Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

sclimbic sometimes does not detect left basal forebrain
by Miriam Taza 31 Aug '22

31 Aug '22

External Email - Use Caution Hello, I noticed 20 out of ~240 subjects left basal forebrain volumes were not picked up after running ScLimbic. These are healthy adults and their scans look good. Also, I noticed often when this occurs NAcc is also 0 or other regions. I am concerned if there is a systematic issue with left volumes ending up smaller than they should relative to right. Thanks, Miriam

2 12

Re: [Freesurfer] Bus error using VM (#@# Nu Intensity Correction)
by fsbuild 31 Aug '22

31 Aug '22

External Email - Use Caution Hard to look at the error w/o a core dump file, but I suspect “bus error” is from the VM and not from commands in the recon-all acting differently during your 2nd run. It reads like you created a shared folder for the VM to use, and set SUBJECTS_DIR to it so the recon-all will write files to the D: drive which I assume has a windows file system (NTFS) and not a linux file system (ext4). Bus error could be from the VM not being able to do something on the D drive when it needed to.  It’s not going to work by default for something running in the linux VM to create a soft link on a Windows file system.  There are some postings about how to enable this, but it’s a pain, https://secure-web.cisco.com/1o9_6RQMC4nKOlu3EcHHOdySIipng3hEcPD… I would avoid pointing SUBJECTS_DIR to a windows file system for the linux VM to write to.   If you want disk space usage on your C  drive, consider locating the VM on your external D drive (which should also help the VM run faster since it won’t be running from the boot drive)..   You can take your existing VM on the C drive and clone it to a new folder/destination on your D drive using the VirtualBox application.  Then you should have 2 instances of the VM.  Test bringing up the one on the D drive and then delete the one on the C drive including all its files. - R. On Aug 31, 2022, at 18:32, daedalus39(a)aol.com wrote:        External Email - Use Caution        Hello FreeSurfer Developers,In an effort to relieve strain on my local C:/ drive, I was testing "export" to an existing shared folder on my SSD drive (D:/)Guidance came from:https://secure-web.cisco.com/1QmDaWnb5IenddSg9grDpAn0XIRiC9e5PGBGJG3oU… SUBJECTS_DIR=/media/sf_0007_Subjects-FS/subjectsI had tested the FS-7.2 VM on this same image leaving the SUBJECTS_DIR environment variable as default and this MRI was processed and ran to completion without error. While certain early portions for FS ran without issue for this 2nd test (shared folder in the VM set up upon installation), the recon-all run exited with errors at the Nu Intensity Correction step. Bus error Command exited with non-zero status 1 I don't understand how "mri_binarize" could crash and I'm hoping you can provide some guidance.  Did I need to use a variation of the command:mkdir -p /home/developer/guest_shared/sf_0007_Subjects-FS/subjects(?)I am running all this on the VM FS_Ubuntu_18_04_06.Thanks in advance for any insight.-RandyPS. I only know enough Linux to get into trouble-------- freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurfer/7.2.0FSFAST_HOME       /usr/local/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /usr/local/freesurfer/7.2.0/subjectsMNI_DIR           /usr/local/freesurfer/7.2.0/mnixxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx from recon-all.log xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx#@# Nu Intensity Correction Wed Aug 31 14:19:28 EDT 2022 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /usr/bin/bc/media/sf_0007_Subjects-FS/subjects/WBI-FES_S_0862x/mri/usr/local/freesurfer/7.2.0/bin/mri_nu_correct.mni--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4nIters 2mri_nu_correct.mni 7.2.0Linux developer-VirtualBox 5.4.0-124-generic #140~18.04.1-Ubuntu SMP Fri Aug 5 11:43:34 UTC 2022 x86_64 x86_64 x86_64 GNU/LinuxWed Aug 31 14:19:28 EDT 2022tmpdir is ./tmp.mri_nu_correct.mni.6181cd /media/sf_0007_Subjects-FS/subjects/WBI-FES_S_0862x/mriAntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.6181/nu0.mgz --dtype ucharAntsN4BiasFieldCorrectionFs donemri_binarize --i ./tmp.mri_nu_correct.mni.6181/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.6181/ones.mgzBus error Command exited with non-zero status 1@#@FSTIME  2022:08:31:14:19:28 mri_nu_correct.mni N 9 e 139.45 S 1.50 U 137.65 P 99% M 508172 F 1 R 155334 W 0 c 291 w 1359 I 720 O 0 L 0.91 0.50 0.26@#@FSLOADPOST 2022:08:31:14:21:48 mri_nu_correct.mni N 9 2.37 1.22 0.56Linux developer-VirtualBox 5.4.0-124-generic #140~18.04.1-Ubuntu SMP Fri Aug 5 11:43:34 UTC 2022 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s WBI-FES_S_0862x exited with ERRORS at Wed Aug 31 14:21:48 EDT 2022To report a problem, see http://secure-web.cisco.com/1G6QB2un2v7wb_To8cD-QTSpsFjZXmTfsa3vpNWripVw16C… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Bus error using VM (#@# Nu Intensity Correction)
by daedalus39＠aol.com 31 Aug '22

