah, I see. Try this tutorial. It is for fMRI, but it applies to any modality https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
to clarify better, i need to compare myelin water fraction in cortex of control and patients to find out the areas with reduced MWF in patients cortex compared with controls, that is the reason i want to have cortex in inflated format.
For this reason i used bbregister to have register.dat, and then mri_vol2surf to resample MWI cortex to surface. As i need to have all surfaces in fsaverage space for group analysis, i am using mri_preproc7mri_surf2surf (according to the group analysis wiki you sent me).
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh
<reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Wednesday, July 17, 2019 4:26:21 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use Caution
I am trying to compare MWI(sampled on the surface) between couple patients and controls using group analysis, therefore i need to have all inflated surface_on_same space (according to the wiki of group analysis you sent me, i should use mris_preproc to put my data on fsaverage).
Could you now tell me whether my mris_prepoc is right? and one other question i have asked in last email?
Thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
*Sent:* Wednesday, July 17, 2019 4:14:41 PM *To:* Reza Rahmanzadeh; Freesurfer support list;
greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] need for help It is not clear to me what you are trying to do. Do you want to do a morphometry study (ie, comparing thickness, area, and/or volume across subjects)? Or do you want to compare MWI (sampled on the surface) across subjects?
On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote:
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Dear Doug,
I took the back slash away and ran
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white** MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white** ERROR: reading curvature file*
Then i changed it to --meas : mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgz --meas area
Then, as i need to register my the inflated cortex of myelin water image (MWI) to the surface_registered_on_fsaverage (could it be the output of command-line above?), should i use this output "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling myelin water image to lh.white of my subject FSP10 before registration to fsaverage) for mri_surf2surf (to resample the latter to the former, to have MWI to surface_fsaverage)
Looking forward to answers
Thanks
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza
Rahmanzadeh <reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch
mailto:reza.rahmanzadeh@unibas.ch>
*Sent:* Wednesday, July 17, 2019 9:56:00 AM *To:* Freesurfer support list *Cc:* DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help External Email - Use Caution
Thanks Tim,
Then if i would resample my data to fsaverage and surfaces are of main importance to my work, what should i use for -meas ?
Reza
On 17 Jul 2019, at 09:39, Tim Schäfer <ts+ml@rcmd.org mailto:ts+ml@rcmd.org
mailto:ts+ml@rcmd.org> wrote:
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I guess '-meas' expects a measure (like 'thickness' or 'area'), not
a surface (like 'white').
Best,
Tim
> On July 17, 2019 at 9:03 AM Reza Rahmanzadeh
<reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> wrote:
> > > External Email - Use Caution > > I removed the back slash and the command line i executed is: > > > mris_preproc --target fsaverage --hemi lh --s FSP010 --out
lh.FSP10.white.mgh --meas white
> > > but i got the error: > > Reading curvature file
/usr/local/freesurfer/subjects/FSP010/surf/lh.white
> MRISreadBinaryCurvature: incompatible vertex number in file
/usr/local/freesurfer/subjects/FSP010/surf/lh.white
> ERROR: reading curvature file > > I have added --srcfmt mgh as the last argument, but again i got
the error:
> Reading source surface reg
/usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg
> Loading source data > No such file or directory > ERROR: could not read
/usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3
> > > What is wrong with my mris_prepoc command line? > > Reza > > > ________________________________ > From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
> Sent: Tuesday, July 16, 2019 10:01:15 PM > To: Reza Rahmanzadeh; Freesurfer support list;
greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
> Subject: Re: need for help > > don't include the back slash (ie, fsaverage not fsaverage/ same
for FSP010)
> >> On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote: >> >> External Email - Use Caution >> >> Thanks a lot Doug, >> >> >> I started to proceed with FS group analysis wiki you sent to me. >> Accordingly, i have to resample all my data (output of recon-all
for a
>> given subject for example) into fsaverage using mris_preproc. My >> commandline for a subject was: >> >> mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out >> lh.FSP10.white.mgh --meas white >> >> >> and i got the error: >> >> * >> * >> *Reading source surface reg >>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>> No such file or directory >> mri_surf2surf: could not read surface >>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>> No such file or directory* >> * >> * >> As there was no**lh.fsaverage/.sphere.reg* *folder, i found one
file
>> in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder >> with the name lh.fsaverage and i copied/pasted the mentiomed file
into
>> this folder and i changed the file name to: ./sphere.reg. I got the >> error: >> * >> * >> *Reading curvature file >> /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere >> MRISreadBinaryCurvature: incompatible vertex number in file >> /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere* >> * >> * >> * >> * >> What is the problem with my mris_preproc command-line? >> >> Reza >> >>
>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu >> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
>> <freesurfer-bounces@nmr.mgh.harvard.edu >> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
>> N.,Ph.D. <DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> >> *Sent:* Tuesday, July 16, 2019 7:01:30 PM >> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>> *Subject:* Re: [Freesurfer] need for help >> >> >>> On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote: >>> >>> External Email - Use Caution >>> >>> (I assume now we are discussing in FS list, if no please let
me how
>>> possible?) >>> >>> >>> Thanks Doug, now i could see the inflate surface, this means
that my
>>> mri_vol2surf works well. As i would do GLM analysis over inflated >>> cortex of patients and controls in Qdec, >>> >>> >>> 1- should i input my surfaces to Qdec as inflated surface or just >>> inputting the output_of_vol2surf.mgz to Qdec? >>> >>> if inflated one is the input, then how could i get them?
mris_inflate
>>> gives error. >>> >> QDEC is no longer being supported. Use the command line stream >> (mri_surf2surf, mri_glmfit, mri_glmfit-sim). >> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis >>> >>> >>> 2- should i input all patients and controls surfaces in standard >>> surface before entering to Qdec? >>> >>> >>> 3- I would like to resample whole cortex (whole cortical
thickness, in
>>> other words: the average of all projfrac between 0 and 1), is it >>> possible? or i am limited to resample one given depth of
cortex into
>>> inflated surface only? >>> >> Run mri_vol2surf with --help and look for --projfrac-avg >>> >>> >>> thanks a lot, >>> >>> Reza >>> >>> >>>
>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>> *Sent:* Tuesday, July 16, 2019 6:22:56 PM >>> *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu >>> mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
>>> *Subject:* Re: need for help >>> The command should be something like >>> tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz >>> Also, tksurfer is also obsolete (but should work). You should be
using
>>> freeview (or tksurferfv, a freeview front end that takes the same >>> command line args as tksurfer) >>> Also, please remember to respond to the fs list >>> >>>> On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote: >>>> >>>> External Email - Use Caution >>>> >>>> I got the mri_vol2surf output with .mgz: >>>> >>>> >>>> my tksurfer command: >>>> >>>> tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of >>>> mri_vol2surf was lh.inflated_MWI.mgz) >>>> >>>> >>>> and the error i got: >>>> >>>> *freadFloat: fread failed** >>>> No such file or directory* >>>> >>>> To me, opening the surfer in tksurfer is only a way to get
sure my
>>>> vol2surf worked well. the main problem is i got this error
for all
>>>> mris_smooth, mris_inflate, mris_sphere ... >>>> >>>> >>>> Do you think that means the output of mri_vol2surf is not
correct, or
>>>> otherwise i could proceed with that , even when tksurfer
could not
>>>> open it, for GLM in Qdec? >>>> >>>> >>>> Thanks, >>>> >>>> Reza >>>> >>>> >>
>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>> *Sent:* Tuesday, July 16, 2019 6:01:15 PM >>>> *To:* Reza Rahmanzadeh >>>> *Subject:* Re: need for help >>>> what is your tksurfer command line? Also, the .w file is somewhat >>>> obsolete (it should still work); instead you can use .mgz
file (and
>>>> don't spec --paint) >>>> >>>>> On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> Thanks Doug, >>>>> >>>>> >>>>> I used the one without --inflated also, again the tksurfer
could not
>>>>> open it and i got the same error. Where is the problem with my
cmd.?
>>>>> >>>>> >>>>> In addition, i wanted to make the output of mri_vol2surf
inflated
>>>>> using mris_inflate but i got the same error: >>>>> >>>>> *freadFloat: fread failed >>>>> No such file or directory* >>>>> * >>>>> * >>>>> *could you let me know what is the problem in registering my mwi >>>>> volumes to surface that i getonly such errors.* >>>>> * >>>>> * >>>>> *Thanks,* >>>>> *reza >>>>> * >>>>> >>>>> >>>
>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >>>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >>>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>> *Cc:* greve@nmr.mgh.harvard.edu >>>>> mailto:greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu
>>>>> *Subject:* Re: need for help >>>>> Don't use --inflated. The inflated surface is not a biological >>>>> surface. The default is the white surface, which is the one
you want
>>>>> (--projfrac 0.5 will project it to the middle between the
white and
>>> pial) >>>>> >>>>>> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: >>>>>> >>>>>> External Email - Use Caution >>>>>> >>>>>> Dear Freesurfer, >>>>>> >>>>>> I have a batch of myelin water image (MWI) from patients and >>>>>> controls, and trying to have inflated cortex registered on
standard
>>>>>> surface for GLM (Qdec). >>>>>> >>>>>> With the commandlines below i get my inflated surface of MWI
map of
>>>>>> my patients and controls. >>>>>> >>>>>> 1-using bbregister to put MWI into FS space and to calculate >>>>>> register.dat: >>>>>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg
register.dat
>>>>>> --o mwf_FS --t1 >>>>>> >>>>>> 2-using mri_vol2surf to extract inflated surface of MWI: >>>>>> mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 >>>>>> --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type >>>>>> paint--inflated (*or*--surf sphere) >>>>>> >>>>>> However the tksurfer could not open the inflated surface
and the
>>>>>> error message is: >>>>>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! >>>>>> Probably trying to use a scalar data file as a surface!* >>>>>> >>>>>> I used the commandline below for #2: >>>>>> mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o >>>>>> mwf-lh.w --out_type paint >>>>>> and i got the error: >>>>>> >>>>>> *ERROR: MRISread: file >>>>>> '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has
many
>>>>>> more faces than vertices!** >>>>>> Probably trying to use a scalar data file as a surface!* >>>>>> * >>>>>> * >>>>>> As tksurfer could not open my surfaces with errors above, i
think
>>>>>> perhaps the vol2surf procedure is not done properly. Where
is the
>>>>>> problem? i need to get the inflated cortex and then putting ob >>>>>> sphere (using mris_sphere) and the registering to standard
surface
>>>>>> using mris_register for GLM in Qdec, right? >>>>>> >>>>>> >>>>>> It is two weeks i am struggling with these commands, any helps >>>>>> highly appreciated. * >>>>>> * >>>>>> * >>>>>> * >>>>>> * >>>>>> * >>>>>> Best, >>>>>> Reza >>>>>> >>>>> >>>>> The information in this e-mail is intended only for the
person to
>>>>> whom it is >>>>> addressed. If you believe this e-mail was sent to you in
error and
>>>>> the e-mail >>>>> contains patient information, please contact the Partners
Compliance
>>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was
sent to
>>>>> you in error >>>>> but does not contain patient information, please contact the
sender
>>>>> and properly >>>>> dispose of the e-mail. >>>>> >>>> >>> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and
Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main,
Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thanks Doug,
The script works well for projfrac-avg. but the problem is: when i use mris_preproc to assemble my MWIs and put them on fsaverage, as .fsgd file is only the order of my controls and subjects and i would have the inflated cortex of MWI on fsaverage, then anyway i have to specify my volume and registration files (tkregister2 output). Then there’s an error: i shouldn’t use both -fsgd and - iv together. Then i decided not to use fsgd file for mris_preproc and only using that for mri_glmfit. In mris_preproc, i write all “-iv volumes and registration files” in the same order as in fsgd file but i don’t write -fsgd argument. Is this way correct?
Thanks, Reza
On 29 Jul 2019, at 23:32, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote:
Oh, I guess that's a problem! I've created a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc See if that works. You should compare the output to using the max or -projfrac 0.5 to make sure they are at least similar since I have not run it even once:)
On 7/29/19 5:08 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks
But mris_prepoc will not accept “projfrac-avg” and there’s an error: argument unrecognized!
Then how can i compute the average via mris_preproc? As based on tutorial, first i used tkregister/bbregister to compute the registration matrix and then i should put input images with transformation matrix in mris_preproc. I mean i shouldn’t use mri_vol2surf (that allows me to use projfrac-avg) in group analysis and that’s the reason i have problem with mris_proproc to compute the average.
What should i do?
Thanks, Reza
On 29 Jul 2019, at 23:03, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
one computes the average, the other computes the maximum
On 7/29/19 9:03 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionDear Doug,
I appreciat if you reply my question in the previous e-mail with this:
can not i use projfrac-avg in mris_preproc? Is --projfrac-max min max delta just the same?
Best,
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh <reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Monday, July 29, 2019 11:37:46 AM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionDear Doug,
Thanks, the tutorial was super helpful. As i would compare the MWF value in cortex between control subjects and patients. Now my problem is how to make the contrast matrix for mris_preproc to do the comparison in both direction (in 1, the outcome should be voxels in which MWf value in control>patients & in 2, reversed).
The explanations in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
is for one group analysis and in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is not clear about contrast.
I remember for -randomise command-line, there was possibility to make contrast and design matrix (something like FSGD) via design_ttest2. Can i use still design_ttest2 for producing contrast and design matrix?
Best,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> *Sent:* Wednesday, July 17, 2019 5:31:27 PM *To:* Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help Ah, I see. Try this tutorial. It is for fMRI, but it applies to any modality https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote:
External Email - Use Cautionto clarify better, i need to compare myelin water fraction in cortex of control and patients to find out the areas with reduced MWF in patients cortex compared with controls, that is the reason i want to have cortex in inflated format.
For this reason i used bbregister to have register.dat, and then mri_vol2surf to resample MWI cortex to surface. As i need to have all surfaces in fsaverage space for group analysis, i am using mri_preproc7mri_surf2surf (according to the group analysis wiki you sent me).
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh
<reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Wednesday, July 17, 2019 4:26:21 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionI am trying to compare MWI(sampled on the surface) between couple patients and controls using group analysis, therefore i need to have all inflated surface_on_same space (according to the wiki of group analysis you sent me, i should use mris_preproc to put my data on fsaverage).
Could you now tell me whether my mris_prepoc is right? and one other question i have asked in last email?
Thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
*Sent:* Wednesday, July 17, 2019 4:14:41 PM *To:* Reza Rahmanzadeh; Freesurfer support list;
greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] need for help It is not clear to me what you are trying to do. Do you want to do a morphometry study (ie, comparing thickness, area, and/or volume across subjects)? Or do you want to compare MWI (sampled on the surface) across subjects?
On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionDear Doug,
I took the back slash away and ran
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white** MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white** ERROR: reading curvature file*
Then i changed it to --meas : mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgz --meas area
Then, as i need to register my the inflated cortex of myelin water image (MWI) to the surface_registered_on_fsaverage (could it be the output of command-line above?), should i use this output "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling myelin water image to lh.white of my subject FSP10 before registration to fsaverage) for mri_surf2surf (to resample the latter to the former, to have MWI to surface_fsaverage)
Looking forward to answers
Thanks
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza
Rahmanzadeh <reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch
mailto:reza.rahmanzadeh@unibas.ch>
*Sent:* Wednesday, July 17, 2019 9:56:00 AM *To:* Freesurfer support list *Cc:* DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help External Email - Use Caution
Thanks Tim,
Then if i would resample my data to fsaverage and surfaces are of main importance to my work, what should i use for -meas ?
Reza
> On 17 Jul 2019, at 09:39, Tim Schäfer <ts+ml@rcmd.org > mailto:ts+ml@rcmd.org
mailto:ts+ml@rcmd.org> wrote:
> > External Email - Use Caution > > I guess '-meas' expects a measure (like 'thickness' or 'area'), not a surface (like 'white'). > > Best, > > Tim > >> On July 17, 2019 at 9:03 AM Reza Rahmanzadeh <reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> wrote: >> >> >> External Email - Use Caution >> >> I removed the back slash and the command line i executed is: >> >> >> mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white >> >> >> but i got the error: >> >> Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white >> MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white >> ERROR: reading curvature file >> >> I have added --srcfmt mgh as the last argument, but again i got the error: >> Reading source surface reg /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg >> Loading source data >> No such file or directory >> ERROR: could not read /usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3 >> >> >> What is wrong with my mris_prepoc command line? >> >> Reza >> >> >> ________________________________ >> From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>> Sent: Tuesday, July 16, 2019 10:01:15 PM >> To: Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >> Subject: Re: need for help >> >> don't include the back slash (ie, fsaverage not fsaverage/ same for FSP010) >> >>> On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote: >>> >>> External Email - Use Caution >>> >>> Thanks a lot Doug, >>> >>> >>> I started to proceed with FS group analysis wiki you sent to me. >>> Accordingly, i have to resample all my data (output of recon-all for a >>> given subject for example) into fsaverage using mris_preproc. My >>> commandline for a subject was: >>> >>> mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out >>> lh.FSP10.white.mgh --meas white >>> >>> >>> and i got the error: >>> >>> * >>> * >>> *Reading source surface reg >>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>> No such file or directory >>> mri_surf2surf: could not read surface >>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>> No such file or directory* >>> * >>> * >>> As there was no**lh.fsaverage/.sphere.reg* *folder, i found one
file
>>> in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder >>> with the name lh.fsaverage and i copied/pasted the mentiomed file into >>> this folder and i changed the file name to: ./sphere.reg. I got the >>> error: >>> * >>> * >>> *Reading curvature file >>> /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere >>> MRISreadBinaryCurvature: incompatible vertex number in file >>> /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere* >>> * >>> * >>> * >>> * >>> What is the problem with my mris_preproc command-line? >>> >>> Reza >>> >>>
>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
>>> <freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
>>> N.,Ph.D. <DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> >>> *Sent:* Tuesday, July 16, 2019 7:01:30 PM >>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>> *Subject:* Re: [Freesurfer] need for help >>> >>> >>>> On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote: >>>> >>>> External Email - Use Caution >>>> >>>> (I assume now we are discussing in FS list, if no please let
me how
>>>> possible?) >>>> >>>> >>>> Thanks Doug, now i could see the inflate surface, this means
that my
>>>> mri_vol2surf works well. As i would do GLM analysis over inflated >>>> cortex of patients and controls in Qdec, >>>> >>>> >>>> 1- should i input my surfaces to Qdec as inflated surface or just >>>> inputting the output_of_vol2surf.mgz to Qdec? >>>> >>>> if inflated one is the input, then how could i get them? mris_inflate >>>> gives error. >>>> >>> QDEC is no longer being supported. Use the command line stream >>> (mri_surf2surf, mri_glmfit, mri_glmfit-sim). >>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis >>>> >>>> >>>> 2- should i input all patients and controls surfaces in standard >>>> surface before entering to Qdec? >>>> >>>> >>>> 3- I would like to resample whole cortex (whole cortical thickness, in >>>> other words: the average of all projfrac between 0 and 1), is it >>>> possible? or i am limited to resample one given depth of
cortex into
>>>> inflated surface only? >>>> >>> Run mri_vol2surf with --help and look for --projfrac-avg >>>> >>>> >>>> thanks a lot, >>>> >>>> Reza >>>> >>>> >>>>
>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>> *Sent:* Tuesday, July 16, 2019 6:22:56 PM >>>> *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu >>>> mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
>>>> *Subject:* Re: need for help >>>> The command should be something like >>>> tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz >>>> Also, tksurfer is also obsolete (but should work). You should be using >>>> freeview (or tksurferfv, a freeview front end that takes the same >>>> command line args as tksurfer) >>>> Also, please remember to respond to the fs list >>>> >>>>> On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> I got the mri_vol2surf output with .mgz: >>>>> >>>>> >>>>> my tksurfer command: >>>>> >>>>> tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of >>>>> mri_vol2surf was lh.inflated_MWI.mgz) >>>>> >>>>> >>>>> and the error i got: >>>>> >>>>> *freadFloat: fread failed** >>>>> No such file or directory* >>>>> >>>>> To me, opening the surfer in tksurfer is only a way to get
sure my
>>>>> vol2surf worked well. the main problem is i got this error
for all
>>>>> mris_smooth, mris_inflate, mris_sphere ... >>>>> >>>>> >>>>> Do you think that means the output of mri_vol2surf is not correct, or >>>>> otherwise i could proceed with that , even when tksurfer
could not
>>>>> open it, for GLM in Qdec? >>>>> >>>>> >>>>> Thanks, >>>>> >>>>> Reza >>>>> >>>>> >>>
>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>> *Sent:* Tuesday, July 16, 2019 6:01:15 PM >>>>> *To:* Reza Rahmanzadeh >>>>> *Subject:* Re: need for help >>>>> what is your tksurfer command line? Also, the .w file is somewhat >>>>> obsolete (it should still work); instead you can use .mgz
file (and
>>>>> don't spec --paint) >>>>> >>>>>> On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote: >>>>>> >>>>>> External Email - Use Caution >>>>>> >>>>>> Thanks Doug, >>>>>> >>>>>> >>>>>> I used the one without --inflated also, again the tksurfer could not >>>>>> open it and i got the same error. Where is the problem with my cmd.? >>>>>> >>>>>> >>>>>> In addition, i wanted to make the output of mri_vol2surf
inflated
>>>>>> using mris_inflate but i got the same error: >>>>>> >>>>>> *freadFloat: fread failed >>>>>> No such file or directory* >>>>>> * >>>>>> * >>>>>> *could you let me know what is the problem in registering my mwi >>>>>> volumes to surface that i getonly such errors.* >>>>>> * >>>>>> * >>>>>> *Thanks,* >>>>>> *reza >>>>>> * >>>>>> >>>>>> >>>>
>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>>> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >>>>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>> *Cc:* greve@nmr.mgh.harvard.edu >>>>>> mailto:greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu
>>>>>> *Subject:* Re: need for help >>>>>> Don't use --inflated. The inflated surface is not a biological >>>>>> surface. The default is the white surface, which is the one you want >>>>>> (--projfrac 0.5 will project it to the middle between the white and >>>> pial) >>>>>> >>>>>>> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: >>>>>>> >>>>>>> External Email - Use Caution >>>>>>> >>>>>>> Dear Freesurfer, >>>>>>> >>>>>>> I have a batch of myelin water image (MWI) from patients and >>>>>>> controls, and trying to have inflated cortex registered on standard >>>>>>> surface for GLM (Qdec). >>>>>>> >>>>>>> With the commandlines below i get my inflated surface of MWI map of >>>>>>> my patients and controls. >>>>>>> >>>>>>> 1-using bbregister to put MWI into FS space and to calculate >>>>>>> register.dat: >>>>>>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg register.dat >>>>>>> --o mwf_FS --t1 >>>>>>> >>>>>>> 2-using mri_vol2surf to extract inflated surface of MWI: >>>>>>> mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 >>>>>>> --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type >>>>>>> paint--inflated (*or*--surf sphere) >>>>>>> >>>>>>> However the tksurfer could not open the inflated surface
and the
>>>>>>> error message is: >>>>>>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! >>>>>>> Probably trying to use a scalar data file as a surface!* >>>>>>> >>>>>>> I used the commandline below for #2: >>>>>>> mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o >>>>>>> mwf-lh.w --out_type paint >>>>>>> and i got the error: >>>>>>> >>>>>>> *ERROR: MRISread: file >>>>>>> '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has many >>>>>>> more faces than vertices!** >>>>>>> Probably trying to use a scalar data file as a surface!* >>>>>>> * >>>>>>> * >>>>>>> As tksurfer could not open my surfaces with errors above, i
think
>>>>>>> perhaps the vol2surf procedure is not done properly. Where
is the
>>>>>>> problem? i need to get the inflated cortex and then putting ob >>>>>>> sphere (using mris_sphere) and the registering to standard surface >>>>>>> using mris_register for GLM in Qdec, right? >>>>>>> >>>>>>> >>>>>>> It is two weeks i am struggling with these commands, any helps >>>>>>> highly appreciated. * >>>>>>> * >>>>>>> * >>>>>>> * >>>>>>> * >>>>>>> * >>>>>>> Best, >>>>>>> Reza >>>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the
person to
>>>>>> whom it is >>>>>> addressed. If you believe this e-mail was sent to you in
error and
>>>>>> the e-mail >>>>>> contains patient information, please contact the Partners Compliance >>>>>> HelpLine at >>>>>> http://www.partners.org/complianceline . If the e-mail was
sent to
>>>>>> you in error >>>>>> but does not contain patient information, please contact the sender >>>>>> and properly >>>>>> dispose of the e-mail. >>>>>> >>>>> >>>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Dr. Tim Schäfer > Postdoc Computational Neuroimaging > Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy > University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
... One problem when i use the new mris_preproc:
Always the output of mri_glmfit when the input is the result of new mris_preproc is:
Found 0 voxels in mask ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input
I think it means that something is perhaps wrong with the script. I tried both projfrac 0.5 and projfrac-avg 0 1 0.25 and i got the same error. I did not get the error when i used old mris_preproc using projfrac 0.5.
The other thing that could be the reason is my fsgd file. I have problem how to specify the name of subjects, Now it is sth like:
GroupDescriptorFile 1 Class Group1 CLASS Group2 Input FSC001 Group1 Input FSC002 Group1 Input FSC003 Group1 .
.
.
Input FSP001 Group2 Input FSP002 Group2 Input FSP003 Group2 .
.
The oeder is thew same with mris_preproc, now the subject name is FSC0xx for controls and FSP00x for patients, these are the name of folders containing FS outputs, but my input volume is MWIs and the registration files are not stored in this folder. Does it matter how to name subjects when i am using fsgd file only in mri_glmfit ( to get aware of order)?
Thanks,
Reza
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza Rahmanzadeh reza.rahmanzadeh@unibas.ch Sent: Tuesday, July 30, 2019 2:44:25 PM To: Greve, Douglas N.,Ph.D. Cc: Freesurfer support list; greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] need for help
External Email - Use Caution
Thanks Doug,
The script works well for projfrac-avg. but the problem is: when i use mris_preproc to assemble my MWIs and put them on fsaverage, as .fsgd file is only the order of my controls and subjects and i would have the inflated cortex of MWI on fsaverage, then anyway i have to specify my volume and registration files (tkregister2 output). Then there’s an error: i shouldn’t use both -fsgd and - iv together. Then i decided not to use fsgd file for mris_preproc and only using that for mri_glmfit. In mris_preproc, i write all “-iv volumes and registration files” in the same order as in fsgd file but i don’t write -fsgd argument. Is this way correct?
Thanks, Reza
On 29 Jul 2019, at 23:32, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote:
Oh, I guess that's a problem! I've created a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc See if that works. You should compare the output to using the max or -projfrac 0.5 to make sure they are at least similar since I have not run it even once:)
On 7/29/19 5:08 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks
But mris_prepoc will not accept “projfrac-avg” and there’s an error: argument unrecognized!
Then how can i compute the average via mris_preproc? As based on tutorial, first i used tkregister/bbregister to compute the registration matrix and then i should put input images with transformation matrix in mris_preproc. I mean i shouldn’t use mri_vol2surf (that allows me to use projfrac-avg) in group analysis and that’s the reason i have problem with mris_proproc to compute the average.
What should i do?
Thanks, Reza
On 29 Jul 2019, at 23:03, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
one computes the average, the other computes the maximum
On 7/29/19 9:03 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionDear Doug,
I appreciat if you reply my question in the previous e-mail with this:
can not i use projfrac-avg in mris_preproc? Is --projfrac-max min max delta just the same?
Best,
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh <reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Monday, July 29, 2019 11:37:46 AM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionDear Doug,
Thanks, the tutorial was super helpful. As i would compare the MWF value in cortex between control subjects and patients. Now my problem is how to make the contrast matrix for mris_preproc to do the comparison in both direction (in 1, the outcome should be voxels in which MWf value in control>patients & in 2, reversed).
The explanations in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
is for one group analysis and in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is not clear about contrast.
I remember for -randomise command-line, there was possibility to make contrast and design matrix (something like FSGD) via design_ttest2. Can i use still design_ttest2 for producing contrast and design matrix?
Best,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> *Sent:* Wednesday, July 17, 2019 5:31:27 PM *To:* Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help Ah, I see. Try this tutorial. It is for fMRI, but it applies to any modality https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote:
External Email - Use Cautionto clarify better, i need to compare myelin water fraction in cortex of control and patients to find out the areas with reduced MWF in patients cortex compared with controls, that is the reason i want to have cortex in inflated format.
For this reason i used bbregister to have register.dat, and then mri_vol2surf to resample MWI cortex to surface. As i need to have all surfaces in fsaverage space for group analysis, i am using mri_preproc7mri_surf2surf (according to the group analysis wiki you sent me).
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh
<reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Wednesday, July 17, 2019 4:26:21 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionI am trying to compare MWI(sampled on the surface) between couple patients and controls using group analysis, therefore i need to have all inflated surface_on_same space (according to the wiki of group analysis you sent me, i should use mris_preproc to put my data on fsaverage).
Could you now tell me whether my mris_prepoc is right? and one other question i have asked in last email?
Thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
*Sent:* Wednesday, July 17, 2019 4:14:41 PM *To:* Reza Rahmanzadeh; Freesurfer support list;
greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] need for help It is not clear to me what you are trying to do. Do you want to do a morphometry study (ie, comparing thickness, area, and/or volume across subjects)? Or do you want to compare MWI (sampled on the surface) across subjects?
On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionDear Doug,
I took the back slash away and ran
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white** MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white** ERROR: reading curvature file*
Then i changed it to --meas : mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgz --meas area
Then, as i need to register my the inflated cortex of myelin water image (MWI) to the surface_registered_on_fsaverage (could it be the output of command-line above?), should i use this output "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling myelin water image to lh.white of my subject FSP10 before registration to fsaverage) for mri_surf2surf (to resample the latter to the former, to have MWI to surface_fsaverage)
Looking forward to answers
Thanks
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza
Rahmanzadeh <reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch
mailto:reza.rahmanzadeh@unibas.ch>
*Sent:* Wednesday, July 17, 2019 9:56:00 AM *To:* Freesurfer support list *Cc:* DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help External Email - Use Caution
Thanks Tim,
Then if i would resample my data to fsaverage and surfaces are of main importance to my work, what should i use for -meas ?
