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 >>> >> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
