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30130 discussions

Valid options.txt file for mris_pmake (and maybe .dsh.yml too)
by Garikoitz Lerma-Usabiaga 16 May '24

16 May '24

External Email - Use Caution Hi list! I was reading the documentation on mris_pmake (by the way, it is outdated, the documentation still asks for --surface00, at least in 7.3.2), and I would like to have a valid options.txt file to make it work with dsh (a valid example .dsh*.yml would be greatly appreciated too. I want to speed up a simple vertex to vertex calculation, as Bruce said in an old thread, I am able to run it line by line but there is a lot of overhead reading the surfaces, so it would be great to just do the calculations. Thanks!! Gari

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Issue related to converting .nii.gz file to .mgz using FreeSurfer's mri_convert
by Tsigaras, Thanos 15 May '24

15 May '24

External Email - Use Caution Hello FreeSurfer Developers, I am using FastSurfer for this processing, but the issue is related to FreeSurfer's mri_convert function. I wanted to perform some manual segmentation edits on the "aparc.DKTatlas+aseg.deep.mgz" output file of FastSurfer. Since ITK-SNAP can't open .mgz files, I used the mri_convert function to convert the .mgz file to .nii.gz. I performed the edits and tried to rerun FastSurfer using the manually edited .nii.gz file. I got the error: "ERROR: Specified segmentation output and conformed image output do not have same file type. You passed --asegdkt_segfile directory/to/aparc.DKTatlas+aseg.deep.nii.gz and --conformed_name directory/to/orig.mgz. Make sure these have the same file-format and adjust the names passed to the flags accordingly!" So I used mri_convert once again to convert the .nii.gz file back to .mgz. When tried to rerun FastSurfer, I got the error: "You passed --surf_only or --no_asegdkt, but the whole-brain segmentation (directory/to/aparc.DKTatlas+aseg.deep.edited.mgz) could not be found." I also tried opening the .mgz edited file using MRIcron, but I get an error there as well: "Error: first value in a MGH header should be 1 (got 1) and data type should be in the range 1..4. (got 10)", which is not the case when I open the original .mgz file. The way I am using the mri_convert function is simply "mri_convert aparc.DKTatlas+aseg.deep.edited.nii.gz aparc.DKTatlas+aseg.deep.edited.mgz". I've searched the list and no similar errors have been reported. Please let me know if you need more details to help me troubleshoot this issue. For your time and help I would like to thank you in advance! Best regards Thanos Tsigaras ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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error using mri_em_register
by Michal Zamberg-Elad 15 May '24

15 May '24

External Email - Use Caution It does not create the nu.mgz file. Error logs are attached. The result is that when running recon all it cannot find the LH and RH files and then collapses. Darwin Kernel Version 21.3.0 iMac-Pro 21.3.0 Root: xnu-8019.80.24~20/RELEASE_X86_64 x86_64 Thank you, Michal

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Hippocampus subfield LUT
by karl landheer 14 May '24

14 May '24

External Email - Use Caution Hello, I am looking for the LUT which converts the indices in images like lh.hippoAmygLabels-T.v22.mgz to region name. Is this available anywhere? I can’t find it

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Retinotopy error computing contrast matrices
by Mesquita, Tiago 14 May '24