Reza
> On 17 Jul 2019, at 09:39, Tim Schäfer <ts+ml@rcmd.org > mailto:ts+ml@rcmd.org
mailto:ts+ml@rcmd.org> wrote:
> > External Email - Use Caution > > I guess '-meas' expects a measure (like 'thickness' or 'area'), not a surface (like 'white'). > > Best, > > Tim > >> On July 17, 2019 at 9:03 AM Reza Rahmanzadeh <reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> wrote: >> >> >> External Email - Use Caution >> >> I removed the back slash and the command line i executed is: >> >> >> mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white >> >> >> but i got the error: >> >> Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white >> MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white >> ERROR: reading curvature file >> >> I have added --srcfmt mgh as the last argument, but again i got the error: >> Reading source surface reg /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg >> Loading source data >> No such file or directory >> ERROR: could not read /usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3 >> >> >> What is wrong with my mris_prepoc command line? >> >> Reza >> >> >> ________________________________ >> From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>> Sent: Tuesday, July 16, 2019 10:01:15 PM >> To: Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >> Subject: Re: need for help >> >> don't include the back slash (ie, fsaverage not fsaverage/ same for FSP010) >> >>> On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote: >>> >>> External Email - Use Caution >>> >>> Thanks a lot Doug, >>> >>> >>> I started to proceed with FS group analysis wiki you sent to me. >>> Accordingly, i have to resample all my data (output of recon-all for a >>> given subject for example) into fsaverage using mris_preproc. My >>> commandline for a subject was: >>> >>> mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out >>> lh.FSP10.white.mgh --meas white >>> >>> >>> and i got the error: >>> >>> * >>> * >>> *Reading source surface reg >>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>> No such file or directory >>> mri_surf2surf: could not read surface >>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>> No such file or directory* >>> * >>> * >>> As there was no**lh.fsaverage/.sphere.reg* *folder, i found one
file
>>> in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder >>> with the name lh.fsaverage and i copied/pasted the mentiomed file into >>> this folder and i changed the file name to: ./sphere.reg. I got the >>> error: >>> * >>> * >>> *Reading curvature file >>> /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere >>> MRISreadBinaryCurvature: incompatible vertex number in file >>> /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere* >>> * >>> * >>> * >>> * >>> What is the problem with my mris_preproc command-line? >>> >>> Reza >>> >>>
>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
>>> <freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
>>> N.,Ph.D. <DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> >>> *Sent:* Tuesday, July 16, 2019 7:01:30 PM >>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>> *Subject:* Re: [Freesurfer] need for help >>> >>> >>>> On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote: >>>> >>>> External Email - Use Caution >>>> >>>> (I assume now we are discussing in FS list, if no please let
me how
>>>> possible?) >>>> >>>> >>>> Thanks Doug, now i could see the inflate surface, this means
that my
>>>> mri_vol2surf works well. As i would do GLM analysis over inflated >>>> cortex of patients and controls in Qdec, >>>> >>>> >>>> 1- should i input my surfaces to Qdec as inflated surface or just >>>> inputting the output_of_vol2surf.mgz to Qdec? >>>> >>>> if inflated one is the input, then how could i get them? mris_inflate >>>> gives error. >>>> >>> QDEC is no longer being supported. Use the command line stream >>> (mri_surf2surf, mri_glmfit, mri_glmfit-sim). >>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis >>>> >>>> >>>> 2- should i input all patients and controls surfaces in standard >>>> surface before entering to Qdec? >>>> >>>> >>>> 3- I would like to resample whole cortex (whole cortical thickness, in >>>> other words: the average of all projfrac between 0 and 1), is it >>>> possible? or i am limited to resample one given depth of
cortex into
>>>> inflated surface only? >>>> >>> Run mri_vol2surf with --help and look for --projfrac-avg >>>> >>>> >>>> thanks a lot, >>>> >>>> Reza >>>> >>>> >>>>
>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>> *Sent:* Tuesday, July 16, 2019 6:22:56 PM >>>> *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu >>>> mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
>>>> *Subject:* Re: need for help >>>> The command should be something like >>>> tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz >>>> Also, tksurfer is also obsolete (but should work). You should be using >>>> freeview (or tksurferfv, a freeview front end that takes the same >>>> command line args as tksurfer) >>>> Also, please remember to respond to the fs list >>>> >>>>> On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> I got the mri_vol2surf output with .mgz: >>>>> >>>>> >>>>> my tksurfer command: >>>>> >>>>> tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of >>>>> mri_vol2surf was lh.inflated_MWI.mgz) >>>>> >>>>> >>>>> and the error i got: >>>>> >>>>> *freadFloat: fread failed** >>>>> No such file or directory* >>>>> >>>>> To me, opening the surfer in tksurfer is only a way to get
sure my
>>>>> vol2surf worked well. the main problem is i got this error
for all
>>>>> mris_smooth, mris_inflate, mris_sphere ... >>>>> >>>>> >>>>> Do you think that means the output of mri_vol2surf is not correct, or >>>>> otherwise i could proceed with that , even when tksurfer
could not
>>>>> open it, for GLM in Qdec? >>>>> >>>>> >>>>> Thanks, >>>>> >>>>> Reza >>>>> >>>>> >>>
>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>> *Sent:* Tuesday, July 16, 2019 6:01:15 PM >>>>> *To:* Reza Rahmanzadeh >>>>> *Subject:* Re: need for help >>>>> what is your tksurfer command line? Also, the .w file is somewhat >>>>> obsolete (it should still work); instead you can use .mgz
file (and
>>>>> don't spec --paint) >>>>> >>>>>> On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote: >>>>>> >>>>>> External Email - Use Caution >>>>>> >>>>>> Thanks Doug, >>>>>> >>>>>> >>>>>> I used the one without --inflated also, again the tksurfer could not >>>>>> open it and i got the same error. Where is the problem with my cmd.? >>>>>> >>>>>> >>>>>> In addition, i wanted to make the output of mri_vol2surf
inflated
>>>>>> using mris_inflate but i got the same error: >>>>>> >>>>>> *freadFloat: fread failed >>>>>> No such file or directory* >>>>>> * >>>>>> * >>>>>> *could you let me know what is the problem in registering my mwi >>>>>> volumes to surface that i getonly such errors.* >>>>>> * >>>>>> * >>>>>> *Thanks,* >>>>>> *reza >>>>>> * >>>>>> >>>>>> >>>>
>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>>> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >>>>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>> *Cc:* greve@nmr.mgh.harvard.edu >>>>>> mailto:greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu
>>>>>> *Subject:* Re: need for help >>>>>> Don't use --inflated. The inflated surface is not a biological >>>>>> surface. The default is the white surface, which is the one you want >>>>>> (--projfrac 0.5 will project it to the middle between the white and >>>> pial) >>>>>> >>>>>>> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: >>>>>>> >>>>>>> External Email - Use Caution >>>>>>> >>>>>>> Dear Freesurfer, >>>>>>> >>>>>>> I have a batch of myelin water image (MWI) from patients and >>>>>>> controls, and trying to have inflated cortex registered on standard >>>>>>> surface for GLM (Qdec). >>>>>>> >>>>>>> With the commandlines below i get my inflated surface of MWI map of >>>>>>> my patients and controls. >>>>>>> >>>>>>> 1-using bbregister to put MWI into FS space and to calculate >>>>>>> register.dat: >>>>>>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg register.dat >>>>>>> --o mwf_FS --t1 >>>>>>> >>>>>>> 2-using mri_vol2surf to extract inflated surface of MWI: >>>>>>> mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 >>>>>>> --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type >>>>>>> paint--inflated (*or*--surf sphere) >>>>>>> >>>>>>> However the tksurfer could not open the inflated surface
and the
>>>>>>> error message is: >>>>>>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! >>>>>>> Probably trying to use a scalar data file as a surface!* >>>>>>> >>>>>>> I used the commandline below for #2: >>>>>>> mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o >>>>>>> mwf-lh.w --out_type paint >>>>>>> and i got the error: >>>>>>> >>>>>>> *ERROR: MRISread: file >>>>>>> '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has many >>>>>>> more faces than vertices!** >>>>>>> Probably trying to use a scalar data file as a surface!* >>>>>>> * >>>>>>> * >>>>>>> As tksurfer could not open my surfaces with errors above, i
think
>>>>>>> perhaps the vol2surf procedure is not done properly. Where
is the
>>>>>>> problem? i need to get the inflated cortex and then putting ob >>>>>>> sphere (using mris_sphere) and the registering to standard surface >>>>>>> using mris_register for GLM in Qdec, right? >>>>>>> >>>>>>> >>>>>>> It is two weeks i am struggling with these commands, any helps >>>>>>> highly appreciated. * >>>>>>> * >>>>>>> * >>>>>>> * >>>>>>> * >>>>>>> * >>>>>>> Best, >>>>>>> Reza >>>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the
person to
>>>>>> whom it is >>>>>> addressed. If you believe this e-mail was sent to you in
error and
>>>>>> the e-mail >>>>>> contains patient information, please contact the Partners Compliance >>>>>> HelpLine at >>>>>> http://www.partners.org/complianceline . If the e-mail was
sent to
>>>>>> you in error >>>>>> but does not contain patient information, please contact the sender >>>>>> and properly >>>>>> dispose of the e-mail. >>>>>> >>>>> >>>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Dr. Tim Schäfer > Postdoc Computational Neuroimaging > Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy > University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
(sorry for bombaeding you with e-mails)
It seems that the error happens only when i use NODDI diffusion image e.g. NDI map i get that error, but for MWIs the new mris_preproc works well.
Should i do anything special for NODDI images? BTW, the bbregister works well for NODDI and i entered the correct registration file into mris_preproc.
Thanks,
Reza
________________________________ From: Reza Rahmanzadeh Sent: Tuesday, July 30, 2019 6:17:22 PM To: Greve, Douglas N.,Ph.D.; Freesurfer support list Cc: greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] need for help
... One problem when i use the new mris_preproc:
Always the output of mri_glmfit when the input is the result of new mris_preproc is:
Found 0 voxels in mask ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input
I think it means that something is perhaps wrong with the script. I tried both projfrac 0.5 and projfrac-avg 0 1 0.25 and i got the same error. I did not get the error when i used old mris_preproc using projfrac 0.5.
The other thing that could be the reason is my fsgd file. I have problem how to specify the name of subjects, Now it is sth like:
GroupDescriptorFile 1 Class Group1 CLASS Group2 Input FSC001 Group1 Input FSC002 Group1 Input FSC003 Group1 .
.
.
Input FSP001 Group2 Input FSP002 Group2 Input FSP003 Group2 .
.
The oeder is thew same with mris_preproc, now the subject name is FSC0xx for controls and FSP00x for patients, these are the name of folders containing FS outputs, but my input volume is MWIs and the registration files are not stored in this folder. Does it matter how to name subjects when i am using fsgd file only in mri_glmfit ( to get aware of order)?
Thanks,
Reza
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza Rahmanzadeh reza.rahmanzadeh@unibas.ch Sent: Tuesday, July 30, 2019 2:44:25 PM To: Greve, Douglas N.,Ph.D. Cc: Freesurfer support list; greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] need for help
External Email - Use Caution
Thanks Doug,
The script works well for projfrac-avg. but the problem is: when i use mris_preproc to assemble my MWIs and put them on fsaverage, as .fsgd file is only the order of my controls and subjects and i would have the inflated cortex of MWI on fsaverage, then anyway i have to specify my volume and registration files (tkregister2 output). Then there’s an error: i shouldn’t use both -fsgd and - iv together. Then i decided not to use fsgd file for mris_preproc and only using that for mri_glmfit. In mris_preproc, i write all “-iv volumes and registration files” in the same order as in fsgd file but i don’t write -fsgd argument. Is this way correct?
Thanks, Reza
On 29 Jul 2019, at 23:32, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote:
Oh, I guess that's a problem! I've created a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc See if that works. You should compare the output to using the max or -projfrac 0.5 to make sure they are at least similar since I have not run it even once:)
On 7/29/19 5:08 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks
But mris_prepoc will not accept “projfrac-avg” and there’s an error: argument unrecognized!
Then how can i compute the average via mris_preproc? As based on tutorial, first i used tkregister/bbregister to compute the registration matrix and then i should put input images with transformation matrix in mris_preproc. I mean i shouldn’t use mri_vol2surf (that allows me to use projfrac-avg) in group analysis and that’s the reason i have problem with mris_proproc to compute the average.
What should i do?
Thanks, Reza
On 29 Jul 2019, at 23:03, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
one computes the average, the other computes the maximum
On 7/29/19 9:03 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionDear Doug,
I appreciat if you reply my question in the previous e-mail with this:
can not i use projfrac-avg in mris_preproc? Is --projfrac-max min max delta just the same?
Best,
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh <reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Monday, July 29, 2019 11:37:46 AM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionDear Doug,
Thanks, the tutorial was super helpful. As i would compare the MWF value in cortex between control subjects and patients. Now my problem is how to make the contrast matrix for mris_preproc to do the comparison in both direction (in 1, the outcome should be voxels in which MWf value in control>patients & in 2, reversed).
The explanations in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
is for one group analysis and in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is not clear about contrast.
I remember for -randomise command-line, there was possibility to make contrast and design matrix (something like FSGD) via design_ttest2. Can i use still design_ttest2 for producing contrast and design matrix?
Best,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> *Sent:* Wednesday, July 17, 2019 5:31:27 PM *To:* Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help Ah, I see. Try this tutorial. It is for fMRI, but it applies to any modality https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote:
External Email - Use Cautionto clarify better, i need to compare myelin water fraction in cortex of control and patients to find out the areas with reduced MWF in patients cortex compared with controls, that is the reason i want to have cortex in inflated format.
For this reason i used bbregister to have register.dat, and then mri_vol2surf to resample MWI cortex to surface. As i need to have all surfaces in fsaverage space for group analysis, i am using mri_preproc7mri_surf2surf (according to the group analysis wiki you sent me).
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh
<reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Wednesday, July 17, 2019 4:26:21 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionI am trying to compare MWI(sampled on the surface) between couple patients and controls using group analysis, therefore i need to have all inflated surface_on_same space (according to the wiki of group analysis you sent me, i should use mris_preproc to put my data on fsaverage).
Could you now tell me whether my mris_prepoc is right? and one other question i have asked in last email?
Thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
*Sent:* Wednesday, July 17, 2019 4:14:41 PM *To:* Reza Rahmanzadeh; Freesurfer support list;
greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] need for help It is not clear to me what you are trying to do. Do you want to do a morphometry study (ie, comparing thickness, area, and/or volume across subjects)? Or do you want to compare MWI (sampled on the surface) across subjects?
On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionDear Doug,
I took the back slash away and ran
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white
but i got error:
*Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white** MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white** ERROR: reading curvature file*
Then i changed it to --meas : mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgz --meas area
Then, as i need to register my the inflated cortex of myelin water image (MWI) to the surface_registered_on_fsaverage (could it be the output of command-line above?), should i use this output "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling myelin water image to lh.white of my subject FSP10 before registration to fsaverage) for mri_surf2surf (to resample the latter to the former, to have MWI to surface_fsaverage)
Looking forward to answers
Thanks
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza
Rahmanzadeh <reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch
mailto:reza.rahmanzadeh@unibas.ch>
*Sent:* Wednesday, July 17, 2019 9:56:00 AM *To:* Freesurfer support list *Cc:* DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help External Email - Use Caution
Thanks Tim,
Then if i would resample my data to fsaverage and surfaces are of main importance to my work, what should i use for -meas ?
Reza
> On 17 Jul 2019, at 09:39, Tim Schäfer <ts+ml@rcmd.org > mailto:ts+ml@rcmd.org
mailto:ts+ml@rcmd.org> wrote:
> > External Email - Use Caution > > I guess '-meas' expects a measure (like 'thickness' or 'area'), not a surface (like 'white'). > > Best, > > Tim > >> On July 17, 2019 at 9:03 AM Reza Rahmanzadeh <reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> wrote: >> >> >> External Email - Use Caution >> >> I removed the back slash and the command line i executed is: >> >> >> mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh --meas white >> >> >> but i got the error: >> >> Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white >> MRISreadBinaryCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/FSP010/surf/lh.white >> ERROR: reading curvature file >> >> I have added --srcfmt mgh as the last argument, but again i got the error: >> Reading source surface reg /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg >> Loading source data >> No such file or directory >> ERROR: could not read /usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3 >> >> >> What is wrong with my mris_prepoc command line? >> >> Reza >> >> >> ________________________________ >> From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>> Sent: Tuesday, July 16, 2019 10:01:15 PM >> To: Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >> Subject: Re: need for help >> >> don't include the back slash (ie, fsaverage not fsaverage/ same for FSP010) >> >>> On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote: >>> >>> External Email - Use Caution >>> >>> Thanks a lot Doug, >>> >>> >>> I started to proceed with FS group analysis wiki you sent to me. >>> Accordingly, i have to resample all my data (output of recon-all for a >>> given subject for example) into fsaverage using mris_preproc. My >>> commandline for a subject was: >>> >>> mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out >>> lh.FSP10.white.mgh --meas white >>> >>> >>> and i got the error: >>> >>> * >>> * >>> *Reading source surface reg >>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>> No such file or directory >>> mri_surf2surf: could not read surface >>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>> No such file or directory* >>> * >>> * >>> As there was no**lh.fsaverage/.sphere.reg* *folder, i found one
file
>>> in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder >>> with the name lh.fsaverage and i copied/pasted the mentiomed file into >>> this folder and i changed the file name to: ./sphere.reg. I got the >>> error: >>> * >>> * >>> *Reading curvature file >>> /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere >>> MRISreadBinaryCurvature: incompatible vertex number in file >>> /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere* >>> * >>> * >>> * >>> * >>> What is the problem with my mris_preproc command-line? >>> >>> Reza >>> >>>
>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
>>> <freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
>>> N.,Ph.D. <DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> >>> *Sent:* Tuesday, July 16, 2019 7:01:30 PM >>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>> *Subject:* Re: [Freesurfer] need for help >>> >>> >>>> On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote: >>>> >>>> External Email - Use Caution >>>> >>>> (I assume now we are discussing in FS list, if no please let
me how
>>>> possible?) >>>> >>>> >>>> Thanks Doug, now i could see the inflate surface, this means
that my
>>>> mri_vol2surf works well. As i would do GLM analysis over inflated >>>> cortex of patients and controls in Qdec, >>>> >>>> >>>> 1- should i input my surfaces to Qdec as inflated surface or just >>>> inputting the output_of_vol2surf.mgz to Qdec? >>>> >>>> if inflated one is the input, then how could i get them? mris_inflate >>>> gives error. >>>> >>> QDEC is no longer being supported. Use the command line stream >>> (mri_surf2surf, mri_glmfit, mri_glmfit-sim). >>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis >>>> >>>> >>>> 2- should i input all patients and controls surfaces in standard >>>> surface before entering to Qdec? >>>> >>>> >>>> 3- I would like to resample whole cortex (whole cortical thickness, in >>>> other words: the average of all projfrac between 0 and 1), is it >>>> possible? or i am limited to resample one given depth of
cortex into
>>>> inflated surface only? >>>> >>> Run mri_vol2surf with --help and look for --projfrac-avg >>>> >>>> >>>> thanks a lot, >>>> >>>> Reza >>>> >>>> >>>>
>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>> *Sent:* Tuesday, July 16, 2019 6:22:56 PM >>>> *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu >>>> mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
>>>> *Subject:* Re: need for help >>>> The command should be something like >>>> tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz >>>> Also, tksurfer is also obsolete (but should work). You should be using >>>> freeview (or tksurferfv, a freeview front end that takes the same >>>> command line args as tksurfer) >>>> Also, please remember to respond to the fs list >>>> >>>>> On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> I got the mri_vol2surf output with .mgz: >>>>> >>>>> >>>>> my tksurfer command: >>>>> >>>>> tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of >>>>> mri_vol2surf was lh.inflated_MWI.mgz) >>>>> >>>>> >>>>> and the error i got: >>>>> >>>>> *freadFloat: fread failed** >>>>> No such file or directory* >>>>> >>>>> To me, opening the surfer in tksurfer is only a way to get
sure my
>>>>> vol2surf worked well. the main problem is i got this error
for all
>>>>> mris_smooth, mris_inflate, mris_sphere ... >>>>> >>>>> >>>>> Do you think that means the output of mri_vol2surf is not correct, or >>>>> otherwise i could proceed with that , even when tksurfer
could not
>>>>> open it, for GLM in Qdec? >>>>> >>>>> >>>>> Thanks, >>>>> >>>>> Reza >>>>> >>>>> >>>
>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>> *Sent:* Tuesday, July 16, 2019 6:01:15 PM >>>>> *To:* Reza Rahmanzadeh >>>>> *Subject:* Re: need for help >>>>> what is your tksurfer command line? Also, the .w file is somewhat >>>>> obsolete (it should still work); instead you can use .mgz
file (and
>>>>> don't spec --paint) >>>>> >>>>>> On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote: >>>>>> >>>>>> External Email - Use Caution >>>>>> >>>>>> Thanks Doug, >>>>>> >>>>>> >>>>>> I used the one without --inflated also, again the tksurfer could not >>>>>> open it and i got the same error. Where is the problem with my cmd.? >>>>>> >>>>>> >>>>>> In addition, i wanted to make the output of mri_vol2surf
inflated
>>>>>> using mris_inflate but i got the same error: >>>>>> >>>>>> *freadFloat: fread failed >>>>>> No such file or directory* >>>>>> * >>>>>> * >>>>>> *could you let me know what is the problem in registering my mwi >>>>>> volumes to surface that i getonly such errors.* >>>>>> * >>>>>> * >>>>>> *Thanks,* >>>>>> *reza >>>>>> * >>>>>> >>>>>> >>>>
>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>>> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >>>>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>> *Cc:* greve@nmr.mgh.harvard.edu >>>>>> mailto:greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu
>>>>>> *Subject:* Re: need for help >>>>>> Don't use --inflated. The inflated surface is not a biological >>>>>> surface. The default is the white surface, which is the one you want >>>>>> (--projfrac 0.5 will project it to the middle between the white and >>>> pial) >>>>>> >>>>>>> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: >>>>>>> >>>>>>> External Email - Use Caution >>>>>>> >>>>>>> Dear Freesurfer, >>>>>>> >>>>>>> I have a batch of myelin water image (MWI) from patients and >>>>>>> controls, and trying to have inflated cortex registered on standard >>>>>>> surface for GLM (Qdec). >>>>>>> >>>>>>> With the commandlines below i get my inflated surface of MWI map of >>>>>>> my patients and controls. >>>>>>> >>>>>>> 1-using bbregister to put MWI into FS space and to calculate >>>>>>> register.dat: >>>>>>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg register.dat >>>>>>> --o mwf_FS --t1 >>>>>>> >>>>>>> 2-using mri_vol2surf to extract inflated surface of MWI: >>>>>>> mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 >>>>>>> --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type >>>>>>> paint--inflated (*or*--surf sphere) >>>>>>> >>>>>>> However the tksurfer could not open the inflated surface
and the
>>>>>>> error message is: >>>>>>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! >>>>>>> Probably trying to use a scalar data file as a surface!* >>>>>>> >>>>>>> I used the commandline below for #2: >>>>>>> mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o >>>>>>> mwf-lh.w --out_type paint >>>>>>> and i got the error: >>>>>>> >>>>>>> *ERROR: MRISread: file >>>>>>> '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has many >>>>>>> more faces than vertices!** >>>>>>> Probably trying to use a scalar data file as a surface!* >>>>>>> * >>>>>>> * >>>>>>> As tksurfer could not open my surfaces with errors above, i
think
>>>>>>> perhaps the vol2surf procedure is not done properly. Where
is the
>>>>>>> problem? i need to get the inflated cortex and then putting ob >>>>>>> sphere (using mris_sphere) and the registering to standard surface >>>>>>> using mris_register for GLM in Qdec, right? >>>>>>> >>>>>>> >>>>>>> It is two weeks i am struggling with these commands, any helps >>>>>>> highly appreciated. * >>>>>>> * >>>>>>> * >>>>>>> * >>>>>>> * >>>>>>> * >>>>>>> Best, >>>>>>> Reza >>>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the
person to
>>>>>> whom it is >>>>>> addressed. If you believe this e-mail was sent to you in
error and
>>>>>> the e-mail >>>>>> contains patient information, please contact the Partners Compliance >>>>>> HelpLine at >>>>>> http://www.partners.org/complianceline . If the e-mail was
sent to
>>>>>> you in error >>>>>> but does not contain patient information, please contact the sender >>>>>> and properly >>>>>> dispose of the e-mail. >>>>>> >>>>> >>>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Dr. Tim Schäfer > Postdoc Computational Neuroimaging > Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy > University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I don't know what is in the NODDI maps. The way mri_glmfit works is that if any subject has a 0-value at a vertex, then it will mask out that vertex for all subjects. Is NODDI something that might have a lot of 0-values? It also may be that one subject has all 0s (eg, if the regitration was really bad), so you can check the map created by mris_preproc (load it in as an overlay, then hit the configure button, then change the frame number to scroll through your subjects)
On 7/30/19 12:46 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution
(sorry for bombaeding you with e-mails)
It seems that the error happens only when i use NODDI diffusion image e.g. NDI map i get that error, but for MWIs the new mris_preproc works well.
Should i do anything special for NODDI images? BTW, the bbregister works well for NODDI and i entered the correct registration file into mris_preproc.
Thanks,
Reza
*From:* Reza Rahmanzadeh *Sent:* Tuesday, July 30, 2019 6:17:22 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
... One problem when i use the new mris_preproc:
Always the output of mri_glmfit when the input is the result of new mris_preproc is:
*F**ound 0 voxels in mask ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input*
I think it means that something is perhaps wrong with the script. I tried both projfrac 0.5 and projfrac-avg 0 1 0.25 and i got the same error. I did not get the error when i used old mris_preproc using projfrac 0.5.*
*The other thing that could be the reason is my fsgd file. I have problem how to specify the name of subjects,
Now it is sth like:
GroupDescriptorFile 1 Class Group1 CLASS Group2 Input FSC001 Group1 Input FSC002 Group1 Input FSC003 Group1 .
.
.
Input FSP001 Group2 Input FSP002 Group2 Input FSP003 Group2 .
.
The oeder is thew same with mris_preproc, now the subject name is FSC0xx for controls and FSP00x for patients, these are the name of folders containing FS outputs, but my input volume is MWIs and the registration files are not stored in this folder. Does it matter how to name subjects when i am using fsgd file only in mri_glmfit ( to get aware of order)?
Thanks,
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza Rahmanzadeh reza.rahmanzadeh@unibas.ch *Sent:* Tuesday, July 30, 2019 2:44:25 PM *To:* Greve, Douglas N.,Ph.D. *Cc:* Freesurfer support list; greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help External Email - Use Caution
Thanks Doug,
The script works well for projfrac-avg. but the problem is: when i use mris_preproc to assemble my MWIs and put them on fsaverage, as .fsgd file is only the order of my controls and subjects and i would have the inflated cortex of MWI on fsaverage, then anyway i have to specify my volume and registration files (tkregister2 output). Then there’s an error: i shouldn’t use both -fsgd and - iv together. Then i decided not to use fsgd file for mris_preproc and only using that for mri_glmfit. In mris_preproc, i write all “-iv volumes and registration files” in the same order as in fsgd file but i don’t write -fsgd argument. Is this way correct?
Thanks, Reza
On 29 Jul 2019, at 23:32, Greve, Douglas N.,Ph.D.
DGREVE@mgh.harvard.edu wrote:
Oh, I guess that's a problem! I've created a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc See if that works. You should compare the output to using the max or -projfrac 0.5 to make sure they are at least similar since I have not run it even once:)
On 7/29/19 5:08 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Thanks
But mris_prepoc will not accept “projfrac-avg” and there’s an error: argument unrecognized!
Then how can i compute the average via mris_preproc? As based on tutorial, first i used tkregister/bbregister to compute the registration matrix and then i should put input images with transformation matrix in mris_preproc. I mean i shouldn’t use mri_vol2surf (that allows me to use projfrac-avg) in group analysis and that’s the reason i have problem with mris_proproc to compute the average.
What should i do?
Thanks, Reza
On 29 Jul 2019, at 23:03, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
one computes the average, the other computes the maximum
On 7/29/19 9:03 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Dear Doug,
I appreciat if you reply my question in the previous e-mail with
this:
can not i use projfrac-avg in mris_preproc? Is --projfrac-max min max delta just the same?
Best,
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh <reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Monday, July 29, 2019 11:37:46 AM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use Caution
Dear Doug,
Thanks, the tutorial was super helpful. As i would compare the MWF value in cortex between control subjects and patients. Now my problem is how to make the contrast matrix for mris_preproc to do the comparison in both direction (in 1, the outcome should be voxels in which MWf value in control>patients & in 2, reversed).
The explanations in
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
is for one group analysis and in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is not clear about contrast.
I remember for -randomise command-line, there was possibility to make contrast and design matrix (something like FSGD) via design_ttest2. Can i use still design_ttest2 for producing contrast and design
matrix?
Best,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> *Sent:* Wednesday, July 17, 2019 5:31:27 PM *To:* Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help Ah, I see. Try this tutorial. It is for fMRI, but it applies to any modality
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
to clarify better, i need to compare myelin water fraction in cortex of control and patients to find out the areas with reduced MWF in patients cortex compared with controls, that is the reason i want to have cortex in inflated format.
For this reason i used bbregister to have register.dat, and then mri_vol2surf to resample MWI cortex to surface. As i need to
have all
surfaces in fsaverage space for group analysis, i am using mri_preproc7mri_surf2surf (according to the group analysis wiki you sent me).
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh
<reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Wednesday, July 17, 2019 4:26:21 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use Caution
I am trying to compare MWI(sampled on the surface) between couple patients and controls using group analysis, therefore i need to have all inflated surface_on_same space (according to the wiki of group analysis you sent me, i should use mris_preproc to put my data on fsaverage).
Could you now tell me whether my mris_prepoc is right? and one other question i have asked in last email?
Thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
*Sent:* Wednesday, July 17, 2019 4:14:41 PM *To:* Reza Rahmanzadeh; Freesurfer support list;
greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] need for help It is not clear to me what you are trying to do. Do you want to do a morphometry study (ie, comparing thickness, area, and/or volume
across
subjects)? Or do you want to compare MWI (sampled on the surface) across subjects?
