Freesurfer

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Issues with set-up and configuration on Linux
by Collins Jones, Liam 15 Aug '19

15 Aug '19

External Email - Use Caution Dear FreeSurfer developers, I am having trouble with FreeSurfer set up and configuration on Linux. The installation appears to have completed without any problems, though when pasting the lines export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh into the terminal command window I am seeing the following:- -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni bash: tr: No such file or directory bash: grep: No such file or directory bash: tr: No such file or directory bash: sed: No such file or directory FSL_DIR /usr/share/fsl/5.0 Following this, when running the first command from the "Test your FreeSurfer installation" section of the Download website, I'm seeing this error:- Command 'cp' is available in '/bin/cp' The command could not be located because '/bin' is not included in the PATH environment variable. I am not sure why this error is occurring and have been through the archive but could not find a similar problem. In addition to this I'm unable to run basic Linux commands (eg ls) in the same terminal window. Is there a way to overcome this so that I can run FreeSurfer functions? Any help would be greatly appreciated. Here are some background details:- 1) Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 2) Platform: Ubuntu 18.04.2 LTS 3) uname -a: Linux bodhi 4.15.0-55-generic #60-Ubuntu SMP Tue Jul 2 18:22:20 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Many thanks, Liam Collins-Jones.

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Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: need for help
by Greve, Douglas N.,Ph.D. 15 Aug '19

