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
