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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.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
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