Freesurfer October 2020

freesurfer@nmr.mgh.harvard.edu

112 participants
180 discussions

Re: [Freesurfer] Tracula error: run list is longer than subject list
by Yendiki, Anastasia 04 Nov '20

04 Nov '20

What goes after "-c" in the trac-all command should be the configuration file, not the nifti file. ________________________________ From: Shanika Jayakody <shanika.jayakody(a)einsteinmed.org> Sent: Monday, October 26, 2020 5:01 PM To: Yendiki, Anastasia <AYENDIKI(a)mgh.harvard.edu> Subject: Fw: Tracula error: run list is longer than subject list External Email - Use Caution Hi Anastasia Thanks for your reply. That file was a Dicom but it was named as "IM_0017". Anyways I tried with the extension (renamed the file too as IM_007.dcm) Just to see if there is a different outcome, I ran trac-all on another subject too but still I get the same error. I have two things to double check with you 1) our pre-processed files are nii, not dcm-I have changed the configuration file, bvals and bvec files as instructed in FreeSurfer wiki (attached) and did trac-all- this way the first error I get is illigal variable name. I am not sure if nii files won't work or if there is something wrong with my configuration file. 2) I ran trac-all on the same subjects dicom files (changed the configuration file accordingly) Either way I get the same error (log file attached). It would be really great if you can suggest something-looking forward to hear from you. Many thanks, Oshadi ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia <AYENDIKI(a)mgh.harvard.edu> Sent: Monday, October 26, 2020 11:05 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list Hi Oshadi - The first error in your log file is this: ERROR: cannot find /home/admin/freesrufer/subjects/30141/30141Diffusion/IM_0017 Does that file exist? Does the file name have an extension that you're omitting? Best, Anastasia. ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Shanika Jayakody <shanika.jayakody(a)einsteinmed.org> Sent: Monday, October 26, 2020 10:06 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>; Yendiki, Anastasia <AYENDIKI(a)mgh.harvard.edu> Subject: [Freesurfer] Fw: Tracula error: run list is longer than subject list External Email - Use Caution Hi Anastasia Thanks again for helping with troubleshooting the error- I was wondering if you have any suggestions for me to try. I have also tried running TRACULA on freesurfer tutorial data but get the same error Best regards, Oshadi ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Shanika Jayakody <shanika.jayakody(a)einsteinmed.org> Sent: Tuesday, October 20, 2020 9:56 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails. External Email - Use Caution Hi Anastasia Thanks for your reply. It was subjlist (sorry that was a typo in my email) I have attached the 1) log file 2) cognfiuration file 3) bvec and bval files I have used. I hope that's what you need- I am very new to FreeSurfer please let me know if you want me to send any more files. Thank you for your help Best regards Oshadi ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia <AYENDIKI(a)mgh.harvard.edu> Sent: Monday, October 19, 2020 8:33 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list Make sure to use "subjlist", not "sublist". If that is not the issue, then please attach your log file and configuration file - it's hard to guess the issue without more information. Best, Anastasia. ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Shanika Jayakody <shanika.jayakody(a)einsteinmed.org> Sent: Monday, October 19, 2020 2:43 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Tracula error: run list is longer than subject list External Email - Use Caution Hello, I have been trying to run trac-all on a DWI of a participant, but I keep getting the error "run list is longer than subject list" I have created a configuration file setting sublist and runlist to just one subject so I am not sure what the error is about. I wonder if anyone can help me figure out a solution. Many thanks Oshadi

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Tracula error
by Michele Valotti 02 Nov '20

02 Nov '20

External Email - Use Caution Hello all, I am trying to run Tracula for one of my subjects and after creating the configuration file I run trac-all -prep -c /path/to/config/file but I am getting this error: FSLDIR: Undefined variable. I have run the SetUpFreeSurfer.sh script and echo $FSLDIR prints my fls directory. Adding export FSLDIR=/my/fls/path also does not fix the error, Any suggestions? Thank you very much, Michele

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Error in QDEC
by Koustav Chatterjee 02 Nov '20

02 Nov '20

External Email - Use Caution Hello, I have found the following error while click on 'Generate Stats Data Tables' to import the aseg and aparc data from the FreeSurfer-processed group data, Could you please suggest how to overcome the issue? [image: image.png] Thank you, KC

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resolution greater than 1 mm segmentation
by Gonzalo Rojas Costa 02 Nov '20

02 Nov '20

External Email - Use Caution Hi: I know that using an mprage image with greater than 1 mm resolution, freesurfer converts it to 1 mm previous segmentation. There is any option that freesurfer uses the original resolution of the image? Any other software that do such a thing ? Especially hippocampal segmentation. Sincerely, Gonzalo Rojas Costa