14 May '24

External Email - Use Caution Hello FreeSurfer Developers, I am trying to do a retinotopy analysis. My retinotopy has 8 bars, this bars swipe the visual field from the 8 possible directions (all multiple of 45 degrees angle). One complete swipe takes 24 sec. I have 16 different positions per swipe. So I have tried using -retinotopy 24 (period of a complete swipe) or 1.5 (period of each individual bar) in every case i always end up having the same error. For some reason Xcond = NaN (normalized). I tried eccen pos, eccen neg even polar neg and pos in my paradigm files and get always the same result. Can someone help me? this is what i get: Creating Design Matrix ... creation time = 0.006 sec DoMCFit = 1 ntptot = 119, nX = 35, DOF = 84 Saving X matrix to ~/Project/Sess02/bold/rtopy.self.lh/pr001/Xtmp.mat XCond = NaN (normalized) Warning: Matrix is singular to working precision. > In fast_selxavg3b (line 403) Computing contrast matrices Warning: Matrix is singular to working precision. > In fast_selxavg3b (line 441) Warning: Matrix is singular to working precision. > In fast_selxavg3b (line 441) OLS Beta Pass run 1 t= 0.0 reading data ... 0.820008 Global Mean 146.10 Global In-Mask Mean = 146.104 (NaN) Rescale Target = 100 RescaleFactor = 0.684444 OLS Residual Pass run 1 t= 0.0 reading data ... 0.776954 Saving rho1 Found 0 voxels with corrected AR1 > 0.90 Not Whitening Warning: Matrix is singular to working precision. > In fast_glmfit (line 54) In fast_selxavg3b (line 999) Found 7921 zero-valued voxels Computing contrasts Starting contrasts eccen J=2 ------------- Warning: Matrix is singular to working precision. > In fast_fratiow (line 86) In fast_selxavg3b (line 1161) Warning: Matrix is singular, close to singular or badly scaled. Results may be inaccurate. RCOND = NaN. > In fast_fratiow (line 86) In fast_selxavg3b (line 1161) Error using betainc X must be in the interval [0,1]. Error in FTest (line 51) p = betainc(z, dof2/2, dof1/2); Error in fast_selxavg3b (line 1163) pmat = FTest(dof1, dof2, Fmat); If i look into the X.mat m betainc is filled witn NaN. I have atteched my analysis info and X.mat. Let me know if you need more informations about my analysis. Best, Tiago Mesquita

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Harmonization (Site/Scanner) for FreeSurfer Area Data
by Tejaswi D. Sudhakar 13 May '24

13 May '24

External Email - Use Caution Hi FreeSurfer experts, I have harmonized across site and scanners on both thickness and area for a large cohort (500+ subjects). We are seeing high covariance values when comparing the harmonized and non-harmonized area datasets and trying to understand what this means. Can this be due to how area is calculated (the mean area of the adjacent triangles at a vertex)? Are all of the triangles the same size? Can you explain the calculation of area further in the context of how thickness and area are related? Secondly, we haven’t seen much literature on harmonizing freesurfer area, though harmonization is well reported for thickness measures. Are you familiar with harmonization of area data? Best, Tejaswi

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Subcortical surfaces from volume features.
by Sam Maddox (CMP - Postgraduate Researcher) 10 May '24

10 May '24

External Email - Use Caution Dear Freesurfer Experts, I am looking into generating subcortical surfaces from the subcortical volumes generated from recon-all. The reason for this is I am trying to create a vertex based Morphological Similarity Network generated from both cortical and subcortical regions. Ideally I would avoid Volume Based Statistics as, from what I can see, I am limited to just thickness features. I have run recon-all for all of my participants, and ideally my set up for surface subcortical features would be done in freesurfer as well, although I am aware of other tools such as: https://secure-web.cisco.com/1Naw6TVmVSgW4iHi_BvEcAItpkOmdAs3fMgTWn1abKwPfB… https://secure-web.cisco.com/1u1Ru_EifdWYQsjg7F-GHFGBp-Vkvjk_3iHSqwgV0CTWKw… https://secure-web.cisco.com/1yhlZBs4CaRuE7OrwrGVtEsQL33d47WfL9Yu02tKHEzKqG… https://secure-web.cisco.com/1SH8G6D-66tFkOVdkMhKlZU3DoZJWFrankZvFbDjhud520… inaivu/aseg2srf at master * aestrivex/inaivu * GitHub<https://secure-web.cisco.com/1Dfh65Cci0nD0VovbWbYJTBewgjEMy6UwWY0YW-6fsinPT…> The above tools may be able to generate subcortical surfaces, but I would then need to convert them back to freesurfer formats to run mris_anatomical_stats, which I am lost with. If anyone has any advice for this, this would be great! Within freesurfer, I am aware of tools such as mri_vol2surf, as well as other such as mris_sample_parc - Free Surfer Wiki (harvard.edu)<https://secure-web.cisco.com/1zui1UwPJX5g6ACi-dDQWDrdF2r3cGq_2t5-DhB34ZuQ87…>. I am a bit lost as to how to use these tools, as the documentation is limited, and threads are more looking at generating these surfaces for visualizations rather than anatomical statistics. I am also wondering if there are any additional processing steps, perhaps normalization, that may be required before creating the MSN. If anyone has tried this before or has any advice, I would love to hear. I am relatively new to this area, using freesurfer past recon-all, so any help is appreciated! Many thanks, Sam

