Freesurfer December 2024

freesurfer@nmr.mgh.harvard.edu

45 participants
62 discussions

Recon all across different image dimensions of different clinical subjects!
by JM 10 Dec '24

10 Dec '24

External Email - Use Caution Hi FreeSurfer experts, In our hospital research settings, we collected structural MRI data from patients while they were admitted for treatment. Some of the patients were scanned before contrast agent was injected and some were scanned after contrast agent was injected. There was no consistent protocol used. Some patients had 3D T1 data collected (with dimensions 512 x 512 x 248 with voxel size 0.47 x 0.47 x 0.7), some had Ax-T1 data (with dimensions 512 x 512 x 32 with voxel size 0.4 x 0.4 x 5) and some had only Sag-T1 data collected (with dimensions 256 x 256 x 25 with voxel size 0.85 x 0.85 x 6). Interestingly, recon-all works fine without any error across all three sets (i.e., 3D T1, Ax-T1 and Sag-T1). I would greatly appreciate your thoughts/suggestions/answers with the following: 1. Does it matter whether images are analyzed (i.e., recon-all 'd) on pre-contrast images or post-contrast images (in terms of output morphometry values [e.g., thickness, volume])? In other words, would it be OK if estimated pre-contrast morphometry values and estimated post-contrast morphometry values can further be analyzed in group level analysis OR subjects with pre-contrast can't be in the same group as subjects with post-contrast for further analysis (e.g., morphometry vs behavior values)? 2. Similarly, would it be OK if estimated 3D-T1 morphometry values and estimated Ax-T1 and Sag-T1 morphometry values can further be analyzed in group level analysis? Otherway, I was thinking was to resample the images to isotropic voxel size, then run recon all, and then combine subjects with 3D-T1, Ax-T1 and Sag-T1. OR subjects with 3D-T1 can't be in the same group as subjects with Ax-T1 and Sag-T1 for further analysis (e.g., morphometry vs behavior values)? In addition, any other suggestions on how I can utilize Ax-T1 and Sag-T1 data for morphometry analysis would be very helpful. I would greatly appreciate your response at your earliest convenience. Thanks!

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Error in longitudinal hippocampal fields processing
by Mark Wagshul 09 Dec '24

09 Dec '24

External Email - Use Caution Hi, I'm running into an error running segmentHA_T1_long, it processes the left side just fine, but gives the following error and fails to produce the requisite output files for the right: "Unable to perform assignment because the left and right sides have a different number of elements." I've attached the log file, in case that helps in diagnosing the issue. Thanks! Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einsteinmed.edu<mailto:mark.wagshul@einsteinmed.edu> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

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Re: [Freesurfer] TRACULA error /bin/tcsh: bad interpreter: No such file or directory
by fsbuild 09 Dec '24

09 Dec '24

External Email - Use Caution Tcsh and other programs/files freesurfer uses are not installed by default on Ubuntu linux.  So to install fresurfer and also have the system install what freesurfer needs to run, you should use one of the freesurfer  .deb package installers available from,https://secure-web.cisco.com/1rgwwg0ZifTyCWJ3xhoWAUKZbDTEFuO5WZbY_1_dw…; To install the 7.4.1 release on Ubuntu 22, you would download,https://secure-web.cisco.com/1EZiIcgCiIUVcrk2eIaKVHB6rJya2cl1VbO03… On your machine you would change directories to where you downloaded that file and run the installer with the command,$ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb That will install tcsh, other system files and install freesurfer under /usr/local/freesurfer/7.4.1.  Then you would set FREESURFER_HOME to /usr/local/freesurfer/7.4.1 and (re)set SUBJECTS_DIR to a path you can write to, e.g.,$ bash$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1$ source $FREESURFER_HOME/SetUpFreeSurfer.sh… output deleted ...$ export SUBJECTS_DIR=$HOME/subjects$ mkdir -p $HOME/subjects - R. On Dec 9, 2024, at 11:39, Barletta, Valeria <VBARLETTA(a)mgh.harvard.edu> wrote:Hello Freesurfers, I am trying to launch trac-all -prep on Ubuntu 22 but I am getting this error: -bash: /home/local/PARTNERS/vb922/freesurfer/bin/trac-all: /bin/tcsh: bad interpreter: No such file or directory Can you please help me figure out what is going on? Thank you,Valeria_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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TRACULA error /bin/tcsh: bad interpreter: No such file or directory
by Barletta, Valeria 09 Dec '24

09 Dec '24

Hello Freesurfers, I am trying to launch trac-all -prep on Ubuntu 22 but I am getting this error: -bash: /home/local/PARTNERS/vb922/freesurfer/bin/trac-all: /bin/tcsh: bad interpreter: No such file or directory Can you please help me figure out what is going on? Thank you, Valeria

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LME matrix design
by Bondi, Daniel 06 Dec '24