31 Aug '22

External Email - Use Caution Hello FreeSurfer Developers, In an effort to relieve strain on my local C:/ drive, I was testing "export" to an existing shared folder on my SSD drive (D:/) Guidance came from:https://secure-web.cisco.com/1YO7E9aNxbSzoJwOfWqQ9yCQ_LqmLvnOvokKgrEEl… export SUBJECTS_DIR=/media/sf_0007_Subjects-FS/subjects I had tested the FS-7.2 VM on this same image leaving the SUBJECTS_DIR environment variable as default and this MRI was processed and ran to completion without error. While certain early portions for FS ran without issue for this 2nd test (shared folder in the VM set up upon installation), the recon-all run exited with errors at the Nu Intensity Correction step. Bus error Command exited with non-zero status 1 I don't understand how "mri_binarize" could crash and I'm hoping you can provide some guidance. Did I need to use a variation of the command:mkdir -p /home/developer/guest_shared/sf_0007_Subjects-FS/subjects(?) I am running all this on the VM FS_Ubuntu_18_04_06. Thanks in advance for any insight. -Randy PS. I only know enough Linux to get into trouble -------- freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME /usr/local/freesurfer/7.2.0FSFAST_HOME /usr/local/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR /usr/local/freesurfer/7.2.0/subjectsMNI_DIR /usr/local/freesurfer/7.2.0/mni xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx from recon-all.log xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx #@# Nu Intensity Correction Wed Aug 31 14:19:28 EDT 2022 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /usr/bin/bc/media/sf_0007_Subjects-FS/subjects/WBI-FES_S_0862x/mri/usr/local/freesurfer/7.2.0/bin/mri_nu_correct.mni--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4nIters 2mri_nu_correct.mni 7.2.0Linux developer-VirtualBox 5.4.0-124-generic #140~18.04.1-Ubuntu SMP Fri Aug 5 11:43:34 UTC 2022 x86_64 x86_64 x86_64 GNU/LinuxWed Aug 31 14:19:28 EDT 2022tmpdir is ./tmp.mri_nu_correct.mni.6181cd /media/sf_0007_Subjects-FS/subjects/WBI-FES_S_0862x/mriAntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.6181/nu0.mgz --dtype ucharAntsN4BiasFieldCorrectionFs donemri_binarize --i ./tmp.mri_nu_correct.mni.6181/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.6181/ones.mgzBus error Command exited with non-zero status 1@#@FSTIME 2022:08:31:14:19:28 mri_nu_correct.mni N 9 e 139.45 S 1.50 U 137.65 P 99% M 508172 F 1 R 155334 W 0 c 291 w 1359 I 720 O 0 L 0.91 0.50 0.26@#@FSLOADPOST 2022:08:31:14:21:48 mri_nu_correct.mni N 9 2.37 1.22 0.56Linux developer-VirtualBox 5.4.0-124-generic #140~18.04.1-Ubuntu SMP Fri Aug 5 11:43:34 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux recon-all -s WBI-FES_S_0862x exited with ERRORS at Wed Aug 31 14:21:48 EDT 2022 To report a problem, see http://secure-web.cisco.com/1tbOYcer_KUstAn7EZVPpXMoWbZAIoBPdPn197RvvssZ6nk…

1 0

LENS-Italy Postdoc Opportunity
by Mora, Jocelyn S. 31 Aug '22

31 Aug '22

Hi all, The biophotonics group at LENS is looking for a biologist to study human brain neuroanatomy using fluorescence microscopy techniques. Please see the below posting. Feel free to forward to anyone you know who might be interested. Thanks, Jocelyn The biophotonics group at LENS, is looking for a biologist to study human brain neuroanatomy using fluorescence microscopy techniques. Detailed information can be found on the LENS website: https://lens.unifi.it/media/albo/2022/08/000059184-LENSCLE-4fa83b7a-c8ca-41…<https://secure-web.cisco.com/1nHgs_cv5noFpfAFeZl1_rBbF1SSzORl2yMyBfMuOPDTlm…> The deadline for submitting the application for selection is 16/09/2022. Description: One of the greatest scientific challenges of our day is to gain a complete understanding of the human brain. In this regard, the candidate will have the main purpose of developing, adapting and elaborating techniques for the study of brain anatomy in 3D. In particular, the candidate's work will be focused on the preparation, acquisition and analysis of human brain samples using high-resolution fluorescence microscopy techniques. To carry out the cytoarchitectonic study of the samples, the candidate will have to develop sample clearing techniques and advanced immunohistochemical techniques. To examine the specimens in three dimensions, the candidate will need to use advanced fluorescence microscopy techniques such as confocal, two-photon and light sheet microscopy. Finally, to obtain the mapping of neurons and fibers, the candidate will have to analyze the data with analysis techniques based on machine learning. The nominated protocols are to be applied by the candidate to brain samples from healthy subjects and subjects with focal cortical dysplasias. If you have any questions please write to costantini(a)lens.unifi.it<mailto:costantini@lens.unifi.it>

