no idea until you tell me what you did, including command lines and terminal output
On 8/7/19 11:08 AM, Reza Rahmanzadeh wrote: > External Email - Use Caution > > Thanks, I saw that before, what could be the reason for that and how could i > do mris_preproc correctly for NDI maps? > > Thanks, > Reza > >> On 7 Aug 2019, at 17:05, Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> >> wrote: >> >> Every vertex of every subject is 0 in lh.NDI_inflated.avg.05.mgh >> >>> 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
