Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

Asymmetry analysis
by Carlos Alcocer 20 Jul '23

20 Jul '23

External Email - Use Caution Hello, I am trying to do an asymmetry analysis using steps detailed in https://secure-web.cisco.com/1E9BKFPFixB_mpRwvgfFNlEN0qYfJdo8MVLo6aeqDf-afy… However, step 1.3 starts with running: mris_apply_reg --src lh.map.mgh --trg lh.map.lh.fsaverage_sym.mgh --streg $SUBJECTS_DIR/subject/surf/lh.fsaverage_sym.sphere.reg $FREESURFER_HOME/subjects/fsaverage_sym/surf/lh.sphere.reg What is this lh.map.mgh file? and where can I find it/how can i make it? Thank you, Carlos

2 3

Extracting cortical thickness values for each subject using labels
by Akansha Mahesh Naraindas 20 Jul '23

20 Jul '23

External Email - Use Caution Hi I have made custom labels to use as ROIs, I was wondering if there was any way to get thickness values at each vertex for a participant but just within the areas covered by specific label files, So from the lh.thickness.fwhm0.fsaverage.mgh file, would I be able to extract thickness values from this file, but just within the region covered by aparc-rh-046.label ? Do you know of a way to do this? Thanks Akansha

3 3

Fwd: error in recon all
by alanood alsaleh 20 Jul '23

20 Jul '23

External Email - Use Caution Hello Freesurfer developer I tried to run a recon all commands for 36 subjects, and 30 finished without any issues. However, 6 of them were terminated with the ERROR (Talairach failed!). Can you please help me to sort this problem out? Please find the attachments (I attached the recon all script I used and the log file that I got for the subject with an error ). Regards Alanood

2 1

Variation in volume when recon-all is run 1416 times on the same subject
by 神保岳大 20 Jul '23

20 Jul '23

External Email - Use Caution Dear FreeSurfer team, We were interested in the reproducibility of multiple runs of recon-all and repeated recon-all 1416 times on the same subject. We then checked the left and right brain results for the volume obtained from the Aseg process. The right brain showed exactly the same volume, while the left brain showed a small variation. We thought that the variation in volume between the left and right brains would be the same. But why is this not the case in reality? The volume_attemps1416.csv is attached. For example, the Left-Lateral-Ventricle in this file has variation, but the Right-Lateral-Ventricle has no variation, as shown below. *Left-Lateral-Ventricle*12377.8 12375.9 12375.9 12380 12376.4 ... *Right-Lateral-Ventricle*7514.7 7514.7 7514.7 7514.7 7514.7 ... 1) FreeSufer vesion: 7.2.0 2) Platform: Red Hat Enterprise Linux 8.6 3) uname -a: Linux fn01sv01 4.18.0-372.36.1.el8_6.x86_64 #1 SMP Thu Nov 17 16:37:07 EST 2022 x86_64 x86_64 x86_64 GNU/Linux 4) volume_attemps1416.csv: Summarized results of 1416 aseg.stats. ───────────────────────────────── Takehiro Jimbo, Ph.D. TEL: 050-5308-1575 Email: info(a)jras.co.jp URL: https://secure-web.cisco.com/1v12MsuoCVOvbnqcvpETpiPtEYjXBUvx9IxdD0D4EvElKE… ─────────────────────────────────

2 1

mri_glmfit-sim cluster output issue
by jordan wagner 20 Jul '23

20 Jul '23

External Email - Use Caution Hello, My name is Jordan and I am working on cluster correction between two groups. I ran the step before: "freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=sig.mgh". I was able to find many significant values of p<0.05. However, when I ran the cluster correction there were no significant cluster in any of my group comparisons. I had to run mri_glmit-sim in the terminal each time for every directory because running the script that looped resulted in "cwp: command not found". I was wondering if there is something I could look for that is causing an issue or something else I can do to fix this. I wanted to reach out to make sure my results aren't completely null. Thank you, Jordan Wagner

2 1

Re: [Freesurfer] Error running hippocampus subfields and amygdala nuclei segmentation pipeline
by fsbuild 20 Jul '23