> On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > > Dear Doug, > > > I took the back slash away and ran > > mris_preproc --target fsaverage --hemi lh --s FSP010 --out > lh.FSP10.white.mgh --meas white > > > but i got error: > > *Reading curvature file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white** > MRISreadBinaryCurvature: incompatible vertex number in file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white** > ERROR: reading curvature file* > > > Then i changed it to --meas : mris_preproc --target fsaverage
--hemi
> lh --s FSP010 --out lh.FSP10.white.mgz --meas area > > > Then, as i need to register my the inflated cortex of myelin water > image (MWI) to the surface_registered_on_fsaverage (could it be the > output of command-line above?), should i use this output > "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling > myelin water image to lh.white of my subject FSP10 before > registration to fsaverage) for mri_surf2surf (to resample the
latter
> to the former, to have MWI to surface_fsaverage) > > > > Looking forward to answers > > Thanks > > Reza > > > > > >
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu > mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu > mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza
> Rahmanzadeh <reza.rahmanzadeh@unibas.ch > mailto:reza.rahmanzadeh@unibas.ch
mailto:reza.rahmanzadeh@unibas.ch>
> *Sent:* Wednesday, July 17, 2019 9:56:00 AM > *To:* Freesurfer support list > *Cc:* DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu > *Subject:* Re: [Freesurfer] need for help > External Email - Use Caution > > Thanks Tim, > > Then if i would resample my data to fsaverage and surfaces are of > main importance to my work, what should i use for -meas ? > > Reza > >> On 17 Jul 2019, at 09:39, Tim Schäfer <ts+ml@rcmd.org >> mailto:ts+ml@rcmd.org
mailto:ts+ml@rcmd.org> wrote:
>> >> External Email - Use Caution >> >> I guess '-meas' expects a measure (like 'thickness' or
'area'), not
> a surface (like 'white'). >> >> Best, >> >> Tim >> >>> On July 17, 2019 at 9:03 AM Reza Rahmanzadeh > <reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch > mailto:reza.rahmanzadeh@unibas.ch> wrote: >>> >>> >>> External Email - Use Caution >>> >>> I removed the back slash and the command line i executed is: >>> >>> >>> mris_preproc --target fsaverage --hemi lh --s FSP010 --out > lh.FSP10.white.mgh --meas white >>> >>> >>> but i got the error: >>> >>> Reading curvature file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white >>> MRISreadBinaryCurvature: incompatible vertex number in file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white >>> ERROR: reading curvature file >>> >>> I have added --srcfmt mgh as the last argument, but again i got > the error: >>> Reading source surface reg > /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg >>> Loading source data >>> No such file or directory >>> ERROR: could not read > /usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3 >>> >>> >>> What is wrong with my mris_prepoc command line? >>> >>> Reza >>> >>> >>> ________________________________ >>> From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>> Sent: Tuesday, July 16, 2019 10:01:15 PM >>> To: Reza Rahmanzadeh; Freesurfer support list; > greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > mailto:greve@nmr.mgh.harvard.edu >>> Subject: Re: need for help >>> >>> don't include the back slash (ie, fsaverage not fsaverage/ same > for FSP010) >>> >>>> On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote: >>>> >>>> External Email - Use Caution >>>> >>>> Thanks a lot Doug, >>>> >>>> >>>> I started to proceed with FS group analysis wiki you sent to me. >>>> Accordingly, i have to resample all my data (output of recon-all > for a >>>> given subject for example) into fsaverage using mris_preproc. My >>>> commandline for a subject was: >>>> >>>> mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out >>>> lh.FSP10.white.mgh --meas white >>>> >>>> >>>> and i got the error: >>>> >>>> * >>>> * >>>> *Reading source surface reg >>>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>>> No such file or directory >>>> mri_surf2surf: could not read surface >>>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>>> No such file or directory* >>>> * >>>> * >>>> As there was no**lh.fsaverage/.sphere.reg* *folder, i found one
file
>>>> in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a
folder
>>>> with the name lh.fsaverage and i copied/pasted the mentiomed
file
> into >>>> this folder and i changed the file name to: ./sphere.reg. I
got the
>>>> error: >>>> * >>>> * >>>> *Reading curvature file >>>> /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere >>>> MRISreadBinaryCurvature: incompatible vertex number in file >>>> /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere* >>>> * >>>> * >>>> * >>>> * >>>> What is the problem with my mris_preproc command-line? >>>> >>>> Reza >>>> >>>> >
>>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu >>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
>>>> <freesurfer-bounces@nmr.mgh.harvard.edu >>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
>>>> N.,Ph.D. <DGREVE@mgh.harvard.edu >>>> mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> >>>> *Sent:* Tuesday, July 16, 2019 7:01:30 PM >>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>> *Subject:* Re: [Freesurfer] need for help >>>> >>>> >>>>> On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> (I assume now we are discussing in FS list, if no please let
me how
>>>>> possible?) >>>>> >>>>> >>>>> Thanks Doug, now i could see the inflate surface, this means
that my
>>>>> mri_vol2surf works well. As i would do GLM analysis over
inflated
>>>>> cortex of patients and controls in Qdec, >>>>> >>>>> >>>>> 1- should i input my surfaces to Qdec as inflated surface
or just
>>>>> inputting the output_of_vol2surf.mgz to Qdec? >>>>> >>>>> if inflated one is the input, then how could i get them? > mris_inflate >>>>> gives error. >>>>> >>>> QDEC is no longer being supported. Use the command line stream >>>> (mri_surf2surf, mri_glmfit, mri_glmfit-sim). >>>>
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>>>>> >>>>> >>>>> 2- should i input all patients and controls surfaces in
standard
>>>>> surface before entering to Qdec? >>>>> >>>>> >>>>> 3- I would like to resample whole cortex (whole cortical > thickness, in >>>>> other words: the average of all projfrac between 0 and 1),
is it
>>>>> possible? or i am limited to resample one given depth of
cortex into
>>>>> inflated surface only? >>>>> >>>> Run mri_vol2surf with --help and look for --projfrac-avg >>>>> >>>>> >>>>> thanks a lot, >>>>> >>>>> Reza >>>>> >>>>> >>>>> >
>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>> *Sent:* Tuesday, July 16, 2019 6:22:56 PM >>>>> *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu >>>>> mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
>>>>> *Subject:* Re: need for help >>>>> The command should be something like >>>>> tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz >>>>> Also, tksurfer is also obsolete (but should work). You
should be
> using >>>>> freeview (or tksurferfv, a freeview front end that takes
the same
>>>>> command line args as tksurfer) >>>>> Also, please remember to respond to the fs list >>>>> >>>>>> On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote: >>>>>> >>>>>> External Email - Use Caution >>>>>> >>>>>> I got the mri_vol2surf output with .mgz: >>>>>> >>>>>> >>>>>> my tksurfer command: >>>>>> >>>>>> tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of >>>>>> mri_vol2surf was lh.inflated_MWI.mgz) >>>>>> >>>>>> >>>>>> and the error i got: >>>>>> >>>>>> *freadFloat: fread failed** >>>>>> No such file or directory* >>>>>> >>>>>> To me, opening the surfer in tksurfer is only a way to get
sure my
>>>>>> vol2surf worked well. the main problem is i got this error
for all
>>>>>> mris_smooth, mris_inflate, mris_sphere ... >>>>>> >>>>>> >>>>>> Do you think that means the output of mri_vol2surf is not > correct, or >>>>>> otherwise i could proceed with that , even when tksurfer
could not
>>>>>> open it, for GLM in Qdec? >>>>>> >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Reza >>>>>> >>>>>> >>>> >
>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>>> *Sent:* Tuesday, July 16, 2019 6:01:15 PM >>>>>> *To:* Reza Rahmanzadeh >>>>>> *Subject:* Re: need for help >>>>>> what is your tksurfer command line? Also, the .w file is
somewhat
>>>>>> obsolete (it should still work); instead you can use .mgz
file (and
>>>>>> don't spec --paint) >>>>>> >>>>>>> On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote: >>>>>>> >>>>>>> External Email - Use Caution >>>>>>> >>>>>>> Thanks Doug, >>>>>>> >>>>>>> >>>>>>> I used the one without --inflated also, again the tksurfer > could not >>>>>>> open it and i got the same error. Where is the problem
with my
> cmd.? >>>>>>> >>>>>>> >>>>>>> In addition, i wanted to make the output of mri_vol2surf
inflated
>>>>>>> using mris_inflate but i got the same error: >>>>>>> >>>>>>> *freadFloat: fread failed >>>>>>> No such file or directory* >>>>>>> * >>>>>>> * >>>>>>> *could you let me know what is the problem in registering
my mwi
>>>>>>> volumes to surface that i getonly such errors.* >>>>>>> * >>>>>>> * >>>>>>> *Thanks,* >>>>>>> *reza >>>>>>> * >>>>>>> >>>>>>> >>>>> >
>>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>>>> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >>>>>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>> *Cc:* greve@nmr.mgh.harvard.edu >>>>>>> mailto:greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu
>>>>>>> *Subject:* Re: need for help >>>>>>> Don't use --inflated. The inflated surface is not a
biological
>>>>>>> surface. The default is the white surface, which is the one > you want >>>>>>> (--projfrac 0.5 will project it to the middle between the > white and >>>>> pial) >>>>>>> >>>>>>>> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: >>>>>>>> >>>>>>>> External Email - Use Caution >>>>>>>> >>>>>>>> Dear Freesurfer, >>>>>>>> >>>>>>>> I have a batch of myelin water image (MWI) from patients and >>>>>>>> controls, and trying to have inflated cortex registered on > standard >>>>>>>> surface for GLM (Qdec). >>>>>>>> >>>>>>>> With the commandlines below i get my inflated surface of MWI > map of >>>>>>>> my patients and controls. >>>>>>>> >>>>>>>> 1-using bbregister to put MWI into FS space and to calculate >>>>>>>> register.dat: >>>>>>>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg > register.dat >>>>>>>> --o mwf_FS --t1 >>>>>>>> >>>>>>>> 2-using mri_vol2surf to extract inflated surface of MWI: >>>>>>>> mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 >>>>>>>> --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type >>>>>>>> paint--inflated (*or*--surf sphere) >>>>>>>> >>>>>>>> However the tksurfer could not open the inflated surface
and the
>>>>>>>> error message is: >>>>>>>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! >>>>>>>> Probably trying to use a scalar data file as a surface!* >>>>>>>> >>>>>>>> I used the commandline below for #2: >>>>>>>> mri_vol2surf --src mwf.nii --srcreg register.dat --hemi
lh --o
>>>>>>>> mwf-lh.w --out_type paint >>>>>>>> and i got the error: >>>>>>>> >>>>>>>> *ERROR: MRISread: file >>>>>>>>
'/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has
> many >>>>>>>> more faces than vertices!** >>>>>>>> Probably trying to use a scalar data file as a surface!* >>>>>>>> * >>>>>>>> * >>>>>>>> As tksurfer could not open my surfaces with errors above, i
think
>>>>>>>> perhaps the vol2surf procedure is not done properly. Where
is the
>>>>>>>> problem? i need to get the inflated cortex and then
putting ob
>>>>>>>> sphere (using mris_sphere) and the registering to standard > surface >>>>>>>> using mris_register for GLM in Qdec, right? >>>>>>>> >>>>>>>> >>>>>>>> It is two weeks i am struggling with these commands, any
helps
>>>>>>>> highly appreciated. * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> Best, >>>>>>>> Reza >>>>>>>> >>>>>>> >>>>>>> The information in this e-mail is intended only for the
person to
>>>>>>> whom it is >>>>>>> addressed. If you believe this e-mail was sent to you in
error and
>>>>>>> the e-mail >>>>>>> contains patient information, please contact the Partners > Compliance >>>>>>> HelpLine at >>>>>>> http://www.partners.org/complianceline . If the e-mail was
sent to
>>>>>>> you in error >>>>>>> but does not contain patient information, please contact the > sender >>>>>>> and properly >>>>>>> dispose of the e-mail. >>>>>>> >>>>>> >>>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Dr. Tim Schäfer >> Postdoc Computational Neuroimaging >> Department of Child and Adolescent Psychiatry, Psychosomatics and > Psychotherapy >> University Hospital Frankfurt, Goethe University Frankfurt am
Main,
> Germany >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Dear Doug,
NODDI is diffusion imaging and we have vakue regarding neurite density (NDI in NDI map) and orientation dispersion (ODI value in ODI map). I do not know why mris_preproc works well on MWI maps but not on NODDI maps (both NDI and ODI maps). Beside using projfrac-avg 0 1 0.25 , i have run mris_preproc with projfrac 0.5 but again i got this error:
ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input
I have run mris_preproc on three patients that i am sure about registration quality, again when i scroll through them , there is no value in none of them. How that is possible?
NODDI does not have a lot of zero value but all values in cortex are between 0.2-0.4.
Thanks, Reza
________________________________ From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Wednesday, July 31, 2019 12:50:45 AM To: Reza Rahmanzadeh; Freesurfer support list Cc: greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] need for help
I don't know what is in the NODDI maps. The way mri_glmfit works is that if any subject has a 0-value at a vertex, then it will mask out that vertex for all subjects. Is NODDI something that might have a lot of 0-values? It also may be that one subject has all 0s (eg, if the regitration was really bad), so you can check the map created by mris_preproc (load it in as an overlay, then hit the configure button, then change the frame number to scroll through your subjects)
On 7/30/19 12:46 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution(sorry for bombaeding you with e-mails)
It seems that the error happens only when i use NODDI diffusion image e.g. NDI map i get that error, but for MWIs the new mris_preproc works well.
Should i do anything special for NODDI images? BTW, the bbregister works well for NODDI and i entered the correct registration file into mris_preproc.
Thanks,
Reza
*From:* Reza Rahmanzadeh *Sent:* Tuesday, July 30, 2019 6:17:22 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
... One problem when i use the new mris_preproc:
Always the output of mri_glmfit when the input is the result of new mris_preproc is:
*F**ound 0 voxels in mask ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input*
I think it means that something is perhaps wrong with the script. I tried both projfrac 0.5 and projfrac-avg 0 1 0.25 and i got the same error. I did not get the error when i used old mris_preproc using projfrac 0.5.*
*The other thing that could be the reason is my fsgd file. I have problem how to specify the name of subjects,
Now it is sth like:
GroupDescriptorFile 1 Class Group1 CLASS Group2 Input FSC001 Group1 Input FSC002 Group1 Input FSC003 Group1 .
.
.
Input FSP001 Group2 Input FSP002 Group2 Input FSP003 Group2 .
.
The oeder is thew same with mris_preproc, now the subject name is FSC0xx for controls and FSP00x for patients, these are the name of folders containing FS outputs, but my input volume is MWIs and the registration files are not stored in this folder. Does it matter how to name subjects when i am using fsgd file only in mri_glmfit ( to get aware of order)?
Thanks,
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza Rahmanzadeh reza.rahmanzadeh@unibas.ch *Sent:* Tuesday, July 30, 2019 2:44:25 PM *To:* Greve, Douglas N.,Ph.D. *Cc:* Freesurfer support list; greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help External Email - Use Caution
Thanks Doug,
The script works well for projfrac-avg. but the problem is: when i use mris_preproc to assemble my MWIs and put them on fsaverage, as .fsgd file is only the order of my controls and subjects and i would have the inflated cortex of MWI on fsaverage, then anyway i have to specify my volume and registration files (tkregister2 output). Then there’s an error: i shouldn’t use both -fsgd and - iv together. Then i decided not to use fsgd file for mris_preproc and only using that for mri_glmfit. In mris_preproc, i write all “-iv volumes and registration files” in the same order as in fsgd file but i don’t write -fsgd argument. Is this way correct?
Thanks, Reza
On 29 Jul 2019, at 23:32, Greve, Douglas N.,Ph.D.
DGREVE@mgh.harvard.edu wrote:
Oh, I guess that's a problem! I've created a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc See if that works. You should compare the output to using the max or -projfrac 0.5 to make sure they are at least similar since I have not run it even once:)
On 7/29/19 5:08 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks
But mris_prepoc will not accept “projfrac-avg” and there’s an error: argument unrecognized!
Then how can i compute the average via mris_preproc? As based on tutorial, first i used tkregister/bbregister to compute the registration matrix and then i should put input images with transformation matrix in mris_preproc. I mean i shouldn’t use mri_vol2surf (that allows me to use projfrac-avg) in group analysis and that’s the reason i have problem with mris_proproc to compute the average.
What should i do?
Thanks, Reza
On 29 Jul 2019, at 23:03, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
one computes the average, the other computes the maximum
On 7/29/19 9:03 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionDear Doug,
I appreciat if you reply my question in the previous e-mail with
this:
can not i use projfrac-avg in mris_preproc? Is --projfrac-max min max delta just the same?
Best,
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh <reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Monday, July 29, 2019 11:37:46 AM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionDear Doug,
Thanks, the tutorial was super helpful. As i would compare the MWF value in cortex between control subjects and patients. Now my problem is how to make the contrast matrix for mris_preproc to do the comparison in both direction (in 1, the outcome should be voxels in which MWf value in control>patients & in 2, reversed).
The explanations in
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
is for one group analysis and in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is not clear about contrast.
I remember for -randomise command-line, there was possibility to make contrast and design matrix (something like FSGD) via design_ttest2. Can i use still design_ttest2 for producing contrast and design
matrix?
Best,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> *Sent:* Wednesday, July 17, 2019 5:31:27 PM *To:* Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help Ah, I see. Try this tutorial. It is for fMRI, but it applies to any modality
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote:
External Email - Use Cautionto clarify better, i need to compare myelin water fraction in cortex of control and patients to find out the areas with reduced MWF in patients cortex compared with controls, that is the reason i want to have cortex in inflated format.
For this reason i used bbregister to have register.dat, and then mri_vol2surf to resample MWI cortex to surface. As i need to
have all
surfaces in fsaverage space for group analysis, i am using mri_preproc7mri_surf2surf (according to the group analysis wiki you sent me).
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh
<reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Wednesday, July 17, 2019 4:26:21 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionI am trying to compare MWI(sampled on the surface) between couple patients and controls using group analysis, therefore i need to have all inflated surface_on_same space (according to the wiki of group analysis you sent me, i should use mris_preproc to put my data on fsaverage).
Could you now tell me whether my mris_prepoc is right? and one other question i have asked in last email?
Thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
*Sent:* Wednesday, July 17, 2019 4:14:41 PM *To:* Reza Rahmanzadeh; Freesurfer support list;
greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] need for help It is not clear to me what you are trying to do. Do you want to do a morphometry study (ie, comparing thickness, area, and/or volume
across
subjects)? Or do you want to compare MWI (sampled on the surface) across subjects?
> On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > > Dear Doug, > > > I took the back slash away and ran > > mris_preproc --target fsaverage --hemi lh --s FSP010 --out > lh.FSP10.white.mgh --meas white > > > but i got error: > > *Reading curvature file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white** > MRISreadBinaryCurvature: incompatible vertex number in file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white** > ERROR: reading curvature file* > > > Then i changed it to --meas : mris_preproc --target fsaverage
--hemi
> lh --s FSP010 --out lh.FSP10.white.mgz --meas area > > > Then, as i need to register my the inflated cortex of myelin water > image (MWI) to the surface_registered_on_fsaverage (could it be the > output of command-line above?), should i use this output > "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling > myelin water image to lh.white of my subject FSP10 before > registration to fsaverage) for mri_surf2surf (to resample the
latter
> to the former, to have MWI to surface_fsaverage) > > > > Looking forward to answers > > Thanks > > Reza > > > > > >
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu > mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu > mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza
> Rahmanzadeh <reza.rahmanzadeh@unibas.ch > mailto:reza.rahmanzadeh@unibas.ch
mailto:reza.rahmanzadeh@unibas.ch>
> *Sent:* Wednesday, July 17, 2019 9:56:00 AM > *To:* Freesurfer support list > *Cc:* DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu > *Subject:* Re: [Freesurfer] need for help > External Email - Use Caution > > Thanks Tim, > > Then if i would resample my data to fsaverage and surfaces are of > main importance to my work, what should i use for -meas ? > > Reza > >> On 17 Jul 2019, at 09:39, Tim Schäfer <ts+ml@rcmd.org >> mailto:ts+ml@rcmd.org
mailto:ts+ml@rcmd.org> wrote:
>> >> External Email - Use Caution >> >> I guess '-meas' expects a measure (like 'thickness' or
'area'), not
> a surface (like 'white'). >> >> Best, >> >> Tim >> >>> On July 17, 2019 at 9:03 AM Reza Rahmanzadeh > <reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch > mailto:reza.rahmanzadeh@unibas.ch> wrote: >>> >>> >>> External Email - Use Caution >>> >>> I removed the back slash and the command line i executed is: >>> >>> >>> mris_preproc --target fsaverage --hemi lh --s FSP010 --out > lh.FSP10.white.mgh --meas white >>> >>> >>> but i got the error: >>> >>> Reading curvature file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white >>> MRISreadBinaryCurvature: incompatible vertex number in file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white >>> ERROR: reading curvature file >>> >>> I have added --srcfmt mgh as the last argument, but again i got > the error: >>> Reading source surface reg > /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg >>> Loading source data >>> No such file or directory >>> ERROR: could not read > /usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3 >>> >>> >>> What is wrong with my mris_prepoc command line? >>> >>> Reza >>> >>> >>> ________________________________ >>> From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>> Sent: Tuesday, July 16, 2019 10:01:15 PM >>> To: Reza Rahmanzadeh; Freesurfer support list; > greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > mailto:greve@nmr.mgh.harvard.edu >>> Subject: Re: need for help >>> >>> don't include the back slash (ie, fsaverage not fsaverage/ same > for FSP010) >>> >>>> On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote: >>>> >>>> External Email - Use Caution >>>> >>>> Thanks a lot Doug, >>>> >>>> >>>> I started to proceed with FS group analysis wiki you sent to me. >>>> Accordingly, i have to resample all my data (output of recon-all > for a >>>> given subject for example) into fsaverage using mris_preproc. My >>>> commandline for a subject was: >>>> >>>> mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out >>>> lh.FSP10.white.mgh --meas white >>>> >>>> >>>> and i got the error: >>>> >>>> * >>>> * >>>> *Reading source surface reg >>>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>>> No such file or directory >>>> mri_surf2surf: could not read surface >>>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>>> No such file or directory* >>>> * >>>> * >>>> As there was no**lh.fsaverage/.sphere.reg* *folder, i found one
file
>>>> in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a
folder
>>>> with the name lh.fsaverage and i copied/pasted the mentiomed
file
> into >>>> this folder and i changed the file name to: ./sphere.reg. I
got the
>>>> error: >>>> * >>>> * >>>> *Reading curvature file >>>> /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere >>>> MRISreadBinaryCurvature: incompatible vertex number in file >>>> /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere* >>>> * >>>> * >>>> * >>>> * >>>> What is the problem with my mris_preproc command-line? >>>> >>>> Reza >>>> >>>> >
>>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu >>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
>>>> <freesurfer-bounces@nmr.mgh.harvard.edu >>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
>>>> N.,Ph.D. <DGREVE@mgh.harvard.edu >>>> mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> >>>> *Sent:* Tuesday, July 16, 2019 7:01:30 PM >>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>> *Subject:* Re: [Freesurfer] need for help >>>> >>>> >>>>> On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> (I assume now we are discussing in FS list, if no please let
me how
>>>>> possible?) >>>>> >>>>> >>>>> Thanks Doug, now i could see the inflate surface, this means
that my
>>>>> mri_vol2surf works well. As i would do GLM analysis over
inflated
>>>>> cortex of patients and controls in Qdec, >>>>> >>>>> >>>>> 1- should i input my surfaces to Qdec as inflated surface
or just
>>>>> inputting the output_of_vol2surf.mgz to Qdec? >>>>> >>>>> if inflated one is the input, then how could i get them? > mris_inflate >>>>> gives error. >>>>> >>>> QDEC is no longer being supported. Use the command line stream >>>> (mri_surf2surf, mri_glmfit, mri_glmfit-sim). >>>>
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>>>>> >>>>> >>>>> 2- should i input all patients and controls surfaces in
standard
>>>>> surface before entering to Qdec? >>>>> >>>>> >>>>> 3- I would like to resample whole cortex (whole cortical > thickness, in >>>>> other words: the average of all projfrac between 0 and 1),
is it
>>>>> possible? or i am limited to resample one given depth of
cortex into
>>>>> inflated surface only? >>>>> >>>> Run mri_vol2surf with --help and look for --projfrac-avg >>>>> >>>>> >>>>> thanks a lot, >>>>> >>>>> Reza >>>>> >>>>> >>>>> >
>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>> *Sent:* Tuesday, July 16, 2019 6:22:56 PM >>>>> *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu >>>>> mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
>>>>> *Subject:* Re: need for help >>>>> The command should be something like >>>>> tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz >>>>> Also, tksurfer is also obsolete (but should work). You
should be
> using >>>>> freeview (or tksurferfv, a freeview front end that takes
the same
>>>>> command line args as tksurfer) >>>>> Also, please remember to respond to the fs list >>>>> >>>>>> On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote: >>>>>> >>>>>> External Email - Use Caution >>>>>> >>>>>> I got the mri_vol2surf output with .mgz: >>>>>> >>>>>> >>>>>> my tksurfer command: >>>>>> >>>>>> tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of >>>>>> mri_vol2surf was lh.inflated_MWI.mgz) >>>>>> >>>>>> >>>>>> and the error i got: >>>>>> >>>>>> *freadFloat: fread failed** >>>>>> No such file or directory* >>>>>> >>>>>> To me, opening the surfer in tksurfer is only a way to get
sure my
>>>>>> vol2surf worked well. the main problem is i got this error
for all
>>>>>> mris_smooth, mris_inflate, mris_sphere ... >>>>>> >>>>>> >>>>>> Do you think that means the output of mri_vol2surf is not > correct, or >>>>>> otherwise i could proceed with that , even when tksurfer
could not
>>>>>> open it, for GLM in Qdec? >>>>>> >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Reza >>>>>> >>>>>> >>>> >
>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>>> *Sent:* Tuesday, July 16, 2019 6:01:15 PM >>>>>> *To:* Reza Rahmanzadeh >>>>>> *Subject:* Re: need for help >>>>>> what is your tksurfer command line? Also, the .w file is
somewhat
>>>>>> obsolete (it should still work); instead you can use .mgz
file (and
>>>>>> don't spec --paint) >>>>>> >>>>>>> On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote: >>>>>>> >>>>>>> External Email - Use Caution >>>>>>> >>>>>>> Thanks Doug, >>>>>>> >>>>>>> >>>>>>> I used the one without --inflated also, again the tksurfer > could not >>>>>>> open it and i got the same error. Where is the problem
with my
> cmd.? >>>>>>> >>>>>>> >>>>>>> In addition, i wanted to make the output of mri_vol2surf
inflated
>>>>>>> using mris_inflate but i got the same error: >>>>>>> >>>>>>> *freadFloat: fread failed >>>>>>> No such file or directory* >>>>>>> * >>>>>>> * >>>>>>> *could you let me know what is the problem in registering
my mwi
>>>>>>> volumes to surface that i getonly such errors.* >>>>>>> * >>>>>>> * >>>>>>> *Thanks,* >>>>>>> *reza >>>>>>> * >>>>>>> >>>>>>> >>>>> >
>>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>>>> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >>>>>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>> *Cc:* greve@nmr.mgh.harvard.edu >>>>>>> mailto:greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu
>>>>>>> *Subject:* Re: need for help >>>>>>> Don't use --inflated. The inflated surface is not a
biological
>>>>>>> surface. The default is the white surface, which is the one > you want >>>>>>> (--projfrac 0.5 will project it to the middle between the > white and >>>>> pial) >>>>>>> >>>>>>>> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: >>>>>>>> >>>>>>>> External Email - Use Caution >>>>>>>> >>>>>>>> Dear Freesurfer, >>>>>>>> >>>>>>>> I have a batch of myelin water image (MWI) from patients and >>>>>>>> controls, and trying to have inflated cortex registered on > standard >>>>>>>> surface for GLM (Qdec). >>>>>>>> >>>>>>>> With the commandlines below i get my inflated surface of MWI > map of >>>>>>>> my patients and controls. >>>>>>>> >>>>>>>> 1-using bbregister to put MWI into FS space and to calculate >>>>>>>> register.dat: >>>>>>>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg > register.dat >>>>>>>> --o mwf_FS --t1 >>>>>>>> >>>>>>>> 2-using mri_vol2surf to extract inflated surface of MWI: >>>>>>>> mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 >>>>>>>> --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type >>>>>>>> paint--inflated (*or*--surf sphere) >>>>>>>> >>>>>>>> However the tksurfer could not open the inflated surface
and the
>>>>>>>> error message is: >>>>>>>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! >>>>>>>> Probably trying to use a scalar data file as a surface!* >>>>>>>> >>>>>>>> I used the commandline below for #2: >>>>>>>> mri_vol2surf --src mwf.nii --srcreg register.dat --hemi
lh --o
>>>>>>>> mwf-lh.w --out_type paint >>>>>>>> and i got the error: >>>>>>>> >>>>>>>> *ERROR: MRISread: file >>>>>>>>
'/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has
> many >>>>>>>> more faces than vertices!** >>>>>>>> Probably trying to use a scalar data file as a surface!* >>>>>>>> * >>>>>>>> * >>>>>>>> As tksurfer could not open my surfaces with errors above, i
think
>>>>>>>> perhaps the vol2surf procedure is not done properly. Where
is the
>>>>>>>> problem? i need to get the inflated cortex and then
putting ob
>>>>>>>> sphere (using mris_sphere) and the registering to standard > surface >>>>>>>> using mris_register for GLM in Qdec, right? >>>>>>>> >>>>>>>> >>>>>>>> It is two weeks i am struggling with these commands, any
helps
>>>>>>>> highly appreciated. * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> Best, >>>>>>>> Reza >>>>>>>> >>>>>>> >>>>>>> The information in this e-mail is intended only for the
person to
>>>>>>> whom it is >>>>>>> addressed. If you believe this e-mail was sent to you in
error and
>>>>>>> the e-mail >>>>>>> contains patient information, please contact the Partners > Compliance >>>>>>> HelpLine at >>>>>>> http://www.partners.org/complianceline . If the e-mail was
sent to
>>>>>>> you in error >>>>>>> but does not contain patient information, please contact the > sender >>>>>>> and properly >>>>>>> dispose of the e-mail. >>>>>>> >>>>>> >>>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Dr. Tim Schäfer >> Postdoc Computational Neuroimaging >> Department of Child and Adolescent Psychiatry, Psychosomatics and > Psychotherapy >> University Hospital Frankfurt, Goethe University Frankfurt am
Main,
> Germany >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
did you check each subject to make sure they had a non-zero map?
On 8/2/2019 6:25 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Dear Doug,
NODDI is diffusion imaging and we have vakue regarding neurite density (NDI in NDI map) and orientation dispersion (ODI value in ODI map). I do not know why mris_preproc works well on MWI maps but not on NODDI maps (both NDI and ODI maps). Beside using projfrac-avg 0 1 0.25 , i have run mris_preproc with projfrac 0.5 but again i got this error:
ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input
I have run mris_preproc on three patients that i am sure about registration quality, again when i scroll through them , there is no value in none of them. How that is possible?
NODDI does not have a lot of zero value but all values in cortex are between 0.2-0.4.
Thanks, Reza
________________________________ From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Wednesday, July 31, 2019 12:50:45 AM To: Reza Rahmanzadeh; Freesurfer support list Cc: greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] need for help
I don't know what is in the NODDI maps. The way mri_glmfit works is that if any subject has a 0-value at a vertex, then it will mask out that vertex for all subjects. Is NODDI something that might have a lot of 0-values? It also may be that one subject has all 0s (eg, if the regitration was really bad), so you can check the map created by mris_preproc (load it in as an overlay, then hit the configure button, then change the frame number to scroll through your subjects)
On 7/30/19 12:46 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution(sorry for bombaeding you with e-mails)
It seems that the error happens only when i use NODDI diffusion image e.g. NDI map i get that error, but for MWIs the new mris_preproc works well.
Should i do anything special for NODDI images? BTW, the bbregister works well for NODDI and i entered the correct registration file into mris_preproc.
Thanks,
Reza
*From:* Reza Rahmanzadeh *Sent:* Tuesday, July 30, 2019 6:17:22 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list *Cc:* greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
... One problem when i use the new mris_preproc:
Always the output of mri_glmfit when the input is the result of new mris_preproc is:
*F**ound 0 voxels in mask ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input*
I think it means that something is perhaps wrong with the script. I tried both projfrac 0.5 and projfrac-avg 0 1 0.25 and i got the same error. I did not get the error when i used old mris_preproc using projfrac 0.5.*
*The other thing that could be the reason is my fsgd file. I have problem how to specify the name of subjects,
Now it is sth like:
GroupDescriptorFile 1 Class Group1 CLASS Group2 Input FSC001 Group1 Input FSC002 Group1 Input FSC003 Group1 .
.
.
Input FSP001 Group2 Input FSP002 Group2 Input FSP003 Group2 .
.
The oeder is thew same with mris_preproc, now the subject name is FSC0xx for controls and FSP00x for patients, these are the name of folders containing FS outputs, but my input volume is MWIs and the registration files are not stored in this folder. Does it matter how to name subjects when i am using fsgd file only in mri_glmfit ( to get aware of order)?
Thanks,
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza Rahmanzadeh reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch *Sent:* Tuesday, July 30, 2019 2:44:25 PM *To:* Greve, Douglas N.,Ph.D. *Cc:* Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help External Email - Use Caution
Thanks Doug,
The script works well for projfrac-avg. but the problem is: when i use mris_preproc to assemble my MWIs and put them on fsaverage, as .fsgd file is only the order of my controls and subjects and i would have the inflated cortex of MWI on fsaverage, then anyway i have to specify my volume and registration files (tkregister2 output). Then there’s an error: i shouldn’t use both -fsgd and - iv together. Then i decided not to use fsgd file for mris_preproc and only using that for mri_glmfit. In mris_preproc, i write all “-iv volumes and registration files” in the same order as in fsgd file but i don’t write -fsgd argument. Is this way correct?
Thanks, Reza
On 29 Jul 2019, at 23:32, Greve, Douglas N.,Ph.D.
DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu wrote:
Oh, I guess that's a problem! I've created a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc See if that works. You should compare the output to using the max or -projfrac 0.5 to make sure they are at least similar since I have not run it even once:)
On 7/29/19 5:08 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks
But mris_prepoc will not accept “projfrac-avg” and there’s an error: argument unrecognized!
Then how can i compute the average via mris_preproc? As based on tutorial, first i used tkregister/bbregister to compute the registration matrix and then i should put input images with transformation matrix in mris_preproc. I mean i shouldn’t use mri_vol2surf (that allows me to use projfrac-avg) in group analysis and that’s the reason i have problem with mris_proproc to compute the average.
What should i do?
Thanks, Reza
On 29 Jul 2019, at 23:03, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
one computes the average, the other computes the maximum
On 7/29/19 9:03 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionDear Doug,
I appreciat if you reply my question in the previous e-mail with
this:
can not i use projfrac-avg in mris_preproc? Is --projfrac-max min max delta just the same?
Best,
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh <reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Monday, July 29, 2019 11:37:46 AM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionDear Doug,
Thanks, the tutorial was super helpful. As i would compare the MWF value in cortex between control subjects and patients. Now my problem is how to make the contrast matrix for mris_preproc to do the comparison in both direction (in 1, the outcome should be voxels in which MWf value in control>patients & in 2, reversed).
The explanations in
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
is for one group analysis and in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is not clear about contrast.
I remember for -randomise command-line, there was possibility to make contrast and design matrix (something like FSGD) via design_ttest2. Can i use still design_ttest2 for producing contrast and design
matrix?
Best,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> *Sent:* Wednesday, July 17, 2019 5:31:27 PM *To:* Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help Ah, I see. Try this tutorial. It is for fMRI, but it applies to any modality
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote:
External Email - Use Cautionto clarify better, i need to compare myelin water fraction in cortex of control and patients to find out the areas with reduced MWF in patients cortex compared with controls, that is the reason i want to have cortex in inflated format.
For this reason i used bbregister to have register.dat, and then mri_vol2surf to resample MWI cortex to surface. As i need to
have all
surfaces in fsaverage space for group analysis, i am using mri_preproc7mri_surf2surf (according to the group analysis wiki you sent me).
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh
<reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Wednesday, July 17, 2019 4:26:21 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionI am trying to compare MWI(sampled on the surface) between couple patients and controls using group analysis, therefore i need to have all inflated surface_on_same space (according to the wiki of group analysis you sent me, i should use mris_preproc to put my data on fsaverage).
Could you now tell me whether my mris_prepoc is right? and one other question i have asked in last email?
Thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
*Sent:* Wednesday, July 17, 2019 4:14:41 PM *To:* Reza Rahmanzadeh; Freesurfer support list;
greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] need for help It is not clear to me what you are trying to do. Do you want to do a morphometry study (ie, comparing thickness, area, and/or volume
across
subjects)? Or do you want to compare MWI (sampled on the surface) across subjects?
