Right, you can't use both --fsgd and --iv. You have to use --iv, so make sure the order is the same as in the fsgd file.
On 7/30/19 8:44 AM, Reza Rahmanzadeh wrote: > 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
