Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

How many regions does "aparc.DKTatlas+aseg.mgz" have?
by Kei Nishimaki 21 Nov '23

21 Nov '23

External Email - Use Caution Hello FreeSurfer Developers, We ran recon-all on a 3D T1-weighted image, by default. ls *.nii | parallel -–jobs 2 recon-all -s {.} -i {} -all -qcache Our question is very simple. How many regions does "aparc+aseg.mgz" and "aparc.DKTatlas+aseg.mgz" and "aparc.a2009s+aseg.mgz" have in each? We checked the links below. And we want to renumber the region index from 0 as shown in the photo below. https://secure-web.cisco.com/1fBJMEihMTm8S1YZKy0FxnEoJxLOAxKaZC0-l90ulKxJmi… However, the number of regions varies slightly depending on the subjects (103~106 in aparc.DKTatlas+aseg.mgz). Therefore, we want to know the number of regions in three parcellation map. 1) FreeSurfer version: freesurfer-linux-ubuntu20_amd64-7.4.1.tar.gz 2) Linux ~~~ 5.15.0-76-generic #83~20.04.1-Ubuntu SMP Wed Jun 21 20:23:31 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux [cid:2d03e569-3221-4f8d-b86f-c8d38cf75b2e] Thanks, Kei

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Large discrepancy in left and right volumes of perirhinal/entorhinal cortices on FreeSurfer 7.1
by Marawi, Tulip 21 Nov '23

21 Nov '23

External Email - Use Caution Dear FreeSurfer developers, Our research group used the FreeSurfer's recon-all tool to reconstruct 74 anatomical images from cognitively healthy older individuals and parcellate the cortex based on the Desikan-Killiany atlas. However, we are running into a consistent issue with the perirhinal volumes on the annot stats from BA_exvivo_thresh.stats, where there is a large discrepancy between the left and right hemispheres (larger left hemisphere). Upon visual and numerical investigation, it appears that this could be due to mis-labelling the right perirhinal vertices as entorhinal, resulting in an unusually small right perirhinal cortex, and unusually large right entorhinal cortex. Could you please clarify why this could be happening, and advise on next steps? We have used FreeSurfer 7.1 for this analysis. Sincerely, Tulip Marawi This e-mail is intended only for the named recipient(s) and may contain confidential, personal and/or health information (information which may be subject to legal restrictions on use, retention and/or disclosure). No waiver of confidence is intended by virtue of communication via the internet. Any review or distribution by anyone other than the person(s) for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and destroy all copies.

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Re: [Freesurfer] Doubts about GLM contrasts
by Laura Willers de Souza 21 Nov '23

21 Nov '23

External Email - Use Caution Great, thanks so much! But I am having difficulty understanding how to construct the contrast to answer the following question "Is the interaction between group (CU/CI) and cortisol significant regressing out the effect of sex, age, APOE_carrier, abeta and ptau?" It seems like the contrast would be the same as before.. Can you help me with this? Thanks again! Laura Willers de Souza PhD Student in Pharmacology and Therapeutics Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil ----- Douglas N. Greve<https://secure-web.cisco.com/1yYgRLzmOCtuh8UFLaxt4ucohab6Ii9cqIDNXc9_tUgQIT…> Wed, 15 Nov 2023 06:54:36 -0800<https://secure-web.cisco.com/1YP7c0yUfORmuLGAmHVodnKa9al2_Y0u_TMgwZ8HHpNLBo…> Yes, that looks right (assuming that cortisol is your first variable) ---- On 11/7/2023 3:49 PM, Laura Willers de Souza wrote: External Email - Use Caution Hello FreeSurfer Developers, Following the FSGD examples on the website, I built the following test: Question: Is there an association between cortisol and cortical thickness regressing out the effect of sex, age, APOE4_carrier (1=1 or 2 alleles, 0=no alleles), abeta, ptau, diagnosis (CU and CI)? Regressors: 2 factors (sex, diagnosis) with 2 levels each, 5 covariates (age, APOE4_carrier (1=1 or 2 alleles, 0=no alleles), abeta, ptau, cortisol) >> 24 regressors Contrast: 0 0 0 0 0.5 -0.5 0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 FSGD: GroupDescriptorFile 1 Title CSF_semgrupos Class MaleCU Class MaleCI Class FemaleCU Class FemaleCI Variables Cortisol Age ABETA ptau APOE4_carrier Input 098_S_4003_I224603 MaleCI 11 81.3 741.5 22.83 1 Does this feel right to you? I am having difficulty understanding how to construct the contrast to answer the following question "Is the interaction between group (CU/CI) and cortisol significant regressing out the effect of sex, age, APOE_carrier, abeta and ptau?" It seems like the contrast would be the same as before.. Can you guys help me with this? Thanks in advance! *Laura Willers de Souza * PhD Student in Pharmacology and Therapeutics Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

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recon-all error
by Carlos Alcocer 21 Nov '23

21 Nov '23

External Email - Use Caution Reposting due to issue with email bouncing. I am receiving following error on my subjects. Recon-all still continues after error and finishes "without error" I have attached the recon-all log as well. mri_convert /path/to/inputt1.nii /path/to/mri/orig/001.mgz mri_convert /path/to/anat_t1.nii /path/to/mri/orig/001.mgz reading from /path/to/anat_t1.nii... NaN found at voxel (0, 0, 244, 0) error: No such file or directory error: WARNING: 319676 NaNs found in volume /path/to/anat_t1.nii... Thank you, Carlos