> On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > > Dear Doug, > > > I took the back slash away and ran > > mris_preproc --target fsaverage --hemi lh --s FSP010 --out > lh.FSP10.white.mgh --meas white > > > but i got error: > > *Reading curvature file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white** > MRISreadBinaryCurvature: incompatible vertex number in file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white** > ERROR: reading curvature file* > > > Then i changed it to --meas : mris_preproc --target fsaverage
--hemi
> lh --s FSP010 --out lh.FSP10.white.mgz --meas area > > > Then, as i need to register my the inflated cortex of myelin water > image (MWI) to the surface_registered_on_fsaverage (could it be the > output of command-line above?), should i use this output > "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling > myelin water image to lh.white of my subject FSP10 before > registration to fsaverage) for mri_surf2surf (to resample the
latter
> to the former, to have MWI to surface_fsaverage) > > > > Looking forward to answers > > Thanks > > Reza > > > > > >
> *From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu > mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu > mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza
> Rahmanzadeh <reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch > mailto:reza.rahmanzadeh@unibas.ch
mailto:reza.rahmanzadeh@unibas.ch>
> *Sent:* Wednesday, July 17, 2019 9:56:00 AM > *To:* Freesurfer support list > *Cc:* DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu > *Subject:* Re: [Freesurfer] need for help > External Email - Use Caution > > Thanks Tim, > > Then if i would resample my data to fsaverage and surfaces are of > main importance to my work, what should i use for -meas ? > > Reza > >> On 17 Jul 2019, at 09:39, Tim Schäfer <ts+ml@rcmd.orgmailto:ts+ml@rcmd.org >> mailto:ts+ml@rcmd.org
mailto:ts+ml@rcmd.org> wrote:
>> >> External Email - Use Caution >> >> I guess '-meas' expects a measure (like 'thickness' or
'area'), not
> a surface (like 'white'). >> >> Best, >> >> Tim >> >>> On July 17, 2019 at 9:03 AM Reza Rahmanzadeh > <reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch > mailto:reza.rahmanzadeh@unibas.ch> wrote: >>> >>> >>> External Email - Use Caution >>> >>> I removed the back slash and the command line i executed is: >>> >>> >>> mris_preproc --target fsaverage --hemi lh --s FSP010 --out > lh.FSP10.white.mgh --meas white >>> >>> >>> but i got the error: >>> >>> Reading curvature file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white >>> MRISreadBinaryCurvature: incompatible vertex number in file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white >>> ERROR: reading curvature file >>> >>> I have added --srcfmt mgh as the last argument, but again i got > the error: >>> Reading source surface reg > /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg >>> Loading source data >>> No such file or directory >>> ERROR: could not read > /usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3 >>> >>> >>> What is wrong with my mris_prepoc command line? >>> >>> Reza >>> >>> >>> ________________________________ >>> From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>> Sent: Tuesday, July 16, 2019 10:01:15 PM >>> To: Reza Rahmanzadeh; Freesurfer support list; > greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > mailto:greve@nmr.mgh.harvard.edu >>> Subject: Re: need for help >>> >>> don't include the back slash (ie, fsaverage not fsaverage/ same > for FSP010) >>> >>>> On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote: >>>> >>>> External Email - Use Caution >>>> >>>> Thanks a lot Doug, >>>> >>>> >>>> I started to proceed with FS group analysis wiki you sent to me. >>>> Accordingly, i have to resample all my data (output of recon-all > for a >>>> given subject for example) into fsaverage using mris_preproc. My >>>> commandline for a subject was: >>>> >>>> mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out >>>> lh.FSP10.white.mgh --meas white >>>> >>>> >>>> and i got the error: >>>> >>>> * >>>> * >>>> *Reading source surface reg >>>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>>> No such file or directory >>>> mri_surf2surf: could not read surface >>>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>>> No such file or directory* >>>> * >>>> * >>>> As there was no**lh.fsaverage/.sphere.reg* *folder, i found one
file
>>>> in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a
folder
>>>> with the name lh.fsaverage and i copied/pasted the mentiomed
file
> into >>>> this folder and i changed the file name to: ./sphere.reg. I
got the
>>>> error: >>>> * >>>> * >>>> *Reading curvature file >>>> /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere >>>> MRISreadBinaryCurvature: incompatible vertex number in file >>>> /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere* >>>> * >>>> * >>>> * >>>> * >>>> What is the problem with my mris_preproc command-line? >>>> >>>> Reza >>>> >>>> >
>>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu >>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
>>>> <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu >>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
>>>> N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >>>> mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> >>>> *Sent:* Tuesday, July 16, 2019 7:01:30 PM >>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>> *Subject:* Re: [Freesurfer] need for help >>>> >>>> >>>>> On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> (I assume now we are discussing in FS list, if no please let
me how
>>>>> possible?) >>>>> >>>>> >>>>> Thanks Doug, now i could see the inflate surface, this means
that my
>>>>> mri_vol2surf works well. As i would do GLM analysis over
inflated
>>>>> cortex of patients and controls in Qdec, >>>>> >>>>> >>>>> 1- should i input my surfaces to Qdec as inflated surface
or just
>>>>> inputting the output_of_vol2surf.mgz to Qdec? >>>>> >>>>> if inflated one is the input, then how could i get them? > mris_inflate >>>>> gives error. >>>>> >>>> QDEC is no longer being supported. Use the command line stream >>>> (mri_surf2surf, mri_glmfit, mri_glmfit-sim). >>>>
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>>>>> >>>>> >>>>> 2- should i input all patients and controls surfaces in
standard
>>>>> surface before entering to Qdec? >>>>> >>>>> >>>>> 3- I would like to resample whole cortex (whole cortical > thickness, in >>>>> other words: the average of all projfrac between 0 and 1),
is it
>>>>> possible? or i am limited to resample one given depth of
cortex into
>>>>> inflated surface only? >>>>> >>>> Run mri_vol2surf with --help and look for --projfrac-avg >>>>> >>>>> >>>>> thanks a lot, >>>>> >>>>> Reza >>>>> >>>>> >>>>> >
>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>> *Sent:* Tuesday, July 16, 2019 6:22:56 PM >>>>> *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu >>>>> mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
>>>>> *Subject:* Re: need for help >>>>> The command should be something like >>>>> tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz >>>>> Also, tksurfer is also obsolete (but should work). You
should be
> using >>>>> freeview (or tksurferfv, a freeview front end that takes
the same
>>>>> command line args as tksurfer) >>>>> Also, please remember to respond to the fs list >>>>> >>>>>> On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote: >>>>>> >>>>>> External Email - Use Caution >>>>>> >>>>>> I got the mri_vol2surf output with .mgz: >>>>>> >>>>>> >>>>>> my tksurfer command: >>>>>> >>>>>> tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of >>>>>> mri_vol2surf was lh.inflated_MWI.mgz) >>>>>> >>>>>> >>>>>> and the error i got: >>>>>> >>>>>> *freadFloat: fread failed** >>>>>> No such file or directory* >>>>>> >>>>>> To me, opening the surfer in tksurfer is only a way to get
sure my
>>>>>> vol2surf worked well. the main problem is i got this error
for all
>>>>>> mris_smooth, mris_inflate, mris_sphere ... >>>>>> >>>>>> >>>>>> Do you think that means the output of mri_vol2surf is not > correct, or >>>>>> otherwise i could proceed with that , even when tksurfer
could not
>>>>>> open it, for GLM in Qdec? >>>>>> >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Reza >>>>>> >>>>>> >>>> >
>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >>>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>>> *Sent:* Tuesday, July 16, 2019 6:01:15 PM >>>>>> *To:* Reza Rahmanzadeh >>>>>> *Subject:* Re: need for help >>>>>> what is your tksurfer command line? Also, the .w file is
somewhat
>>>>>> obsolete (it should still work); instead you can use .mgz
file (and
>>>>>> don't spec --paint) >>>>>> >>>>>>> On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote: >>>>>>> >>>>>>> External Email - Use Caution >>>>>>> >>>>>>> Thanks Doug, >>>>>>> >>>>>>> >>>>>>> I used the one without --inflated also, again the tksurfer > could not >>>>>>> open it and i got the same error. Where is the problem
with my
> cmd.? >>>>>>> >>>>>>> >>>>>>> In addition, i wanted to make the output of mri_vol2surf
inflated
>>>>>>> using mris_inflate but i got the same error: >>>>>>> >>>>>>> *freadFloat: fread failed >>>>>>> No such file or directory* >>>>>>> * >>>>>>> * >>>>>>> *could you let me know what is the problem in registering
my mwi
>>>>>>> volumes to surface that i getonly such errors.* >>>>>>> * >>>>>>> * >>>>>>> *Thanks,* >>>>>>> *reza >>>>>>> * >>>>>>> >>>>>>> >>>>> >
>>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >>>>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>>>> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >>>>>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>> *Cc:* greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>>>>>> mailto:greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu
>>>>>>> *Subject:* Re: need for help >>>>>>> Don't use --inflated. The inflated surface is not a
biological
>>>>>>> surface. The default is the white surface, which is the one > you want >>>>>>> (--projfrac 0.5 will project it to the middle between the > white and >>>>> pial) >>>>>>> >>>>>>>> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: >>>>>>>> >>>>>>>> External Email - Use Caution >>>>>>>> >>>>>>>> Dear Freesurfer, >>>>>>>> >>>>>>>> I have a batch of myelin water image (MWI) from patients and >>>>>>>> controls, and trying to have inflated cortex registered on > standard >>>>>>>> surface for GLM (Qdec). >>>>>>>> >>>>>>>> With the commandlines below i get my inflated surface of MWI > map of >>>>>>>> my patients and controls. >>>>>>>> >>>>>>>> 1-using bbregister to put MWI into FS space and to calculate >>>>>>>> register.dat: >>>>>>>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg > register.dat >>>>>>>> --o mwf_FS --t1 >>>>>>>> >>>>>>>> 2-using mri_vol2surf to extract inflated surface of MWI: >>>>>>>> mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 >>>>>>>> --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type >>>>>>>> paint--inflated (*or*--surf sphere) >>>>>>>> >>>>>>>> However the tksurfer could not open the inflated surface
and the
>>>>>>>> error message is: >>>>>>>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! >>>>>>>> Probably trying to use a scalar data file as a surface!* >>>>>>>> >>>>>>>> I used the commandline below for #2: >>>>>>>> mri_vol2surf --src mwf.nii --srcreg register.dat --hemi
lh --o
>>>>>>>> mwf-lh.w --out_type paint >>>>>>>> and i got the error: >>>>>>>> >>>>>>>> *ERROR: MRISread: file >>>>>>>>
'/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has
> many >>>>>>>> more faces than vertices!** >>>>>>>> Probably trying to use a scalar data file as a surface!* >>>>>>>> * >>>>>>>> * >>>>>>>> As tksurfer could not open my surfaces with errors above, i
think
>>>>>>>> perhaps the vol2surf procedure is not done properly. Where
is the
>>>>>>>> problem? i need to get the inflated cortex and then
putting ob
>>>>>>>> sphere (using mris_sphere) and the registering to standard > surface >>>>>>>> using mris_register for GLM in Qdec, right? >>>>>>>> >>>>>>>> >>>>>>>> It is two weeks i am struggling with these commands, any
helps
>>>>>>>> highly appreciated. * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> Best, >>>>>>>> Reza >>>>>>>> >>>>>>> >>>>>>> The information in this e-mail is intended only for the
person to
>>>>>>> whom it is >>>>>>> addressed. If you believe this e-mail was sent to you in
error and
>>>>>>> the e-mail >>>>>>> contains patient information, please contact the Partners > Compliance >>>>>>> HelpLine at >>>>>>> http://www.partners.org/complianceline . If the e-mail was
sent to
>>>>>>> you in error >>>>>>> but does not contain patient information, please contact the > sender >>>>>>> and properly >>>>>>> dispose of the e-mail. >>>>>>> >>>>>> >>>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Dr. Tim Schäfer >> Postdoc Computational Neuroimaging >> Department of Child and Adolescent Psychiatry, Psychosomatics and > Psychotherapy >> University Hospital Frankfurt, Goethe University Frankfurt am
Main,
> Germany >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
yes, I have the page below for all patients.
I think it means all values are zero. My registration for bbregister is fine and i wrote my mris_preproc the same as MWF maps.
Thanks,
Reza
________________________________ From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Friday, August 2, 2019 3:35:45 PM To: Reza Rahmanzadeh; Freesurfer support list Cc: greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] need for help
did you check each subject to make sure they had a non-zero map?
On 8/2/2019 6:25 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Dear Doug,
NODDI is diffusion imaging and we have vakue regarding neurite density (NDI in NDI map) and orientation dispersion (ODI value in ODI map). I do not know why mris_preproc works well on MWI maps but not on NODDI maps (both NDI and ODI maps). Beside using projfrac-avg 0 1 0.25 , i have run mris_preproc with projfrac 0.5 but again i got this error:
ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input
I have run mris_preproc on three patients that i am sure about registration quality, again when i scroll through them , there is no value in none of them. How that is possible?
NODDI does not have a lot of zero value but all values in cortex are between 0.2-0.4.
Thanks, Reza
________________________________ From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Wednesday, July 31, 2019 12:50:45 AM To: Reza Rahmanzadeh; Freesurfer support list Cc: greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] need for help
I don't know what is in the NODDI maps. The way mri_glmfit works is that if any subject has a 0-value at a vertex, then it will mask out that vertex for all subjects. Is NODDI something that might have a lot of 0-values? It also may be that one subject has all 0s (eg, if the regitration was really bad), so you can check the map created by mris_preproc (load it in as an overlay, then hit the configure button, then change the frame number to scroll through your subjects)
On 7/30/19 12:46 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution(sorry for bombaeding you with e-mails)
It seems that the error happens only when i use NODDI diffusion image e.g. NDI map i get that error, but for MWIs the new mris_preproc works well.
Should i do anything special for NODDI images? BTW, the bbregister works well for NODDI and i entered the correct registration file into mris_preproc.
Thanks,
Reza
*From:* Reza Rahmanzadeh *Sent:* Tuesday, July 30, 2019 6:17:22 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list *Cc:* greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
... One problem when i use the new mris_preproc:
Always the output of mri_glmfit when the input is the result of new mris_preproc is:
*F**ound 0 voxels in mask ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input*
I think it means that something is perhaps wrong with the script. I tried both projfrac 0.5 and projfrac-avg 0 1 0.25 and i got the same error. I did not get the error when i used old mris_preproc using projfrac 0.5.*
*The other thing that could be the reason is my fsgd file. I have problem how to specify the name of subjects,
Now it is sth like:
GroupDescriptorFile 1 Class Group1 CLASS Group2 Input FSC001 Group1 Input FSC002 Group1 Input FSC003 Group1 .
.
.
Input FSP001 Group2 Input FSP002 Group2 Input FSP003 Group2 .
.
The oeder is thew same with mris_preproc, now the subject name is FSC0xx for controls and FSP00x for patients, these are the name of folders containing FS outputs, but my input volume is MWIs and the registration files are not stored in this folder. Does it matter how to name subjects when i am using fsgd file only in mri_glmfit ( to get aware of order)?
Thanks,
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza Rahmanzadeh reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch *Sent:* Tuesday, July 30, 2019 2:44:25 PM *To:* Greve, Douglas N.,Ph.D. *Cc:* Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help External Email - Use Caution
Thanks Doug,
The script works well for projfrac-avg. but the problem is: when i use mris_preproc to assemble my MWIs and put them on fsaverage, as .fsgd file is only the order of my controls and subjects and i would have the inflated cortex of MWI on fsaverage, then anyway i have to specify my volume and registration files (tkregister2 output). Then there’s an error: i shouldn’t use both -fsgd and - iv together. Then i decided not to use fsgd file for mris_preproc and only using that for mri_glmfit. In mris_preproc, i write all “-iv volumes and registration files” in the same order as in fsgd file but i don’t write -fsgd argument. Is this way correct?
Thanks, Reza
On 29 Jul 2019, at 23:32, Greve, Douglas N.,Ph.D.
DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu wrote:
Oh, I guess that's a problem! I've created a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc See if that works. You should compare the output to using the max or -projfrac 0.5 to make sure they are at least similar since I have not run it even once:)
On 7/29/19 5:08 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks
But mris_prepoc will not accept “projfrac-avg” and there’s an error: argument unrecognized!
Then how can i compute the average via mris_preproc? As based on tutorial, first i used tkregister/bbregister to compute the registration matrix and then i should put input images with transformation matrix in mris_preproc. I mean i shouldn’t use mri_vol2surf (that allows me to use projfrac-avg) in group analysis and that’s the reason i have problem with mris_proproc to compute the average.
What should i do?
Thanks, Reza
On 29 Jul 2019, at 23:03, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
one computes the average, the other computes the maximum
On 7/29/19 9:03 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionDear Doug,
I appreciat if you reply my question in the previous e-mail with
this:
can not i use projfrac-avg in mris_preproc? Is --projfrac-max min max delta just the same?
Best,
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh <reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Monday, July 29, 2019 11:37:46 AM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionDear Doug,
Thanks, the tutorial was super helpful. As i would compare the MWF value in cortex between control subjects and patients. Now my problem is how to make the contrast matrix for mris_preproc to do the comparison in both direction (in 1, the outcome should be voxels in which MWf value in control>patients & in 2, reversed).
The explanations in
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
is for one group analysis and in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is not clear about contrast.
I remember for -randomise command-line, there was possibility to make contrast and design matrix (something like FSGD) via design_ttest2. Can i use still design_ttest2 for producing contrast and design
matrix?
Best,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> *Sent:* Wednesday, July 17, 2019 5:31:27 PM *To:* Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help Ah, I see. Try this tutorial. It is for fMRI, but it applies to any modality
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote:
External Email - Use Cautionto clarify better, i need to compare myelin water fraction in cortex of control and patients to find out the areas with reduced MWF in patients cortex compared with controls, that is the reason i want to have cortex in inflated format.
For this reason i used bbregister to have register.dat, and then mri_vol2surf to resample MWI cortex to surface. As i need to
have all
surfaces in fsaverage space for group analysis, i am using mri_preproc7mri_surf2surf (according to the group analysis wiki you sent me).
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh
<reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Wednesday, July 17, 2019 4:26:21 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionI am trying to compare MWI(sampled on the surface) between couple patients and controls using group analysis, therefore i need to have all inflated surface_on_same space (according to the wiki of group analysis you sent me, i should use mris_preproc to put my data on fsaverage).
Could you now tell me whether my mris_prepoc is right? and one other question i have asked in last email?
Thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
*Sent:* Wednesday, July 17, 2019 4:14:41 PM *To:* Reza Rahmanzadeh; Freesurfer support list;
greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] need for help It is not clear to me what you are trying to do. Do you want to do a morphometry study (ie, comparing thickness, area, and/or volume
across
subjects)? Or do you want to compare MWI (sampled on the surface) across subjects?
> On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > > Dear Doug, > > > I took the back slash away and ran > > mris_preproc --target fsaverage --hemi lh --s FSP010 --out > lh.FSP10.white.mgh --meas white > > > but i got error: > > *Reading curvature file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white** > MRISreadBinaryCurvature: incompatible vertex number in file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white** > ERROR: reading curvature file* > > > Then i changed it to --meas : mris_preproc --target fsaverage
--hemi
> lh --s FSP010 --out lh.FSP10.white.mgz --meas area > > > Then, as i need to register my the inflated cortex of myelin water > image (MWI) to the surface_registered_on_fsaverage (could it be the > output of command-line above?), should i use this output > "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling > myelin water image to lh.white of my subject FSP10 before > registration to fsaverage) for mri_surf2surf (to resample the
latter
> to the former, to have MWI to surface_fsaverage) > > > > Looking forward to answers > > Thanks > > Reza > > > > > >
> *From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu > mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu > mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza
> Rahmanzadeh <reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch > mailto:reza.rahmanzadeh@unibas.ch
mailto:reza.rahmanzadeh@unibas.ch>
> *Sent:* Wednesday, July 17, 2019 9:56:00 AM > *To:* Freesurfer support list > *Cc:* DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu > *Subject:* Re: [Freesurfer] need for help > External Email - Use Caution > > Thanks Tim, > > Then if i would resample my data to fsaverage and surfaces are of > main importance to my work, what should i use for -meas ? > > Reza > >> On 17 Jul 2019, at 09:39, Tim Schäfer <ts+ml@rcmd.orgmailto:ts+ml@rcmd.org >> mailto:ts+ml@rcmd.org
mailto:ts+ml@rcmd.org> wrote:
>> >> External Email - Use Caution >> >> I guess '-meas' expects a measure (like 'thickness' or
'area'), not
> a surface (like 'white'). >> >> Best, >> >> Tim >> >>> On July 17, 2019 at 9:03 AM Reza Rahmanzadeh > <reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch > mailto:reza.rahmanzadeh@unibas.ch> wrote: >>> >>> >>> External Email - Use Caution >>> >>> I removed the back slash and the command line i executed is: >>> >>> >>> mris_preproc --target fsaverage --hemi lh --s FSP010 --out > lh.FSP10.white.mgh --meas white >>> >>> >>> but i got the error: >>> >>> Reading curvature file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white >>> MRISreadBinaryCurvature: incompatible vertex number in file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white >>> ERROR: reading curvature file >>> >>> I have added --srcfmt mgh as the last argument, but again i got > the error: >>> Reading source surface reg > /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg >>> Loading source data >>> No such file or directory >>> ERROR: could not read > /usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3 >>> >>> >>> What is wrong with my mris_prepoc command line? >>> >>> Reza >>> >>> >>> ________________________________ >>> From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>> Sent: Tuesday, July 16, 2019 10:01:15 PM >>> To: Reza Rahmanzadeh; Freesurfer support list; > greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > mailto:greve@nmr.mgh.harvard.edu >>> Subject: Re: need for help >>> >>> don't include the back slash (ie, fsaverage not fsaverage/ same > for FSP010) >>> >>>> On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote: >>>> >>>> External Email - Use Caution >>>> >>>> Thanks a lot Doug, >>>> >>>> >>>> I started to proceed with FS group analysis wiki you sent to me. >>>> Accordingly, i have to resample all my data (output of recon-all > for a >>>> given subject for example) into fsaverage using mris_preproc. My >>>> commandline for a subject was: >>>> >>>> mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out >>>> lh.FSP10.white.mgh --meas white >>>> >>>> >>>> and i got the error: >>>> >>>> * >>>> * >>>> *Reading source surface reg >>>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>>> No such file or directory >>>> mri_surf2surf: could not read surface >>>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>>> No such file or directory* >>>> * >>>> * >>>> As there was no**lh.fsaverage/.sphere.reg* *folder, i found one
file
>>>> in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a
folder
>>>> with the name lh.fsaverage and i copied/pasted the mentiomed
file
> into >>>> this folder and i changed the file name to: ./sphere.reg. I
got the
>>>> error: >>>> * >>>> * >>>> *Reading curvature file >>>> /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere >>>> MRISreadBinaryCurvature: incompatible vertex number in file >>>> /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere* >>>> * >>>> * >>>> * >>>> * >>>> What is the problem with my mris_preproc command-line? >>>> >>>> Reza >>>> >>>> >
>>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu >>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
>>>> <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu >>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
>>>> N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >>>> mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> >>>> *Sent:* Tuesday, July 16, 2019 7:01:30 PM >>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>> *Subject:* Re: [Freesurfer] need for help >>>> >>>> >>>>> On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> (I assume now we are discussing in FS list, if no please let
me how
>>>>> possible?) >>>>> >>>>> >>>>> Thanks Doug, now i could see the inflate surface, this means
that my
>>>>> mri_vol2surf works well. As i would do GLM analysis over
inflated
>>>>> cortex of patients and controls in Qdec, >>>>> >>>>> >>>>> 1- should i input my surfaces to Qdec as inflated surface
or just
>>>>> inputting the output_of_vol2surf.mgz to Qdec? >>>>> >>>>> if inflated one is the input, then how could i get them? > mris_inflate >>>>> gives error. >>>>> >>>> QDEC is no longer being supported. Use the command line stream >>>> (mri_surf2surf, mri_glmfit, mri_glmfit-sim). >>>>
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>>>>> >>>>> >>>>> 2- should i input all patients and controls surfaces in
standard
>>>>> surface before entering to Qdec? >>>>> >>>>> >>>>> 3- I would like to resample whole cortex (whole cortical > thickness, in >>>>> other words: the average of all projfrac between 0 and 1),
is it
>>>>> possible? or i am limited to resample one given depth of
cortex into
>>>>> inflated surface only? >>>>> >>>> Run mri_vol2surf with --help and look for --projfrac-avg >>>>> >>>>> >>>>> thanks a lot, >>>>> >>>>> Reza >>>>> >>>>> >>>>> >
>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>> *Sent:* Tuesday, July 16, 2019 6:22:56 PM >>>>> *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu >>>>> mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
>>>>> *Subject:* Re: need for help >>>>> The command should be something like >>>>> tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz >>>>> Also, tksurfer is also obsolete (but should work). You
should be
> using >>>>> freeview (or tksurferfv, a freeview front end that takes
the same
>>>>> command line args as tksurfer) >>>>> Also, please remember to respond to the fs list >>>>> >>>>>> On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote: >>>>>> >>>>>> External Email - Use Caution >>>>>> >>>>>> I got the mri_vol2surf output with .mgz: >>>>>> >>>>>> >>>>>> my tksurfer command: >>>>>> >>>>>> tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of >>>>>> mri_vol2surf was lh.inflated_MWI.mgz) >>>>>> >>>>>> >>>>>> and the error i got: >>>>>> >>>>>> *freadFloat: fread failed** >>>>>> No such file or directory* >>>>>> >>>>>> To me, opening the surfer in tksurfer is only a way to get
sure my
>>>>>> vol2surf worked well. the main problem is i got this error
for all
>>>>>> mris_smooth, mris_inflate, mris_sphere ... >>>>>> >>>>>> >>>>>> Do you think that means the output of mri_vol2surf is not > correct, or >>>>>> otherwise i could proceed with that , even when tksurfer
could not
>>>>>> open it, for GLM in Qdec? >>>>>> >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Reza >>>>>> >>>>>> >>>> >
>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >>>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>>> *Sent:* Tuesday, July 16, 2019 6:01:15 PM >>>>>> *To:* Reza Rahmanzadeh >>>>>> *Subject:* Re: need for help >>>>>> what is your tksurfer command line? Also, the .w file is
somewhat
>>>>>> obsolete (it should still work); instead you can use .mgz
file (and
>>>>>> don't spec --paint) >>>>>> >>>>>>> On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote: >>>>>>> >>>>>>> External Email - Use Caution >>>>>>> >>>>>>> Thanks Doug, >>>>>>> >>>>>>> >>>>>>> I used the one without --inflated also, again the tksurfer > could not >>>>>>> open it and i got the same error. Where is the problem
with my
> cmd.? >>>>>>> >>>>>>> >>>>>>> In addition, i wanted to make the output of mri_vol2surf
inflated
>>>>>>> using mris_inflate but i got the same error: >>>>>>> >>>>>>> *freadFloat: fread failed >>>>>>> No such file or directory* >>>>>>> * >>>>>>> * >>>>>>> *could you let me know what is the problem in registering
my mwi
>>>>>>> volumes to surface that i getonly such errors.* >>>>>>> * >>>>>>> * >>>>>>> *Thanks,* >>>>>>> *reza >>>>>>> * >>>>>>> >>>>>>> >>>>> >
>>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >>>>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>>>> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >>>>>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>> *Cc:* greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>>>>>> mailto:greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu
>>>>>>> *Subject:* Re: need for help >>>>>>> Don't use --inflated. The inflated surface is not a
biological
>>>>>>> surface. The default is the white surface, which is the one > you want >>>>>>> (--projfrac 0.5 will project it to the middle between the > white and >>>>> pial) >>>>>>> >>>>>>>> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: >>>>>>>> >>>>>>>> External Email - Use Caution >>>>>>>> >>>>>>>> Dear Freesurfer, >>>>>>>> >>>>>>>> I have a batch of myelin water image (MWI) from patients and >>>>>>>> controls, and trying to have inflated cortex registered on > standard >>>>>>>> surface for GLM (Qdec). >>>>>>>> >>>>>>>> With the commandlines below i get my inflated surface of MWI > map of >>>>>>>> my patients and controls. >>>>>>>> >>>>>>>> 1-using bbregister to put MWI into FS space and to calculate >>>>>>>> register.dat: >>>>>>>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg > register.dat >>>>>>>> --o mwf_FS --t1 >>>>>>>> >>>>>>>> 2-using mri_vol2surf to extract inflated surface of MWI: >>>>>>>> mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 >>>>>>>> --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type >>>>>>>> paint--inflated (*or*--surf sphere) >>>>>>>> >>>>>>>> However the tksurfer could not open the inflated surface
and the
>>>>>>>> error message is: >>>>>>>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! >>>>>>>> Probably trying to use a scalar data file as a surface!* >>>>>>>> >>>>>>>> I used the commandline below for #2: >>>>>>>> mri_vol2surf --src mwf.nii --srcreg register.dat --hemi
lh --o
>>>>>>>> mwf-lh.w --out_type paint >>>>>>>> and i got the error: >>>>>>>> >>>>>>>> *ERROR: MRISread: file >>>>>>>>
'/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has
> many >>>>>>>> more faces than vertices!** >>>>>>>> Probably trying to use a scalar data file as a surface!* >>>>>>>> * >>>>>>>> * >>>>>>>> As tksurfer could not open my surfaces with errors above, i
think
>>>>>>>> perhaps the vol2surf procedure is not done properly. Where
is the
>>>>>>>> problem? i need to get the inflated cortex and then
putting ob
>>>>>>>> sphere (using mris_sphere) and the registering to standard > surface >>>>>>>> using mris_register for GLM in Qdec, right? >>>>>>>> >>>>>>>> >>>>>>>> It is two weeks i am struggling with these commands, any
helps
>>>>>>>> highly appreciated. * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> Best, >>>>>>>> Reza >>>>>>>> >>>>>>> >>>>>>> The information in this e-mail is intended only for the
person to
>>>>>>> whom it is >>>>>>> addressed. If you believe this e-mail was sent to you in
error and
>>>>>>> the e-mail >>>>>>> contains patient information, please contact the Partners > Compliance >>>>>>> HelpLine at >>>>>>> http://www.partners.org/complianceline . If the e-mail was
sent to
>>>>>>> you in error >>>>>>> but does not contain patient information, please contact the > sender >>>>>>> and properly >>>>>>> dispose of the e-mail. >>>>>>> >>>>>> >>>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Dr. Tim Schäfer >> Postdoc Computational Neuroimaging >> Department of Child and Adolescent Psychiatry, Psychosomatics and > Psychotherapy >> University Hospital Frankfurt, Goethe University Frankfurt am
Main,
> Germany >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Can you upload the input (ie, argument to --y) here: ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Also, send your mri_glmfit command line.
On 8/2/2019 9:41 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
yes, I have the page below for all patients.
I think it means all values are zero. My registration for bbregister is fine and i wrote my mris_preproc the same as MWF maps.
Thanks,
Reza
________________________________ From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Friday, August 2, 2019 3:35:45 PM To: Reza Rahmanzadeh; Freesurfer support list Cc: greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] need for help
did you check each subject to make sure they had a non-zero map?
On 8/2/2019 6:25 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Dear Doug,
NODDI is diffusion imaging and we have vakue regarding neurite density (NDI in NDI map) and orientation dispersion (ODI value in ODI map). I do not know why mris_preproc works well on MWI maps but not on NODDI maps (both NDI and ODI maps). Beside using projfrac-avg 0 1 0.25 , i have run mris_preproc with projfrac 0.5 but again i got this error:
ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input
I have run mris_preproc on three patients that i am sure about registration quality, again when i scroll through them , there is no value in none of them. How that is possible?
NODDI does not have a lot of zero value but all values in cortex are between 0.2-0.4.
Thanks, Reza
________________________________ From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Wednesday, July 31, 2019 12:50:45 AM To: Reza Rahmanzadeh; Freesurfer support list Cc: greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] need for help
I don't know what is in the NODDI maps. The way mri_glmfit works is that if any subject has a 0-value at a vertex, then it will mask out that vertex for all subjects. Is NODDI something that might have a lot of 0-values? It also may be that one subject has all 0s (eg, if the regitration was really bad), so you can check the map created by mris_preproc (load it in as an overlay, then hit the configure button, then change the frame number to scroll through your subjects)
On 7/30/19 12:46 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution(sorry for bombaeding you with e-mails)
It seems that the error happens only when i use NODDI diffusion image e.g. NDI map i get that error, but for MWIs the new mris_preproc works well.
Should i do anything special for NODDI images? BTW, the bbregister works well for NODDI and i entered the correct registration file into mris_preproc.
Thanks,
Reza
*From:* Reza Rahmanzadeh *Sent:* Tuesday, July 30, 2019 6:17:22 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list *Cc:* greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
... One problem when i use the new mris_preproc:
Always the output of mri_glmfit when the input is the result of new mris_preproc is:
*F**ound 0 voxels in mask ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input*
I think it means that something is perhaps wrong with the script. I tried both projfrac 0.5 and projfrac-avg 0 1 0.25 and i got the same error. I did not get the error when i used old mris_preproc using projfrac 0.5.*
*The other thing that could be the reason is my fsgd file. I have problem how to specify the name of subjects,
Now it is sth like:
GroupDescriptorFile 1 Class Group1 CLASS Group2 Input FSC001 Group1 Input FSC002 Group1 Input FSC003 Group1 .
.
.
Input FSP001 Group2 Input FSP002 Group2 Input FSP003 Group2 .
.
The oeder is thew same with mris_preproc, now the subject name is FSC0xx for controls and FSP00x for patients, these are the name of folders containing FS outputs, but my input volume is MWIs and the registration files are not stored in this folder. Does it matter how to name subjects when i am using fsgd file only in mri_glmfit ( to get aware of order)?