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Contrast files - 2 groups, 4 covariates
by Liliana Wu 10 May '24

10 May '24

External Email - Use Caution Hello! I am having trouble with creating my contrast files. I did go over FsfdExamples (https://secure-web.cisco.com/1ezcK_pFVwJfmWpdVsJeZORU_8kaDi3SfZnw3BO98zpMkJ…) However, I am unsure how should I create my contrast files if I want do a 2 group comparison while controlling 4 covariates: Class: Patients, healthy control variables are: Age,gender,episodes,residuals, Here is how I set up my contrast files: 1 -1 0 0 0 0 0 0 0 0 - Contrast1 (measure group differences) 1 -1 0.125 0.125 0.125 0.125 0.125 0.125 0.125 0.125 – Contrast 2 (measure group differences while accounting for covariates) For some reason I think I am setting up those contrast files wrong… Any help is appreciated. Best, Liliana

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mri_segment_hypothalamic_subunits 7.4.1 issue
by Antonio Di Renzo 10 May '24

10 May '24

External Email - Use Caution Dear FreeSurfer developers, I have just tested the Segmentation of hypothalamic subunits, but unfortunately it does not work. I simply wrote: mri_segment_hypothalamic_subunits --s subject_folder or mri_segment_hypothalamic_subunits --s subject_folder/T1.nii or mri_segment_hypothalamic_subunits --s recon_all_processed_folder Every time the message is: Illegal instruction (core dumped). Moreover when I asked the help option: mri_segment_hypothalamic_subunits -h I obtained again: Illegal instruction (core dumped). I installed tensorflow as answered using: fspython -m pip install tensorflow but these libraries are installed already because the messages are: Requirement already satisfied written on every row. How can I use this function? Thank you in advance, Antonio ps. I used the following softwares Freesurfer version 7.4.1 Ubuntu 22.04.4 LTS Oracle virtual box for Windows 10 pro

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Re: [Freesurfer] MCR install for parcellation
by fsbuild 09 May '24

09 May '24

External Email - Use Caution  Hello Antonio, With the 7.4.1 release, you can install R2014b or R2019b matlab runtime environment into the freesurfer tree.  Earlier freesurfer releases use R2014b.  I would setup the freesurfer environment first, and then pass in the value of FREESURFER_HOME on the command line as listed below.  Below, I have shown using R2019b with a linux install of Freesurfer 7.4.1 using bash shell. - R. - - - - -  $ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1                  <--- linux install path $ source $FREESURFER_HOME/SetUpFreeSurfer.sh <... output deleted ... showing SUBJECTS_DIR and other environment variables> $ cd  $FREESURFER_HOME/bin $ sudo FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2019b I believe this sets things up (for R2019b) so the libmwm* libraries are installed under $FREESURFER_HOME/MCRv97/bin/glnxa64.  You can try adding that path (or any path the fs_install_mcr script output recommends) to the start of LD_LIBRARY_PATH.  You should remove any other entries to a different MATLAB distribution other than the one you actually install. On May 9, 2024, at 12:45, Antonio Di Renzo <antoniomp777(a)hotmail.it> wrote:        External Email - Use Caution        Messers FreeSurfer developers,I dowloaded MCR zip file for linux in /home/vboxuser/Downloads from MatLab website.I extracted files in new foldern named Matlab_Component_Runtime_R2014b in Downloads.I am trying to install Matlab Component Runtime, but the the following command: fs_install_mcr R2014b does not work.Where can I find the right step by step MCR installation guide?Thank you,Antonio_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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