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Running autorecon2-wm after wm edits makes no difference in final surface
by Fernanda Hansen P. de Moraes 21 Nov '23

21 Nov '23

External Email - Use Caution Dear FreeSurfer experts, I have been trying to manually correct a wm volume to further fix the wm and pial surfaces, but when I ran *recon-all -subjid SUBJxxx -autorecon2-wm -autorecon3* nothing happened to the surfaces. I found an unknown-args.txt file under scripts, and it seems the autorecon2-wm flag is not recognized. How can I create new surfaces and overcome this issue? Here attached is the complete recon-all log file from the beginning, including all steps attempted. I would be very glad if you could help me overcoming this error to include as much subjects as possible in my project. Best regards, Fernanda Hansen P. de Moraes fernandahmoraes(a)gmail.com Pesquisadora no Instituto de Física da UFRJ | metaBIO (IF-UFRJ) Doutora em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino

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recon-all error
by Carlos Alcocer 20 Nov '23

20 Nov '23

External Email - Use Caution Hi, For some of my subjects I get the following error at the beginning of recon-all: mri_convert /path/to/inputt1.nii /path/to/mri/orig/001.mgz mri_convert /path/to/anat_t1.nii /path/to/mri/orig/001.mgz reading from /path/to/anat_t1.nii... NaN found at voxel (0, 0, 244, 0) error: No such file or directory error: WARNING: 319676 NaNs found in volume /path/to/anat_t1.nii... However, recon-all will keep running and then later finish without error. What exactly is going on? This is only happens on some subjects. Thank you, Carlos

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2 PhD positions in Prenatal programming of neurodevelopment in childhood
by Klara Mareckova 20 Nov '23

20 Nov '23

External Email - Use Caution Hello, I'm offering two PhD positions at the Faculty of Medicine, Masaryk University, Czech Republic, to study Prenatal programming of neurodevelopment in childhood. See more information at the links below and email me your CV at klara.mareckova(a)gmail.com if interested! :) Thanks, Klara Mareckova https://secure-web.cisco.com/1Md08Dmcg7DmgC-QMZFtqmVaw1faa3Fbv26fmwvBE4aZUH… https://secure-web.cisco.com/104yy20ksfCRxwDE7lc4YW3rRpd9GuI26hH_Oh8M5yBhov…

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Re: [Freesurfer] license issue with the updated version
by fsbuild 19 Nov '23

19 Nov '23

External Email - Use Caution  Please let us know if you are running MacOS 14 (Sonoma) on an Intel or silicon Mac (M1, M2 chip).    The system requirements at https://secure-web.cisco.com/10qwlQRot-nOOCuaXBtxsk1Ua4Tfh-PQlj0cP9-E6KzZM5… list MacOS 13 (Ventura) as the latest supported MacOS for the 7.4.1 release. - R. On Nov 18, 2023, at 18:29, Atena Akbari <atenaakbary(a)gmail.com> wrote:QObject::killTimer: Timers cannot be stopped from another thread

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license issue with the updated version
by Atena Akbari 18 Nov '23

18 Nov '23

External Email - Use Caution Dear freesurfer team I have uninstalled the previous versions of freesurfer on my mac (Sonoma 14.1), and have installed a new version 7.4.1 based on the step by step freesurfer installation info on the website. I have set the freesurfer home directory as follows: export FREESURFER_HOME=/Applications/freesurfer/7.4.1/ export SUBJECTS_DIR=path/to/my/data source $FREESURFER_HOME/SetUpFreeSurfer.sh and the license is in the /Applications/freesurfer/7.4.1. But when I run a freesurfer command I get the following error: ERROR: FreeSurfer license file /Applications/freesurfer/7.2.0/license.txt not found. QObject::killTimer: Timers cannot be stopped from another thread QObject::~QObject: Timers cannot be stopped from another thread /Applications/freesurfer/7.4.1//bin/freeview: line 2: 2938 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" Could you help me with this issue? thanks so much. Best, Atena

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Re: [Freesurfer] Unable to run recon-all
by fsbuild 17 Nov '23

17 Nov '23

External Email - Use Caution  The install location of freesurfer under /usr/local is on purpose read only (like the location of most Linux package installs) so you should not be trying to process and write subject data there.  We provide example subjects under /usr/local/freesurfer/7.4.0/subjects for read only purposes. Neither can you set SUBJECTS_DIR or write files in the process of running recon-all to your mounted or shared C drive.  This is because the the Windows file system does not support creating soft links. So please try the following.  In your Ubuntu linux terminal window,  go to your HOME directory and create a subjects directory there, i.e., you can always read/write to your HOME directory.   Then copy in your subject data to be processed there via recon-all and set SUBJECTS_DIR appropriately or pass the path on the recon-all command line. … in WSL linux terminal window …$ cd $HOME$ mkdir subjects$ cd subjects$ pwd/home/naily/subjects$ export SUBJECTS_DIR=/home/naily/subjects… copy in your data to process for recon-all to live under SUBJECTS_DIR … It also looks like your license file is not being found.  You can set the environment variable FS_LICENSE to point to that so it will be found and read, $ export FS_LICENSE=/home/naiy/license.txt$ head -1 $FS_LICENSEyou(a)somewhere.com       <---- email address you used to register … then try running some Freesurfer commands again … - R. On Nov 17, 2023, at 17:49, Nai, Ying Hwey <naiy@wustl..edu> wrote:<FSissues.txt>

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