Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

(no subject)
by Peng Liu 06 Apr '20

06 Apr '20

External Email - Use Caution Dear Freesurfer experts, I am trying to customize a colour map of my own, with five colours and scale from -12.5 to 12.5, since when using Heat (with default options), the scale is correct but it is shown in only four colours. However after I created the .lut file (attached below), when loading it into freeview, the colour scale is from 0 to 6. [image: image.png] Does this mean I should also include scale information in the .lut file? Any help would be much appreciated. Peng Liu

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Permutation with Non-Orthogonal Matrices
by Hua, Jessica 06 Apr '20

06 Apr '20

External Email - Use Caution Hi FreeSurfer Experts, Reposting this message. I am trying to correct for multiple comparisons by running a permutation for a non-orthogonal design. Based on reading through the blog, I came up with the following script: mri_glmfit-sim --glmdir rh.volume.AgeSex.10.glmdir --sim perm-resid 1000 3.0 --sim-sign abs --cwp 0.05 --2spaces I am getting the following error message: ERROR: Flag abs unrecognized. And when I tried to put the "abs" after "1000 3.0," I got the error message saying that I needed to specify the --sim-sign. Could you please let me know how I need to edit my script? I have already run mris_preproc and mri_glmfit. Thanks! Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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mri_glmfit-sim FWHM error
by s7675854＠stud.uni-frankfurt.de 06 Apr '20

06 Apr '20

External Email - Use Caution Dear Freesurfer experts, I'm trying to run a simulation (--> mri_glmfit-sim) with cached LGI data (fwhm10), but get an error due to the estimated fwhm kernel. The folder corresponding to the fwhm value (-->37) does not exist, I guess because it's a pretty unusual value...? DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 36.855100 ERROR: cannot find /apps/prod/x86_64/freesurfer-6.0.1/average/mult-comp-cor/fsaverage/lh/cortex/fwhm37/abs/th20/mc-z.csd I've seen mails describing similar issues in the archive and from your explanation I more or less understand that you cannot define this value as it is estimated in the process...? However, I did not see if there is a solution to this problem. What could I do about it now? I attached the logfiles and would be very grateful for your help, thanks a lot and stay healthy, Doro

2 1

Customizing colour map
by Peng Liu 06 Apr '20

06 Apr '20

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Converting .mgz (or .nii) file to .hdr file (.hdr and .img)
by Kim, Gwang-Won 04 Apr '20

04 Apr '20

Dear expert, I'd like to convert .mgz (or .nii) file to .hdr file (.hdr and .img) to use .hdr in SPM software. I tried to convert the file using "mri_convert". But, there were the error messages below. Please, let me know how to onvert .mgz (or .nii) file to .hdr file (.hdr and .img). 1) convert .nii file to .hdr file (.hdr and .img) [latifah:kim] (nmr-stable6-env) mri_convert -it nii -ot spm BB.nii RE mri_convert.bin -it nii -ot spm BB.nii RE $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from BB.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to RE... ANALYZE FORMAT ERROR: ncols 163842 in volume exceeds 32768 2) convert .mgh file to .hdr file (.hdr and .img) [latifah:kim] (nmr-stable6-env) mri_convert -it mgh -ot spm AA.mgh RE.hdr mri_convert.bin -it mgh -ot spm AA.mgh RE.hdr $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from AA.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to RE.hdr... ANALYZE FORMAT ERROR: ncols 163842 in volume exceeds 32768

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Re: [Freesurfer] Freesurfer with Catalina
by fsbuild 03 Apr '20

