Oh, I guess that's a problem! I've created a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc See if that works. You should compare the output to using the max or -projfrac 0.5 to make sure they are at least similar since I have not run it even once:)
On 7/29/19 5:08 PM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > Thanks > > But mris_prepoc will not accept “projfrac-avg” and there’s an error: > argument unrecognized! > > Then how can i compute the average via mris_preproc? As based on > tutorial, first i used tkregister/bbregister to compute the > registration matrix and then i should put input images with > transformation matrix in mris_preproc. I mean i shouldn’t use > mri_vol2surf (that allows me to use projfrac-avg) in group analysis > and that’s the reason i have problem with mris_proproc to compute the > average. > > What should i do? > > Thanks, > Reza > > On 29 Jul 2019, at 23:03, Greve, Douglas N.,Ph.D. > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > >> one computes the average, the other computes the maximum >> >> On 7/29/19 9:03 AM, Reza Rahmanzadeh wrote: >>> >>> External Email - Use Caution >>> >>> Dear Doug, >>> >>> >>> I appreciat if you reply my question in the previous e-mail with this: >>> >>> >>> can not i use projfrac-avg in mris_preproc? Is --projfrac-max min max >>> delta just the same? >>> >>> >>> Best, >>> >>> Reza >>> >>> ------------------------------------------------------------------------ >>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu >>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >>> <freesurfer-boun...@nmr.mgh.harvard.edu >>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Reza >>> Rahmanzadeh >>> <reza.rahmanza...@unibas.ch <mailto:reza.rahmanza...@unibas.ch>> >>> *Sent:* Monday, July 29, 2019 11:37:46 AM >>> *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; >>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>> *Subject:* Re: [Freesurfer] need for help >>> >>> 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 >>> <mailto:dgr...@mgh.harvard.edu> >>> <mailto:dgr...@mgh.harvard.edu>> >>> *Sent:* Wednesday, July 17, 2019 5:31:27 PM >>> *To:* Reza Rahmanzadeh; Freesurfer support list; >>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>> <mailto: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 >>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >>>> <freesurfer-boun...@nmr.mgh.harvard.edu >>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Reza >>> Rahmanzadeh >>>> <reza.rahmanza...@unibas.ch <mailto:reza.rahmanza...@unibas.ch> >>>> <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> >>>> <mailto: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 >>>> <mailto:dgr...@mgh.harvard.edu> >>> <mailto:dgr...@mgh.harvard.edu>> >>>> *Sent:* Wednesday, July 17, 2019 4:14:41 PM >>>> *To:* Reza Rahmanzadeh; Freesurfer support list; >>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>> <mailto: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 >>>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >>>>> <freesurfer-boun...@nmr.mgh.harvard.edu >>>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Reza >>>>> Rahmanzadeh <reza.rahmanza...@unibas.ch >>>>> <mailto:reza.rahmanza...@unibas.ch> >>> <mailto:reza.rahmanza...@unibas.ch>> >>>>> *Sent:* Wednesday, July 17, 2019 9:56:00 AM >>>>> *To:* Freesurfer support list >>>>> *Cc:* dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu> >>>>> <mailto: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 >>>>>> <mailto:ts...@rcmd.org> >>> <mailto: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 <mailto:reza.rahmanza...@unibas.ch> >>>>> <mailto: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 >>>>>>> <mailto:dgr...@mgh.harvard.edu> >>> <mailto:dgr...@mgh.harvard.edu>> >>>>>>> Sent: Tuesday, July 16, 2019 10:01:15 PM >>>>>>> To: Reza Rahmanzadeh; Freesurfer support list; >>>>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>>>> <mailto: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 >>>>>>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >>>>>>>> <freesurfer-boun...@nmr.mgh.harvard.edu >>>>>>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Greve, >>> Douglas >>>>>>>> N.,Ph.D. <dgr...@mgh.harvard.edu >>>>>>>> <mailto:dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu>> >>>>>>>> *Sent:* Tuesday, July 16, 2019 7:01:30 PM >>>>>>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto: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 >>>>>>>>> <mailto:dgr...@mgh.harvard.edu> >>> <mailto:dgr...@mgh.harvard.edu>> >>>>>>>>> *Sent:* Tuesday, July 16, 2019 6:22:56 PM >>>>>>>>> *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu >>>>>>>>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>> <mailto: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 >>>>>>>>>> <mailto:dgr...@mgh.harvard.edu> >>> <mailto: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 >>>>>>>>>>> <mailto:dgr...@mgh.harvard.edu> >>> <mailto:dgr...@mgh.harvard.edu>> >>>>>>>>>>> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >>>>>>>>>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>>> *Cc:* gr...@nmr.mgh.harvard.edu >>>>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu> >>> <mailto: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 >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto: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 >>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> <mailto: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