15 Aug '19

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. <DGREVE(a)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. <DGREVE(a)mgh.harvard.edu> >>> *Sent:* Monday, August 5, 2019 5:55:18 PM >>> *To:* Reza Rahmanzadeh; Freesurfer support list >>> *Cc:* greve(a)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. <DGREVE(a)mgh.harvard.edu> >>>> *Sent:* Friday, August 2, 2019 3:35:45 PM >>>> *To:* Reza Rahmanzadeh; Freesurfer support list >>>> *Cc:* greve(a)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. <DGREVE(a)mgh.harvard.edu> >>>>> *Sent:* Wednesday, July 31, 2019 12:50:45 AM >>>>> *To:* Reza Rahmanzadeh; Freesurfer support list >>>>> *Cc:* greve(a)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:* greve(a)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-bounces(a)nmr.mgh.harvard.edu >>>>>> <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Reza >>>>> Rahmanzadeh >>>>>> <reza.rahmanzadeh(a)unibas.ch> >>>>>> *Sent:* Tuesday, July 30, 2019 2:44:25 PM >>>>>> *To:* Greve, Douglas N.,Ph.D. >>>>>> *Cc:* Freesurfer support list; greve(a)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. >>>>>> <DGREVE(a)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. >>>>>>>> <DGREVE(a)mgh.harvard.edu <mailto:DGREVE@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-bounces(a)nmr.mgh.harvard.edu >>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >>>>>>>>>> <freesurfer-bounces(a)nmr.mgh.harvard.edu >>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of >>>>> Reza >>>>>>>>>> Rahmanzadeh >>>>>>>>>> <reza.rahmanzadeh(a)unibas.ch <mailto:reza.rahmanzadeh@unibas.ch>> >>>>>>>>>> *Sent:* Monday, July 29, 2019 11:37:46 AM >>>>>>>>>> *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; >>>>>>>>>> greve(a)nmr.mgh.harvard.edu <mailto:greve@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_fr… >>>>> >>>>>>>>>> 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. <DGREVE(a)mgh.harvard.edu >>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu> >>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu>> >>>>>>>>>> *Sent:* Wednesday, July 17, 2019 5:31:27 PM >>>>>>>>>> *To:* Reza Rahmanzadeh; Freesurfer support list; >>>>>>>>>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:greve@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_fr… >>>>>>>>>> >>>>>>>>>>> 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-bounces(a)nmr.mgh.harvard.edu >>>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >>>>>>>>>>> <freesurfer-bounces(a)nmr.mgh.harvard.edu >>>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of >>>>> Reza >>>>>>>>>> Rahmanzadeh >>>>>>>>>>> <reza.rahmanzadeh(a)unibas.ch <mailto:reza.rahmanzadeh@unibas.ch> >>>>>>>>>>> <mailto:reza.rahmanzadeh@unibas.ch>> >>>>>>>>>>> *Sent:* Wednesday, July 17, 2019 4:26:21 PM >>>>>>>>>>> *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; >>>>>>>>>>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>>>>>>>>>> <mailto:greve@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. <DGREVE(a)mgh.harvard.edu >>>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu> >>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu>> >>>>>>>>>>> *Sent:* Wednesday, July 17, 2019 4:14:41 PM >>>>>>>>>>> *To:* Reza Rahmanzadeh; Freesurfer support list; >>>>>>>>>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:greve@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-bounces(a)nmr.mgh.harvard.edu >>>>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >>>>>>>>>>>> <freesurfer-bounces(a)nmr.mgh.harvard.edu >>>>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of >>>>> Reza >>>>>>>>>>>> Rahmanzadeh <reza.rahmanzadeh(a)unibas.ch >>>>>>>>>>>> <mailto:reza.rahmanzadeh@unibas.ch> >>>>>>>>>> <mailto:reza.rahmanzadeh@unibas.ch>> >>>>>>>>>>>> *Sent:* Wednesday, July 17, 2019 9:56:00 AM >>>>>>>>>>>> *To:* Freesurfer support list >>>>>>>>>>>> *Cc:* DGREVE(a)mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>>>>>>>>>>> <mailto:DGREVE@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+ml(a)rcmd.org >>>>>>>>>>>>> <mailto:ts+ml@rcmd.org> >>>>>>>>>> <mailto:ts+ml@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.rahmanzadeh(a)unibas.ch <mailto:reza.rahmanzadeh@unibas.ch> >>>>>>>>>>>> <mailto:reza.rahmanzadeh@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. <DGREVE(a)mgh.harvard.edu >>>>>>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu> >>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu>> >>>>>>>>>>>>>> Sent: Tuesday, July 16, 2019 10:01:15 PM >>>>>>>>>>>>>> To: Reza Rahmanzadeh; Freesurfer support list; >>>>>>>>>>>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>>>>>>>>>>> <mailto:greve@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-bounces(a)nmr.mgh.harvard.edu >>>>>>>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >>>>>>>>>>>>>>> <freesurfer-bounces(a)nmr.mgh.harvard.edu >>>>>>>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of >>>>> Greve, >>>>>>>>>> Douglas >>>>>>>>>>>>>>> N.,Ph.D. <DGREVE(a)mgh.harvard.edu >>>>>>>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu> >>>>> <mailto:DGREVE@mgh.harvard.edu>> >>>>>>>>>>>>>>> *Sent:* Tuesday, July 16, 2019 7:01:30 PM >>>>>>>>>>>>>>> *To:* Reza Rahmanzadeh; Freesurfer(a)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. <DGREVE(a)mgh.harvard.edu >>>>>>>>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu> >>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu>> >>>>>>>>>>>>>>>> *Sent:* Tuesday, July 16, 2019 6:22:56 PM >>>>>>>>>>>>>>>> *To:* Reza Rahmanzadeh; freesurfer(a)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. <DGREVE(a)mgh.harvard.edu >>>>>>>>>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu> >>>>>>>>>> <mailto:DGREVE@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. <DGREVE(a)mgh.harvard.edu >>>>>>>>>>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu> >>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu>> >>>>>>>>>>>>>>>>>> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >>>>>>>>>>>>>>>>>> *To:* Reza Rahmanzadeh; Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>>>>>>>>>> *Cc:* greve(a)nmr.mgh.harvard.edu >>>>>>>>>>>>>>>>>> <mailto:greve@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:greve@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(a)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(a)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(a)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(a)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(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Using Freesurfer Commands for Neonate
by Mahshid Fouladivanda 15 Aug '19

15 Aug '19

External Email - Use Caution Dear Lilla, Thanks for your help. I have used the same command in the recon-all.log file (seen bellow), but I have a doubt for the highlighted part in the command: "mri_aparc2aseg --s SBJ1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gcamri/aseg.auto_noCCseg.label_intensities.txt" which used a predefined file from freesurfer folder. Actually, I used the mri_aparc2aseg command with some changes, seen bellow: mri_aparc2aseg --s mysubj --annot aparc --o $SUBJECTS_DIR/mysubj/mri/parc.mgz so, I am wondered if it reads the ' /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca' automatically. I would appreciate it of you could help on how to correct this part. Regards, Mahshid

