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_freeview
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-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh > <reza.rahmanza...@unibas.ch> > *Sent:* Wednesday, July 17, 2019 4:26:21 PM > *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; > gr...@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. <dgr...@mgh.harvard.edu> > *Sent:* Wednesday, July 17, 2019 4:14:41 PM > *To:* Reza Rahmanzadeh; Freesurfer support list; gr...@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-boun...@nmr.mgh.harvard.edu >> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Reza >> Rahmanzadeh <reza.rahmanza...@unibas.ch> >> *Sent:* Wednesday, July 17, 2019 9:56:00 AM >> *To:* Freesurfer support list >> *Cc:* dgr...@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...@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.rahmanza...@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. <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 >> >> >> >> _______________________________________________ >> >> 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 > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