Thanks,
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza Rahmanzadeh reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch *Sent:* Tuesday, July 30, 2019 2:44:25 PM *To:* Greve, Douglas N.,Ph.D. *Cc:* Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help External Email - Use Caution
Thanks Doug,
The script works well for projfrac-avg. but the problem is: when i use mris_preproc to assemble my MWIs and put them on fsaverage, as .fsgd file is only the order of my controls and subjects and i would have the inflated cortex of MWI on fsaverage, then anyway i have to specify my volume and registration files (tkregister2 output). Then there’s an error: i shouldn’t use both -fsgd and - iv together. Then i decided not to use fsgd file for mris_preproc and only using that for mri_glmfit. In mris_preproc, i write all “-iv volumes and registration files” in the same order as in fsgd file but i don’t write -fsgd argument. Is this way correct?
Thanks, Reza
On 29 Jul 2019, at 23:32, Greve, Douglas N.,Ph.D.
DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu wrote:
Oh, I guess that's a problem! I've created a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc See if that works. You should compare the output to using the max or -projfrac 0.5 to make sure they are at least similar since I have not run it even once:)
On 7/29/19 5:08 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks
But mris_prepoc will not accept “projfrac-avg” and there’s an error: argument unrecognized!
Then how can i compute the average via mris_preproc? As based on tutorial, first i used tkregister/bbregister to compute the registration matrix and then i should put input images with transformation matrix in mris_preproc. I mean i shouldn’t use mri_vol2surf (that allows me to use projfrac-avg) in group analysis and that’s the reason i have problem with mris_proproc to compute the average.
What should i do?
Thanks, Reza
On 29 Jul 2019, at 23:03, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
one computes the average, the other computes the maximum
On 7/29/19 9:03 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionDear Doug,
I appreciat if you reply my question in the previous e-mail with
this:
can not i use projfrac-avg in mris_preproc? Is --projfrac-max min max delta just the same?
Best,
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh <reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Monday, July 29, 2019 11:37:46 AM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionDear Doug,
Thanks, the tutorial was super helpful. As i would compare the MWF value in cortex between control subjects and patients. Now my problem is how to make the contrast matrix for mris_preproc to do the comparison in both direction (in 1, the outcome should be voxels in which MWf value in control>patients & in 2, reversed).
The explanations in
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
is for one group analysis and in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is not clear about contrast.
I remember for -randomise command-line, there was possibility to make contrast and design matrix (something like FSGD) via design_ttest2. Can i use still design_ttest2 for producing contrast and design
matrix?
Best,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> *Sent:* Wednesday, July 17, 2019 5:31:27 PM *To:* Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help Ah, I see. Try this tutorial. It is for fMRI, but it applies to any modality
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote:
External Email - Use Cautionto clarify better, i need to compare myelin water fraction in cortex of control and patients to find out the areas with reduced MWF in patients cortex compared with controls, that is the reason i want to have cortex in inflated format.
For this reason i used bbregister to have register.dat, and then mri_vol2surf to resample MWI cortex to surface. As i need to
have all
surfaces in fsaverage space for group analysis, i am using mri_preproc7mri_surf2surf (according to the group analysis wiki you sent me).
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh
<reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Wednesday, July 17, 2019 4:26:21 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionI am trying to compare MWI(sampled on the surface) between couple patients and controls using group analysis, therefore i need to have all inflated surface_on_same space (according to the wiki of group analysis you sent me, i should use mris_preproc to put my data on fsaverage).
Could you now tell me whether my mris_prepoc is right? and one other question i have asked in last email?
Thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
*Sent:* Wednesday, July 17, 2019 4:14:41 PM *To:* Reza Rahmanzadeh; Freesurfer support list;
greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] need for help It is not clear to me what you are trying to do. Do you want to do a morphometry study (ie, comparing thickness, area, and/or volume
across
subjects)? Or do you want to compare MWI (sampled on the surface) across subjects?
> On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > > Dear Doug, > > > I took the back slash away and ran > > mris_preproc --target fsaverage --hemi lh --s FSP010 --out > lh.FSP10.white.mgh --meas white > > > but i got error: > > *Reading curvature file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white** > MRISreadBinaryCurvature: incompatible vertex number in file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white** > ERROR: reading curvature file* > > > Then i changed it to --meas : mris_preproc --target fsaverage
--hemi
> lh --s FSP010 --out lh.FSP10.white.mgz --meas area > > > Then, as i need to register my the inflated cortex of myelin water > image (MWI) to the surface_registered_on_fsaverage (could it be the > output of command-line above?), should i use this output > "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling > myelin water image to lh.white of my subject FSP10 before > registration to fsaverage) for mri_surf2surf (to resample the
latter
> to the former, to have MWI to surface_fsaverage) > > > > Looking forward to answers > > Thanks > > Reza > > > > > >
> *From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu > mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu > mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza
> Rahmanzadeh <reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch > mailto:reza.rahmanzadeh@unibas.ch
mailto:reza.rahmanzadeh@unibas.ch>
> *Sent:* Wednesday, July 17, 2019 9:56:00 AM > *To:* Freesurfer support list > *Cc:* DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu > *Subject:* Re: [Freesurfer] need for help > External Email - Use Caution > > Thanks Tim, > > Then if i would resample my data to fsaverage and surfaces are of > main importance to my work, what should i use for -meas ? > > Reza > >> On 17 Jul 2019, at 09:39, Tim Schäfer <ts+ml@rcmd.orgmailto:ts+ml@rcmd.org >> mailto:ts+ml@rcmd.org
mailto:ts+ml@rcmd.org> wrote:
>> >> External Email - Use Caution >> >> I guess '-meas' expects a measure (like 'thickness' or
'area'), not
> a surface (like 'white'). >> >> Best, >> >> Tim >> >>> On July 17, 2019 at 9:03 AM Reza Rahmanzadeh > <reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch > mailto:reza.rahmanzadeh@unibas.ch> wrote: >>> >>> >>> External Email - Use Caution >>> >>> I removed the back slash and the command line i executed is: >>> >>> >>> mris_preproc --target fsaverage --hemi lh --s FSP010 --out > lh.FSP10.white.mgh --meas white >>> >>> >>> but i got the error: >>> >>> Reading curvature file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white >>> MRISreadBinaryCurvature: incompatible vertex number in file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white >>> ERROR: reading curvature file >>> >>> I have added --srcfmt mgh as the last argument, but again i got > the error: >>> Reading source surface reg > /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg >>> Loading source data >>> No such file or directory >>> ERROR: could not read > /usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3 >>> >>> >>> What is wrong with my mris_prepoc command line? >>> >>> Reza >>> >>> >>> ________________________________ >>> From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>> Sent: Tuesday, July 16, 2019 10:01:15 PM >>> To: Reza Rahmanzadeh; Freesurfer support list; > greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > mailto:greve@nmr.mgh.harvard.edu >>> Subject: Re: need for help >>> >>> don't include the back slash (ie, fsaverage not fsaverage/ same > for FSP010) >>> >>>> On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote: >>>> >>>> External Email - Use Caution >>>> >>>> Thanks a lot Doug, >>>> >>>> >>>> I started to proceed with FS group analysis wiki you sent to me. >>>> Accordingly, i have to resample all my data (output of recon-all > for a >>>> given subject for example) into fsaverage using mris_preproc. My >>>> commandline for a subject was: >>>> >>>> mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out >>>> lh.FSP10.white.mgh --meas white >>>> >>>> >>>> and i got the error: >>>> >>>> * >>>> * >>>> *Reading source surface reg >>>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>>> No such file or directory >>>> mri_surf2surf: could not read surface >>>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>>> No such file or directory* >>>> * >>>> * >>>> As there was no**lh.fsaverage/.sphere.reg* *folder, i found one
file
>>>> in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a
folder
>>>> with the name lh.fsaverage and i copied/pasted the mentiomed
file
> into >>>> this folder and i changed the file name to: ./sphere.reg. I
got the
>>>> error: >>>> * >>>> * >>>> *Reading curvature file >>>> /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere >>>> MRISreadBinaryCurvature: incompatible vertex number in file >>>> /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere* >>>> * >>>> * >>>> * >>>> * >>>> What is the problem with my mris_preproc command-line? >>>> >>>> Reza >>>> >>>> >
>>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu >>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
>>>> <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu >>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
>>>> N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >>>> mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> >>>> *Sent:* Tuesday, July 16, 2019 7:01:30 PM >>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>> *Subject:* Re: [Freesurfer] need for help >>>> >>>> >>>>> On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> (I assume now we are discussing in FS list, if no please let
me how
>>>>> possible?) >>>>> >>>>> >>>>> Thanks Doug, now i could see the inflate surface, this means
that my
>>>>> mri_vol2surf works well. As i would do GLM analysis over
inflated
>>>>> cortex of patients and controls in Qdec, >>>>> >>>>> >>>>> 1- should i input my surfaces to Qdec as inflated surface
or just
>>>>> inputting the output_of_vol2surf.mgz to Qdec? >>>>> >>>>> if inflated one is the input, then how could i get them? > mris_inflate >>>>> gives error. >>>>> >>>> QDEC is no longer being supported. Use the command line stream >>>> (mri_surf2surf, mri_glmfit, mri_glmfit-sim). >>>>
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>>>>> >>>>> >>>>> 2- should i input all patients and controls surfaces in
standard
>>>>> surface before entering to Qdec? >>>>> >>>>> >>>>> 3- I would like to resample whole cortex (whole cortical > thickness, in >>>>> other words: the average of all projfrac between 0 and 1),
is it
>>>>> possible? or i am limited to resample one given depth of
cortex into
>>>>> inflated surface only? >>>>> >>>> Run mri_vol2surf with --help and look for --projfrac-avg >>>>> >>>>> >>>>> thanks a lot, >>>>> >>>>> Reza >>>>> >>>>> >>>>> >
>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>> *Sent:* Tuesday, July 16, 2019 6:22:56 PM >>>>> *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu >>>>> mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
>>>>> *Subject:* Re: need for help >>>>> The command should be something like >>>>> tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz >>>>> Also, tksurfer is also obsolete (but should work). You
should be
> using >>>>> freeview (or tksurferfv, a freeview front end that takes
the same
>>>>> command line args as tksurfer) >>>>> Also, please remember to respond to the fs list >>>>> >>>>>> On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote: >>>>>> >>>>>> External Email - Use Caution >>>>>> >>>>>> I got the mri_vol2surf output with .mgz: >>>>>> >>>>>> >>>>>> my tksurfer command: >>>>>> >>>>>> tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of >>>>>> mri_vol2surf was lh.inflated_MWI.mgz) >>>>>> >>>>>> >>>>>> and the error i got: >>>>>> >>>>>> *freadFloat: fread failed** >>>>>> No such file or directory* >>>>>> >>>>>> To me, opening the surfer in tksurfer is only a way to get
sure my
>>>>>> vol2surf worked well. the main problem is i got this error
for all
>>>>>> mris_smooth, mris_inflate, mris_sphere ... >>>>>> >>>>>> >>>>>> Do you think that means the output of mri_vol2surf is not > correct, or >>>>>> otherwise i could proceed with that , even when tksurfer
could not
>>>>>> open it, for GLM in Qdec? >>>>>> >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Reza >>>>>> >>>>>> >>>> >
>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >>>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>>> *Sent:* Tuesday, July 16, 2019 6:01:15 PM >>>>>> *To:* Reza Rahmanzadeh >>>>>> *Subject:* Re: need for help >>>>>> what is your tksurfer command line? Also, the .w file is
somewhat
>>>>>> obsolete (it should still work); instead you can use .mgz
file (and
>>>>>> don't spec --paint) >>>>>> >>>>>>> On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote: >>>>>>> >>>>>>> External Email - Use Caution >>>>>>> >>>>>>> Thanks Doug, >>>>>>> >>>>>>> >>>>>>> I used the one without --inflated also, again the tksurfer > could not >>>>>>> open it and i got the same error. Where is the problem
with my
> cmd.? >>>>>>> >>>>>>> >>>>>>> In addition, i wanted to make the output of mri_vol2surf
inflated
>>>>>>> using mris_inflate but i got the same error: >>>>>>> >>>>>>> *freadFloat: fread failed >>>>>>> No such file or directory* >>>>>>> * >>>>>>> * >>>>>>> *could you let me know what is the problem in registering
my mwi
>>>>>>> volumes to surface that i getonly such errors.* >>>>>>> * >>>>>>> * >>>>>>> *Thanks,* >>>>>>> *reza >>>>>>> * >>>>>>> >>>>>>> >>>>> >
>>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >>>>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>>>> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >>>>>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>> *Cc:* greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>>>>>> mailto:greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu
>>>>>>> *Subject:* Re: need for help >>>>>>> Don't use --inflated. The inflated surface is not a
biological
>>>>>>> surface. The default is the white surface, which is the one > you want >>>>>>> (--projfrac 0.5 will project it to the middle between the > white and >>>>> pial) >>>>>>> >>>>>>>> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: >>>>>>>> >>>>>>>> External Email - Use Caution >>>>>>>> >>>>>>>> Dear Freesurfer, >>>>>>>> >>>>>>>> I have a batch of myelin water image (MWI) from patients and >>>>>>>> controls, and trying to have inflated cortex registered on > standard >>>>>>>> surface for GLM (Qdec). >>>>>>>> >>>>>>>> With the commandlines below i get my inflated surface of MWI > map of >>>>>>>> my patients and controls. >>>>>>>> >>>>>>>> 1-using bbregister to put MWI into FS space and to calculate >>>>>>>> register.dat: >>>>>>>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg > register.dat >>>>>>>> --o mwf_FS --t1 >>>>>>>> >>>>>>>> 2-using mri_vol2surf to extract inflated surface of MWI: >>>>>>>> mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 >>>>>>>> --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type >>>>>>>> paint--inflated (*or*--surf sphere) >>>>>>>> >>>>>>>> However the tksurfer could not open the inflated surface
and the
>>>>>>>> error message is: >>>>>>>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! >>>>>>>> Probably trying to use a scalar data file as a surface!* >>>>>>>> >>>>>>>> I used the commandline below for #2: >>>>>>>> mri_vol2surf --src mwf.nii --srcreg register.dat --hemi
lh --o
>>>>>>>> mwf-lh.w --out_type paint >>>>>>>> and i got the error: >>>>>>>> >>>>>>>> *ERROR: MRISread: file >>>>>>>>
'/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has
> many >>>>>>>> more faces than vertices!** >>>>>>>> Probably trying to use a scalar data file as a surface!* >>>>>>>> * >>>>>>>> * >>>>>>>> As tksurfer could not open my surfaces with errors above, i
think
>>>>>>>> perhaps the vol2surf procedure is not done properly. Where
is the
>>>>>>>> problem? i need to get the inflated cortex and then
putting ob
>>>>>>>> sphere (using mris_sphere) and the registering to standard > surface >>>>>>>> using mris_register for GLM in Qdec, right? >>>>>>>> >>>>>>>> >>>>>>>> It is two weeks i am struggling with these commands, any
helps
>>>>>>>> highly appreciated. * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> Best, >>>>>>>> Reza >>>>>>>> >>>>>>> >>>>>>> The information in this e-mail is intended only for the
person to
>>>>>>> whom it is >>>>>>> addressed. If you believe this e-mail was sent to you in
error and
>>>>>>> the e-mail >>>>>>> contains patient information, please contact the Partners > Compliance >>>>>>> HelpLine at >>>>>>> http://www.partners.org/complianceline . If the e-mail was
sent to
>>>>>>> you in error >>>>>>> but does not contain patient information, please contact the > sender >>>>>>> and properly >>>>>>> dispose of the e-mail. >>>>>>> >>>>>> >>>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Dr. Tim Schäfer >> Postdoc Computational Neuroimaging >> Department of Child and Adolescent Psychiatry, Psychosomatics and > Psychotherapy >> University Hospital Frankfurt, Goethe University Frankfurt am
Main,
> Germany >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Doug,
When i click on the link you sent me for uploading the files, there is no bottom/way to upload something there. That is why i attached the outputs.
My command lines sequentially for the analysis are: ( I have done just the same command lines for MWF maps and it worked very good, but for NDI and ODI maps of NODDI does not work).
1-mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 --out lh.NDI_inflated.avg.mgh (i used the new mris_preproc you sent me).
2-mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex --sval lh.NDI_inflated.avg.mgh --tval lh.NDI_inflated.avg.05.mgh
3-mri_glmfit --y lh.NDI_inflated.avg.05.mgh --surf fsaverage lh --C contrast --fsgd fsgd.fsgd --cortex --glmdir lh.NDI_inflated.avg.05.glmdir
The outputs of all three steps are attached.
Looking forward for your helps
Reza
________________________________ From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Monday, August 5, 2019 5:55:18 PM To: Reza Rahmanzadeh; Freesurfer support list Cc: greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] need for help
Can you upload the input (ie, argument to --y) here: ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Also, send your mri_glmfit command line.
On 8/2/2019 9:41 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
yes, I have the page below for all patients.
I think it means all values are zero. My registration for bbregister is fine and i wrote my mris_preproc the same as MWF maps.
Thanks,
Reza
________________________________ From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Friday, August 2, 2019 3:35:45 PM To: Reza Rahmanzadeh; Freesurfer support list Cc: greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] need for help
did you check each subject to make sure they had a non-zero map?
On 8/2/2019 6:25 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Dear Doug,
NODDI is diffusion imaging and we have vakue regarding neurite density (NDI in NDI map) and orientation dispersion (ODI value in ODI map). I do not know why mris_preproc works well on MWI maps but not on NODDI maps (both NDI and ODI maps). Beside using projfrac-avg 0 1 0.25 , i have run mris_preproc with projfrac 0.5 but again i got this error:
ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input
I have run mris_preproc on three patients that i am sure about registration quality, again when i scroll through them , there is no value in none of them. How that is possible?
NODDI does not have a lot of zero value but all values in cortex are between 0.2-0.4.
Thanks, Reza
________________________________ From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Wednesday, July 31, 2019 12:50:45 AM To: Reza Rahmanzadeh; Freesurfer support list Cc: greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] need for help
I don't know what is in the NODDI maps. The way mri_glmfit works is that if any subject has a 0-value at a vertex, then it will mask out that vertex for all subjects. Is NODDI something that might have a lot of 0-values? It also may be that one subject has all 0s (eg, if the regitration was really bad), so you can check the map created by mris_preproc (load it in as an overlay, then hit the configure button, then change the frame number to scroll through your subjects)
On 7/30/19 12:46 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution(sorry for bombaeding you with e-mails)
It seems that the error happens only when i use NODDI diffusion image e.g. NDI map i get that error, but for MWIs the new mris_preproc works well.
Should i do anything special for NODDI images? BTW, the bbregister works well for NODDI and i entered the correct registration file into mris_preproc.
Thanks,
Reza
*From:* Reza Rahmanzadeh *Sent:* Tuesday, July 30, 2019 6:17:22 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list *Cc:* greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
... One problem when i use the new mris_preproc:
Always the output of mri_glmfit when the input is the result of new mris_preproc is:
*F**ound 0 voxels in mask ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input*
I think it means that something is perhaps wrong with the script. I tried both projfrac 0.5 and projfrac-avg 0 1 0.25 and i got the same error. I did not get the error when i used old mris_preproc using projfrac 0.5.*
*The other thing that could be the reason is my fsgd file. I have problem how to specify the name of subjects,
Now it is sth like:
GroupDescriptorFile 1 Class Group1 CLASS Group2 Input FSC001 Group1 Input FSC002 Group1 Input FSC003 Group1 .
.
.
Input FSP001 Group2 Input FSP002 Group2 Input FSP003 Group2 .
.
The oeder is thew same with mris_preproc, now the subject name is FSC0xx for controls and FSP00x for patients, these are the name of folders containing FS outputs, but my input volume is MWIs and the registration files are not stored in this folder. Does it matter how to name subjects when i am using fsgd file only in mri_glmfit ( to get aware of order)?
Thanks,
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza Rahmanzadeh reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch *Sent:* Tuesday, July 30, 2019 2:44:25 PM *To:* Greve, Douglas N.,Ph.D. *Cc:* Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help External Email - Use Caution
Thanks Doug,
The script works well for projfrac-avg. but the problem is: when i use mris_preproc to assemble my MWIs and put them on fsaverage, as .fsgd file is only the order of my controls and subjects and i would have the inflated cortex of MWI on fsaverage, then anyway i have to specify my volume and registration files (tkregister2 output). Then there’s an error: i shouldn’t use both -fsgd and - iv together. Then i decided not to use fsgd file for mris_preproc and only using that for mri_glmfit. In mris_preproc, i write all “-iv volumes and registration files” in the same order as in fsgd file but i don’t write -fsgd argument. Is this way correct?
Thanks, Reza
On 29 Jul 2019, at 23:32, Greve, Douglas N.,Ph.D.
DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu wrote:
Oh, I guess that's a problem! I've created a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc See if that works. You should compare the output to using the max or -projfrac 0.5 to make sure they are at least similar since I have not run it even once:)
On 7/29/19 5:08 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks
But mris_prepoc will not accept “projfrac-avg” and there’s an error: argument unrecognized!
Then how can i compute the average via mris_preproc? As based on tutorial, first i used tkregister/bbregister to compute the registration matrix and then i should put input images with transformation matrix in mris_preproc. I mean i shouldn’t use mri_vol2surf (that allows me to use projfrac-avg) in group analysis and that’s the reason i have problem with mris_proproc to compute the average.
What should i do?
Thanks, Reza
On 29 Jul 2019, at 23:03, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
one computes the average, the other computes the maximum
On 7/29/19 9:03 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionDear Doug,
I appreciat if you reply my question in the previous e-mail with
this:
can not i use projfrac-avg in mris_preproc? Is --projfrac-max min max delta just the same?
Best,
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh <reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Monday, July 29, 2019 11:37:46 AM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionDear Doug,
Thanks, the tutorial was super helpful. As i would compare the MWF value in cortex between control subjects and patients. Now my problem is how to make the contrast matrix for mris_preproc to do the comparison in both direction (in 1, the outcome should be voxels in which MWf value in control>patients & in 2, reversed).
The explanations in
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
is for one group analysis and in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is not clear about contrast.
I remember for -randomise command-line, there was possibility to make contrast and design matrix (something like FSGD) via design_ttest2. Can i use still design_ttest2 for producing contrast and design
matrix?
Best,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> *Sent:* Wednesday, July 17, 2019 5:31:27 PM *To:* Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help Ah, I see. Try this tutorial. It is for fMRI, but it applies to any modality
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote:
External Email - Use Cautionto clarify better, i need to compare myelin water fraction in cortex of control and patients to find out the areas with reduced MWF in patients cortex compared with controls, that is the reason i want to have cortex in inflated format.
For this reason i used bbregister to have register.dat, and then mri_vol2surf to resample MWI cortex to surface. As i need to
have all
surfaces in fsaverage space for group analysis, i am using mri_preproc7mri_surf2surf (according to the group analysis wiki you sent me).
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh
<reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Wednesday, July 17, 2019 4:26:21 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionI am trying to compare MWI(sampled on the surface) between couple patients and controls using group analysis, therefore i need to have all inflated surface_on_same space (according to the wiki of group analysis you sent me, i should use mris_preproc to put my data on fsaverage).
Could you now tell me whether my mris_prepoc is right? and one other question i have asked in last email?
Thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
*Sent:* Wednesday, July 17, 2019 4:14:41 PM *To:* Reza Rahmanzadeh; Freesurfer support list;
greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] need for help It is not clear to me what you are trying to do. Do you want to do a morphometry study (ie, comparing thickness, area, and/or volume
across
subjects)? Or do you want to compare MWI (sampled on the surface) across subjects?
> On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > > Dear Doug, > > > I took the back slash away and ran > > mris_preproc --target fsaverage --hemi lh --s FSP010 --out > lh.FSP10.white.mgh --meas white > > > but i got error: > > *Reading curvature file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white** > MRISreadBinaryCurvature: incompatible vertex number in file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white** > ERROR: reading curvature file* > > > Then i changed it to --meas : mris_preproc --target fsaverage
--hemi
> lh --s FSP010 --out lh.FSP10.white.mgz --meas area > > > Then, as i need to register my the inflated cortex of myelin water > image (MWI) to the surface_registered_on_fsaverage (could it be the > output of command-line above?), should i use this output > "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling > myelin water image to lh.white of my subject FSP10 before > registration to fsaverage) for mri_surf2surf (to resample the
latter
> to the former, to have MWI to surface_fsaverage) > > > > Looking forward to answers > > Thanks > > Reza > > > > > >
> *From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu > mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu > mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza
> Rahmanzadeh <reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch > mailto:reza.rahmanzadeh@unibas.ch
mailto:reza.rahmanzadeh@unibas.ch>
> *Sent:* Wednesday, July 17, 2019 9:56:00 AM > *To:* Freesurfer support list > *Cc:* DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu > *Subject:* Re: [Freesurfer] need for help > External Email - Use Caution > > Thanks Tim, > > Then if i would resample my data to fsaverage and surfaces are of > main importance to my work, what should i use for -meas ? > > Reza > >> On 17 Jul 2019, at 09:39, Tim Schäfer <ts+ml@rcmd.orgmailto:ts+ml@rcmd.org >> mailto:ts+ml@rcmd.org
mailto:ts+ml@rcmd.org> wrote:
>> >> External Email - Use Caution >> >> I guess '-meas' expects a measure (like 'thickness' or
'area'), not
> a surface (like 'white'). >> >> Best, >> >> Tim >> >>> On July 17, 2019 at 9:03 AM Reza Rahmanzadeh > <reza.rahmanzadeh@unibas.chmailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch > mailto:reza.rahmanzadeh@unibas.ch> wrote: >>> >>> >>> External Email - Use Caution >>> >>> I removed the back slash and the command line i executed is: >>> >>> >>> mris_preproc --target fsaverage --hemi lh --s FSP010 --out > lh.FSP10.white.mgh --meas white >>> >>> >>> but i got the error: >>> >>> Reading curvature file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white >>> MRISreadBinaryCurvature: incompatible vertex number in file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white >>> ERROR: reading curvature file >>> >>> I have added --srcfmt mgh as the last argument, but again i got > the error: >>> Reading source surface reg > /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg >>> Loading source data >>> No such file or directory >>> ERROR: could not read > /usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3 >>> >>> >>> What is wrong with my mris_prepoc command line? >>> >>> Reza >>> >>> >>> ________________________________ >>> From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>> Sent: Tuesday, July 16, 2019 10:01:15 PM >>> To: Reza Rahmanzadeh; Freesurfer support list; > greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > mailto:greve@nmr.mgh.harvard.edu >>> Subject: Re: need for help >>> >>> don't include the back slash (ie, fsaverage not fsaverage/ same > for FSP010) >>> >>>> On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote: >>>> >>>> External Email - Use Caution >>>> >>>> Thanks a lot Doug, >>>> >>>> >>>> I started to proceed with FS group analysis wiki you sent to me. >>>> Accordingly, i have to resample all my data (output of recon-all > for a >>>> given subject for example) into fsaverage using mris_preproc. My >>>> commandline for a subject was: >>>> >>>> mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out >>>> lh.FSP10.white.mgh --meas white >>>> >>>> >>>> and i got the error: >>>> >>>> * >>>> * >>>> *Reading source surface reg >>>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>>> No such file or directory >>>> mri_surf2surf: could not read surface >>>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>>> No such file or directory* >>>> * >>>> * >>>> As there was no**lh.fsaverage/.sphere.reg* *folder, i found one
file
>>>> in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a
folder
>>>> with the name lh.fsaverage and i copied/pasted the mentiomed
file
> into >>>> this folder and i changed the file name to: ./sphere.reg. I
got the
>>>> error: >>>> * >>>> * >>>> *Reading curvature file >>>> /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere >>>> MRISreadBinaryCurvature: incompatible vertex number in file >>>> /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere* >>>> * >>>> * >>>> * >>>> * >>>> What is the problem with my mris_preproc command-line? >>>> >>>> Reza >>>> >>>> >
>>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu >>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
>>>> <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu >>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
>>>> N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >>>> mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> >>>> *Sent:* Tuesday, July 16, 2019 7:01:30 PM >>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>> *Subject:* Re: [Freesurfer] need for help >>>> >>>> >>>>> On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> (I assume now we are discussing in FS list, if no please let
me how
>>>>> possible?) >>>>> >>>>> >>>>> Thanks Doug, now i could see the inflate surface, this means
that my
>>>>> mri_vol2surf works well. As i would do GLM analysis over
inflated
>>>>> cortex of patients and controls in Qdec, >>>>> >>>>> >>>>> 1- should i input my surfaces to Qdec as inflated surface
or just
>>>>> inputting the output_of_vol2surf.mgz to Qdec? >>>>> >>>>> if inflated one is the input, then how could i get them? > mris_inflate >>>>> gives error. >>>>> >>>> QDEC is no longer being supported. Use the command line stream >>>> (mri_surf2surf, mri_glmfit, mri_glmfit-sim). >>>>
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>>>>> >>>>> >>>>> 2- should i input all patients and controls surfaces in
standard
>>>>> surface before entering to Qdec? >>>>> >>>>> >>>>> 3- I would like to resample whole cortex (whole cortical > thickness, in >>>>> other words: the average of all projfrac between 0 and 1),
is it
>>>>> possible? or i am limited to resample one given depth of
cortex into
>>>>> inflated surface only? >>>>> >>>> Run mri_vol2surf with --help and look for --projfrac-avg >>>>> >>>>> >>>>> thanks a lot, >>>>> >>>>> Reza >>>>> >>>>> >>>>> >
>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>> *Sent:* Tuesday, July 16, 2019 6:22:56 PM >>>>> *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu >>>>> mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
>>>>> *Subject:* Re: need for help >>>>> The command should be something like >>>>> tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz >>>>> Also, tksurfer is also obsolete (but should work). You
should be
> using >>>>> freeview (or tksurferfv, a freeview front end that takes
the same
>>>>> command line args as tksurfer) >>>>> Also, please remember to respond to the fs list >>>>> >>>>>> On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote: >>>>>> >>>>>> External Email - Use Caution >>>>>> >>>>>> I got the mri_vol2surf output with .mgz: >>>>>> >>>>>> >>>>>> my tksurfer command: >>>>>> >>>>>> tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of >>>>>> mri_vol2surf was lh.inflated_MWI.mgz) >>>>>> >>>>>> >>>>>> and the error i got: >>>>>> >>>>>> *freadFloat: fread failed** >>>>>> No such file or directory* >>>>>> >>>>>> To me, opening the surfer in tksurfer is only a way to get
sure my
>>>>>> vol2surf worked well. the main problem is i got this error
for all
>>>>>> mris_smooth, mris_inflate, mris_sphere ... >>>>>> >>>>>> >>>>>> Do you think that means the output of mri_vol2surf is not > correct, or >>>>>> otherwise i could proceed with that , even when tksurfer
could not
>>>>>> open it, for GLM in Qdec? >>>>>> >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Reza >>>>>> >>>>>> >>>> >
>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >>>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>>> *Sent:* Tuesday, July 16, 2019 6:01:15 PM >>>>>> *To:* Reza Rahmanzadeh >>>>>> *Subject:* Re: need for help >>>>>> what is your tksurfer command line? Also, the .w file is
somewhat
>>>>>> obsolete (it should still work); instead you can use .mgz
file (and
>>>>>> don't spec --paint) >>>>>> >>>>>>> On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote: >>>>>>> >>>>>>> External Email - Use Caution >>>>>>> >>>>>>> Thanks Doug, >>>>>>> >>>>>>> >>>>>>> I used the one without --inflated also, again the tksurfer > could not >>>>>>> open it and i got the same error. Where is the problem
with my
> cmd.? >>>>>>> >>>>>>> >>>>>>> In addition, i wanted to make the output of mri_vol2surf
inflated
>>>>>>> using mris_inflate but i got the same error: >>>>>>> >>>>>>> *freadFloat: fread failed >>>>>>> No such file or directory* >>>>>>> * >>>>>>> * >>>>>>> *could you let me know what is the problem in registering
my mwi
>>>>>>> volumes to surface that i getonly such errors.* >>>>>>> * >>>>>>> * >>>>>>> *Thanks,* >>>>>>> *reza >>>>>>> * >>>>>>> >>>>>>> >>>>> >
>>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >>>>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>>>> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >>>>>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>> *Cc:* greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>>>>>> mailto:greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu
>>>>>>> *Subject:* Re: need for help >>>>>>> Don't use --inflated. The inflated surface is not a
biological
>>>>>>> surface. The default is the white surface, which is the one > you want >>>>>>> (--projfrac 0.5 will project it to the middle between the > white and >>>>> pial) >>>>>>> >>>>>>>> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: >>>>>>>> >>>>>>>> External Email - Use Caution >>>>>>>> >>>>>>>> Dear Freesurfer, >>>>>>>> >>>>>>>> I have a batch of myelin water image (MWI) from patients and >>>>>>>> controls, and trying to have inflated cortex registered on > standard >>>>>>>> surface for GLM (Qdec). >>>>>>>> >>>>>>>> With the commandlines below i get my inflated surface of MWI > map of >>>>>>>> my patients and controls. >>>>>>>> >>>>>>>> 1-using bbregister to put MWI into FS space and to calculate >>>>>>>> register.dat: >>>>>>>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg > register.dat >>>>>>>> --o mwf_FS --t1 >>>>>>>> >>>>>>>> 2-using mri_vol2surf to extract inflated surface of MWI: >>>>>>>> mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 >>>>>>>> --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type >>>>>>>> paint--inflated (*or*--surf sphere) >>>>>>>> >>>>>>>> However the tksurfer could not open the inflated surface
and the
>>>>>>>> error message is: >>>>>>>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! >>>>>>>> Probably trying to use a scalar data file as a surface!* >>>>>>>> >>>>>>>> I used the commandline below for #2: >>>>>>>> mri_vol2surf --src mwf.nii --srcreg register.dat --hemi
lh --o
>>>>>>>> mwf-lh.w --out_type paint >>>>>>>> and i got the error: >>>>>>>> >>>>>>>> *ERROR: MRISread: file >>>>>>>>
'/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has
> many >>>>>>>> more faces than vertices!** >>>>>>>> Probably trying to use a scalar data file as a surface!* >>>>>>>> * >>>>>>>> * >>>>>>>> As tksurfer could not open my surfaces with errors above, i
think
>>>>>>>> perhaps the vol2surf procedure is not done properly. Where
is the
>>>>>>>> problem? i need to get the inflated cortex and then
putting ob
>>>>>>>> sphere (using mris_sphere) and the registering to standard > surface >>>>>>>> using mris_register for GLM in Qdec, right? >>>>>>>> >>>>>>>> >>>>>>>> It is two weeks i am struggling with these commands, any
helps
>>>>>>>> highly appreciated. * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> Best, >>>>>>>> Reza >>>>>>>> >>>>>>> >>>>>>> The information in this e-mail is intended only for the
person to
>>>>>>> whom it is >>>>>>> addressed. If you believe this e-mail was sent to you in
error and
>>>>>>> the e-mail >>>>>>> contains patient information, please contact the Partners > Compliance >>>>>>> HelpLine at >>>>>>> http://www.partners.org/complianceline . If the e-mail was
sent to
>>>>>>> you in error >>>>>>> but does not contain patient information, please contact the > sender >>>>>>> and properly >>>>>>> dispose of the e-mail. >>>>>>> >>>>>> >>>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Dr. Tim Schäfer >> Postdoc Computational Neuroimaging >> Department of Child and Adolescent Psychiatry, Psychosomatics and > Psychotherapy >> University Hospital Frankfurt, Goethe University Frankfurt am
Main,
> Germany >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You can try it from the command line, ftp surfer.nmr.mgh.harvard.edut It will ask you for a user name; use your email address It will ask you for a password; use "anonymous" (no quotes) cd transfer/incoming put file.tar
On 8/6/19 6:30 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Hi Doug,
When i click on the link you sent me for uploading the files, there is no bottom/way to upload something there. That is why i attached the outputs.