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Re: [Freesurfer] How to Divide the Brain Surface Parcells to more regions
by Mahshid Fouladivanda 15 Aug '19

15 Aug '19

External Email - Use Caution Dear Doug, Special appreciation for your help. Actually, I have created the annotation and the color table files and finally I have divided the parcels. Also, I checked the primary and the division parcels on the .pial surface that they were correct. But as I bring them from surface to volume using mri_aparc2aseg (as mentioned in the email, Subject: How to Create Cortex Parcellation Using "mri_aparc2aseg"?) it fail. I mean that the parcels are not placed where they should be there. In other word, I expect it when a primary region had been divided to for example two other regions finally, the two regions with each other form the primary region with the same shape and position in the brain cortex. But, it does not happen!!! All newly resulted regions are in the brain cortex and seem well in total but they do not placed correctly based on primary regions and have movement and region shape deformation when put them beside each other to have a one region as one of the primaries. So that I doubt about the freesurfer commands that basically are used for adults, while I use neonate images. I am really confused, I would appreciate it if you could help me. Best Regards, Mahshid

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Re: [Freesurfer] How to Create Cortex Parcellation Using "mri_aparc2aseg"?
by Mahshid Fouladivanda 15 Aug '19

15 Aug '19

External Email - Use Caution Dear Doug, Here is the emails: Message: 6 Date: Fri, 2 Aug 2019 01:55:34 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> Subject: Re: [Freesurfer] How to Create Cortex Parcellation Using "mri_aparc2aseg"? To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <183e8a60-1cc2-1680-26a7-bce8a1d03315(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" If you look in the recon-all.log file for any subject, you will see a mri_aparc2aseg command line. YOu can use that specifying your annot and the new output name. On 8/1/2019 4:58 PM, Mahshid Fouladivanda wrote: External Email - Use Caution Dear experts, I have a segmentation file of all the tissues in the brain and the ribbon file which were extracted by another toolbox rather than freesurfer. Also, I have created the annotation file using "write_annotation.m". Now, I wanna create a parcellation file based on the segmentation and annotation files using "mri_aparc2aseg" in freesurfer. Bellow is the command I entered in the terminal and extract the parcels: mri_aparc2aseg --s subject name --annot annotation name --o output name and I used the segmentation file as the "aseg.mgz" for the above command. Now, I am wondered that do I select the right aseg file or not?? Any help would be appreciated. Regards, Mahshid

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mri_vol2surf error
by Pratik Kashyap 14 Aug '19

14 Aug '19

External Email - Use Caution mri_vol2surf --cortex --hemi lh --interp trilinear --o rest2.nii.gz --out_type niigz --reg register.dat --projfrac-avg 0.500 --mov rest2.nii --surfreg sphere.reg --trgsubject fsaverage A source volume path must be supplied Hey, I'm running the above command, getting an error 'A source volume path must be specified' I checked all the source paths, they exist. But the output path doesn't , which is weird as it isn't a source path. Please help, PK

2 1

multimodal analysis (pet and cortical thickness relationship) using --pvr
by miracle ozzoude 14 Aug '19

14 Aug '19

External Email - Use Caution Hello Experts, I am performing an analysis looking at the relationship between amyloid uptake and cortical thickness using --pvr flag in mri_glmfit. I've 2 groups and 2 variables (age and education). I want to run a within group analysis while regressing out age and education (i.e. Within group 1, is there a negative relationship between amyloid uptake and cortical thickness regressing out the effects of age and education). However, i'm not sure how my pvr contrasts will look like. Below are my fsgd and an attempt at creating contrasts. Please, can you let me know if my contrasts are correct based on my questions. Thank you. Best, Paul The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2 Variable Age Education Input XX1 g1 60 16 Input XX2 g1 58 14 Input YY1 g2 62 20 Input YY1 g2 62 20 ------------------------------------------------------------- matrix for group1: pvrgroup1= 1 0 0 0 0 0 0 is there a relationship between amyloid-thickness in group1 regressing out age and education? matrix for group2: pvrgroup2= 0 1 0 0 0 0 0 is there a relationship between amyloid-thickness in group2 regressing out age and education?

