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. >> >
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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
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