03 Apr '20

External Email - Use Caution Hello Stephan, I’m assuming you’re running the freesurfer 6.0.0 release and used the Mac pkg file to install it on your Mac from,freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg You would need admin/root privileges to use the “Security and Privacy” tab from the System preferences window on the Mac to give the pkg file permission to install freesurfer as /Applications/freesurfer I have just done this install on a machine running Catalina (Mac OS 10.15.2).  Then I ran the commands below.  Please try them and see if you get the same results.  The first command I typed is “bash” to start a bash shell. % bash The default interactive shell is now zsh. To update your account to use zsh, please run `chsh -s /bin/zsh`. For more details, please visit https://support.apple.com/kb/HT208050. Mac:~>  Mac:~> export FREESURFER_HOME=/Applications/freesurfer Mac:~> source /Applications/freesurfer/SetUpFreeSurfer.sh -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer FSFAST_HOME       /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/subjects MNI_DIR           /Applications/freesurfer/mni Mac:~> which mri_convert /Applications/freesurfer/bin/mri_convert Mac:~> file `which mri_convert` /Applications/freesurfer/bin/mri_convert: Bourne-Again shell script text executable, ASCII text Mac:~> which mri_convert.bin /Applications/freesurfer/bin/mri_convert.bin Mac:~> file `which mri_convert.bin` /Applications/freesurfer/bin/mri_convert.bin: Mach-O 64-bit executable x86_64 Mac:~> bash -x /Applications/freesurfer/bin/mri_convert --help + source /Applications/freesurfer/sources.sh +++ uname -s ++ '[' Darwin == Darwin ']' ++ source /Applications/freesurfer/SetUpFreeSurfer.sh +++ '[' -z /Applications/freesurfer ']' +++ '[' -z /Applications/freesurfer/subjects ']' +++ '[' -z /Applications/freesurfer/sessions ']' +++ source /Applications/freesurfer/FreeSurferEnv..sh ++++ VERSION='$Id: FreeSurferEnv.sh,v 1.61 2016/06/09 14:54:31 zkaufman Exp $' ++++ '[' 1 -gt 1 ']' +++++ uname -s ++++ os=Darwin ++++ export OS=Darwin ++++ OS=Darwin ++++ '[' -n '' ']' ++++ output=1 ++++ [[ -z synpro ]] ++++ [[ -z '' ]] ++++ output=0 ++++ '[' -z /Applications/freesurfer ']' ++++ '[' '!' -d /Applications/freesurfer ']' ++++ [[ 0 == 1 ]] ++++ '[' -z /Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/synpro/bin ']' ++++ '[' -z 0 ']' ++++ [[ -z /Applications/freesurfer/fsfast ]] ++++ [[ 0 != 0 ]] ++++ [[ -z /Applications/freesurfer/subjects ]] ++++ [[ 0 != 0 ]] ++++ [[ -z '' ]] ++++ [[ -z /Applications/freesurfer/mni/bin ]] ++++ [[ 0 != 0 ]] ++++ [[ -z '' ]] ++++ [[ -z /Applications/freesurfer/mni/lib ]] ++++ [[ 0 != 0 ]] ++++ [[ -z '' ]] ++++ [[ -z /Applications/freesurfer/mni/data ]] ++++ [[ 0 != 0 ]] ++++ [[ -z '' ]] ++++ '[' -n '' ']' ++++ '[' -e /Applications/freesurfer/fsl ']' ++++ '[' -e /usr/pubsw/packages/fsl/current ']' ++++ '[' -e /usr/local/pubsw/packages/fsl/current ']' ++++ '[' -e /usr/local/fsl ']' ++++ export FREESURFER_HOME=/Applications/freesurfer ++++ FREESURFER_HOME=/Applications/freesurfer ++++ export LOCAL_DIR=/Applications/freesurfer/local ++++ LOCAL_DIR=/Applications/freesurfer/local ++++ for d in '"$FSFAST_HOME"' '"$SUBJECTS_DIR"' ++++ '[' '!' -d /Applications/freesurfer/fsfast ']' ++++ for d in '"$FSFAST_HOME"' '"$SUBJECTS_DIR"' ++++ '[' '!' -d /Applications/freesurfer/subjects ']' ++++ [[ -z nii.gz ]] ++++ [[ 0 != 0 ]] ++++ [[ 0 == 1 ]] ++++ [[ 0 == 1 ]] ++++ [[ -z '' ]] ++++ export FMRI_ANALYSIS_DIR=/Applications/freesurfer/fsfast ++++ FMRI_ANALYSIS_DIR=/Applications/freesurfer/fsfast ++++ SUF=/Users/synpro/matlab/startup.m ++++ '[' '!' -e /Users/synpro/matlab/startup.m ']' +++++ grep FSFAST_HOME /Users/synpro/matlab/startup.m +++++ wc -l ++++ tmp1='       1' +++++ grep FMRI_ANALYSIS_DIR /Users/synpro/matlab/startup.m +++++ wc -l ++++ tmp2='       0' +++++ grep FREESURFER_HOME /Users/synpro/matlab/startup.m +++++ wc -l ++++ tmp3='       1' ++++ [[        1 == 0 ]] ++++ [[ 0 == 1 ]] ++++ '[' -z '' ']' ++++ '[' -n /Applications/freesurfer/mni/bin ']' ++++ '[' '!' -d /Applications/freesurfer/mni/bin ']' ++++ '[' -n /Applications/freesurfer/mni/lib ']' ++++ '[' '!' -d /Applications/freesurfer/mni/lib ']' ++++ '[' -z /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.12.3 ']' ++++ '[' -z /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.12.3 ']' ++++ '[' /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.12.3 '!=' /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.12.3 ']' ++++ '[' -z '' ']' ++++ '[' -n /Applications/freesurfer/mni/bin ']' ++++ PATH=/Applications/freesurfer/mni/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/synpro/bin ++++ '[' -d /Applications/freesurfer/lib/misc/bin ']' ++++ '[' -d /Applications/freesurfer/lib/misc/lib ']' ++++ [[ 0 == 1 ]] ++++ '[' -d /Applications/freesurfer/bin/freeview.app ']' ++++ '[' -d /Applications/freesurfer/lib/gcc/lib ']' ++++ '[' -z '' ']' ++++ export DYLD_LIBRARY_PATH=/Applications/freesurfer/lib/gcc/lib ++++ DYLD_LIBRARY_PATH=/Applications/freesurfer/lib/gcc/lib ++++ '[' -n '' ']' ++++ [[ 0 == 1 ]] ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ [[ 0 == 1 ]] ++++ '[' -d /Applications/freesurfer/tktools ']' ++++ PATH=/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/synpro/bin ++++ export PATH=/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/synpro/bin ++++ PATH=/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/synpro/bin ++++ export FIX_VERTEX_AREA= ++++ FIX_VERTEX_AREA= ++++ return 0 + mri_convert.bin --help mri_convert.bin --help  Help NAME mri_convert SYNOPSIS mri_convert [options] <in volume> <out volume> … rest of output deleted … On Apr 3, 2020, at 11:28, Stephan <stephan.wunderlich22(a)gmail.com> wrote:        External Email - Use Caution        Hi Freesurer team,I am trying to run mri_convert (and recon_all) with a Macbook Pro 2019 with Catalina.Running mri_convert always leads to the following error://Users/neurolab/Desktop/Stephan/Programmes/freesurfer/bin/mri_convert: line 3: //Users/neurolab/Desktop/Stephan/Programmes/freesurfer/bin/mri_convert.bin: cannot execute binary fileAll security changes haven't helped yet.Best,Stephan_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_robust_template: Internal Error: Rotation should not scale.
by Sebille, Sophie 03 Apr '20