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Re: [Freesurfer] How to Create Cortex Parcellation Using "mri_aparc2aseg"?
by Mahshid Fouladivanda 14 Aug '19

14 Aug '19

External Email - Use Caution Dear Doug, Thanks for your reply. I have used the same command in the recon-all.log file (seen bellow), but I have a doubt for the highlighted part in the command: "mri_aparc2aseg --s SBJ1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt" which used a predefined file from freesurfer folder. Actually, I used the mri_aparc2aseg command with some changes, seen bellow: mri_aparc2aseg --s mysubj --annot aparc --o $SUBJECTS_DIR/mysubj/mri/parc.mgz so, I am wondered if it reads the ' /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca' automatically. I would appreciate it of you could help on. Regards, Mahshid

2 1

Questions about pial surfaces segmentation
by Hsin-Hung Li 14 Aug '19

14 Aug '19

External Email - Use Caution Hello FreeSurfer Developers, I run recon-all on the T1 and T2 images of a few new human subjects. After running recon-all, I followed the freesurfer troubleshooting tutorial, and started visually checking the segmentation of the pial surfaces and white surfaces. I found similar errors among a few subjects, and would like to make sure that what I am thinking is correct before proceeding: The figures I attached are the coronal view of the same subject (from the left column to the right column: posterior to anterior). These errors mainly occurred at the occipital cortex, and at the boundary between the left and right hemisphere. It seems that the pial surface included a piece of dura matter that should not be there. It is indicated by the green arrows in the images. It also seems to happen at the places indicated by the blue arrows, but not as visible. Is what I'm thinking correct? I also attached an image containing three different views of the same subject. In general, will running -gcut in this example help reducing the errors above? -The recon-all is run on a server with freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -uname -m x86_64 -recon-all.log: see attached Thank you so much. HHL

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Re: [Freesurfer] Help with MRI segstats
by Greve, Douglas N.,Ph.D. 14 Aug '19

