Sorry, that should be ftp surfer.nmr.mgh.harvard.edu On 8/6/19 12:39 PM, Douglas N. Greve wrote: > You can try it from the command line, > ftp surfer.nmr.mgh.harvard.edut > It will ask you for a user name; use your email address > It will ask you for a password; use "anonymous" (no quotes) > cd transfer/incoming > put file.tar > > > On 8/6/19 6:30 AM, Reza Rahmanzadeh wrote: >> >> External Email - Use Caution >> >> Hi Doug, >> >> >> When i click on the link you sent me for uploading the files, there >> is no bottom/way to upload something there. That is why i attached >> the outputs. >> >> >> My command lines sequentially for the analysis are: ( I have done >> just the same command lines for MWF maps and it worked very good, but >> for NDI and ODI maps of NODDI does not work). >> >> 1-mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 >> --out lh.NDI_inflated.avg.mgh (i used the new mris_preproc you sent me). >> >> 2-mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex --sval >> lh.NDI_inflated.avg.mgh --tval lh.NDI_inflated.avg.05.mgh >> >> 3-mri_glmfit --y lh.NDI_inflated.avg.05.mgh --surf fsaverage lh --C >> contrast --fsgd fsgd.fsgd --cortex --glmdir >> lh.NDI_inflated.avg.05.glmdir >> >> >> >> The outputs of all three steps are attached. >> >> >> >> Looking forward for your helps >> >> Reza >> >> >> >> >> >> >> >> ------------------------------------------------------------------------ >> *From:* Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> >> *Sent:* Monday, August 5, 2019 5:55:18 PM >> *To:* Reza Rahmanzadeh; Freesurfer support list >> *Cc:* gr...@nmr.mgh.harvard.edu >> *Subject:* Re: [Freesurfer] need for help >> Can you upload the input (ie, argument to --y) here: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming >> Also, send your mri_glmfit command line. >> >> On 8/2/2019 9:41 AM, Reza Rahmanzadeh wrote: >>> >>> External Email - Use Caution >>> >>> yes, I have the page below for all patients. >>> >>> >>> I think it means all values are zero. My registration for bbregister >>> is fine and i wrote my mris_preproc the same as MWF maps. >>> >>> >>> Thanks, >>> >>> Reza >>> >>> ------------------------------------------------------------------------ >>> >>> *From:* Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> >>> *Sent:* Friday, August 2, 2019 3:35:45 PM >>> *To:* Reza Rahmanzadeh; Freesurfer support list >>> *Cc:* gr...@nmr.mgh.harvard.edu >>> *Subject:* Re: [Freesurfer] need for help >>> did you check each subject to make sure they had a non-zero map? >>> >>> On 8/2/2019 6:25 AM, Reza Rahmanzadeh wrote: >>>> >>>> External Email - Use Caution >>>> >>>> Dear Doug, >>>> >>>> >>>> NODDI is diffusion imaging and we have vakue regarding neurite >>>> density (NDI in NDI map) and orientation dispersion (ODI value in >>>> ODI map). I do not know why mris_preproc works well on MWI maps but >>>> not on NODDI maps (both NDI and ODI maps). Beside using >>>> projfrac-avg 0 1 0.25 , i have run mris_preproc with projfrac 0.5 >>>> but again i got this error: >>>> >>>> ERROR: no voxels found in the mask >>>> make sure at least one voxel has a non-zero value for each input >>>> >>>> I have run mris_preproc on three patients that i am sure about >>>> registration quality, again when i scroll through them , there is >>>> no value in none of them. How that is possible? >>>> >>>> NODDI does not have a lot of zero value but all values in cortex >>>> are between 0.2-0.4. >>>> >>>> >>>> Thanks, >>>> Reza >>>> >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> *From:* Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> >>>> *Sent:* Wednesday, July 31, 2019 12:50:45 AM >>>> *To:* Reza Rahmanzadeh; Freesurfer support list >>>> *Cc:* gr...@nmr.mgh.harvard.edu >>>> *Subject:* Re: [Freesurfer] need for help >>>> 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 >>>> <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 >>>> >>> >> >
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