06 Dec '24

External Email - Use Caution Hello FreeSurfer experts, I am currently working through the linear mixed effects pipeline to assess longitudinal cortical thickness changes in non-contact/contact athletes and have some questions. My design matrix is as follows: X = [ones(size(M,1), 1), M(:,1), M(:,2), M(:,3), M(:,1).*M(:,3), M(:,4), M(:,1).*M(:,4), M(:,5), M(:,6), M(:,7), M(:,8), M(:,9)]; M(:,1) = group M(:,2) = scan time from baseline M(:,3) = age With the rest of the columns in X being other covariates from M or *time interaction, and the random intercept term being the only random effect. 1. I'm using the spatiotemporal approach, but would vertex-wise yield more powerful results? I know that a previous thread had a similar question, but I am wondering if one would be more favourable for looking at regional CT changes. 2. As well, the two groups have different distributions in timepoints and size. The contact athlete group is about double the size (42 vs 21) and has significantly more athletes with multi-year participation (2- or 3-years), whereas the non-contact athlete group is almost entirely single-year participation (one set of pre- and post-season scans). Is this something that the LME can inherently account for? 3. My main goal is to test if there is a significant difference in the slopes of the two groups (using lme_mass_F). I currently have this setup for my contrast matrix: CM.C = [0 1 zeros(1,10)]. Since I only have two groups, is it logical to use a single row? Additionally, I am a bit unsure of how to assign beta weights. 4. After running the F-test, I am correcting the multiple comparisons using FDR2. Are there any other corrections/tests I should utilize before plotting data in tksurfer? Thank you in advance, Daniel

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Re: [Freesurfer] TRACULA exited with ERROR /home/vbarletta/ants-2.5.4/bin/antsRegistrationSyNQuick.sh: Permission denied.
by fsbuild 04 Dec '24

04 Dec '24

External Email - Use Caution Not sure how you setup/installed ants in your home directory, but it could be the install permissions are wrong on antsRegistrationSyNQuick.sh.  You could try making that script executable with, $ chmod 755 /home/vbarletta/ants-2.5.4/bin/antsRegistrationSyNQuick.sh - R. On Dec 4, 2024, at 16:48, Barletta, Valeria <VBARLETTA(a)mgh.harvard.edu> wrote:Dear Freesurfers,Do you know how to fix this error in trac-all? (I'm using Ubuntu 18.04) #@# Inter-subject registration Wed Dec  4 22:37:52 CET 2024/home/vbarletta/ants-2.5.4/bin/antsRegistrationSyNQuick.sh -d 3 -m trac/R01121_SCAN/dmri/dtifit_FA.nii.gz -f /home/vbarletta/tester/freesurfer/trctrain/hcp/MGH35_HCP_FA_template.nii.gz -o trac/R01121_SCAN/dmri/xfms/diff2syn/home/vbarletta/ants-2.5.4/bin/antsRegistrationSyNQuick.sh: Permission denied. trac-preproc exited with ERRORS at Wed Dec  4 22:37:52 CET 2024 Alternatively, is there a way to run Tracula without using ants? Thank you for your help,Valeria _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail..nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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TRACULA exited with ERROR /home/vbarletta/ants-2.5.4/bin/antsRegistrationSyNQuick.sh: Permission denied.
by Barletta, Valeria 04 Dec '24

04 Dec '24

Dear Freesurfers, Do you know how to fix this error in trac-all? (I'm using Ubuntu 18.04) #@# Inter-subject registration Wed Dec 4 22:37:52 CET 2024 /home/vbarletta/ants-2.5.4/bin/antsRegistrationSyNQuick.sh -d 3 -m trac/R01121_SCAN/dmri/dtifit_FA.nii.gz -f /home/vbarletta/tester/freesurfer/trctrain/hcp/MGH35_HCP_FA_template.nii.gz -o trac/R01121_SCAN/dmri/xfms/diff2syn /home/vbarletta/ants-2.5.4/bin/antsRegistrationSyNQuick.sh: Permission denied. trac-preproc exited with ERRORS at Wed Dec 4 22:37:52 CET 2024 Alternatively, is there a way to run Tracula without using ants? Thank you for your help, Valeria

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use and registration of FLAIR in recon-all and segmentHA
by Simone Cauzzo 04 Dec '24

04 Dec '24

External Email - Use Caution Hi all I am running Freesurfer 7.4 I use recon-all with the -FLAIRpial option. 1) I wonder whether the FLAIR to T1 registration is handled by recon-all or whether I need to supply a FLAIR image already registered to T1. 2) in case recon-all handles the registration, is there a way I can check the registration quality? which file should I use in freeview? 3) in case I already have a reliable FLAIR to T1 registration, is there a way to make recon-all skip the FLAIR to T1 registration? In addition, I would like to use segmentHA_T2.sh 4) in case recon-all handles the registration, which file can I give to segmentHA_T2 as additional scan? I guess I should select the FLAIR already registered to T1.. 5) Is there a reason why I should prefer a T2 image to a FLAIR for segmentHA_T2? Thank you Simone Cauzzo, PhD University of Padova

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Re: [Freesurfer] mri_coreg threads parallel processing clarification
by fsbuild 04 Dec '24

