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. <dgr...@mgh.harvard.edu> Sent: Tuesday, July 16, 2019 10:01:15 PM To: Reza Rahmanzadeh; Freesurfer support list; gr...@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-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas > N.,Ph.D. <dgr...@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. <dgr...@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. <dgr...@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. <dgr...@mgh.harvard.edu> > > >> *Sent:* Tuesday, July 16, 2019 5:37:17 PM > > >> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu > > >> *Cc:* gr...@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
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