My command lines sequentially for the analysis are: ( I have done just the same command lines for MWF maps and it worked very good, but for NDI and ODI maps of NODDI does not work).
1-mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 --out lh.NDI_inflated.avg.mgh (i used the new mris_preproc you sent me).
2-mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex --sval lh.NDI_inflated.avg.mgh --tval lh.NDI_inflated.avg.05.mgh
3-mri_glmfit --y lh.NDI_inflated.avg.05.mgh --surf fsaverage lh --C contrast --fsgd fsgd.fsgd --cortex --glmdir lh.NDI_inflated.avg.05.glmdir
The outputs of all three steps are attached.
Looking forward for your helps
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Monday, August 5, 2019 5:55:18 PM *To:* Reza Rahmanzadeh; Freesurfer support list *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help Can you upload the input (ie, argument to --y) here: ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Also, send your mri_glmfit command line.
On 8/2/2019 9:41 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
yes, I have the page below for all patients.
I think it means all values are zero. My registration for bbregister is fine and i wrote my mris_preproc the same as MWF maps.
Thanks,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Friday, August 2, 2019 3:35:45 PM *To:* Reza Rahmanzadeh; Freesurfer support list *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help did you check each subject to make sure they had a non-zero map?
On 8/2/2019 6:25 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Dear Doug,
NODDI is diffusion imaging and we have vakue regarding neurite density (NDI in NDI map) and orientation dispersion (ODI value in ODI map). I do not know why mris_preproc works well on MWI maps but not on NODDI maps (both NDI and ODI maps). Beside using projfrac-avg 0 1 0.25 , i have run mris_preproc with projfrac 0.5 but again i got this error:
ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input
I have run mris_preproc on three patients that i am sure about registration quality, again when i scroll through them , there is no value in none of them. How that is possible?
NODDI does not have a lot of zero value but all values in cortex are between 0.2-0.4.
Thanks, Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Wednesday, July 31, 2019 12:50:45 AM *To:* Reza Rahmanzadeh; Freesurfer support list *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help I don't know what is in the NODDI maps. The way mri_glmfit works is that if any subject has a 0-value at a vertex, then it will mask out that vertex for all subjects. Is NODDI something that might have a lot of 0-values? It also may be that one subject has all 0s (eg, if the regitration was really bad), so you can check the map created by mris_preproc (load it in as an overlay, then hit the configure button, then change the frame number to scroll through your subjects)
On 7/30/19 12:46 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution
(sorry for bombaeding you with e-mails)
It seems that the error happens only when i use NODDI diffusion image e.g. NDI map i get that error, but for MWIs the new mris_preproc
works
well.
Should i do anything special for NODDI images? BTW, the bbregister works well for NODDI and i entered the correct registration file into mris_preproc.
Thanks,
Reza
*From:* Reza Rahmanzadeh *Sent:* Tuesday, July 30, 2019 6:17:22 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
... One problem when i use the new mris_preproc:
Always the output of mri_glmfit when the input is the result of new mris_preproc is:
*F**ound 0 voxels in mask ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input*
I think it means that something is perhaps wrong with the script. I tried both projfrac 0.5 and projfrac-avg 0 1 0.25 and i got the same error. I did not get the error when i used old mris_preproc using projfrac 0.5.*
*The other thing that could be the reason is my fsgd file. I have problem how to specify the name of subjects,
Now it is sth like:
GroupDescriptorFile 1 Class Group1 CLASS Group2 Input FSC001 Group1 Input FSC002 Group1 Input FSC003 Group1 .
.
.
Input FSP001 Group2 Input FSP002 Group2 Input FSP003 Group2 .
.
The oeder is thew same with mris_preproc, now the subject name is FSC0xx for controls and FSP00x for patients, these are the name of folders containing FS outputs, but my input volume is MWIs and the registration files are not stored in this folder. Does it matter how to name subjects when i am using fsgd file only in mri_glmfit ( to
get
aware of order)?
Thanks,
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza
Rahmanzadeh
reza.rahmanzadeh@unibas.ch *Sent:* Tuesday, July 30, 2019 2:44:25 PM *To:* Greve, Douglas N.,Ph.D. *Cc:* Freesurfer support list; greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help External Email - Use Caution
Thanks Doug,
The script works well for projfrac-avg. but the problem is: when i
use
mris_preproc to assemble my MWIs and put them on fsaverage, as .fsgd file is only the order of my controls and subjects and i would have the inflated cortex of MWI on fsaverage, then anyway i have to
specify
my volume and registration files (tkregister2 output). Then
there’s an
error: i shouldn’t use both -fsgd and - iv together. Then i decided not to use fsgd file for mris_preproc and only using that for mri_glmfit. In mris_preproc, i write all “-iv volumes and
registration
files” in the same order as in fsgd file but i don’t write -fsgd argument. Is this way correct?
Thanks, Reza
On 29 Jul 2019, at 23:32, Greve, Douglas N.,Ph.D.
DGREVE@mgh.harvard.edu wrote:
Oh, I guess that's a problem! I've created a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc See if that works. You should compare the output to using the max or -projfrac 0.5 to make sure they are at least similar since I
have not
run it even once:)
On 7/29/19 5:08 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Thanks
But mris_prepoc will not accept “projfrac-avg” and there’s an
error:
argument unrecognized!
Then how can i compute the average via mris_preproc? As based on tutorial, first i used tkregister/bbregister to compute the registration matrix and then i should put input images with transformation matrix in mris_preproc. I mean i shouldn’t use mri_vol2surf (that allows me to use projfrac-avg) in group analysis and that’s the reason i have problem with mris_proproc to
compute the
average.
What should i do?
Thanks, Reza
On 29 Jul 2019, at 23:03, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
> one computes the average, the other computes the maximum > >> On 7/29/19 9:03 AM, Reza Rahmanzadeh wrote: >> >> External Email - Use Caution >> >> Dear Doug, >> >> >> I appreciat if you reply my question in the previous e-mail with
this:
>> >> >> can not i use projfrac-avg in mris_preproc? Is --projfrac-max
min max
>> delta just the same? >> >> >> Best, >> >> Reza >> >>
>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu >> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >> <freesurfer-bounces@nmr.mgh.harvard.edu >> mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
Reza
>> Rahmanzadeh >> <reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> >> *Sent:* Monday, July 29, 2019 11:37:46 AM >> *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; >> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >> *Subject:* Re: [Freesurfer] need for help >> >> External Email - Use Caution >> >> Dear Doug, >> >> >> Thanks, the tutorial was super helpful. As i would compare
the MWF
>> value in cortex between control subjects and patients. Now my
problem
>> is how to make the contrast matrix for mris_preproc to do the >> comparison in both direction (in 1, the outcome should be
voxels in
>> which MWf value in control>patients & in 2, reversed). >> >> >> The explanations in >>
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
>> >> is for one group analysis and in >>
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is
>> not clear about contrast. >> >> I remember for -randomise command-line, there was possibility
to make
>> contrast and design matrix (something like FSGD) via
design_ttest2.
>> Can i use still design_ttest2 for producing contrast and design
matrix?
>> >> >> >> Best, >> >> Reza >> >>
>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu> >> *Sent:* Wednesday, July 17, 2019 5:31:27 PM >> *To:* Reza Rahmanzadeh; Freesurfer support list; >> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >> mailto:greve@nmr.mgh.harvard.edu >> *Subject:* Re: [Freesurfer] need for help >> Ah, I see. Try this tutorial. It is for fMRI, but it applies
to any
>> modality >>
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
>> >> >>> On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote: >>> >>> External Email - Use Caution >>> >>> to clarify better, i need to compare myelin water fraction
in cortex
>>> of control and patients to find out the areas with reduced
MWF in
>>> patients cortex compared with controls, that is the reason i
want to
>>> have cortex in inflated format. >>> >>> >>> For this reason i used bbregister to have register.dat, and then >>> mri_vol2surf to resample MWI cortex to surface. As i need to
have all
>>> surfaces in fsaverage space for group analysis, i am using >>> mri_preproc7mri_surf2surf (according to the group analysis
wiki you
>>> sent me). >>> >>>
>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>> <freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >> mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
Reza
>> Rahmanzadeh >>> <reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch >>> mailto:reza.rahmanzadeh@unibas.ch> >>> *Sent:* Wednesday, July 17, 2019 4:26:21 PM >>> *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; >>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>> mailto:greve@nmr.mgh.harvard.edu >>> *Subject:* Re: [Freesurfer] need for help >>> >>> External Email - Use Caution >>> >>> I am trying to compare MWI(sampled on the surface) between
couple
>>> patients and controls using group analysis, therefore i need
to have
>>> all inflated surface_on_same space (according to the wiki of
group
>>> analysis you sent me, i should use mris_preproc to put my
data on
>>> fsaverage). >>> >>> >>> Could you now tell me whether my mris_prepoc is right? and
one other
>>> question i have asked in last email? >>> >>> >>> Thanks a lot, >>> >>> Reza >>> >>>
>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu> >>> *Sent:* Wednesday, July 17, 2019 4:14:41 PM >>> *To:* Reza Rahmanzadeh; Freesurfer support list; >> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >> mailto:greve@nmr.mgh.harvard.edu >>> *Subject:* Re: [Freesurfer] need for help >>> It is not clear to me what you are trying to do. Do you want
to do a
>>> morphometry study (ie, comparing thickness, area, and/or volume
across
>>> subjects)? Or do you want to compare MWI (sampled on the
surface)
>>> across subjects? >>> >>>> On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote: >>>> >>>> External Email - Use Caution >>>> >>>> >>>> Dear Doug, >>>> >>>> >>>> I took the back slash away and ran >>>> >>>> mris_preproc --target fsaverage --hemi lh --s FSP010 --out >>>> lh.FSP10.white.mgh --meas white >>>> >>>> >>>> but i got error: >>>> >>>> *Reading curvature file >>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.white** >>>> MRISreadBinaryCurvature: incompatible vertex number in file >>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.white** >>>> ERROR: reading curvature file* >>>> >>>> >>>> Then i changed it to --meas : mris_preproc --target fsaverage
--hemi
>>>> lh --s FSP010 --out lh.FSP10.white.mgz --meas area >>>> >>>> >>>> Then, as i need to register my the inflated cortex of
myelin water
>>>> image (MWI) to the surface_registered_on_fsaverage (could
it be the
>>>> output of command-line above?), should i use this output >>>> "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling >>>> myelin water image to lh.white of my subject FSP10 before >>>> registration to fsaverage) for mri_surf2surf (to resample the
latter
>>>> to the former, to have MWI to surface_fsaverage) >>>> >>>> >>>> >>>> Looking forward to answers >>>> >>>> Thanks >>>> >>>> Reza >>>> >>>> >>>> >>>> >>>> >>>> >>
>>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu >>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>>> <freesurfer-bounces@nmr.mgh.harvard.edu >>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >> mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
Reza
>>>> Rahmanzadeh <reza.rahmanzadeh@unibas.ch >>>> mailto:reza.rahmanzadeh@unibas.ch >> mailto:reza.rahmanzadeh@unibas.ch> >>>> *Sent:* Wednesday, July 17, 2019 9:56:00 AM >>>> *To:* Freesurfer support list >>>> *Cc:* DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu >>>> mailto:DGREVE@mgh.harvard.edu >>>> *Subject:* Re: [Freesurfer] need for help >>>> External Email - Use Caution >>>> >>>> Thanks Tim, >>>> >>>> Then if i would resample my data to fsaverage and surfaces
are of
>>>> main importance to my work, what should i use for -meas ? >>>> >>>> Reza >>>> >>>>> On 17 Jul 2019, at 09:39, Tim Schäfer <ts+ml@rcmd.org >>>>> mailto:ts+ml@rcmd.org >> mailto:ts+ml@rcmd.org> wrote: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> I guess '-meas' expects a measure (like 'thickness' or
'area'), not
>>>> a surface (like 'white'). >>>>> >>>>> Best, >>>>> >>>>> Tim >>>>> >>>>>> On July 17, 2019 at 9:03 AM Reza Rahmanzadeh >>>> <reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch >>>> mailto:reza.rahmanzadeh@unibas.ch> wrote: >>>>>> >>>>>> >>>>>> External Email - Use Caution >>>>>> >>>>>> I removed the back slash and the command line i executed is: >>>>>> >>>>>> >>>>>> mris_preproc --target fsaverage --hemi lh --s FSP010 --out >>>> lh.FSP10.white.mgh --meas white >>>>>> >>>>>> >>>>>> but i got the error: >>>>>> >>>>>> Reading curvature file >>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.white >>>>>> MRISreadBinaryCurvature: incompatible vertex number in file >>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.white >>>>>> ERROR: reading curvature file >>>>>> >>>>>> I have added --srcfmt mgh as the last argument, but again
i got
>>>> the error: >>>>>> Reading source surface reg >>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg >>>>>> Loading source data >>>>>> No such file or directory >>>>>> ERROR: could not read >>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3 >>>>>> >>>>>> >>>>>> What is wrong with my mris_prepoc command line? >>>>>> >>>>>> Reza >>>>>> >>>>>> >>>>>> ________________________________ >>>>>> From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>> mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu> >>>>>> Sent: Tuesday, July 16, 2019 10:01:15 PM >>>>>> To: Reza Rahmanzadeh; Freesurfer support list; >>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>>> mailto:greve@nmr.mgh.harvard.edu >>>>>> Subject: Re: need for help >>>>>> >>>>>> don't include the back slash (ie, fsaverage not
fsaverage/ same
>>>> for FSP010) >>>>>> >>>>>>> On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote: >>>>>>> >>>>>>> External Email - Use Caution >>>>>>> >>>>>>> Thanks a lot Doug, >>>>>>> >>>>>>> >>>>>>> I started to proceed with FS group analysis wiki you
sent to me.
>>>>>>> Accordingly, i have to resample all my data (output of
recon-all
>>>> for a >>>>>>> given subject for example) into fsaverage using
mris_preproc. My
>>>>>>> commandline for a subject was: >>>>>>> >>>>>>> mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out >>>>>>> lh.FSP10.white.mgh --meas white >>>>>>> >>>>>>> >>>>>>> and i got the error: >>>>>>> >>>>>>> * >>>>>>> * >>>>>>> *Reading source surface reg >>>>>>> >>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>>>>>> No such file or directory >>>>>>> mri_surf2surf: could not read surface >>>>>>> >>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>>>>>> No such file or directory* >>>>>>> * >>>>>>> * >>>>>>> As there was no**lh.fsaverage/.sphere.reg* *folder, i
found one
>> file >>>>>>> in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a
folder
>>>>>>> with the name lh.fsaverage and i copied/pasted the
mentiomed
file
>>>> into >>>>>>> this folder and i changed the file name to: ./sphere.reg. I
got the
>>>>>>> error: >>>>>>> * >>>>>>> * >>>>>>> *Reading curvature file >>>>>>> /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere >>>>>>> MRISreadBinaryCurvature: incompatible vertex number in file >>>>>>> /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere* >>>>>>> * >>>>>>> * >>>>>>> * >>>>>>> * >>>>>>> What is the problem with my mris_preproc command-line? >>>>>>> >>>>>>> Reza >>>>>>> >>>>>>> >>>> >>
>>>>>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu >>>>>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>>>>>> <freesurfer-bounces@nmr.mgh.harvard.edu >>>>>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >> mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
Greve,
>> Douglas >>>>>>> N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>>>> *Sent:* Tuesday, July 16, 2019 7:01:30 PM >>>>>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>> *Subject:* Re: [Freesurfer] need for help >>>>>>> >>>>>>> >>>>>>>> On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote: >>>>>>>> >>>>>>>> External Email - Use Caution >>>>>>>> >>>>>>>> (I assume now we are discussing in FS list, if no
please let
>> me how >>>>>>>> possible?) >>>>>>>> >>>>>>>> >>>>>>>> Thanks Doug, now i could see the inflate surface, this
means
>> that my >>>>>>>> mri_vol2surf works well. As i would do GLM analysis over
inflated
>>>>>>>> cortex of patients and controls in Qdec, >>>>>>>> >>>>>>>> >>>>>>>> 1- should i input my surfaces to Qdec as inflated surface
or just
>>>>>>>> inputting the output_of_vol2surf.mgz to Qdec? >>>>>>>> >>>>>>>> if inflated one is the input, then how could i get them? >>>> mris_inflate >>>>>>>> gives error. >>>>>>>> >>>>>>> QDEC is no longer being supported. Use the command line
stream
>>>>>>> (mri_surf2surf, mri_glmfit, mri_glmfit-sim). >>>>>>>
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>>>>>>>> >>>>>>>> >>>>>>>> 2- should i input all patients and controls surfaces in
standard
>>>>>>>> surface before entering to Qdec? >>>>>>>> >>>>>>>> >>>>>>>> 3- I would like to resample whole cortex (whole cortical >>>> thickness, in >>>>>>>> other words: the average of all projfrac between 0 and 1),
is it
>>>>>>>> possible? or i am limited to resample one given depth of >> cortex into >>>>>>>> inflated surface only? >>>>>>>> >>>>>>> Run mri_vol2surf with --help and look for --projfrac-avg >>>>>>>> >>>>>>>> >>>>>>>> thanks a lot, >>>>>>>> >>>>>>>> Reza >>>>>>>> >>>>>>>> >>>>>>>> >>>> >>
>>>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>>>> mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu> >>>>>>>> *Sent:* Tuesday, July 16, 2019 6:22:56 PM >>>>>>>> *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu >>>>>>>> mailto:freesurfer@nmr.mgh.harvard.edu >> mailto:freesurfer@nmr.mgh.harvard.edu >>>>>>>> *Subject:* Re: need for help >>>>>>>> The command should be something like >>>>>>>> tksurfer mysubject lh inflated -overlay
output_of_vol2surf.mgz
>>>>>>>> Also, tksurfer is also obsolete (but should work). You
should be
>>>> using >>>>>>>> freeview (or tksurferfv, a freeview front end that takes
the same
>>>>>>>> command line args as tksurfer) >>>>>>>> Also, please remember to respond to the fs list >>>>>>>> >>>>>>>>> On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote: >>>>>>>>> >>>>>>>>> External Email - Use Caution >>>>>>>>> >>>>>>>>> I got the mri_vol2surf output with .mgz: >>>>>>>>> >>>>>>>>> >>>>>>>>> my tksurfer command: >>>>>>>>> >>>>>>>>> tksurfer FSP010/ (my subject) lh inflated_MWI.mgz
(output of
>>>>>>>>> mri_vol2surf was lh.inflated_MWI.mgz) >>>>>>>>> >>>>>>>>> >>>>>>>>> and the error i got: >>>>>>>>> >>>>>>>>> *freadFloat: fread failed** >>>>>>>>> No such file or directory* >>>>>>>>> >>>>>>>>> To me, opening the surfer in tksurfer is only a way to get >> sure my >>>>>>>>> vol2surf worked well. the main problem is i got this error >> for all >>>>>>>>> mris_smooth, mris_inflate, mris_sphere ... >>>>>>>>> >>>>>>>>> >>>>>>>>> Do you think that means the output of mri_vol2surf is not >>>> correct, or >>>>>>>>> otherwise i could proceed with that , even when tksurfer >> could not >>>>>>>>> open it, for GLM in Qdec? >>>>>>>>> >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> >>>>>>>>> Reza >>>>>>>>> >>>>>>>>> >>>>>>> >>>> >>
>>>>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>>>>> mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu> >>>>>>>>> *Sent:* Tuesday, July 16, 2019 6:01:15 PM >>>>>>>>> *To:* Reza Rahmanzadeh >>>>>>>>> *Subject:* Re: need for help >>>>>>>>> what is your tksurfer command line? Also, the .w file is
somewhat
>>>>>>>>> obsolete (it should still work); instead you can use .mgz >> file (and >>>>>>>>> don't spec --paint) >>>>>>>>> >>>>>>>>>> On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote: >>>>>>>>>> >>>>>>>>>> External Email - Use Caution >>>>>>>>>> >>>>>>>>>> Thanks Doug, >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> I used the one without --inflated also, again the
tksurfer
>>>> could not >>>>>>>>>> open it and i got the same error. Where is the problem
with my
>>>> cmd.? >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> In addition, i wanted to make the output of mri_vol2surf >> inflated >>>>>>>>>> using mris_inflate but i got the same error: >>>>>>>>>> >>>>>>>>>> *freadFloat: fread failed >>>>>>>>>> No such file or directory* >>>>>>>>>> * >>>>>>>>>> * >>>>>>>>>> *could you let me know what is the problem in
registering
my mwi
>>>>>>>>>> volumes to surface that i getonly such errors.* >>>>>>>>>> * >>>>>>>>>> * >>>>>>>>>> *Thanks,* >>>>>>>>>> *reza >>>>>>>>>> * >>>>>>>>>> >>>>>>>>>> >>>>>>>> >>>> >>
>>>>>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>>>>>> mailto:DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu> >>>>>>>>>> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >>>>>>>>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>> *Cc:* greve@nmr.mgh.harvard.edu >>>>>>>>>> mailto:greve@nmr.mgh.harvard.edu >> mailto:greve@nmr.mgh.harvard.edu >>>>>>>>>> *Subject:* Re: need for help >>>>>>>>>> Don't use --inflated. The inflated surface is not a
biological
>>>>>>>>>> surface. The default is the white surface, which is
the one
>>>> you want >>>>>>>>>> (--projfrac 0.5 will project it to the middle between the >>>> white and >>>>>>>> pial) >>>>>>>>>> >>>>>>>>>>> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: >>>>>>>>>>> >>>>>>>>>>> External Email - Use Caution >>>>>>>>>>> >>>>>>>>>>> Dear Freesurfer, >>>>>>>>>>> >>>>>>>>>>> I have a batch of myelin water image (MWI) from
patients and
>>>>>>>>>>> controls, and trying to have inflated cortex
registered on
>>>> standard >>>>>>>>>>> surface for GLM (Qdec). >>>>>>>>>>> >>>>>>>>>>> With the commandlines below i get my inflated
surface of MWI
>>>> map of >>>>>>>>>>> my patients and controls. >>>>>>>>>>> >>>>>>>>>>> 1-using bbregister to put MWI into FS space and to
calculate
>>>>>>>>>>> register.dat: >>>>>>>>>>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg >>>> register.dat >>>>>>>>>>> --o mwf_FS --t1 >>>>>>>>>>> >>>>>>>>>>> 2-using mri_vol2surf to extract inflated surface of MWI: >>>>>>>>>>> mri_vol2surf --mov mwf.nii --reg register.dat
--projfrac 0.5
>>>>>>>>>>> --interp nearest --hemi lh --o lh.inflated_MWI.w
--out_type
>>>>>>>>>>> paint--inflated (*or*--surf sphere) >>>>>>>>>>> >>>>>>>>>>> However the tksurfer could not open the inflated surface >> and the >>>>>>>>>>> error message is: >>>>>>>>>>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0
vertices!
>>>>>>>>>>> Probably trying to use a scalar data file as a surface!* >>>>>>>>>>> >>>>>>>>>>> I used the commandline below for #2: >>>>>>>>>>> mri_vol2surf --src mwf.nii --srcreg register.dat --hemi
lh --o
>>>>>>>>>>> mwf-lh.w --out_type paint >>>>>>>>>>> and i got the error: >>>>>>>>>>> >>>>>>>>>>> *ERROR: MRISread: file >>>>>>>>>>>
'/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has
>>>> many >>>>>>>>>>> more faces than vertices!** >>>>>>>>>>> Probably trying to use a scalar data file as a surface!* >>>>>>>>>>> * >>>>>>>>>>> * >>>>>>>>>>> As tksurfer could not open my surfaces with errors
above, i
>> think >>>>>>>>>>> perhaps the vol2surf procedure is not done properly.
Where
>> is the >>>>>>>>>>> problem? i need to get the inflated cortex and then
putting ob
>>>>>>>>>>> sphere (using mris_sphere) and the registering to
standard
>>>> surface >>>>>>>>>>> using mris_register for GLM in Qdec, right? >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> It is two weeks i am struggling with these commands,
any
helps
>>>>>>>>>>> highly appreciated. * >>>>>>>>>>> * >>>>>>>>>>> * >>>>>>>>>>> * >>>>>>>>>>> * >>>>>>>>>>> * >>>>>>>>>>> Best, >>>>>>>>>>> Reza >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> The information in this e-mail is intended only for the >> person to >>>>>>>>>> whom it is >>>>>>>>>> addressed. If you believe this e-mail was sent to you in >> error and >>>>>>>>>> the e-mail >>>>>>>>>> contains patient information, please contact the Partners >>>> Compliance >>>>>>>>>> HelpLine at >>>>>>>>>> http://www.partners.org/complianceline
http://www.partners.org/complianceline . If the e-mail was
>> sent to >>>>>>>>>> you in error >>>>>>>>>> but does not contain patient information, please
contact the
>>>> sender >>>>>>>>>> and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> -- >>>>> Dr. Tim Schäfer >>>>> Postdoc Computational Neuroimaging >>>>> Department of Child and Adolescent Psychiatry,
Psychosomatics and
>>>> Psychotherapy >>>>> University Hospital Frankfurt, Goethe University Frankfurt am
Main,
>>>> Germany >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry, that should be ftp surfer.nmr.mgh.harvard.edu
On 8/6/19 12:39 PM, Douglas N. Greve wrote:
You can try it from the command line, ftp surfer.nmr.mgh.harvard.edut It will ask you for a user name; use your email address It will ask you for a password; use "anonymous" (no quotes) cd transfer/incoming put file.tar
On 8/6/19 6:30 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Hi Doug,
When i click on the link you sent me for uploading the files, there is no bottom/way to upload something there. That is why i attached the outputs.
My command lines sequentially for the analysis are: ( I have done just the same command lines for MWF maps and it worked very good, but for NDI and ODI maps of NODDI does not work).
1-mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 --out lh.NDI_inflated.avg.mgh (i used the new mris_preproc you sent me).
2-mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex --sval lh.NDI_inflated.avg.mgh --tval lh.NDI_inflated.avg.05.mgh
3-mri_glmfit --y lh.NDI_inflated.avg.05.mgh --surf fsaverage lh --C contrast --fsgd fsgd.fsgd --cortex --glmdir lh.NDI_inflated.avg.05.glmdir
The outputs of all three steps are attached.
Looking forward for your helps
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Monday, August 5, 2019 5:55:18 PM *To:* Reza Rahmanzadeh; Freesurfer support list *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help Can you upload the input (ie, argument to --y) here: ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Also, send your mri_glmfit command line.
On 8/2/2019 9:41 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
yes, I have the page below for all patients.
I think it means all values are zero. My registration for bbregister is fine and i wrote my mris_preproc the same as MWF maps.
Thanks,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Friday, August 2, 2019 3:35:45 PM *To:* Reza Rahmanzadeh; Freesurfer support list *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help did you check each subject to make sure they had a non-zero map?
On 8/2/2019 6:25 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Dear Doug,
NODDI is diffusion imaging and we have vakue regarding neurite density (NDI in NDI map) and orientation dispersion (ODI value in ODI map). I do not know why mris_preproc works well on MWI maps but not on NODDI maps (both NDI and ODI maps). Beside using projfrac-avg 0 1 0.25 , i have run mris_preproc with projfrac 0.5 but again i got this error:
ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input
I have run mris_preproc on three patients that i am sure about registration quality, again when i scroll through them , there is no value in none of them. How that is possible?
NODDI does not have a lot of zero value but all values in cortex are between 0.2-0.4.
Thanks, Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Wednesday, July 31, 2019 12:50:45 AM *To:* Reza Rahmanzadeh; Freesurfer support list *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help I don't know what is in the NODDI maps. The way mri_glmfit works is that if any subject has a 0-value at a vertex, then it will mask out that vertex for all subjects. Is NODDI something that might have a lot of 0-values? It also may be that one subject has all 0s (eg, if the regitration was really bad), so you can check the map created by mris_preproc (load it in as an overlay, then hit the configure button, then change the frame number to scroll through your subjects)
On 7/30/19 12:46 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution
(sorry for bombaeding you with e-mails)
It seems that the error happens only when i use NODDI diffusion
image
e.g. NDI map i get that error, but for MWIs the new mris_preproc
works
well.
Should i do anything special for NODDI images? BTW, the bbregister works well for NODDI and i entered the correct registration file
into
mris_preproc.
Thanks,
Reza
*From:* Reza Rahmanzadeh *Sent:* Tuesday, July 30, 2019 6:17:22 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
... One problem when i use the new mris_preproc:
Always the output of mri_glmfit when the input is the result of new mris_preproc is:
*F**ound 0 voxels in mask ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input*
I think it means that something is perhaps wrong with the script. I tried both projfrac 0.5 and projfrac-avg 0 1 0.25 and i got the same error. I did not get the error when i used old mris_preproc using projfrac 0.5.*
*The other thing that could be the reason is my fsgd file. I have problem how to specify the name of subjects,
Now it is sth like:
GroupDescriptorFile 1 Class Group1 CLASS Group2 Input FSC001 Group1 Input FSC002 Group1 Input FSC003 Group1 .
.
.
Input FSP001 Group2 Input FSP002 Group2 Input FSP003 Group2 .
.
The oeder is thew same with mris_preproc, now the subject name is FSC0xx for controls and FSP00x for patients, these are the name of folders containing FS outputs, but my input volume is MWIs and the registration files are not stored in this folder. Does it matter how to name subjects when i am using fsgd file only in mri_glmfit (
to get
aware of order)?