04 Dec '24

External Email - Use Caution You could try setting the environment variable OMP_NUM_THREADS, e.g., in zsh/bash shell,  on a machine with 4 performance cores, $ export OMP_NUM_THREADS=4 The test command I ran did not take long to run, but it looks like it used 3 of the 4 performance cores on an M1 Mac with OMP_NUM_THREADS=4.  See attached screenshot, mri_coreg_omp_num_threads.png - R. On Dec 3, 2024, at 17:06, Hemond, Christopher <Christopher.Hemond(a)umassmemorial.org> wrote:        External Email - Use Caution        Dear Doug and team,Thanks very much for your support.  I’ve tried multiple different thread numbers between 1 and 10 with no effect.  I can successfully use multithreading to accelerate other applications like mri_synthseg.I tried adding combinations of both ‘fs_time’ as well as ‘--debug’  to the command, but I do not see any difference in final output, nor any CPU load/usage readout at the end of the command….  Just the usual “mri_coreg RunTimeSec <X> sec”.  Could this be related to the ARM processor in Mac?  It seems to cause many other issues, especially with some SPM commands including processing specification.Many thanks,Chris  From: Hemond, Christopher <Christopher.Hemond(a)umassmemorial.org> Date: Monday, November 25, 2024 at 4:32 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: mri_coreg threads parallel processing clarificationDear experts,Thanks in advance for any help you can provide.  I’m using “mri_coreg” and trying to accelerate it with the “--threads” (and/or “--nthreads”) flags. However in the subsequent command feedback it looks like it is still using just one thread (see output below, “nthreads 1”; and also it is no faster).  Am I doing something obviously wrong?  There are no errors and it executes successfully…   Not sure if relevant but I’m using this for nifty (.nii.gz) files, my command is:“mri_coreg --ref <path/to/ref.nii.gz> --mov <path/to/mov.nii.gz> --reg <path/to/registration.lta> --threads 10” I’m on MacOS running a recent dev download (freesurfer-macOS-darwin_arm64-dev-20241011), but I’ve tried it on 7..4.1 with no success either.  …INFO: using NIfTI-1 sform (sform_code=1)Setting cras translation parameters to align volume centersInit matrix params -0.4553 -6.3123 39.4428  0.0000  0.0000  0.0000  1.0000  1.0000  1.0000  0.0000  0.0000  0.0000 Initial Matrix (RAS2RAS) 1.00000   0.00000   0.00000   0.45535; 0.00000   1.00000   0.00000   6..31235; 0.00000   0.00000   1.00000  -39.44280; 0.00000   0.00000   0.00000   1.00000;Initial parameters to be opt -0.4553 -6.3123 39.4428  0.0000  0.0000  0.0000 Creating random numbers for coordinate ditheringPerforming intensity ditheringPerforming intensity dithering on mov with computed ditherSeparation list (2):  4  2   min = 2DoSmoothing 1DoCoordDither 1DoIntensityDither 1nitersmax 4ftol 1.000e-07linmintol 1.000e-03SatPct 99.990000Hist FWHM 7.000000 7.000000nthreads 1movsat = 3917.0000mov gstd 0.9539 0.9539 0..7422Smoothing mov… The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, transmission, re-transmission, dissemination or other use of, or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_coreg threads parallel processing clarification
by Hemond, Christopher 03 Dec '24

03 Dec '24

External Email - Use Caution Dear experts, Thanks in advance for any help you can provide. I’m using “mri_coreg” and trying to accelerate it with the “--threads” (and/or “--nthreads”) flags. However in the subsequent command feedback it looks like it is still using just one thread (see output below, “nthreads 1”; and also it is no faster). Am I doing something obviously wrong? There are no errors and it executes successfully… Not sure if relevant but I’m using this for nifty (.nii.gz) files, my command is: “mri_coreg --ref <path/to/ref.nii.gz> --mov <path/to/mov.nii.gz> --reg <path/to/registration.lta> --threads 10” I’m on MacOS running a recent dev download (freesurfer-macOS-darwin_arm64-dev-20241011), but I’ve tried it on 7.4.1 with no success either. … INFO: using NIfTI-1 sform (sform_code=1) Setting cras translation parameters to align volume centers Init matrix params -0.4553 -6.3123 39.4428 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Initial Matrix (RAS2RAS) 1.00000 0.00000 0.00000 0.45535; 0.00000 1.00000 0.00000 6.31235; 0.00000 0.00000 1.00000 -39.44280; 0.00000 0.00000 0.00000 1.00000; Initial parameters to be opt -0.4553 -6.3123 39.4428 0.0000 0.0000 0.0000 Creating random numbers for coordinate dithering Performing intensity dithering Performing intensity dithering on mov with computed dither Separation list (2): 4 2 min = 2 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-07 linmintol 1.000e-03 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 3917.0000 mov gstd 0.9539 0.9539 0.7422 Smoothing mov … The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, transmission, re-transmission, dissemination or other use of, or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer.

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