Freesurfer May 2024

freesurfer@nmr.mgh.harvard.edu

56 participants
69 discussions

Request to Edit Page (if possible)
by Emily Popa 19 May '24

19 May '24

External Email - Use Caution Hello, I hope all is great. I ran into many issues using the -make flag with V 7.1 (based on instructions found in https://secure-web.cisco.com/1-msyefLYicmgJRp4aaxIyvNgBvyxq1mdLLjw-c5oMGhWw…) and discovered after investigating erratic behavior/crashes across a bunch of re-processed cases that I had made edits to, that the functionality is no longer supported. I think it might be really helpful to others if at all possible to indicate this on the wiki where it is mentioned as it took some time to find the relevant post in the archives. Thanks! Best, Emily S. Popa, M.S. Programmer Analyst I, Neuroimaging Pacific Brain Health Center | Pacific Neuroscience Institute Foundation | Providence Saint John’s Health Center 1301 20th St. #250 Santa Monica, CA. 90404 (408) 750-7971 (M) [cid3519*image001.jpg(a)01D7EC78.96AA1AC0]<https://secure-web.cisco.com/1sywoT0V8YjrBxyLolh3M6xFLNeV0zhNs_KZrVKcDpGYsj…> [cid3519*image002.jpg(a)01D7EC78.96AA1AC0] <https://secure-web.cisco.com/18aF2I8PTK20vtBR9E_9H31BpGDjhBCja4yiOh-QxkCRHq…> [cid3519*image003.jpg(a)01D7EC78.96AA1AC0] <https://secure-web.cisco.com/1nP2xsoAmMqTxDrqwvMdo5_oVf0Rl3v064B9gfXlPnVOdK…> [cid3519*image004.jpg(a)01D7EC78.96AA1AC0] <https://secure-web.cisco.com/13KwzPRLUTKRpKorxcfsWml1ZEQvZ0tCa1ePVRRywCMbm5…> [cid3519*image005.jpg(a)01D7EC78.96AA1AC0] <https://secure-web.cisco.com/1Ce1VlXCnx6O336wKEGQ3TzL8YB9U8VqME55UBddu-2hgp…>

1 0

Freesurfer on a high-performance cluster (HPC) - MATLAB runtime
by Camilo Castelblanco Riveros 18 May '24

18 May '24

External Email - Use Caution Hi all, I hope your weekend is going great! *Context*: I am trying to run the amygdala/hippocampus segmentation in an hpc. *Issue*: The cluster that I use doesn't have the libmwlaunchermain.so file from MATLAB's 2019b runtime under (/optnfs/freesurfer/7.4.1/MCRv97/bin/glnxa64). Because I don't have permission privileges and standard bin/paths don't apply in the hpc, I can't do something like fs_install_mcr. *Question*: Does someone have the libmwlaunchermain.so file, or is there a way to run the amygdala/hippocampus module without it? Any experience with the hpc is helpful! With gratitude, Camilo ------------------------------------------------------------------------ *Camilo Castelblanco Riveros (He/His)* Integrative Neuroscience at Dartmouth (IND) Ph.D. Student Robertson Lab <https://secure-web.cisco.com/1J85yiocytHpTivZxcZMk7Vqi6lHw5Fk9k8jeONEsfXv5L…> & Bujarski Lab <https://secure-web.cisco.com/1yuSzZ9v0bN8y511sYU8prP1iK-NYHoAYmK7xdIhAPLC2a…> Diversity Student Advisory Board Member e: ccastelblanco.gr(a)dartmouth.edu <camilo.a.castelblanco.riveros.gr(a)dartmouth.edu> [image: Integrative Neuroscience at Dartmouth (IND) (@DartmouthNeuro) / Twitter]

1 0

Post a Postdoctoral Scholars in Neuroimaging at the University of Miami Miller School of Medicine
by Otero Ospina, Andrea 17 May '24

17 May '24

External Email - Use Caution Hello Could you please post a job announcement for a Postdoctoral Scholar Position in Neuroimaging, at the University of Miami Miller School of Medicine, to your mailing list. I'm already inscribed in your mailing list. I'm attaching our post job! Best, Andrea Otero

1 0

mri_watershed Error: read failed
by Schroder, Kirsten 16 May '24

16 May '24

External Email - Use Caution Dear Freesurfer developers, I am currently conducting a research project in which I am running 7T MP2RAGE images in Freesurfer version 6.0.1 but have a run into an issue. For 3 images I receive a watershed error stating “mri_watershed error: GLOBAL region of the brain empty!” which I tried to fix using the -skullstrip -no-wsgcaatlas flag but get different results: 1 image was successful but for 2 images I get mri_watershed Error: read failed (see attachment). It appears that the last file created is the 001.mgz file hence there is no T1.mgz file created and Freesurfer therefore gives this error. I wanted to know if there is way to fix this as I have not been able to find a successful solution from the archive. I have also run the same dataset in Freesurfer version 7.2.0 and receive the same error for some scans. Any help would be appreciated. Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a uname -a: Linux pc8-009.ion.ucl.ac.uk 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Mar 21 12:19:18 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux Thank you, Kirsten

1 0

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

1 0

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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

2 1

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

2 1

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

2 1

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

1 1

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

1 0

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer May 2024