Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30131 discussions

TRACULA - Ball-and-stick model fit running time
by Liliana Wu 02 Sep '22

02 Sep '22

External Email - Use Caution Hi, I have successfully run the preprocessing steps for my DWI data, and I was wondering how long does bedpostx usually take to process DWI? I am running on a high-powered computer (cluster) and a multi-shell data 3 b-values of (b= 1000s/mm2, 34 directions; b= 1600s/mm2, 45 directions; and b= 2600s/mm2, 66 directions). Thank you, Liliana

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Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution
by Trolle, Carl 02 Sep '22

02 Sep '22

Hi, I believe so, I ran the following commands: mris_register -L subject/label/?h.central_sulcus.label $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs S_central subject/surf/?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif subject/surf/?h.sphere.reg.new and then: mris_ca_label subject ?h subject/surf/?h.sphere.reg.new $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs subject/label/?h.aparc.a2009s.annot.new Overlaying the new annot-file over the inflated surface with the sulci visible moved the central sulcus to the designated spot (please see attached). This however seems to have caused the S_front_inf (yellow outline) to split into two. Kind regards, Carl

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Illegal Instruction (mri_segment_hypothalamic_subunits) - VM 7.2.0
by daedalus39＠aol.com 02 Sep '22

02 Sep '22

External Email - Use Caution Dear FreeSurfer developers, I cannot seem to get "mri_segment_hypothalamic_subunits" to work using the virtualbox installation of FS-7.2.0. I have a subject that ran to completion using recon-all, but when I tried to obtain the additional segmentation I keep getting "Illegal instruction (core dumped)". I have tried several permutations of the command (see below)(I did not include some of the extended syntax permutations (--sd, etc) in the list below, but I did try several - -> Illegal etc) It occurred to me that I should just attempt to see if the "help" command would work, so I simply copied the syntax directly from the wiki page mri_segment_hypothalamic_subunits -h... and as you can see below, that also returned "Illegal instruction (core dumped)". I even tried a direct copy of the syntax for "bert". No joy. Is this module actually implemented in the VM?Are there any suggestions regarding syntax, where the command is executed, etc.? Thanks in advance for any help you can offer. -Randy xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx developer@developer-VirtualBox:/$ lsbin dev initrd.img lib64 mnt root snap sys varboot etc initrd.img.old lost+found opt run srv tmp vmlinuzcdrom home lib media proc sbin swapfile usr vmlinuz.old developer@developer-VirtualBox:/$ mri_segment_hypothalamic_subunits --s WBI-FES_S_0862 --write_posteriorsIllegal instruction (core dumped)developer@developer-VirtualBox:/$ pwd/developer@developer-VirtualBox:/$ cd /usr/local/freesurfer/7.2.0/subjects/developer@developer-VirtualBox:/usr/local/freesurfer/7.2.0/subjects$ mri_segment_hypothalamic_subunits --s bertIllegal instruction (core dumped)developer@developer-VirtualBox:/usr/local/freesurfer/7.2.0/subjects$ mri_segment_hypothalamic_subunits --hIllegal instruction (core dumped)developer@developer-VirtualBox:/usr/local/freesurfer/7.2.0/subjects$ mri_segment_hypothalamic_subunits --helpIllegal instruction (core dumped)developer@developer-VirtualBox:/usr/local/freesurfer/7.2.0/subjects$ mri_segment_hypothalamic_subunits -helpIllegal instruction (core dumped)developer@developer-VirtualBox:/usr/local/freesurfer/7.2.0/subjects$ mri_segment_hypothalamic_subunits -hIllegal instruction (core dumped)developer@developer-VirtualBox:/usr/local/freesurfer/7.2.0/subjects$ mri_segment_hypothalamic_subunits --s WBI-WCM_S_0862 --write_posteriors --crop 1000Illegal instruction (core dumped)developer@developer-VirtualBox:/usr/local/freesurfer/7.2.0/subjects$ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx -------- 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/mnideveloper@developer-VirtualBox:~$

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problem with autorecon2-cp
by Mostafa Fakhri 02 Sep '22

02 Sep '22

External Email - Use Caution Hi there, I need just wm.seg.hgz image therefore I used autorecon2-cp: recon-all -sd /share/users/mfakhri/freeSurfer-analys/subjects -subject 102109_3T -i /share/users/mfakhri/freeSurfer-analys/102109_3T/T1w.nii.gz -autorecon2-cp but it doesn't work what's wrong? Thanks for the help! Mostafa

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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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