I don't know what is in the NODDI maps. The way mri_glmfit works is that if any subject has a 0-value at a vertex, then it will mask out that vertex for all subjects. Is NODDI something that might have a lot of 0-values? It also may be that one subject has all 0s (eg, if the regitration was really bad), so you can check the map created by mris_preproc (load it in as an overlay, then hit the configure button, then change the frame number to scroll through your subjects)
On 7/30/19 12:46 PM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > (sorry for bombaeding you with e-mails) > > > It seems that the error happens only when i use NODDI diffusion image > e.g. NDI map i get that error, but for MWIs the new mris_preproc works > well. > > > Should i do anything special for NODDI images? BTW, the bbregister > works well for NODDI and i entered the correct registration file into > mris_preproc. > > > Thanks, > > Reza > > ------------------------------------------------------------------------ > *From:* Reza Rahmanzadeh > *Sent:* Tuesday, July 30, 2019 6:17:22 PM > *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list > *Cc:* gr...@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] need for help > > ... One problem when i use the new mris_preproc: > > Always the output of mri_glmfit when the input is the result of new > mris_preproc is: > > *F**ound 0 voxels in mask > ERROR: no voxels found in the mask > make sure at least one voxel has a non-zero value for each input* > * > * > * > * > I think it means that something is perhaps wrong with the script. I > tried both projfrac 0.5 and projfrac-avg 0 1 0.25 and i got the same > error. I did not get the error when i used old mris_preproc using > projfrac 0.5.* > * > * > * > *The other thing that could be the reason is my fsgd file. I have > problem how to specify the name of subjects, > * > Now it is sth like: > > GroupDescriptorFile 1 > Class Group1 > CLASS Group2 > Input FSC001 Group1 > Input FSC002 Group1 > Input FSC003 Group1 > . > > . > > . > > Input FSP001 Group2 > Input FSP002 Group2 > Input FSP003 Group2 > . > > . > > > The oeder is thew same with mris_preproc, now the subject name is > FSC0xx for controls and FSP00x for patients, these are the name of > folders containing FS outputs, but my input volume is MWIs and the > registration files are not stored in this folder. Does it matter how > to name subjects when i am using fsgd file only in mri_glmfit ( to get > aware of order)? > > > 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:* Tuesday, July 30, 2019 2:44:25 PM > *To:* Greve, Douglas N.,Ph.D. > *Cc:* Freesurfer support list; gr...@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] need for help > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