03 Apr '20

Hi , I'm running Freesurfer's longitudinal pipeline and several of the participants generate the same error for the mri_robust_template step: cmd: mri_robust_template --mov sub-ECTRO103-V1/mri/norm.mgz sub-ECTRO103-V2/mri/norm.mgz /sub-ECTRO103-V3/mri/norm.mgz sub-ECTRO103-V4/mri/norm.mgz --lta sub-ECTRO103/mri/transforms/sub-ECTRO103-V1_to_sub-ECTRO103.lta sub-ECTRO103/mri/transforms/sub-ECTRO103-V2_to_sub-ECTRO103.lta sub-ECTRO103/mri/transforms/sub-ECTRO103-V3_to_sub-ECTRO103.lta sub-ECTRO103/mri/transforms/sub-ECTRO103-V4_to_sub-ECTRO103.lta --template sub-ECTRO103/mri/norm_template.mgz --average 1 --sat 4.685 error: Internal Error for tp 2 -> template Rotation should not scale ( 1.44353e-05 ) Debug Info: A = [ ... 0.9994648269692 0.0051381533060 -0.0325665649690 -0.0062826679505 0.9993709272221 -0.0351399801222 0.0323652536320 0.0353254803840 0.9988599205733 ] R = [ ... 0.9994563704934 0.0051381078439 -0.0325662912834 -0.0062826179162 0.9993626623658 -0.0351396895455 0.0323649840458 0.0353251881385 0.9988516601031 ] S = [ ... 1.0000084609181 0.0000000029711 -0.0000000043613 0.0000000029711 1.0000082701461 0.0000000000049 -0.0000000043613 0.0000000000049 1.0000082701081 ] Internal Error: Rotation should not scale. Looking at the data, I don't see what could be the issue. Does anyone have any thoughts on this? I have attached the recon-all.log of one participant. I can also share the data if you'd like. FreeSurfer version: freesurfer-linux-centos7_x86_64-dev-20200403-65d465d Linux tonetti.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Thanks, Sophie

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White matter hypointensities
by Rockers, Elijah D. 03 Apr '20

03 Apr '20

External Email - Use Caution Hello, When was the wm-hypointeisities label added to the Freesurfer segmentation? Is there any paper that explicitly mentions this, or should I just cite the 2002 paper? Thanks, -Eli Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas and among the top 20 hospitals nationwide. Houston Methodist is the only nationally ranked Honor Roll hospital in the state and is designated as a Magnet hospital for excellence in nursing. houstonmethodist.org | twitter.com/MethodistHosp | facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

1 0

Freesurfer with Catalina
by Stephan 03 Apr '20

03 Apr '20

External Email - Use Caution Hi Freesurer team, I am trying to run mri_convert (and recon_all) with a Macbook Pro 2019 with Catalina. Running mri_convert always leads to the following error: //Users/neurolab/Desktop/Stephan/Programmes/freesurfer/bin/mri_convert: line 3: //Users/neurolab/Desktop/Stephan/Programmes/freesurfer/bin/mri_convert.bin: cannot execute binary file All security changes haven't helped yet. Best, Stephan

1 0

Petsurfer: Gtmstats < 1, voxel wise mean is fine
by Eckbo, Ryan 03 Apr '20

03 Apr '20

Hello experts, I've recently run into a case the gtmstats uptake (reference region: cerebellum) for the pericarlcarine ROI's are as low as 0.40, however computing the voxel wise mean using input.rescaled.nii.gz and mgx.ctxgm.nii.gx and aux/seg.nii.gz, the values are closer to 1, as expected: | vol | psf | roi | gtmstats_uptake | mean_uptake | | --------------------- | --- | -------------------- | --------------- | ----------- | | input.rescaled.nii.gz | 0 | ctx-rh-pericalcarine | 0.807 | 1.226… | | input.rescaled.nii.gz | 0 | ctx-lh-pericalcarine | 0.758 | 1.083… | | input.rescaled.nii.gz | 6 | ctx-rh-pericalcarine | 0.409 | 1.197… | | input.rescaled.nii.gz | 6 | ctx-lh-pericalcarine | 0.470 | 1.058… | | mgx.ctxgm.nii.gz | 0 | ctx-rh-pericalcarine | 0.807 | 1.007… | | mgx.ctxgm.nii.gz | 0 | ctx-lh-pericalcarine | 0.758 | 0.888… | | mgx.ctxgm.nii.gz | 6 | ctx-rh-pericalcarine | 0.409 | 0.915… | | mgx.ctxgm.nii.gz | 6 | ctx-lh-pericalcarine | 0.470 | 0.809… | This is using Freesurfer 6.0, and the PET to anatomical registration looks fine. Any ideas why we get such bad values from the GTM method? Thanks for any help, Ryan

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Freesurfer