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ERROR running mkcontrast
by Nina Khatibi 31 Oct '20

31 Oct '20

External Email - Use Caution Hi, I'm trying to use mkcontrast, but there's an error which I'll send below. I couldn't find any solution to solve it, I hope you help me fix this issue. I'm using freesurfer-darwin-macOS-7.1.1-20200811-8b40551 , on my macbook pro 2018, macOS Mojave 10.14.6 I run "mkcontrast-sess -analysis mpk.fsaverage5Con.lh -contrast NorthSouth -a 4 -c 3" and these appear: INFO: Found 5 Non-Null Conditions INFO: Found 1 Delays Condition Weights: 0 0 -1.00000000000000000000 1.00000000000000000000 0 mkcontrast2 -config mpk.fsaverage5Con.lh/NorthSouth.config -anadir mpk.fsaverage5Con.lh -wcond 0 0 -1.00000000000000000000 1.00000000000000000000 0 -sumconds -o mpk.fsaverage5Con.lh/NorthSouth.mat -prestim 0 -wdelay 1 -no-octave mkcontrast2 7.1.1 cmtxfile mpk.fsaverage5Con.lh/NorthSouth.mat nconds 5, wcond 0 0 -1.00000000000000000000 1.00000000000000000000 0 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau cmtxfile mpk.fsaverage5Con.lh/NorthSouth.mat monly 0 NCond 5 WCond 0 0 -1.00000000000000000000 1.00000000000000000000 0 NDelay 1 WDelay 1 TER 0.050000 sumconds 1 sumdelays 0 nircorr 0 TPreStim 0 RmPreStim 0 rdelta 0 0 rtau 0 0 ndelays 1 CNorm 1 setwdelay 0 setwcond 0 Matlab file is /tmp/mkcontrast2.2236.m ------- matlab output -------------------- MATLAB: Undefined variable. ERROR running mkcontrast mkcontrast2 -config mpk.fsaverage5Con.lh/NorthSouth.config -anadir mpk.fsaverage5Con.lh -wcond 0 0 -1.00000000000000000000 1.00000000000000000000 0 -sumconds -o mpk.fsaverage5Con.lh/NorthSouth.mat -prestim 0 -wdelay 1 -no-octave Thanks, Nina

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Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1
by fsbuild 30 Oct '20