Thanks,
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza
Rahmanzadeh
reza.rahmanzadeh@unibas.ch *Sent:* Tuesday, July 30, 2019 2:44:25 PM *To:* Greve, Douglas N.,Ph.D. *Cc:* Freesurfer support list; greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help External Email - Use Caution
Thanks Doug,
The script works well for projfrac-avg. but the problem is: when
i use
mris_preproc to assemble my MWIs and put them on fsaverage, as .fsgd file is only the order of my controls and subjects and i would have the inflated cortex of MWI on fsaverage, then anyway i have to
specify
my volume and registration files (tkregister2 output). Then
there’s an
error: i shouldn’t use both -fsgd and - iv together. Then i decided not to use fsgd file for mris_preproc and only using that for mri_glmfit. In mris_preproc, i write all “-iv volumes and
registration
files” in the same order as in fsgd file but i don’t write -fsgd argument. Is this way correct?
Thanks, Reza
On 29 Jul 2019, at 23:32, Greve, Douglas N.,Ph.D.
DGREVE@mgh.harvard.edu wrote:
Oh, I guess that's a problem! I've created a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc See if that works. You should compare the output to using the
max or
-projfrac 0.5 to make sure they are at least similar since I
have not
run it even once:)
> On 7/29/19 5:08 PM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > Thanks > > But mris_prepoc will not accept “projfrac-avg” and there’s an
error:
> argument unrecognized! > > Then how can i compute the average via mris_preproc? As based on > tutorial, first i used tkregister/bbregister to compute the > registration matrix and then i should put input images with > transformation matrix in mris_preproc. I mean i shouldn’t use > mri_vol2surf (that allows me to use projfrac-avg) in group
analysis
> and that’s the reason i have problem with mris_proproc to
compute the
> average. > > What should i do? > > Thanks, > Reza > > On 29 Jul 2019, at 23:03, Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote: > >> one computes the average, the other computes the maximum >> >>> On 7/29/19 9:03 AM, Reza Rahmanzadeh wrote: >>> >>> External Email - Use Caution >>> >>> Dear Doug, >>> >>> >>> I appreciat if you reply my question in the previous e-mail
with
this:
>>> >>> >>> can not i use projfrac-avg in mris_preproc? Is
--projfrac-max min max
>>> delta just the same? >>> >>> >>> Best, >>> >>> Reza >>> >>>
>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>> <freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf
of Reza
>>> Rahmanzadeh >>> <reza.rahmanzadeh@unibas.ch
mailto:reza.rahmanzadeh@unibas.ch>
>>> *Sent:* Monday, July 29, 2019 11:37:46 AM >>> *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; >>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>> *Subject:* Re: [Freesurfer] need for help >>> >>> External Email - Use Caution >>> >>> Dear Doug, >>> >>> >>> Thanks, the tutorial was super helpful. As i would compare
the MWF
>>> value in cortex between control subjects and patients. Now
my problem
>>> is how to make the contrast matrix for mris_preproc to do the >>> comparison in both direction (in 1, the outcome should be
voxels in
>>> which MWf value in control>patients & in 2, reversed). >>> >>> >>> The explanations in >>>
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
>>> >>> is for one group analysis and in >>>
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is
>>> not clear about contrast. >>> >>> I remember for -randomise command-line, there was
possibility to make
>>> contrast and design matrix (something like FSGD) via
design_ttest2.
>>> Can i use still design_ttest2 for producing contrast and design
matrix?
>>> >>> >>> >>> Best, >>> >>> Reza >>> >>>
>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu> >>> *Sent:* Wednesday, July 17, 2019 5:31:27 PM >>> *To:* Reza Rahmanzadeh; Freesurfer support list; >>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>> mailto:greve@nmr.mgh.harvard.edu >>> *Subject:* Re: [Freesurfer] need for help >>> Ah, I see. Try this tutorial. It is for fMRI, but it applies
to any
>>> modality >>>
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
>>> >>> >>>> On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote: >>>> >>>> External Email - Use Caution >>>> >>>> to clarify better, i need to compare myelin water fraction
in cortex
>>>> of control and patients to find out the areas with reduced
MWF in
>>>> patients cortex compared with controls, that is the reason
i want to
>>>> have cortex in inflated format. >>>> >>>> >>>> For this reason i used bbregister to have register.dat, and
then
>>>> mri_vol2surf to resample MWI cortex to surface. As i need to
have all
>>>> surfaces in fsaverage space for group analysis, i am using >>>> mri_preproc7mri_surf2surf (according to the group analysis
wiki you
>>>> sent me). >>>> >>>>
>>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu >>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>>> <freesurfer-bounces@nmr.mgh.harvard.edu >>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf
of Reza
>>> Rahmanzadeh >>>> <reza.rahmanzadeh@unibas.ch
mailto:reza.rahmanzadeh@unibas.ch
>>>> mailto:reza.rahmanzadeh@unibas.ch> >>>> *Sent:* Wednesday, July 17, 2019 4:26:21 PM >>>> *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; >>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>>> mailto:greve@nmr.mgh.harvard.edu >>>> *Subject:* Re: [Freesurfer] need for help >>>> >>>> External Email - Use Caution >>>> >>>> I am trying to compare MWI(sampled on the surface) between
couple
>>>> patients and controls using group analysis, therefore i
need to have
>>>> all inflated surface_on_same space (according to the wiki
of group
>>>> analysis you sent me, i should use mris_preproc to put my
data on
>>>> fsaverage). >>>> >>>> >>>> Could you now tell me whether my mris_prepoc is right? and
one other
>>>> question i have asked in last email? >>>> >>>> >>>> Thanks a lot, >>>> >>>> Reza >>>> >>>>
>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>> mailto:DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu> >>>> *Sent:* Wednesday, July 17, 2019 4:14:41 PM >>>> *To:* Reza Rahmanzadeh; Freesurfer support list; >>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>> mailto:greve@nmr.mgh.harvard.edu >>>> *Subject:* Re: [Freesurfer] need for help >>>> It is not clear to me what you are trying to do. Do you
want to do a
>>>> morphometry study (ie, comparing thickness, area, and/or
volume
across
>>>> subjects)? Or do you want to compare MWI (sampled on the
surface)
>>>> across subjects? >>>> >>>>> On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> >>>>> Dear Doug, >>>>> >>>>> >>>>> I took the back slash away and ran >>>>> >>>>> mris_preproc --target fsaverage --hemi lh --s FSP010 --out >>>>> lh.FSP10.white.mgh --meas white >>>>> >>>>> >>>>> but i got error: >>>>> >>>>> *Reading curvature file >>>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.white** >>>>> MRISreadBinaryCurvature: incompatible vertex number in file >>>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.white** >>>>> ERROR: reading curvature file* >>>>> >>>>> >>>>> Then i changed it to --meas : mris_preproc --target fsaverage
--hemi
>>>>> lh --s FSP010 --out lh.FSP10.white.mgz --meas area >>>>> >>>>> >>>>> Then, as i need to register my the inflated cortex of
myelin water
>>>>> image (MWI) to the surface_registered_on_fsaverage (could
it be the
>>>>> output of command-line above?), should i use this output >>>>> "lh.FSP10.white.mgz" and the output of mri_vol2surf
(resampling
>>>>> myelin water image to lh.white of my subject FSP10 before >>>>> registration to fsaverage) for mri_surf2surf (to resample the
latter
>>>>> to the former, to have MWI to surface_fsaverage) >>>>> >>>>> >>>>> >>>>> Looking forward to answers >>>>> >>>>> Thanks >>>>> >>>>> Reza >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>
>>>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu >>>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>>>> <freesurfer-bounces@nmr.mgh.harvard.edu >>>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf
of Reza
>>>>> Rahmanzadeh <reza.rahmanzadeh@unibas.ch >>>>> mailto:reza.rahmanzadeh@unibas.ch >>> mailto:reza.rahmanzadeh@unibas.ch> >>>>> *Sent:* Wednesday, July 17, 2019 9:56:00 AM >>>>> *To:* Freesurfer support list >>>>> *Cc:* DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu >>>>> mailto:DGREVE@mgh.harvard.edu >>>>> *Subject:* Re: [Freesurfer] need for help >>>>> External Email - Use Caution >>>>> >>>>> Thanks Tim, >>>>> >>>>> Then if i would resample my data to fsaverage and surfaces
are of
>>>>> main importance to my work, what should i use for -meas ? >>>>> >>>>> Reza >>>>> >>>>>> On 17 Jul 2019, at 09:39, Tim Schäfer <ts+ml@rcmd.org >>>>>> mailto:ts+ml@rcmd.org >>> mailto:ts+ml@rcmd.org> wrote: >>>>>> >>>>>> External Email - Use Caution >>>>>> >>>>>> I guess '-meas' expects a measure (like 'thickness' or
'area'), not
>>>>> a surface (like 'white'). >>>>>> >>>>>> Best, >>>>>> >>>>>> Tim >>>>>> >>>>>>> On July 17, 2019 at 9:03 AM Reza Rahmanzadeh >>>>> <reza.rahmanzadeh@unibas.ch
mailto:reza.rahmanzadeh@unibas.ch
>>>>> mailto:reza.rahmanzadeh@unibas.ch> wrote: >>>>>>> >>>>>>> >>>>>>> External Email - Use Caution >>>>>>> >>>>>>> I removed the back slash and the command line i executed
is:
>>>>>>> >>>>>>> >>>>>>> mris_preproc --target fsaverage --hemi lh --s FSP010 --out >>>>> lh.FSP10.white.mgh --meas white >>>>>>> >>>>>>> >>>>>>> but i got the error: >>>>>>> >>>>>>> Reading curvature file >>>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.white >>>>>>> MRISreadBinaryCurvature: incompatible vertex number in file >>>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.white >>>>>>> ERROR: reading curvature file >>>>>>> >>>>>>> I have added --srcfmt mgh as the last argument, but
again i got
>>>>> the error: >>>>>>> Reading source surface reg >>>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg >>>>>>> Loading source data >>>>>>> No such file or directory >>>>>>> ERROR: could not read >>>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3 >>>>>>> >>>>>>> >>>>>>> What is wrong with my mris_prepoc command line? >>>>>>> >>>>>>> Reza >>>>>>> >>>>>>> >>>>>>> ________________________________ >>>>>>> From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>>> mailto:DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu> >>>>>>> Sent: Tuesday, July 16, 2019 10:01:15 PM >>>>>>> To: Reza Rahmanzadeh; Freesurfer support list; >>>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>>>> mailto:greve@nmr.mgh.harvard.edu >>>>>>> Subject: Re: need for help >>>>>>> >>>>>>> don't include the back slash (ie, fsaverage not
fsaverage/ same
>>>>> for FSP010) >>>>>>> >>>>>>>> On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote: >>>>>>>> >>>>>>>> External Email - Use Caution >>>>>>>> >>>>>>>> Thanks a lot Doug, >>>>>>>> >>>>>>>> >>>>>>>> I started to proceed with FS group analysis wiki you
sent to me.
>>>>>>>> Accordingly, i have to resample all my data (output of
recon-all
>>>>> for a >>>>>>>> given subject for example) into fsaverage using
mris_preproc. My
>>>>>>>> commandline for a subject was: >>>>>>>> >>>>>>>> mris_preproc --target fsaverage/ --hemi lh --s FSP010/
--out
>>>>>>>> lh.FSP10.white.mgh --meas white >>>>>>>> >>>>>>>> >>>>>>>> and i got the error: >>>>>>>> >>>>>>>> * >>>>>>>> * >>>>>>>> *Reading source surface reg >>>>>>>> >>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>>>>>>> No such file or directory >>>>>>>> mri_surf2surf: could not read surface >>>>>>>> >>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>>>>>>> No such file or directory* >>>>>>>> * >>>>>>>> * >>>>>>>> As there was no**lh.fsaverage/.sphere.reg* *folder, i
found one
>>> file >>>>>>>> in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i
created a
folder
>>>>>>>> with the name lh.fsaverage and i copied/pasted the
mentiomed
file
>>>>> into >>>>>>>> this folder and i changed the file name to:
./sphere.reg. I
got the
>>>>>>>> error: >>>>>>>> * >>>>>>>> * >>>>>>>> *Reading curvature file >>>>>>>> /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere >>>>>>>> MRISreadBinaryCurvature: incompatible vertex number in
file
>>>>>>>> /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere* >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> What is the problem with my mris_preproc command-line? >>>>>>>> >>>>>>>> Reza >>>>>>>> >>>>>>>> >>>>> >>>
>>>>>>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu >>>>>>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>>>>>>> <freesurfer-bounces@nmr.mgh.harvard.edu >>>>>>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf
of Greve,
>>> Douglas >>>>>>>> N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> *Sent:* Tuesday, July 16, 2019 7:01:30 PM >>>>>>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >>>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>> *Subject:* Re: [Freesurfer] need for help >>>>>>>> >>>>>>>> >>>>>>>>> On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote: >>>>>>>>> >>>>>>>>> External Email - Use Caution >>>>>>>>> >>>>>>>>> (I assume now we are discussing in FS list, if no
please let
>>> me how >>>>>>>>> possible?) >>>>>>>>> >>>>>>>>> >>>>>>>>> Thanks Doug, now i could see the inflate surface, this
means
>>> that my >>>>>>>>> mri_vol2surf works well. As i would do GLM analysis over
inflated
>>>>>>>>> cortex of patients and controls in Qdec, >>>>>>>>> >>>>>>>>> >>>>>>>>> 1- should i input my surfaces to Qdec as inflated surface
or just
>>>>>>>>> inputting the output_of_vol2surf.mgz to Qdec? >>>>>>>>> >>>>>>>>> if inflated one is the input, then how could i get them? >>>>> mris_inflate >>>>>>>>> gives error. >>>>>>>>> >>>>>>>> QDEC is no longer being supported. Use the command line
stream
>>>>>>>> (mri_surf2surf, mri_glmfit, mri_glmfit-sim). >>>>>>>>
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>>>>>>>>> >>>>>>>>> >>>>>>>>> 2- should i input all patients and controls surfaces in
standard
>>>>>>>>> surface before entering to Qdec? >>>>>>>>> >>>>>>>>> >>>>>>>>> 3- I would like to resample whole cortex (whole cortical >>>>> thickness, in >>>>>>>>> other words: the average of all projfrac between 0 and
1),
is it
>>>>>>>>> possible? or i am limited to resample one given depth of >>> cortex into >>>>>>>>> inflated surface only? >>>>>>>>> >>>>>>>> Run mri_vol2surf with --help and look for --projfrac-avg >>>>>>>>> >>>>>>>>> >>>>>>>>> thanks a lot, >>>>>>>>> >>>>>>>>> Reza >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>> >>>
>>>>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>>>>> mailto:DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu> >>>>>>>>> *Sent:* Tuesday, July 16, 2019 6:22:56 PM >>>>>>>>> *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu >>>>>>>>> mailto:freesurfer@nmr.mgh.harvard.edu >>> mailto:freesurfer@nmr.mgh.harvard.edu >>>>>>>>> *Subject:* Re: need for help >>>>>>>>> The command should be something like >>>>>>>>> tksurfer mysubject lh inflated -overlay
output_of_vol2surf.mgz
>>>>>>>>> Also, tksurfer is also obsolete (but should work). You
should be
>>>>> using >>>>>>>>> freeview (or tksurferfv, a freeview front end that takes
the same
>>>>>>>>> command line args as tksurfer) >>>>>>>>> Also, please remember to respond to the fs list >>>>>>>>> >>>>>>>>>> On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote: >>>>>>>>>> >>>>>>>>>> External Email - Use Caution >>>>>>>>>> >>>>>>>>>> I got the mri_vol2surf output with .mgz: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> my tksurfer command: >>>>>>>>>> >>>>>>>>>> tksurfer FSP010/ (my subject) lh inflated_MWI.mgz
(output of
>>>>>>>>>> mri_vol2surf was lh.inflated_MWI.mgz) >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> and the error i got: >>>>>>>>>> >>>>>>>>>> *freadFloat: fread failed** >>>>>>>>>> No such file or directory* >>>>>>>>>> >>>>>>>>>> To me, opening the surfer in tksurfer is only a way
to get
>>> sure my >>>>>>>>>> vol2surf worked well. the main problem is i got this
error
>>> for all >>>>>>>>>> mris_smooth, mris_inflate, mris_sphere ... >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Do you think that means the output of mri_vol2surf is
not
>>>>> correct, or >>>>>>>>>> otherwise i could proceed with that , even when tksurfer >>> could not >>>>>>>>>> open it, for GLM in Qdec? >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> >>>>>>>>>> Reza >>>>>>>>>> >>>>>>>>>> >>>>>>>> >>>>> >>>
>>>>>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>>>>>> mailto:DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu> >>>>>>>>>> *Sent:* Tuesday, July 16, 2019 6:01:15 PM >>>>>>>>>> *To:* Reza Rahmanzadeh >>>>>>>>>> *Subject:* Re: need for help >>>>>>>>>> what is your tksurfer command line? Also, the .w file is
somewhat
>>>>>>>>>> obsolete (it should still work); instead you can use
.mgz
>>> file (and >>>>>>>>>> don't spec --paint) >>>>>>>>>> >>>>>>>>>>> On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote: >>>>>>>>>>> >>>>>>>>>>> External Email - Use Caution >>>>>>>>>>> >>>>>>>>>>> Thanks Doug, >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> I used the one without --inflated also, again the
tksurfer
>>>>> could not >>>>>>>>>>> open it and i got the same error. Where is the problem
with my
>>>>> cmd.? >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> In addition, i wanted to make the output of
mri_vol2surf
>>> inflated >>>>>>>>>>> using mris_inflate but i got the same error: >>>>>>>>>>> >>>>>>>>>>> *freadFloat: fread failed >>>>>>>>>>> No such file or directory* >>>>>>>>>>> * >>>>>>>>>>> * >>>>>>>>>>> *could you let me know what is the problem in
registering
my mwi
>>>>>>>>>>> volumes to surface that i getonly such errors.* >>>>>>>>>>> * >>>>>>>>>>> * >>>>>>>>>>> *Thanks,* >>>>>>>>>>> *reza >>>>>>>>>>> * >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>> >>>>> >>>
>>>>>>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>>>>>>> mailto:DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu> >>>>>>>>>>> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >>>>>>>>>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>> *Cc:* greve@nmr.mgh.harvard.edu >>>>>>>>>>> mailto:greve@nmr.mgh.harvard.edu >>> mailto:greve@nmr.mgh.harvard.edu >>>>>>>>>>> *Subject:* Re: need for help >>>>>>>>>>> Don't use --inflated. The inflated surface is not a
biological
>>>>>>>>>>> surface. The default is the white surface, which is
the one
>>>>> you want >>>>>>>>>>> (--projfrac 0.5 will project it to the middle
between the
>>>>> white and >>>>>>>>> pial) >>>>>>>>>>> >>>>>>>>>>>> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: >>>>>>>>>>>> >>>>>>>>>>>> External Email - Use Caution >>>>>>>>>>>> >>>>>>>>>>>> Dear Freesurfer, >>>>>>>>>>>> >>>>>>>>>>>> I have a batch of myelin water image (MWI) from
patients and
>>>>>>>>>>>> controls, and trying to have inflated cortex
registered on
>>>>> standard >>>>>>>>>>>> surface for GLM (Qdec). >>>>>>>>>>>> >>>>>>>>>>>> With the commandlines below i get my inflated
surface of MWI
>>>>> map of >>>>>>>>>>>> my patients and controls. >>>>>>>>>>>> >>>>>>>>>>>> 1-using bbregister to put MWI into FS space and to
calculate
>>>>>>>>>>>> register.dat: >>>>>>>>>>>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg >>>>> register.dat >>>>>>>>>>>> --o mwf_FS --t1 >>>>>>>>>>>> >>>>>>>>>>>> 2-using mri_vol2surf to extract inflated surface of
MWI:
>>>>>>>>>>>> mri_vol2surf --mov mwf.nii --reg register.dat
--projfrac 0.5
>>>>>>>>>>>> --interp nearest --hemi lh --o lh.inflated_MWI.w
--out_type
>>>>>>>>>>>> paint--inflated (*or*--surf sphere) >>>>>>>>>>>> >>>>>>>>>>>> However the tksurfer could not open the inflated
surface
>>> and the >>>>>>>>>>>> error message is: >>>>>>>>>>>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0
vertices!
>>>>>>>>>>>> Probably trying to use a scalar data file as a
surface!*
>>>>>>>>>>>> >>>>>>>>>>>> I used the commandline below for #2: >>>>>>>>>>>> mri_vol2surf --src mwf.nii --srcreg register.dat
--hemi
lh --o
>>>>>>>>>>>> mwf-lh.w --out_type paint >>>>>>>>>>>> and i got the error: >>>>>>>>>>>> >>>>>>>>>>>> *ERROR: MRISread: file >>>>>>>>>>>>
'/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has
>>>>> many >>>>>>>>>>>> more faces than vertices!** >>>>>>>>>>>> Probably trying to use a scalar data file as a
surface!*
>>>>>>>>>>>> * >>>>>>>>>>>> * >>>>>>>>>>>> As tksurfer could not open my surfaces with errors
above, i
>>> think >>>>>>>>>>>> perhaps the vol2surf procedure is not done
properly. Where
>>> is the >>>>>>>>>>>> problem? i need to get the inflated cortex and then
putting ob
>>>>>>>>>>>> sphere (using mris_sphere) and the registering to
standard
>>>>> surface >>>>>>>>>>>> using mris_register for GLM in Qdec, right? >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> It is two weeks i am struggling with these
commands, any
helps
>>>>>>>>>>>> highly appreciated. * >>>>>>>>>>>> * >>>>>>>>>>>> * >>>>>>>>>>>> * >>>>>>>>>>>> * >>>>>>>>>>>> * >>>>>>>>>>>> Best, >>>>>>>>>>>> Reza >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> The information in this e-mail is intended only for the >>> person to >>>>>>>>>>> whom it is >>>>>>>>>>> addressed. If you believe this e-mail was sent to
you in
>>> error and >>>>>>>>>>> the e-mail >>>>>>>>>>> contains patient information, please contact the
Partners
>>>>> Compliance >>>>>>>>>>> HelpLine at >>>>>>>>>>> http://www.partners.org/complianceline
http://www.partners.org/complianceline . If the e-mail was
>>> sent to >>>>>>>>>>> you in error >>>>>>>>>>> but does not contain patient information, please
contact the
>>>>> sender >>>>>>>>>>> and properly >>>>>>>>>>> dispose of the e-mail. >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>> >>>>>> -- >>>>>> Dr. Tim Schäfer >>>>>> Postdoc Computational Neuroimaging >>>>>> Department of Child and Adolescent Psychiatry,
Psychosomatics and
>>>>> Psychotherapy >>>>>> University Hospital Frankfurt, Goethe University
Frankfurt am
Main,
>>>>> Germany >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>> >>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
I tried to log in with the username and password you mentioned, but logging in failed. Could you please have a look into the file already i attached to my previous email, or let me know why i could not log in to transfer the file,
Thanks,
Reza
________________________________ From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Tuesday, August 6, 2019 6:40:28 PM To: Reza Rahmanzadeh; Freesurfer support list Cc: greve@nmr.mgh.harvard.edu Subject: Re: [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: [Freesurfer] need for help
Sorry, that should be ftp surfer.nmr.mgh.harvard.edu
On 8/6/19 12:39 PM, Douglas N. Greve wrote:
You can try it from the command line, ftp surfer.nmr.mgh.harvard.edut It will ask you for a user name; use your email address It will ask you for a password; use "anonymous" (no quotes) cd transfer/incoming put file.tar
On 8/6/19 6:30 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionHi Doug,
When i click on the link you sent me for uploading the files, there is no bottom/way to upload something there. That is why i attached the outputs.
My command lines sequentially for the analysis are: ( I have done just the same command lines for MWF maps and it worked very good, but for NDI and ODI maps of NODDI does not work).
1-mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 --out lh.NDI_inflated.avg.mgh (i used the new mris_preproc you sent me).
2-mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex --sval lh.NDI_inflated.avg.mgh --tval lh.NDI_inflated.avg.05.mgh
3-mri_glmfit --y lh.NDI_inflated.avg.05.mgh --surf fsaverage lh --C contrast --fsgd fsgd.fsgd --cortex --glmdir lh.NDI_inflated.avg.05.glmdir
The outputs of all three steps are attached.
Looking forward for your helps
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Monday, August 5, 2019 5:55:18 PM *To:* Reza Rahmanzadeh; Freesurfer support list *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help Can you upload the input (ie, argument to --y) here: ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Also, send your mri_glmfit command line.
On 8/2/2019 9:41 AM, Reza Rahmanzadeh wrote:
External Email - Use Cautionyes, I have the page below for all patients.
I think it means all values are zero. My registration for bbregister is fine and i wrote my mris_preproc the same as MWF maps.
Thanks,
Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Friday, August 2, 2019 3:35:45 PM *To:* Reza Rahmanzadeh; Freesurfer support list *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help did you check each subject to make sure they had a non-zero map?
On 8/2/2019 6:25 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionDear Doug,
NODDI is diffusion imaging and we have vakue regarding neurite density (NDI in NDI map) and orientation dispersion (ODI value in ODI map). I do not know why mris_preproc works well on MWI maps but not on NODDI maps (both NDI and ODI maps). Beside using projfrac-avg 0 1 0.25 , i have run mris_preproc with projfrac 0.5 but again i got this error:
ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input
I have run mris_preproc on three patients that i am sure about registration quality, again when i scroll through them , there is no value in none of them. How that is possible?
NODDI does not have a lot of zero value but all values in cortex are between 0.2-0.4.
Thanks, Reza
*From:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Wednesday, July 31, 2019 12:50:45 AM *To:* Reza Rahmanzadeh; Freesurfer support list *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help I don't know what is in the NODDI maps. The way mri_glmfit works is that if any subject has a 0-value at a vertex, then it will mask out that vertex for all subjects. Is NODDI something that might have a lot of 0-values? It also may be that one subject has all 0s (eg, if the regitration was really bad), so you can check the map created by mris_preproc (load it in as an overlay, then hit the configure button, then change the frame number to scroll through your subjects)
On 7/30/19 12:46 PM, Reza Rahmanzadeh wrote:
External Email - Use Caution(sorry for bombaeding you with e-mails)
It seems that the error happens only when i use NODDI diffusion
image
e.g. NDI map i get that error, but for MWIs the new mris_preproc
works
well.
Should i do anything special for NODDI images? BTW, the bbregister works well for NODDI and i entered the correct registration file
into
mris_preproc.
Thanks,
Reza
*From:* Reza Rahmanzadeh *Sent:* Tuesday, July 30, 2019 6:17:22 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list *Cc:* greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
... One problem when i use the new mris_preproc:
Always the output of mri_glmfit when the input is the result of new mris_preproc is:
*F**ound 0 voxels in mask ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input*
I think it means that something is perhaps wrong with the script. I tried both projfrac 0.5 and projfrac-avg 0 1 0.25 and i got the same error. I did not get the error when i used old mris_preproc using projfrac 0.5.*
*The other thing that could be the reason is my fsgd file. I have problem how to specify the name of subjects,
Now it is sth like:
GroupDescriptorFile 1 Class Group1 CLASS Group2 Input FSC001 Group1 Input FSC002 Group1 Input FSC003 Group1 .
.
.
Input FSP001 Group2 Input FSP002 Group2 Input FSP003 Group2 .
.
The oeder is thew same with mris_preproc, now the subject name is FSC0xx for controls and FSP00x for patients, these are the name of folders containing FS outputs, but my input volume is MWIs and the registration files are not stored in this folder. Does it matter how to name subjects when i am using fsgd file only in mri_glmfit (
to get
aware of order)?
Thanks,
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza
Rahmanzadeh
reza.rahmanzadeh@unibas.ch *Sent:* Tuesday, July 30, 2019 2:44:25 PM *To:* Greve, Douglas N.,Ph.D. *Cc:* Freesurfer support list; greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help External Email - Use Caution
Thanks Doug,
The script works well for projfrac-avg. but the problem is: when
i use
mris_preproc to assemble my MWIs and put them on fsaverage, as .fsgd file is only the order of my controls and subjects and i would have the inflated cortex of MWI on fsaverage, then anyway i have to
specify
my volume and registration files (tkregister2 output). Then
there’s an
error: i shouldn’t use both -fsgd and - iv together. Then i decided not to use fsgd file for mris_preproc and only using that for mri_glmfit. In mris_preproc, i write all “-iv volumes and
registration
files” in the same order as in fsgd file but i don’t write -fsgd argument. Is this way correct?
Thanks, Reza
On 29 Jul 2019, at 23:32, Greve, Douglas N.,Ph.D.
DGREVE@mgh.harvard.edu wrote:
Oh, I guess that's a problem! I've created a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc See if that works. You should compare the output to using the
max or
-projfrac 0.5 to make sure they are at least similar since I
have not
run it even once:)
> On 7/29/19 5:08 PM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > Thanks > > But mris_prepoc will not accept “projfrac-avg” and there’s an
error:
> argument unrecognized! > > Then how can i compute the average via mris_preproc? As based on > tutorial, first i used tkregister/bbregister to compute the > registration matrix and then i should put input images with > transformation matrix in mris_preproc. I mean i shouldn’t use > mri_vol2surf (that allows me to use projfrac-avg) in group
analysis
> and that’s the reason i have problem with mris_proproc to
compute the
> average. > > What should i do? > > Thanks, > Reza > > On 29 Jul 2019, at 23:03, Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote: > >> one computes the average, the other computes the maximum >> >>> On 7/29/19 9:03 AM, Reza Rahmanzadeh wrote: >>> >>> External Email - Use Caution >>> >>> Dear Doug, >>> >>> >>> I appreciat if you reply my question in the previous e-mail
with
this:
>>> >>> >>> can not i use projfrac-avg in mris_preproc? Is
--projfrac-max min max
>>> delta just the same? >>> >>> >>> Best, >>> >>> Reza >>> >>>
>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>> <freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf
of Reza
>>> Rahmanzadeh >>> <reza.rahmanzadeh@unibas.ch
mailto:reza.rahmanzadeh@unibas.ch>
>>> *Sent:* Monday, July 29, 2019 11:37:46 AM >>> *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; >>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>> *Subject:* Re: [Freesurfer] need for help >>> >>> External Email - Use Caution >>> >>> Dear Doug, >>> >>> >>> Thanks, the tutorial was super helpful. As i would compare
the MWF
>>> value in cortex between control subjects and patients. Now
my problem
>>> is how to make the contrast matrix for mris_preproc to do the >>> comparison in both direction (in 1, the outcome should be
voxels in
>>> which MWf value in control>patients & in 2, reversed). >>> >>> >>> The explanations in >>>
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
>>> >>> is for one group analysis and in >>>
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is
>>> not clear about contrast. >>> >>> I remember for -randomise command-line, there was
possibility to make
>>> contrast and design matrix (something like FSGD) via
design_ttest2.
>>> Can i use still design_ttest2 for producing contrast and design
matrix?