1 0

midsagittal mask
by Sam W 31 Aug '22

31 Aug '22

External Email - Use Caution Hello! I ran recon-all on my subject, is it possible to create a mask of the midsagittal plane using freesurfer? Best regards, Sam

3 4

Thalamus segmentation - segmented thalamus looks bigger than brain.mgz would indicate
by Thalhammer, Melissa 31 Aug '22

31 Aug '22

External Email - Use Caution Dear Freesurfers, I have used the Freesurfer-based thalamus subnuclei segmentation. As a quality control, we have inspected the output files visually in freeview and noticed that some (roughly 5 out of 25 subjects) thalamic volumes are (much) larger than the brain.mgz file would indicate (see attached screenshot showing brain.mgz and ThalamicNuclei.v12.T1.FSvoxelSpace.mgz). This seems to be the case for aseg.mgz as well, i.e., the thalamus in aseg.mgz seems larger than it should be based on the contrast we see in brain.mgz. We have tried to run the segmentation again but this has not led to significantly better results. Is this the right way to visualize the outputs? Is it recommended to exclude these subjects? Is there any recommended quality control pipeline that we could apply? Thank you a lot in advance! Best, Melissa Thalhammer

2 1

samseg dice score is low
by Dilek Özkan 31 Aug '22

31 Aug '22

External Email - Use Caution Hello dear all, I use Freesurfer-Samseg for MS lesion segmentation(cross-sectional). I use the T1 and Flair for this. (just these are inputs) I registered *flair and t1 to DIR *for every patient. (My manual lesion masks are on DIR imaging.) I controlled the registrations At the beginning i didnt change initial threshold of run_samseg. (default value) I created a binary lesion mask using different threshold. *threshold *0.1= *dice* 0,604 *threshold *0.05= *dice *0.611 *threshold *0.001 = *dice *0.599 Do you have any recommendations to increase the dice? It seems that with this way It can't go up about 0.6 Best, Dilek

2 2

Re: [Freesurfer] Thalamic nuclei exited with ERRORS
by fsbuild 30 Aug '22

30 Aug '22

External Email - Use Caution After you install either R2017b or R2019b using the fs_install_mcr script you should end up with either ./freesurfer/MCRv9.3 or ./freesurfer/MCRv9.7   There are no soft links to create manually and there should be no references to MCRv8.4 in DYLD_LIBRARY_PATH or in the shell environment. - R..

2 1

Re: [Freesurfer] Thalamic nuclei exited with ERRORS
by fsbuild 30 Aug '22

30 Aug '22

External Email - Use Caution One error in the logs is from missing symbols in the Matlab java library, and another says to contact the Mathworks for technical support.  But Mathworks is not going to support you because MacOS 10.13 does not meet the system requirements for R2014b. You don’t have to upgrade to MacOS 10.14 or 10.15 to run R2019b per https://secure-web.cisco.com/1A2yZeUgftXNAfIgFAcU_8ADraR51pChpBCWV… but the oldest version of MacOS you can run with R2019b is *exactly* MacOS 10.13.6 and not an earlier version.  You should be able to use the MacOS software update tool to update to 10.13.6 if you are not already running it. I recommend that as I believe that is the last/most stable version of MacOS 10.13.   From the compatibility chart, https://secure-web.cisco.com/1Do0OQV0Uj3IgfgRoxB2s-64lh4FjvAGYa…, it looks like you could also try the older R2017b release.  I think you tried R2019b before with the freesurfer 7.3.2 release but not with the 7.2.0 release which you are now running. You can follow the same instructions below to install R2019b or R2017b with the fs_install_mcr script and see if you get different results.  You should only have one ./freesurfer/MCR* subdir present at any one time.   It’s not clear to me the java libraries included in the Mathworks runtime environment care about the version of Java installed in MacOS, e.g., if it is 1.7 or 1.8.  The errors would seem to indicate the system version of Java is not the issue. - R.

2 1

mri_fwhm and diffusion data
by Igor Nestrašil 30 Aug '22

30 Aug '22

External Email - Use Caution Dear FreeSurfer developers, Can "mri_fwhm" be used to estimate FWHM of b0 images (obtained from diffusion-weighted echo-planar sequences) and is it possible to employ for FWHM estimation from aligned diffusion-weighted images of the same b-value but varying gradient wave vectors? Thank you! Igor Nestrasil U of Minnesota

2 1

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