30 Oct '20

External Email - Use Caution I don't think a script can see/read that shell alias.  That’s why it worked in my example for the slicedelay script to run using a python rev 2  (which was /usr/bin/python = the *first* python returned when searching PATH) while the alias pointed to a completely different python (python3 found in PATH) to run from the terminal when you type “python”. You can put a hash bang line at the top of your scripts to specify them to run with a specific python found in PATH, e.g. below, instead of “python3", “python2” or anaconda python as found in your PATH. - R. - - - ver.py - - -#!/usr/bin/env python3 import sys print(sys.version)- - - ver.py - - - $ ./ver.py3.6.8 (default, Aug  7 2019, 17:28:10)  [GCC 4.8.5 20150623 (Red Hat 4.8.5-39)] On Oct 30, 2020, at 14:42, Peled, Noam <NPELED(a)mgh.harvard.edu> wrote:Thanks,In my system, I aliased the python command to a local anaconda python3.8.So to be able to use slicedelay, should I first alias python to python2? Thanks,Noam From: fsbuild <fsbuild@contbay.com> Sent: Friday, October 30, 2020 2:37 PMTo: freesurfer@nmr.mgh.harvard.eduCc: Peled, Noam <NPELED@mgh.harvard.edu>Subject: Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1         External Email - Use Caution        Please keep in mind that the system python installed on both CentOS6 and CentOS7 (/usr/bin/python) is python 2.X, so scripts aren’t expecting to run a version 3 via the “python” interpreter found in a standard system PATH.  As far as I know only 1 python interpreter can be returned thru PATH (whichever python it finds first according to the order of the entries in PATH).  But you can alias python to be something different in your shell, e.g., here using csh, % alias python python3… or alias to whatever python rev 3 you want to run. If your PATH is set to return system 2.X version, e.g., /usr/bin/python., then any script like slicedeleay should still find /usr/bin/python thru PATH.  But typing python at the terminal will run whatever the alias points to.  The which command will show you this (CentOS7), % which python/usr/bin/python% python --versionPython 2.7..5% alias python python3% python  --versionPython 3.6.8% which pythonpython:                aliased to python3% /usr/local/freesurfer/dev/bin/slicedelay --helpUSAGE: slicedelay --help  --o slicedelayfile  --nslices nslices : total number of slices in the volume  --order order (up,down,odd,even,siemens)  --ngroups ngroups (number of slice groups for SMS)< … rest of output deleted …>% unalias python% which python/usr/bin/python - R.On Oct 29, 2020, at 21:46, Peled, Noam <NPELED(a)mgh.harvard.edu> wrote: Thanks!I’m only working with python3, so I prefer to set python to call python3 and not python2.Is there an option to set the python bin file name used by FreeSurfer (/usr/bin/python2..7 for example)? Thanks,Noam From: fsbuild <fsbuild@contbay.com> Sent: Thursday, October 29, 2020 9:33 PMTo: freesurfer@nmr.mgh.harvard.eduCc: Peled, Noam <NPELED@mgh.harvard.edu>Subject: Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1         External Email - Use Caution        Hello Noam, The python script /usr/local/freesurfer/dev/bin/slicedelay needs to be run with a version of python that is 2.X, i.e., $ file /usr/local/freesurfer/dev/bin/slicedelay/usr/local/freesurfer/dev/bin/slicedelay: Python script, ASCII text executable $ which python2/bin/python2$ python2 /usr/local/freesurfer/dev/bin/slicedelay --helpUSAGE: slicedelay --help  --o slicedelayfile  --nslices nslices : total number of slices in the volume  --order order (up,down,odd,even,siemens)  --ngroups ngroups (number of slice groups for SMS) Creates an FSL custom slice delay file for use with slicetimer (--tcustom=sdfile).It has a single column of values, one for each slice. Each value is the slice delaymeasured as a fraction of the TR and range from +0.5 (beginning of the TR) to -0.5 (end of the TR).. Used for slice-time correction of fMRI. $ which python3/space/freesurfer/python/linux/bin/python3$ python3 /usr/local/freesurfer/dev/bin/slicedelay --help  File "/usr/local/freesurfer/dev/bin/slicedelay", line 9    print "USAGE: slicedelay --help";                                   ^SyntaxError: Missing parentheses in call to 'print'. Did you mean print("USAGE: slicedelay --help")? So I think that means that for you,$ which python- is going to return a python from your PATH such that typing the command “python —version” will report it is rev 3.X and not 2.X. You can try setting the PATH environment variable such that the first python program found in PATH reports it is version 2.X. - R. On Oct 29, 2020, at 20:47, Peled, Noam <NPELED@mgh.harvard..edu> wrote: /usr/local/freesurfer/dev/bin/slicedelay_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh..harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh..harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1
by fsbuild 30 Oct '20

30 Oct '20

External Email - Use Caution Please keep in mind that the system python installed on both CentOS6 and CentOS7 (/usr/bin/python) is python 2.X, so scripts aren’t expecting to run a version 3 via the “python” interpreter found in a standard system PATH.  As far as I know only 1 python interpreter can be returned thru PATH (whichever python it finds first according to the order of the entries in PATH).  But you can alias python to be something different in your shell, e.g., here using csh, % alias python python3… or alias to whatever python rev 3 you want to run. If your PATH is set to return system 2.X version, e.g., /usr/bin/python., then any script like slicedeleay should still find /usr/bin/python thru PATH.  But typing python at the terminal will run whatever the alias points to.  The which command will show you this (CentOS7), % which python/usr/bin/python% python --versionPython 2.7.5% alias python python3% python  --versionPython 3..6.8% which pythonpython:   aliased to python3% /usr/local/freesurfer/dev/bin/slicedelay --helpUSAGE: slicedelay --help  --o slicedelayfile  --nslices nslices : total number of slices in the volume  --order order (up,down,odd,even,siemens)  --ngroups ngroups (number of slice groups for SMS)< … rest of output deleted …>% unalias python% which python/usr/bin/python - R. On Oct 29, 2020, at 21:46, Peled, Noam <NPELED(a)mgh.harvard.edu> wrote:Thanks!I’m only working with python3, so I prefer to set python to call python3 and not python2.Is there an option to set the python bin file name used by FreeSurfer (/usr/bin/python2.7 for example)? Thanks,Noam From: fsbuild <fsbuild@contbay.com> Sent: Thursday, October 29, 2020 9:33 PMTo: freesurfer@nmr.mgh.harvard.eduCc: Peled, Noam <NPELED@mgh.harvard.edu>Subject: Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1         External Email - Use Caution        Hello Noam, The python script /usr/local/freesurfer/dev/bin/slicedelay needs to be run with a version of python that is 2.X, i.e., $ file /usr/local/freesurfer/dev/bin/slicedelay/usr/local/freesurfer/dev/bin/slicedelay: Python script, ASCII text executable$ which python2/bin/python2$ python2 /usr/local/freesurfer/dev/bin/slicedelay --helpUSAGE: slicedelay --help  --o slicedelayfile  --nslices nslices : total number of slices in the volume  --order order (up,down,odd,even,siemens)  --ngroups ngroups (number of slice groups for SMS) Creates an FSL custom slice delay file for use with slicetimer (--tcustom=sdfile).It has a single column of values, one for each slice. Each value is the slice delaymeasured as a fraction of the TR and range from +0.5 (beginning of the TR) to -0.5 (end of the TR). Used for slice-time correction of fMRI. $ which python3/space/freesurfer/python/linux/bin/python3$ python3 /usr/local/freesurfer/dev/bin/slicedelay --help  File "/usr/local/freesurfer/dev/bin/slicedelay", line 9    print "USAGE: slicedelay --help";                                   ^SyntaxError: Missing parentheses in call to 'print'. Did you mean print("USAGE: slicedelay --help")?So I think that means that for you,$ which python- is going to return a python from your PATH such that typing the command “python —version” will report it is rev 3.X and not 2.X. You can try setting the PATH environment variable such that the first python program found in PATH reports it is version 2.X. - R.On Oct 29, 2020, at 20:47, Peled, Noam <NPELED(a)mgh.harvard.edu> wrote: /usr/local/freesurfer/dev/bin/slicedelay_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Accessing posted files
by Daniel Leopold 30 Oct '20

