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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
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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:
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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 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
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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 >
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