Sort of. mri_glmfit will take a design matrix (--X) and contrast matrices (--C), but they need to be in the right format (simple text table). So, you'll have to convert the output of design_ttest2 into that format.
On 7/26/19 8:55 AM, Reza Rahmanzadeh wrote: > > 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_freeview > > 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. <dgr...@mgh.harvard.edu> > *Sent:* Wednesday, July 17, 2019 5:31:27 PM > *To:* Reza Rahmanzadeh; Freesurfer support list; gr...@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_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