>>> >>> >>> >>> Best, >>> >>> Reza >>> >>>
>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu> >>> *Sent:* Wednesday, July 17, 2019 5:31:27 PM >>> *To:* Reza Rahmanzadeh; Freesurfer support list; >>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>> mailto:greve@nmr.mgh.harvard.edu >>> *Subject:* Re: [Freesurfer] need for help >>> Ah, I see. Try this tutorial. It is for fMRI, but it applies
to any
>>> modality >>>
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
>>> >>> >>>> On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote: >>>> >>>> External Email - Use Caution >>>> >>>> to clarify better, i need to compare myelin water fraction
in cortex
>>>> of control and patients to find out the areas with reduced
MWF in
>>>> patients cortex compared with controls, that is the reason
i want to
>>>> have cortex in inflated format. >>>> >>>> >>>> For this reason i used bbregister to have register.dat, and
then
>>>> mri_vol2surf to resample MWI cortex to surface. As i need to
have all
>>>> surfaces in fsaverage space for group analysis, i am using >>>> mri_preproc7mri_surf2surf (according to the group analysis
wiki you
>>>> sent me). >>>> >>>>
>>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu >>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>>> <freesurfer-bounces@nmr.mgh.harvard.edu >>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf
of Reza
>>> Rahmanzadeh >>>> <reza.rahmanzadeh@unibas.ch
mailto:reza.rahmanzadeh@unibas.ch
>>>> mailto:reza.rahmanzadeh@unibas.ch> >>>> *Sent:* Wednesday, July 17, 2019 4:26:21 PM >>>> *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; >>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>>> mailto:greve@nmr.mgh.harvard.edu >>>> *Subject:* Re: [Freesurfer] need for help >>>> >>>> External Email - Use Caution >>>> >>>> I am trying to compare MWI(sampled on the surface) between
couple
>>>> patients and controls using group analysis, therefore i
need to have
>>>> all inflated surface_on_same space (according to the wiki
of group
>>>> analysis you sent me, i should use mris_preproc to put my
data on
>>>> fsaverage). >>>> >>>> >>>> Could you now tell me whether my mris_prepoc is right? and
one other
>>>> question i have asked in last email? >>>> >>>> >>>> Thanks a lot, >>>> >>>> Reza >>>> >>>>
>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>> mailto:DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu> >>>> *Sent:* Wednesday, July 17, 2019 4:14:41 PM >>>> *To:* Reza Rahmanzadeh; Freesurfer support list; >>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>> mailto:greve@nmr.mgh.harvard.edu >>>> *Subject:* Re: [Freesurfer] need for help >>>> It is not clear to me what you are trying to do. Do you
want to do a
>>>> morphometry study (ie, comparing thickness, area, and/or
volume
across
>>>> subjects)? Or do you want to compare MWI (sampled on the
surface)
>>>> across subjects? >>>> >>>>> On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> >>>>> Dear Doug, >>>>> >>>>> >>>>> I took the back slash away and ran >>>>> >>>>> mris_preproc --target fsaverage --hemi lh --s FSP010 --out >>>>> lh.FSP10.white.mgh --meas white >>>>> >>>>> >>>>> but i got error: >>>>> >>>>> *Reading curvature file >>>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.white** >>>>> MRISreadBinaryCurvature: incompatible vertex number in file >>>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.white** >>>>> ERROR: reading curvature file* >>>>> >>>>> >>>>> Then i changed it to --meas : mris_preproc --target fsaverage
--hemi
>>>>> lh --s FSP010 --out lh.FSP10.white.mgz --meas area >>>>> >>>>> >>>>> Then, as i need to register my the inflated cortex of
myelin water
>>>>> image (MWI) to the surface_registered_on_fsaverage (could
it be the
>>>>> output of command-line above?), should i use this output >>>>> "lh.FSP10.white.mgz" and the output of mri_vol2surf
(resampling
>>>>> myelin water image to lh.white of my subject FSP10 before >>>>> registration to fsaverage) for mri_surf2surf (to resample the
latter
>>>>> to the former, to have MWI to surface_fsaverage) >>>>> >>>>> >>>>> >>>>> Looking forward to answers >>>>> >>>>> Thanks >>>>> >>>>> Reza >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>
>>>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu >>>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>>>> <freesurfer-bounces@nmr.mgh.harvard.edu >>>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf
of Reza
>>>>> Rahmanzadeh <reza.rahmanzadeh@unibas.ch >>>>> mailto:reza.rahmanzadeh@unibas.ch >>> mailto:reza.rahmanzadeh@unibas.ch> >>>>> *Sent:* Wednesday, July 17, 2019 9:56:00 AM >>>>> *To:* Freesurfer support list >>>>> *Cc:* DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu >>>>> mailto:DGREVE@mgh.harvard.edu >>>>> *Subject:* Re: [Freesurfer] need for help >>>>> External Email - Use Caution >>>>> >>>>> Thanks Tim, >>>>> >>>>> Then if i would resample my data to fsaverage and surfaces
are of
>>>>> main importance to my work, what should i use for -meas ? >>>>> >>>>> Reza >>>>> >>>>>> On 17 Jul 2019, at 09:39, Tim Schäfer <ts+ml@rcmd.org >>>>>> mailto:ts+ml@rcmd.org >>> mailto:ts+ml@rcmd.org> wrote: >>>>>> >>>>>> External Email - Use Caution >>>>>> >>>>>> I guess '-meas' expects a measure (like 'thickness' or
'area'), not
>>>>> a surface (like 'white'). >>>>>> >>>>>> Best, >>>>>> >>>>>> Tim >>>>>> >>>>>>> On July 17, 2019 at 9:03 AM Reza Rahmanzadeh >>>>> <reza.rahmanzadeh@unibas.ch
mailto:reza.rahmanzadeh@unibas.ch
>>>>> mailto:reza.rahmanzadeh@unibas.ch> wrote: >>>>>>> >>>>>>> >>>>>>> External Email - Use Caution >>>>>>> >>>>>>> I removed the back slash and the command line i executed
is:
>>>>>>> >>>>>>> >>>>>>> mris_preproc --target fsaverage --hemi lh --s FSP010 --out >>>>> lh.FSP10.white.mgh --meas white >>>>>>> >>>>>>> >>>>>>> but i got the error: >>>>>>> >>>>>>> Reading curvature file >>>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.white >>>>>>> MRISreadBinaryCurvature: incompatible vertex number in file >>>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.white >>>>>>> ERROR: reading curvature file >>>>>>> >>>>>>> I have added --srcfmt mgh as the last argument, but
again i got
>>>>> the error: >>>>>>> Reading source surface reg >>>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg >>>>>>> Loading source data >>>>>>> No such file or directory >>>>>>> ERROR: could not read >>>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3 >>>>>>> >>>>>>> >>>>>>> What is wrong with my mris_prepoc command line? >>>>>>> >>>>>>> Reza >>>>>>> >>>>>>> >>>>>>> ________________________________ >>>>>>> From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>>> mailto:DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu> >>>>>>> Sent: Tuesday, July 16, 2019 10:01:15 PM >>>>>>> To: Reza Rahmanzadeh; Freesurfer support list; >>>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>>>> mailto:greve@nmr.mgh.harvard.edu >>>>>>> Subject: Re: need for help >>>>>>> >>>>>>> don't include the back slash (ie, fsaverage not
fsaverage/ same
>>>>> for FSP010) >>>>>>> >>>>>>>> On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote: >>>>>>>> >>>>>>>> External Email - Use Caution >>>>>>>> >>>>>>>> Thanks a lot Doug, >>>>>>>> >>>>>>>> >>>>>>>> I started to proceed with FS group analysis wiki you
sent to me.
>>>>>>>> Accordingly, i have to resample all my data (output of
recon-all
>>>>> for a >>>>>>>> given subject for example) into fsaverage using
mris_preproc. My
>>>>>>>> commandline for a subject was: >>>>>>>> >>>>>>>> mris_preproc --target fsaverage/ --hemi lh --s FSP010/
--out
>>>>>>>> lh.FSP10.white.mgh --meas white >>>>>>>> >>>>>>>> >>>>>>>> and i got the error: >>>>>>>> >>>>>>>> * >>>>>>>> * >>>>>>>> *Reading source surface reg >>>>>>>> >>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>>>>>>> No such file or directory >>>>>>>> mri_surf2surf: could not read surface >>>>>>>> >>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>>>>>>> No such file or directory* >>>>>>>> * >>>>>>>> * >>>>>>>> As there was no**lh.fsaverage/.sphere.reg* *folder, i
found one
>>> file >>>>>>>> in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i
created a
folder
>>>>>>>> with the name lh.fsaverage and i copied/pasted the
mentiomed
file
>>>>> into >>>>>>>> this folder and i changed the file name to:
./sphere.reg. I
got the
>>>>>>>> error: >>>>>>>> * >>>>>>>> * >>>>>>>> *Reading curvature file >>>>>>>> /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere >>>>>>>> MRISreadBinaryCurvature: incompatible vertex number in
file
>>>>>>>> /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere* >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> What is the problem with my mris_preproc command-line? >>>>>>>> >>>>>>>> Reza >>>>>>>> >>>>>>>> >>>>> >>>
>>>>>>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu >>>>>>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>>>>>>> <freesurfer-bounces@nmr.mgh.harvard.edu >>>>>>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf
of Greve,
>>> Douglas >>>>>>>> N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> *Sent:* Tuesday, July 16, 2019 7:01:30 PM >>>>>>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >>>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>> *Subject:* Re: [Freesurfer] need for help >>>>>>>> >>>>>>>> >>>>>>>>> On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote: >>>>>>>>> >>>>>>>>> External Email - Use Caution >>>>>>>>> >>>>>>>>> (I assume now we are discussing in FS list, if no
please let
>>> me how >>>>>>>>> possible?) >>>>>>>>> >>>>>>>>> >>>>>>>>> Thanks Doug, now i could see the inflate surface, this
means
>>> that my >>>>>>>>> mri_vol2surf works well. As i would do GLM analysis over
inflated
>>>>>>>>> cortex of patients and controls in Qdec, >>>>>>>>> >>>>>>>>> >>>>>>>>> 1- should i input my surfaces to Qdec as inflated surface
or just
>>>>>>>>> inputting the output_of_vol2surf.mgz to Qdec? >>>>>>>>> >>>>>>>>> if inflated one is the input, then how could i get them? >>>>> mris_inflate >>>>>>>>> gives error. >>>>>>>>> >>>>>>>> QDEC is no longer being supported. Use the command line
stream
>>>>>>>> (mri_surf2surf, mri_glmfit, mri_glmfit-sim). >>>>>>>>
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>>>>>>>>> >>>>>>>>> >>>>>>>>> 2- should i input all patients and controls surfaces in
standard
>>>>>>>>> surface before entering to Qdec? >>>>>>>>> >>>>>>>>> >>>>>>>>> 3- I would like to resample whole cortex (whole cortical >>>>> thickness, in >>>>>>>>> other words: the average of all projfrac between 0 and
1),
is it
>>>>>>>>> possible? or i am limited to resample one given depth of >>> cortex into >>>>>>>>> inflated surface only? >>>>>>>>> >>>>>>>> Run mri_vol2surf with --help and look for --projfrac-avg >>>>>>>>> >>>>>>>>> >>>>>>>>> thanks a lot, >>>>>>>>> >>>>>>>>> Reza >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>> >>>
>>>>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>>>>> mailto:DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu> >>>>>>>>> *Sent:* Tuesday, July 16, 2019 6:22:56 PM >>>>>>>>> *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu >>>>>>>>> mailto:freesurfer@nmr.mgh.harvard.edu >>> mailto:freesurfer@nmr.mgh.harvard.edu >>>>>>>>> *Subject:* Re: need for help >>>>>>>>> The command should be something like >>>>>>>>> tksurfer mysubject lh inflated -overlay
output_of_vol2surf.mgz
>>>>>>>>> Also, tksurfer is also obsolete (but should work). You
should be
>>>>> using >>>>>>>>> freeview (or tksurferfv, a freeview front end that takes
the same
>>>>>>>>> command line args as tksurfer) >>>>>>>>> Also, please remember to respond to the fs list >>>>>>>>> >>>>>>>>>> On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote: >>>>>>>>>> >>>>>>>>>> External Email - Use Caution >>>>>>>>>> >>>>>>>>>> I got the mri_vol2surf output with .mgz: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> my tksurfer command: >>>>>>>>>> >>>>>>>>>> tksurfer FSP010/ (my subject) lh inflated_MWI.mgz
(output of
>>>>>>>>>> mri_vol2surf was lh.inflated_MWI.mgz) >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> and the error i got: >>>>>>>>>> >>>>>>>>>> *freadFloat: fread failed** >>>>>>>>>> No such file or directory* >>>>>>>>>> >>>>>>>>>> To me, opening the surfer in tksurfer is only a way
to get
>>> sure my >>>>>>>>>> vol2surf worked well. the main problem is i got this
error
>>> for all >>>>>>>>>> mris_smooth, mris_inflate, mris_sphere ... >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Do you think that means the output of mri_vol2surf is
not
>>>>> correct, or >>>>>>>>>> otherwise i could proceed with that , even when tksurfer >>> could not >>>>>>>>>> open it, for GLM in Qdec? >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> >>>>>>>>>> Reza >>>>>>>>>> >>>>>>>>>> >>>>>>>> >>>>> >>>
>>>>>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>>>>>> mailto:DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu> >>>>>>>>>> *Sent:* Tuesday, July 16, 2019 6:01:15 PM >>>>>>>>>> *To:* Reza Rahmanzadeh >>>>>>>>>> *Subject:* Re: need for help >>>>>>>>>> what is your tksurfer command line? Also, the .w file is
somewhat
>>>>>>>>>> obsolete (it should still work); instead you can use
.mgz
>>> file (and >>>>>>>>>> don't spec --paint) >>>>>>>>>> >>>>>>>>>>> On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote: >>>>>>>>>>> >>>>>>>>>>> External Email - Use Caution >>>>>>>>>>> >>>>>>>>>>> Thanks Doug, >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> I used the one without --inflated also, again the
tksurfer
>>>>> could not >>>>>>>>>>> open it and i got the same error. Where is the problem
with my
>>>>> cmd.? >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> In addition, i wanted to make the output of
mri_vol2surf
>>> inflated >>>>>>>>>>> using mris_inflate but i got the same error: >>>>>>>>>>> >>>>>>>>>>> *freadFloat: fread failed >>>>>>>>>>> No such file or directory* >>>>>>>>>>> * >>>>>>>>>>> * >>>>>>>>>>> *could you let me know what is the problem in
registering
my mwi
>>>>>>>>>>> volumes to surface that i getonly such errors.* >>>>>>>>>>> * >>>>>>>>>>> * >>>>>>>>>>> *Thanks,* >>>>>>>>>>> *reza >>>>>>>>>>> * >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>> >>>>> >>>
>>>>>>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>>>>>>> mailto:DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu> >>>>>>>>>>> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >>>>>>>>>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>> *Cc:* greve@nmr.mgh.harvard.edu >>>>>>>>>>> mailto:greve@nmr.mgh.harvard.edu >>> mailto:greve@nmr.mgh.harvard.edu >>>>>>>>>>> *Subject:* Re: need for help >>>>>>>>>>> Don't use --inflated. The inflated surface is not a
biological
>>>>>>>>>>> surface. The default is the white surface, which is
the one
>>>>> you want >>>>>>>>>>> (--projfrac 0.5 will project it to the middle
between the
>>>>> white and >>>>>>>>> pial) >>>>>>>>>>> >>>>>>>>>>>> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: >>>>>>>>>>>> >>>>>>>>>>>> External Email - Use Caution >>>>>>>>>>>> >>>>>>>>>>>> Dear Freesurfer, >>>>>>>>>>>> >>>>>>>>>>>> I have a batch of myelin water image (MWI) from
patients and
>>>>>>>>>>>> controls, and trying to have inflated cortex
registered on
>>>>> standard >>>>>>>>>>>> surface for GLM (Qdec). >>>>>>>>>>>> >>>>>>>>>>>> With the commandlines below i get my inflated
surface of MWI
>>>>> map of >>>>>>>>>>>> my patients and controls. >>>>>>>>>>>> >>>>>>>>>>>> 1-using bbregister to put MWI into FS space and to
calculate
>>>>>>>>>>>> register.dat: >>>>>>>>>>>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg >>>>> register.dat >>>>>>>>>>>> --o mwf_FS --t1 >>>>>>>>>>>> >>>>>>>>>>>> 2-using mri_vol2surf to extract inflated surface of
MWI:
>>>>>>>>>>>> mri_vol2surf --mov mwf.nii --reg register.dat
--projfrac 0.5
>>>>>>>>>>>> --interp nearest --hemi lh --o lh.inflated_MWI.w
--out_type
>>>>>>>>>>>> paint--inflated (*or*--surf sphere) >>>>>>>>>>>> >>>>>>>>>>>> However the tksurfer could not open the inflated
surface
>>> and the >>>>>>>>>>>> error message is: >>>>>>>>>>>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0
vertices!
>>>>>>>>>>>> Probably trying to use a scalar data file as a
surface!*
>>>>>>>>>>>> >>>>>>>>>>>> I used the commandline below for #2: >>>>>>>>>>>> mri_vol2surf --src mwf.nii --srcreg register.dat
--hemi
lh --o
>>>>>>>>>>>> mwf-lh.w --out_type paint >>>>>>>>>>>> and i got the error: >>>>>>>>>>>> >>>>>>>>>>>> *ERROR: MRISread: file >>>>>>>>>>>>
'/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has
>>>>> many >>>>>>>>>>>> more faces than vertices!** >>>>>>>>>>>> Probably trying to use a scalar data file as a
surface!*
>>>>>>>>>>>> * >>>>>>>>>>>> * >>>>>>>>>>>> As tksurfer could not open my surfaces with errors
above, i
>>> think >>>>>>>>>>>> perhaps the vol2surf procedure is not done
properly. Where
>>> is the >>>>>>>>>>>> problem? i need to get the inflated cortex and then
putting ob
>>>>>>>>>>>> sphere (using mris_sphere) and the registering to
standard
>>>>> surface >>>>>>>>>>>> using mris_register for GLM in Qdec, right? >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> It is two weeks i am struggling with these
commands, any
helps
>>>>>>>>>>>> highly appreciated. * >>>>>>>>>>>> * >>>>>>>>>>>> * >>>>>>>>>>>> * >>>>>>>>>>>> * >>>>>>>>>>>> * >>>>>>>>>>>> Best, >>>>>>>>>>>> Reza >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> The information in this e-mail is intended only for the >>> person to >>>>>>>>>>> whom it is >>>>>>>>>>> addressed. If you believe this e-mail was sent to
you in
>>> error and >>>>>>>>>>> the e-mail >>>>>>>>>>> contains patient information, please contact the
Partners
>>>>> Compliance >>>>>>>>>>> HelpLine at >>>>>>>>>>> http://www.partners.org/complianceline
http://www.partners.org/complianceline . If the e-mail was
>>> sent to >>>>>>>>>>> you in error >>>>>>>>>>> but does not contain patient information, please
contact the
>>>>> sender >>>>>>>>>>> and properly >>>>>>>>>>> dispose of the e-mail. >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>> >>>>>> -- >>>>>> Dr. Tim Schäfer >>>>>> Postdoc Computational Neuroimaging >>>>>> Department of Child and Adolescent Psychiatry,
Psychosomatics and
>>>>> Psychotherapy >>>>>> University Hospital Frankfurt, Goethe University
Frankfurt am
Main,
>>>>> Germany >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>> >>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Right, you can't use both --fsgd and --iv. You have to use --iv, so make sure the order is the same as in the fsgd file.
On 7/30/19 8:44 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks Doug,
The script works well for projfrac-avg. but the problem is: when i use mris_preproc to assemble my MWIs and put them on fsaverage, as .fsgd file is only the order of my controls and subjects and i would have the inflated cortex of MWI on fsaverage, then anyway i have to specify my volume and registration files (tkregister2 output). Then there’s an error: i shouldn’t use both -fsgd and - iv together. Then i decided not to use fsgd file for mris_preproc and only using that for mri_glmfit. In mris_preproc, i write all “-iv volumes and registration files” in the same order as in fsgd file but i don’t write -fsgd argument. Is this way correct?
Thanks, Reza
On 29 Jul 2019, at 23:32, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote:
Oh, I guess that's a problem! I've created a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc See if that works. You should compare the output to using the max or -projfrac 0.5 to make sure they are at least similar since I have not run it even once:)
On 7/29/19 5:08 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks
But mris_prepoc will not accept “projfrac-avg” and there’s an error: argument unrecognized!
Then how can i compute the average via mris_preproc? As based on tutorial, first i used tkregister/bbregister to compute the registration matrix and then i should put input images with transformation matrix in mris_preproc. I mean i shouldn’t use mri_vol2surf (that allows me to use projfrac-avg) in group analysis and that’s the reason i have problem with mris_proproc to compute the average.
What should i do?
Thanks, Reza
On 29 Jul 2019, at 23:03, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
one computes the average, the other computes the maximum
On 7/29/19 9:03 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionDear Doug,
I appreciat if you reply my question in the previous e-mail with this:
can not i use projfrac-avg in mris_preproc? Is --projfrac-max min max delta just the same?
Best,
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh <reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Monday, July 29, 2019 11:37:46 AM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionDear Doug,
Thanks, the tutorial was super helpful. As i would compare the MWF value in cortex between control subjects and patients. Now my problem is how to make the contrast matrix for mris_preproc to do the comparison in both direction (in 1, the outcome should be voxels in which MWf value in control>patients & in 2, reversed).
The explanations in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
is for one group analysis and in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is not clear about contrast.
I remember for -randomise command-line, there was possibility to make contrast and design matrix (something like FSGD) via design_ttest2. Can i use still design_ttest2 for producing contrast and design matrix?
Best,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> *Sent:* Wednesday, July 17, 2019 5:31:27 PM *To:* Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help Ah, I see. Try this tutorial. It is for fMRI, but it applies to any modality https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote:
External Email - Use Cautionto clarify better, i need to compare myelin water fraction in cortex of control and patients to find out the areas with reduced MWF in patients cortex compared with controls, that is the reason i want to have cortex in inflated format.
For this reason i used bbregister to have register.dat, and then mri_vol2surf to resample MWI cortex to surface. As i need to have all surfaces in fsaverage space for group analysis, i am using mri_preproc7mri_surf2surf (according to the group analysis wiki you sent me).
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh
<reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Wednesday, July 17, 2019 4:26:21 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionI am trying to compare MWI(sampled on the surface) between couple patients and controls using group analysis, therefore i need to have all inflated surface_on_same space (according to the wiki of group analysis you sent me, i should use mris_preproc to put my data on fsaverage).
Could you now tell me whether my mris_prepoc is right? and one other question i have asked in last email?
Thanks a lot,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
*Sent:* Wednesday, July 17, 2019 4:14:41 PM *To:* Reza Rahmanzadeh; Freesurfer support list;
greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] need for help It is not clear to me what you are trying to do. Do you want to do a morphometry study (ie, comparing thickness, area, and/or volume across subjects)? Or do you want to compare MWI (sampled on the surface) across subjects?
> On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > > Dear Doug, > > > I took the back slash away and ran > > mris_preproc --target fsaverage --hemi lh --s FSP010 --out > lh.FSP10.white.mgh --meas white > > > but i got error: > > *Reading curvature file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white** > MRISreadBinaryCurvature: incompatible vertex number in file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white** > ERROR: reading curvature file* > > > Then i changed it to --meas : mris_preproc --target fsaverage --hemi > lh --s FSP010 --out lh.FSP10.white.mgz --meas area > > > Then, as i need to register my the inflated cortex of myelin water > image (MWI) to the surface_registered_on_fsaverage (could it be the > output of command-line above?), should i use this output > "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling > myelin water image to lh.white of my subject FSP10 before > registration to fsaverage) for mri_surf2surf (to resample the latter > to the former, to have MWI to surface_fsaverage) > > > > Looking forward to answers > > Thanks > > Reza > > > > > >
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu > mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu > mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza
> Rahmanzadeh <reza.rahmanzadeh@unibas.ch > mailto:reza.rahmanzadeh@unibas.ch
mailto:reza.rahmanzadeh@unibas.ch>
> *Sent:* Wednesday, July 17, 2019 9:56:00 AM > *To:* Freesurfer support list > *Cc:* DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu > *Subject:* Re: [Freesurfer] need for help > External Email - Use Caution > > Thanks Tim, > > Then if i would resample my data to fsaverage and surfaces are of > main importance to my work, what should i use for -meas ? > > Reza > >> On 17 Jul 2019, at 09:39, Tim Schäfer <ts+ml@rcmd.org >> mailto:ts+ml@rcmd.org
mailto:ts+ml@rcmd.org> wrote:
>> External Email - Use Caution >> >> I guess '-meas' expects a measure (like 'thickness' or 'area'), not > a surface (like 'white'). >> Best, >> >> Tim >> >>> On July 17, 2019 at 9:03 AM Reza Rahmanzadeh > <reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch > mailto:reza.rahmanzadeh@unibas.ch> wrote: >>> >>> External Email - Use Caution >>> >>> I removed the back slash and the command line i executed is: >>> >>> >>> mris_preproc --target fsaverage --hemi lh --s FSP010 --out > lh.FSP10.white.mgh --meas white >>> >>> but i got the error: >>> >>> Reading curvature file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white >>> MRISreadBinaryCurvature: incompatible vertex number in file > /usr/local/freesurfer/subjects/FSP010/surf/lh.white >>> ERROR: reading curvature file >>> >>> I have added --srcfmt mgh as the last argument, but again i got > the error: >>> Reading source surface reg > /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg >>> Loading source data >>> No such file or directory >>> ERROR: could not read > /usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3 >>> >>> What is wrong with my mris_prepoc command line? >>> >>> Reza >>> >>> >>> ________________________________ >>> From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>> Sent: Tuesday, July 16, 2019 10:01:15 PM >>> To: Reza Rahmanzadeh; Freesurfer support list; > greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > mailto:greve@nmr.mgh.harvard.edu >>> Subject: Re: need for help >>> >>> don't include the back slash (ie, fsaverage not fsaverage/ same > for FSP010) >>>> On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote: >>>> >>>> External Email - Use Caution >>>> >>>> Thanks a lot Doug, >>>> >>>> >>>> I started to proceed with FS group analysis wiki you sent to me. >>>> Accordingly, i have to resample all my data (output of recon-all > for a >>>> given subject for example) into fsaverage using mris_preproc. My >>>> commandline for a subject was: >>>> >>>> mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out >>>> lh.FSP10.white.mgh --meas white >>>> >>>> >>>> and i got the error: >>>> >>>> * >>>> * >>>> *Reading source surface reg >>>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>>> No such file or directory >>>> mri_surf2surf: could not read surface >>>>
/usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>>> No such file or directory* >>>> * >>>> * >>>> As there was no**lh.fsaverage/.sphere.reg* *folder, i found one
file
>>>> in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder >>>> with the name lh.fsaverage and i copied/pasted the mentiomed file > into >>>> this folder and i changed the file name to: ./sphere.reg. I got the >>>> error: >>>> * >>>> * >>>> *Reading curvature file >>>> /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere >>>> MRISreadBinaryCurvature: incompatible vertex number in file >>>> /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere* >>>> * >>>> * >>>> * >>>> * >>>> What is the problem with my mris_preproc command-line? >>>> >>>> Reza >>>> >>>>
>>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu >>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
>>>> <freesurfer-bounces@nmr.mgh.harvard.edu >>>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
>>>> N.,Ph.D. <DGREVE@mgh.harvard.edu >>>> mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> >>>> *Sent:* Tuesday, July 16, 2019 7:01:30 PM >>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>> *Subject:* Re: [Freesurfer] need for help >>>> >>>> >>>>> On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> (I assume now we are discussing in FS list, if no please let
me how
>>>>> possible?) >>>>> >>>>> >>>>> Thanks Doug, now i could see the inflate surface, this means
that my
>>>>> mri_vol2surf works well. As i would do GLM analysis over inflated >>>>> cortex of patients and controls in Qdec, >>>>> >>>>> >>>>> 1- should i input my surfaces to Qdec as inflated surface or just >>>>> inputting the output_of_vol2surf.mgz to Qdec? >>>>> >>>>> if inflated one is the input, then how could i get them? > mris_inflate >>>>> gives error. >>>>> >>>> QDEC is no longer being supported. Use the command line stream >>>> (mri_surf2surf, mri_glmfit, mri_glmfit-sim). >>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis >>>>> >>>>> 2- should i input all patients and controls surfaces in standard >>>>> surface before entering to Qdec? >>>>> >>>>> >>>>> 3- I would like to resample whole cortex (whole cortical > thickness, in >>>>> other words: the average of all projfrac between 0 and 1), is it >>>>> possible? or i am limited to resample one given depth of
cortex into
>>>>> inflated surface only? >>>>> >>>> Run mri_vol2surf with --help and look for --projfrac-avg >>>>> >>>>> thanks a lot, >>>>> >>>>> Reza >>>>> >>>>> >>>>>
>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>> *Sent:* Tuesday, July 16, 2019 6:22:56 PM >>>>> *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu >>>>> mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
>>>>> *Subject:* Re: need for help >>>>> The command should be something like >>>>> tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz >>>>> Also, tksurfer is also obsolete (but should work). You should be > using >>>>> freeview (or tksurferfv, a freeview front end that takes the same >>>>> command line args as tksurfer) >>>>> Also, please remember to respond to the fs list >>>>> >>>>>> On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote: >>>>>> >>>>>> External Email - Use Caution >>>>>> >>>>>> I got the mri_vol2surf output with .mgz: >>>>>> >>>>>> >>>>>> my tksurfer command: >>>>>> >>>>>> tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of >>>>>> mri_vol2surf was lh.inflated_MWI.mgz) >>>>>> >>>>>> >>>>>> and the error i got: >>>>>> >>>>>> *freadFloat: fread failed** >>>>>> No such file or directory* >>>>>> >>>>>> To me, opening the surfer in tksurfer is only a way to get
sure my
>>>>>> vol2surf worked well. the main problem is i got this error
for all
>>>>>> mris_smooth, mris_inflate, mris_sphere ... >>>>>> >>>>>> >>>>>> Do you think that means the output of mri_vol2surf is not > correct, or >>>>>> otherwise i could proceed with that , even when tksurfer
could not
>>>>>> open it, for GLM in Qdec? >>>>>> >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Reza >>>>>> >>>>>>
>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>>> *Sent:* Tuesday, July 16, 2019 6:01:15 PM >>>>>> *To:* Reza Rahmanzadeh >>>>>> *Subject:* Re: need for help >>>>>> what is your tksurfer command line? Also, the .w file is somewhat >>>>>> obsolete (it should still work); instead you can use .mgz
file (and
>>>>>> don't spec --paint) >>>>>> >>>>>>> On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote: >>>>>>> >>>>>>> External Email - Use Caution >>>>>>> >>>>>>> Thanks Doug, >>>>>>> >>>>>>> >>>>>>> I used the one without --inflated also, again the tksurfer > could not >>>>>>> open it and i got the same error. Where is the problem with my > cmd.? >>>>>>> >>>>>>> In addition, i wanted to make the output of mri_vol2surf
inflated
>>>>>>> using mris_inflate but i got the same error: >>>>>>> >>>>>>> *freadFloat: fread failed >>>>>>> No such file or directory* >>>>>>> * >>>>>>> * >>>>>>> *could you let me know what is the problem in registering my mwi >>>>>>> volumes to surface that i getonly such errors.* >>>>>>> * >>>>>>> * >>>>>>> *Thanks,* >>>>>>> *reza >>>>>>> * >>>>>>> >>>>>>>
>>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu >>>>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>>>>>>> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >>>>>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>> *Cc:* greve@nmr.mgh.harvard.edu >>>>>>> mailto:greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu
>>>>>>> *Subject:* Re: need for help >>>>>>> Don't use --inflated. The inflated surface is not a biological >>>>>>> surface. The default is the white surface, which is the one > you want >>>>>>> (--projfrac 0.5 will project it to the middle between the > white and >>>>> pial) >>>>>>>> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: >>>>>>>> >>>>>>>> External Email - Use Caution >>>>>>>> >>>>>>>> Dear Freesurfer, >>>>>>>> >>>>>>>> I have a batch of myelin water image (MWI) from patients and >>>>>>>> controls, and trying to have inflated cortex registered on > standard >>>>>>>> surface for GLM (Qdec). >>>>>>>> >>>>>>>> With the commandlines below i get my inflated surface of MWI > map of >>>>>>>> my patients and controls. >>>>>>>> >>>>>>>> 1-using bbregister to put MWI into FS space and to calculate >>>>>>>> register.dat: >>>>>>>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg > register.dat >>>>>>>> --o mwf_FS --t1 >>>>>>>> >>>>>>>> 2-using mri_vol2surf to extract inflated surface of MWI: >>>>>>>> mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 >>>>>>>> --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type >>>>>>>> paint--inflated (*or*--surf sphere) >>>>>>>> >>>>>>>> However the tksurfer could not open the inflated surface
and the
>>>>>>>> error message is: >>>>>>>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! >>>>>>>> Probably trying to use a scalar data file as a surface!* >>>>>>>> >>>>>>>> I used the commandline below for #2: >>>>>>>> mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o >>>>>>>> mwf-lh.w --out_type paint >>>>>>>> and i got the error: >>>>>>>> >>>>>>>> *ERROR: MRISread: file >>>>>>>> '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has > many >>>>>>>> more faces than vertices!** >>>>>>>> Probably trying to use a scalar data file as a surface!* >>>>>>>> * >>>>>>>> * >>>>>>>> As tksurfer could not open my surfaces with errors above, i
think
>>>>>>>> perhaps the vol2surf procedure is not done properly. Where
is the
>>>>>>>> problem? i need to get the inflated cortex and then putting ob >>>>>>>> sphere (using mris_sphere) and the registering to standard > surface >>>>>>>> using mris_register for GLM in Qdec, right? >>>>>>>> >>>>>>>> >>>>>>>> It is two weeks i am struggling with these commands, any helps >>>>>>>> highly appreciated. * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> * >>>>>>>> Best, >>>>>>>> Reza >>>>>>>> >>>>>>> The information in this e-mail is intended only for the
person to
>>>>>>> whom it is >>>>>>> addressed. If you believe this e-mail was sent to you in
error and
>>>>>>> the e-mail >>>>>>> contains patient information, please contact the Partners > Compliance >>>>>>> HelpLine at >>>>>>> http://www.partners.org/complianceline . If the e-mail was
sent to
>>>>>>> you in error >>>>>>> but does not contain patient information, please contact the > sender >>>>>>> and properly >>>>>>> dispose of the e-mail. >>>>>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> -- >> Dr. Tim Schäfer >> Postdoc Computational Neuroimaging >> Department of Child and Adolescent Psychiatry, Psychosomatics and > Psychotherapy >> University Hospital Frankfurt, Goethe University Frankfurt am Main, > Germany >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Greve, Douglas N.,Ph.D. -
Reza Rahmanzadeh -
Tim Schäfer