14 Aug '19

Can you send a command line and terminal output with the error? On 8/14/19 9:38 AM, Daliah Ross wrote: > > External Email - Use Caution > > Hello, > > I have tried using just one of the arguments, but I'm still not > getting my desired output. I'm not sure if I've explained my question > correctly. I am looking to get anatomical labels on the clusters that > I've already created through mri_surfcluster to find out where in the > cortex each cluster is. How would I go about doing this? I was hoping > that mri_segstats could give an output where it lists each cluster > starting with the biggest and where it is located. I've been able to > get this list, but without anatomical labels. I appreciate your help! > > Thank you, > Daliah > > *Daliah Ross* | dross3(a)mail.yu.edu <mailto:dross3@mail.yu.edu> > > Ph.D. Student, Clinical Psychology with Health Emphasis > Ferkauf Graduate School of Psychology > Yeshiva University > Albert Einstein College of Medicine > > > On Thu, Aug 8, 2019 at 8:01 PM Daliah Ross <dross3(a)mail.yu.edu > <mailto:dross3@mail.yu.edu>> wrote: > > Hi, > > No, we primarily wanted this for the un-permuted case, to be able > to identify the anatomical regions for each cluster. In addition, > we have thought about looking at the spatial cluster distribution > for the permutations to see if there are any regions which are > more prone to false positives, which might be indicative of e.g. > parcellation or imaging issues, but we haven’t yet figured out how > to best go about that step. And, yes, for the permutations we are > running mri_surfcluster and extracting the max cluster size per > permutation. Thank you for the advice! > > Daliah > > *Daliah Ross* | dross3(a)mail.yu.edu <mailto:dross3@mail.yu.edu> > > Ph.D. Student, Clinical Psychology with Health Emphasis > Ferkauf Graduate School of Psychology > Yeshiva University > Albert Einstein College of Medicine > > > On Wed, Aug 7, 2019 at 4:51 PM Greve, Douglas N.,Ph.D. > <DGREVE(a)mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: > > You should only pass one of --seg, --annot, or --slabel to > mri_segstats. I don't understand how you are trying to use > this in the > context of your permutation. Is this something that you are > running on > each iteration? If so, it is probably not what you want to do. > Probably > you want to run mri_surfcluster to get the cluster sizes out. > > On 8/7/19 1:31 PM, Daliah Ross wrote: > > > > External Email - Use Caution > > > > This is the command line: > > mri_segstats --seg F_lhstats_6covars_ > sm5_Interaction_negNumCl_F7.mgh > > --annot lh.aparc.annot lh parc --slabel fsaverage lh cortex > --sum > > F_lhstats_6covars_ sm5_Interaction_negNumCl_F7.txt > > > > We are running the permutations within FS, but because our > model is a > > linear mixed model, and we didn't think that this would be > compatible > > with fspalm. So, we are running the permutations "manually" > (i.e. we > > are generating the random permutations, which in our case is > just > > switching the subject labels for the thickness data. We are > then using > > mri_surfcluster to extract the maximum cluster size per > permutation > > and will use the permutation distribution to determine our the > > statistical significance of our results). In addition, our > analyses > > are a bit out of the ordinary in that the thickness data are an > > independent variable in our model, for which we have a repeated > > non-imaging measure as the outcome. Effectively, we are > using the > > thickness maps to generate vertex-wise regressors, with a fixed > > outcome measure (fixed in the sense that it doesn't vary > across the > > brain). > > > > If you have any thoughts about how we could use fspalm in > our case, > > your advice would be most appreciated. > > > > Thanks again, > > Daliah > > > > *Daliah Ross* | dross3(a)mail.yu.edu > <mailto:dross3@mail.yu.edu> <mailto:dross3@mail.yu.edu > <mailto:dross3@mail.yu.edu>> > > > > Ph.D. Student, Clinical Psychology with Health Emphasis > > Ferkauf Graduate School of Psychology > > Yeshiva University > > Albert Einstein College of Medicine > > > > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> > > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> > > <freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> > > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>> On Behalf Of > > Greve, Douglas N.,Ph.D. > > Sent: Tuesday, August 6, 2019 12:56 PM > > To: freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > Subject: Re: [Freesurfer] Help with MRI segstats > > > > Can you send command lines? Also, are you using the built-in > > permutation tool or trying to do something outside of FS? > > > > On 8/6/19 8:40 AM, Daliah Ross wrote: > > > > > > External Email - Use Caution > > > > > > Hi FreeSurfer experts, > > > > > > I have a couple of questions regarding mri_segstats > tool for an > > > analysis on vertex-wise cortical thickness data. We are > > attempting to > > > compare maximum cluster sizes among permutations. We > are having > > > trouble figuring out how to get the anatomical label > for each > > cluster > > > using the --slabel argument. We are also wondering if the > > difference > > > between cluster sizes between mri_surfcluster and > mri_segstats > > is due > > > to partial volumes, and if so, how to correctly use > the --pv > > argument. > > > It suggests in the wiki page that mri/norm.mgz volume > is usually > > used > > > but I believe we need something surface-based since we > are using > > > thickness data. > > > > > > Thank you in advance for any help you can provide. > > > > > > Best, > > > Daliah > > > > > > *Daliah Ross* | dross3(a)mail.yu.edu > <mailto:dross3@mail.yu.edu> <mailto:dross3@mail.yu.edu > <mailto:dross3@mail.yu.edu>> > > <mailto:dross3@mail.yu.edu <mailto:dross3@mail.yu.edu> > <mailto:dross3@mail.yu.edu <mailto:dross3@mail.yu.edu>>> > > > > > > Ph.D. Student, Clinical Psychology with Health > Emphasis Ferkauf > > > Graduate School of Psychology Yeshiva University > Albert Einstein > > > College of Medicine > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail > > > .nmr.mgh.harvard.edu <http://nmr.mgh.harvard.edu> > > > <http://nmr.mgh.harvard.edu>%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C0 > > > 1%7Cmark.wagshul%40einstein.yu.edu > <http://40einstein.yu.edu> > > > <http://40einstein.yu.edu>%7Cfde693609070412c457808d71a8f16f2% > > > > > > 7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C637007074183066654&sd > > > > ata=ALndUpHJ%2BYhuMzChviSn9ygf8H112mUKvVmJktGoqB4%3D&reserved=0 > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.… > > > > > > The information in this e-mail is intended only for the person > to whom it is > addressed. If you believe this e-mail was sent to you in error > and the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was > sent to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. >

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