20 Jul '23

External Email - Use Caution The  .mexa64 file is a matlab shared library and that error is from the linker saying it is not allowed to link in that library.  Note that it did not say there was a permission denied error or that the .mexa64 file could not be found.   This Mathworks posting indicates that error can happen on systems when SElinux security is enabled, https://secure-web.cisco.com/1mMj5et2sBrHqKCyLNcFSpIV6dYytw3Jjg5sIR39GiUNHH… This part of LD_LIBRARY_PATH looks like the standard setting after running fs_install_mcr script with the Matlab runtime environment installed in the freesurfer distribution.  I'm assuming accessing MALAB runtime environment this way is already known to work on your cluster and does not generate any run time linker errors. LD_LIBRARY_PATH is .:/usr/local/freesurfer/7.1.1//MCRv84//runtime/glnxa64:/usr/local/freesurfer/7.1.1//MCRv84//bin/glnxa64:/usr/local/freesurfer/7.1..1//MCRv84//sys/os/glnxa64:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/usr/local/freesurfer/7.1.1//lib/vtk/lib - but the path to that .mexa64 file is not part of the standard LD_LIBRARY_PATH settings and looks like it is on some temporary mount point, /tmp/MCR_65032579/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64': /tmp/MCR_65032579/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64 - so I'm guessing there is some system and/or security setting that does not allow loading 3rd party libraries from paths like that.   I would ask your IT folks about it.  I could be wrong, but if kvlGEMSMatlab.mexa64 needed to be re-compiled to run on your system, then I would expect to see a different error. -R. On 6/27/23 22:08, Mengjie Huang (mhua0773(a)uni.sydney.edu.au) wrote: Invalid MEX-file '/tmp/MCR_65032579/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64' : failed to map segment from shared object: Operation not permitted

2 1

F.mgh file
by Lyna Mariam El Haffaf 20 Jul '23

20 Jul '23

External Email - Use Caution Dear FreeSurfer team, We are conducting a study with the ADNI database using FreeSurfer g3v1. I was wondering if the mri-segstats can be used to extract statistics from F.mgh file? Also, can the F-value be obtained via this F.mgh file? Thank you in advance! Lyna Mariam El Haffaf Ph.D. student in clinical neuropsychology University of Montreal

2 1

Use synthetic in recon-all pipeline
by Ruifeng Dong 20 Jul '23

20 Jul '23

External Email - Use Caution Hi all, I am running freesurfer 7.3.2 for segmentation of T1 data. It seems like still using the old skull stripping tools by default. How should we change it to using synthstrip? (Question 1) Also, is it a good idea to also turn on the --no-csf flag for cortex and subcortical segmentation? (Question 2) If using synthstrip, do we still need the -T2 option for better treatment of dura regions? (Question 3) Thank you. Best, Ruifeng

3 4

Obliqueness in the input images for recon-all
by Ruifeng Dong 20 Jul '23

20 Jul '23

External Email - Use Caution Dear all, We acquired the images (sagittal, 176*256*256) with obliqueness, because we tried to match the prescription with the subject's head positioning. Then, the obliqueness is shown in the header of the image. We used this image in recon-all. After mri_convert --conform, Freesurfer reoriented the image to RSP and then changed to 256*256*256 FOV. As a result, in orig.mgz, the image is tilted. Wouldn't this make it harder for Freesurfer to register with the template? Why does Freesurfer do this? Does it only expect input images with no obliqueness, i.e. anatomical coordinates and physical coordinates are always aligned? Thank you! Best, Ruifeng

2 1

Generate Stats File for fornix.mgz in T1 weighted MRI ?
by Ahsan Ali 20 Jul '23

20 Jul '23

External Email - Use Caution Dear Sir/Madam, I hope you are doing well. I'm having a ADNI T1 weighted MRI database. I have run the recon-all command successfully and got a couple of default stats files in the stats folder. Then fornix.mgz is estimated using command "mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto_CCseg.mgz -f folder_name" successfully. Now what can be done to generate the stats for only fornix.mgz? I've been struggling with this for a long time, please help me with this. I'm using linux-ubuntu. [image: IMG-20230526-WA0000.jpg] With Regards Ahsan --------------------------------------------- Ahsan Ali Ph.D Scholar Department of Applied Mechanics and Biomedical Engineering (AMBE) Indian Institute of Technology Madras Chennai-600036, Tamil Nadu, INDIA Mob.:- +91-8899605552

2 3

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer