External Email - Use Caution Thanks Doug,
The script works well for projfrac-avg. but the problem is: when i use mris_preproc to assemble my MWIs and put them on fsaverage, as .fsgd file is only the order of my controls and subjects and i would have the inflated cortex of MWI on fsaverage, then anyway i have to specify my volume and registration files (tkregister2 output). Then there’s an error: i shouldn’t use both -fsgd and - iv together. Then i decided not to use fsgd file for mris_preproc and only using that for mri_glmfit. In mris_preproc, i write all “-iv volumes and registration files” in the same order as in fsgd file but i don’t write -fsgd argument. Is this way correct? Thanks, Reza > On 29 Jul 2019, at 23:32, Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> > wrote: > > 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
