Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30085 discussions

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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Re: [Freesurfer] Issue with tkregister command
by Douglas N. Greve 02 Nov '20

02 Nov '20

Please remember to post to the list ... Can you run it with --debug as the first option, then post all of the terminal output? On 10/28/2020 11:21 PM, Elisabetta Ambron wrote: > > External Email - Use Caution > > Dear Prof Greve > I am having an issue running reg-feat2anat and I get the following error > > Initializing exf2anat with header > tkregister2_cmdl_cmdl --targ > /Applications/freesurfer/7.1.1/subjects/sub1/mri/brainmask.mgz --mov > BLOCK1_LEFT.feat/example_func.nii.gz --reg > BLOCK1_LEFT.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout > BLOCK1_LEFT.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader --noedit > tkregister2_cmdl_cmdl: Command not found. > > I saw your answer in > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65643.html > <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65643.html> > I was not able to download the link because it requires an user and > password. > Could you help me with this issue > Thank you > Best > Elisabetta Ambron

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Re: [Freesurfer] Error during skullstripping: numerical result out of range
by Hye Min Shin 02 Nov '20

02 Nov '20

External Email - Use Caution Hello experts, So I did not see brainmask.mgz in mri folder and it looked like reconall stopped at mri_em_register stage because I couldn't find talairach_with_skull.lt in transforms folder. So I tried running mri_em_register again and got the following error: mri_em_register -skull mri/nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca'... average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'mri/nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=10.0 skull bounding box = (46, 56, 29) --> (216, 255, 255) using (103, 122, 142) as brain centroid... mean wm in atlas = 108, using box (82,97,114) --> (123, 146,169) to find MRI wm before smoothing, mri peak at 73 robust fit to distribution - 72 +- 7.4 distribution too broad for accurate scaling - disabling WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=100, mri_peak=108 after smoothing, mri peak at 0, scaling input intensities by inf GCAhistoScaleImageIntensities: could not find wm peak Numerical result out of range

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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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Corticalwhitemattervol versus Cerebralwhitemattervol
by Stephanie K 30 Oct '20

30 Oct '20

External Email - Use Caution *Hi all,* *I'm performing an analysis and I want to look at total white matter volume across various cohorts as an outcome. In most of my cohorts, I find the variable CerebralWhiteMatterVol but in one cohort I cannot find this variable, but I am able to find a variable called CorticalWhiteMatterVol. I am planning to perform a meta-analysis analysis across cohorts. Are these two ("CerebralWhiteMatterVol " and "CorticalWhiteMatterVol" measuring the same thing? I have been advised that the change in labels is due to that cohort using Freesurfer v5.30, that it is measuring the same thing but it may or may not be using a different algorithm. Can I meta-analyse corticalwhitemattervol from one cohort with cerebralwhitemattervol from another cohort?Furthermore, in regression analyses, is it the norm to adjust these for estimated intracranial volume?Sorry, if this is a simple question but neuroanatomy is not my field. I would really appreciate your advice.* Many thanks, Roxanna

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