Freesurfer June 2024

freesurfer@nmr.mgh.harvard.edu

47 participants
51 discussions

Re: [Freesurfer] Question on using thalseg_1.1.h5
by Georgios Argyropoulos 23 May '25

23 May '25

External Email - Use Caution Many thanks and apologies, Henry - I figured it out... I stupidly replaced your improved segmentation script in both the scripts and the bin directory instead of only replacing the former. many thanks for your time, much appreciated g

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run_samseg: Optimizer: maximalDeformation is too small; stopping; killed
by Ringki Marie Siewert 08 Aug '24

08 Aug '24

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LME longitudinal subcortical ROI analysis
by Dan Levitas 03 Jul '24

03 Jul '24

External Email - Use Caution Hello, I recently performed an LME longitudinal mass-univariate (surface) analysis and am now trying to do something similar, but with subcortical (aseg) ROIs instead. I first created an aseg table with the following command: * asegstats2table \ --sd $subjects_dir \ --qdec-long /path/to/long.qdec.table.dat \ --segno 4 10 11 12 17 18 26 43 49 50 51 53 54 58 251 253 255 \ --stats aseg.stats \ --tablefile $output_file* The LME tutorial ( https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) provides information and examples of both a univariate and mass-univariate approach. While univariate seems most appropriate in this case, the example details design matrix setup and testing of a single ROI (hippocampus), whereas I would like to assess several subcortical ROIs. Would I simply create a loop structure to set up design matrices for each ROI (both hemispheres) and test them individually, or can I perform a mass-univariate approach to assess all ROIs at once? Thanks, Dan

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Calculating intensity of Individual voxel
by ERNEST KISSI 02 Jul '24

02 Jul '24

External Email - Use Caution Hi, freesurfer team Is there a way to calculate the intensity of a voxel.Let say, I have a voxel with coordinate 20, 30 and 34 and I wanna know the intensity of it. Can it be done in freesurfer?

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recon-all is shutting down? because of flair?
by egemen gok 30 Jun '24

30 Jun '24

External Email - Use Caution *Hello Freesurfer Developers* recon-all is shutting down for some reason, this is the last lines of the code before shutting down. (It ran approximately 11-12 hours) and fyi = I used flair image because there was no T1 image of the patient [image: image.png] and this is the log file (recon-all.log) = [image: image.png]

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Can find "mri_WMHsynthseg" command in freesurfer 7.4.1
by Byripudi Naveen Kumar ed20d402 28 Jun '24

28 Jun '24

External Email - Use Caution Dear freesurfer experts, I was trying to use synthseg for segmenting and parcellating a heterogeneous brain with lesions. It is advised in the freesurfer synthseg webpage to use mri_WMHsynthseg command for these cases. How ever when I tried to run the command, it shows that command not found. I checked mri_synsthseg command works. What shall I do to resolve this? Is there a way to install the mri_WMHsynthseg or is it part of some existing commands? Regards, Naveen Kumar

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Inquiry about alpha inflation in multiple comparison
by Emma Harper 28 Jun '24

28 Jun '24

External Email - Use Caution Dear Freesufer teams, Does anyone have any recommendations to correct for alpha inflation when doing the multiple comparisons in freesurfer? We are trying to avoid using the Bonferroni Correction so any recommendations for ways beside that would be greatly appreciated. Thanks, Emma Harper

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FreeSurfer atlases
by Savoia, Alice (Stud. FPN) 28 Jun '24

28 Jun '24

External Email - Use Caution Hello, I am looking for a freesufer standard atlas for hippocampal subfields (to be used for a DTI pipeline in FSL) but I cannot find it in fsaversage/label. Does anyone have any suggestion? Thank for the help, Alice

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Error saying cannot find my file for recon-all
by Lydia Luck 28 Jun '24

28 Jun '24

External Email - Use Caution Hello- I am trying to do recon-all on my brain MRI and I’ve rewritten it so many times I have absolutely no clue what is going wrong. Ultimately, the main error message I’m getting is that my file is not found. I’ve tried typing out the complete path, made multiple different folders, renamed the file and the folders, changed the file type, changed the location of the folder, exited terminal and tried again, switched to the other user on the computer (got the same error) even restarted my computer, etc. Kind of at a loss at this point. I am using a Mac with an M1 chip and the 7.4.1 version This is my current line of commands: export FREESURFER_HOME=/Applications/freesurfer/7.4.1 source $FREESURFER_HOME/SetUpFreeSurfer.sh export FS_LICENSE=/opt/freesurfer/license.txt export SUBJECTS_DIR=$Users/lydialuck/3DBRAIN recon-all -s lydiasbrain -i $Users/lydialuck/3DBRAIN/struct.nii.gz -parallel -all And then getting this back: ERROR: cannot find /lydialuck/3DBRAIN/struct.nii.gz Darwin Blazes-MBP.lan 23.4.0 Darwin Kernel Version 23.4.0: Wed Feb 21 21:44:06 PST 2024; root:xnu-10063.101.15~2/RELEASE_ARM64_T8103 arm64 recon-all -s lydiasbrain exited with ERRORS at Thu Jun 27 01:13:56 EDT 2024 If you could help me figure this out that would be great; I’ve probably spent well over 6 hours now trying different things. Thanks so much, Lydia

2 1

The file absence problem of the recon-all -all output
by Quanjiang Liu 28 Jun '24

28 Jun '24

External Email - Use Caution Hi, I ran the recon-all -all command successfully. But the lh.seghead and rh.seghead didn't appear in my output folder. The attachment is the process record. Can you help to solve it? Sorry to bother. Best

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Freesurfer June 2024