30 Oct '20

External Email - Use Caution Dear FS experts, Can you please direct me as to how I can access/download a file suggested in the listserv? I've tried ftp (e.g., https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange) scp, ssh, Googling, clicking on the hyperlink, etc. using combinations of anonymous, my listserv login/password, and my email address, and have been unable to access the needed file. The desired file is the following: https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m Any help would be greatly appreciated. Many thanks, Dan

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Re: [Freesurfer] Moving .nii atlas to surface space and create .annot file
by Douglas N. Greve 30 Oct '20

30 Oct '20

Please remember to post to the list ... Try looking at your atlas on the volume first, eg, tkmeditfv ch2_template1mm nu.mgz -surfs -seg atlas_rh.mgz atlas_rh.mgz will show up as a segmentation and you can see how well it intersects with the surface. Also, you may need a different color table On 10/30/2020 8:44 AM, Maron M. wrote: > > External Email - Use Caution > > Dear Douglas. > > Thank you for your help. > > I did follow your suggestions and performed > > recon-all -all -i ch2.nii.gz -subjid ch2_template1mm > > mri_vol2surf --src 1mm_atlas.nii --out atlas_rh.mgz --hemi rh > --projfrac 0.5 --regheader ch2_template1mm > > mris_seg2annot --seg atlas_rh.mgz --s ch2_template1mm --h rh > --ctab-auto --o rh.atlasfile.annot > > There were no errors. > > However, testing with Freeview, I loaded the > ch2_template1mm/surf/rh.pial.T1 file and overlaid with > rh.atlasfile.annot. > The result is not as anticipated and only covers frontal, parietal and > parts of the visual cortex, missing most parts of the temporal cortex. > I am not sure whether I can upload files here, but I will try to > attach a screenshot. I tried different atlases, which resulted in > different but similar (mismatching) results. > > I also tested the ch2_template1mm/label/rh.aparc.a2009s.annot file, > which looked flawless. > > Any suggestions what I should do to fix this? > > Thanks again! >

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Statistic Difference Region on the Fsaverage Turned into No Statistic Difference after Mapping onto the Subjects
by 李梦君 30 Oct '20

30 Oct '20

External Email - Use Caution Dear FreeSurfer Developers: I compared the thickness, area, volume in the mild traumatic brain injury patients with health control by FreeSurFer, and found a statistic difference region in the cortex area, I defined the statistic difference region as a label on the fsaverage and mapped this label to subjects by Qdec/mri_label2label. The label defined on the fsaverage was mapped onto all subjects successfully, and the label in subjects matched well with the inflated cortex of subjects in Freeview Then the area value of the label in every single subjects was extracted, and I found that there is no statistic difference in the area value between the mild traumatic brain injury patients and health control. I have checked the segmentation of every subjects and it was a good job done by FreeSurFer. FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: macOS High Sierra. Best wishes Mengjun Li Second Xiangya Hospital Central South University

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Freesurfer October 2020