Freesurfer September 2022

freesurfer@nmr.mgh.harvard.edu

92 participants
129 discussions

Stepwise recon-all to get volumes
by Ruifeng Dong 01 Sep '22

01 Sep '22

External Email - Use Caution Hi all, I am computing volumetry using freesurfer using two different runs. 1. I just use recon-all -all, and then look at the aseg.stats file. 2. I ran recon-all only to the 12th step where gca labeling is done. It doesn't generate the aseg.mgz file but only aseg.auto.mgz. I assumed that they are the same and ran the -asegstats step to get the output in aseg.stats. I noticed there are differences between the above two runs on the same image. Firstly, the volumes of WM, GM and ICV are not there from the 2nd run. How does this happen? In which step does Freesurfer compute these? Secondly, the volumes of some subcortical structures are also different between the two runs. Does Freesurfer make corrections to the volume segmentations after step 12? Thank you! Ruifeng

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Re: [Freesurfer] Thalamic nuclei exited with ERRORS
by fsbuild 01 Sep '22

01 Sep '22

External Email - Use Caution For MacOS, the 7.2.0 release was done on MacOS 10.14.6 and it will check for Matlab runtime MCRv84 which you install with R2014b as the argument to fs_install_mcr For MacOS, the 7.3.2 release was done on MacOS 10.15.7 and it will check for Matlab runtime MCRv97 which you install with R2019b as the argument to fs_install_mcr I think we already know your machine running MacOS 10.13 does not match the above but MCRv84 sometimes works for you running the 7.2.0 release.  The errors you posted from Matlab could be an issue with MCRv84 w.r.t MacOS 10.13 or your machine.   Upgrading your OS to match the above could eliminate the matlab errors. If you want to experiment with running different versions of Matlab, e.g.., R2017b, then you can go into the file ./freesurfer/bin/checkMCR.sh and comment out the check for the version of matlab by adding pound sign “#” to the beginning of the lines that do the check.   Then you don’t need to try and bypass the check with soft links.  But we have not done testing for the above releases on MacOS 10.13. I don’t know if you have experience with using multiple boot partitions for MacOS (set via Startup Disk in System Prefeernces).  One test would be to do a clean install of MacOS 10.14 or 10.15 on an empty (internal) disk partition or external disk drive.  Then boot from that partition and install the 7.2.0 or 7.3.2 release with the matching version of Matlab listed above.  You would probably want at least a USB3 connection (or equivalent speed) to an external drive for that to not run slowly.  A clean install should eliminate any issues with the current state of your machine.  Then try running your commands with the matching Freesurfer release in the new/clean version of the OS. - R. On 31 Aug 2022, at 2:12 pm, Yann Quidé <yannquide(a)gmail.com> wrote:This is the error I get when for example, I use MCRv93sub-BA_IGP001     ERROR: cannot find Matlab 2014b runtime in location:     /Applications/freesurfer/7.2.0/MCRv84     It is looking for either:   bin/glnxa64/libmwlaunchermain.so    (Linux 64b) or  bin/maci64/libmwlaunchermain.dylib (Mac 64b) The hippocampal/amygdala and brainstem modules require the (free) Matlab runtime.You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2014b.To do so, please run the following command (you might need root permissions): fs_install_mcr R2014b

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Posting to freesurfer
by Riccardo Iandolo 01 Sep '22

01 Sep '22

External Email - Use Caution Hi, I made a mistake and sent the questions I would like to post to the list. Actually, this is just to activate my email to post on the list. Apologize, Riccardo

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VM passcode
by Beatrice Everall 01 Sep '22

01 Sep '22

External Email - Use Caution Hello, What is the passcode to the archive zip file when downloading the Ubuntu VM? Many thanks Bea

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VM passcode
by Beatrice Everall 01 Sep '22

01 Sep '22

External Email - Use Caution Hello there What is the password to open the archive zip file when downloading the virtual machine? Thanks Bea

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Re: [Freesurfer] Thalamic nuclei exited with ERRORS
by fsbuild 31 Aug '22

31 Aug '22

External Email - Use Caution It’s possible something in 7.2.0 still requires MCRv84.  If so, it is probably not going to work to use a soft link to fake out the name, and using a different version of Matlab run time could explain the crashes..  Please send along the output showing MCRv84 is required. - R.

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FSFAST first level covariates
by Angela Fang 31 Aug '22

31 Aug '22

External Email - Use Caution Hi Freesurfer community, I have run participants through an event-related fMRI task in which subjects rate whether trait adjectives are descriptive of themselves or not, and afterwards asked them to rate each trait word on emotional valence. Is it possible to include these individual level subjective ratings of emotional valence as covariates in the first level contrast in FSFAST? If so, how? Thanks, Angela --- Angela Fang, Ph.D. Assistant Professor Department of Psychology University of Washington Lab website: http://secure-web.cisco.com/1EJiZPvng9zcCEb0OA91-g6prvoE6x8E2RuCN3eRqnJvVyW…<http://secure-web.cisco.com/1EJiZPvng9zcCEb0OA91-g6prvoE6x8E2RuCN3eRqnJvVyW…> Pronouns: she, her, hers

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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

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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

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Freesurfer September 2022