Freesurfer August 2022

freesurfer@nmr.mgh.harvard.edu

85 participants
120 discussions

HELP - pass code for Freesurfer VirtualBox
by Michel Godel 23 Aug '22

23 Aug '22

External Email - Use Caution Hello, I am a PhD candidate in neurosciences at the University of Geneva, I would like to use Freesurfer on my VirtualBox to benefit from the interface between FS and BrainVisa. I write you to ask for the pass code. Thanks a lot ! Michel

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Re: [Freesurfer] Docker for Freesurfer 7.3.2
by fsbuild 22 Aug '22

22 Aug '22

External Email - Use Caution Hello Hudson, It should work with an existing CentOS 7, 8 or Ubuntu 18, 20, 22 OS image that you already have running in docker to download and install the freesurfer 7.3.2 .rpm or .deb package.  You just need to download the Freesurfer 7.3.2 package that matches your OS into the container from https://secure-web.cisco.com/11TR8ua7ZAntd-JOE6C37qMEU6Ni9n2fGmRDikMSPlL_oL… and install it locally, e..g., … inside your container use wget or curl from the command line to fetch the package ... $ cd /tmp $ wget https://secure-web.cisco.com/1Rtxnn-EbC50e49F9QmGbplwoTCpnnGUCFue5MQ4-09g_d… or deb file matching your OS> … for rpm file (RedHat, CentOS) ... $ sudo yum install ./<rpm file matching your OS> … for deb file (Ubuntu) … $ sudo apt-get install ./<deb file matching your OS> … answer yes to queries if you want to commit to installing what will be added to the system … When the installation finishes, look to see you have a subdirectory under /usr/local/freesurfer named after the 7.3.2 release, e.g., something like /usr/local/freesurfer/7.3.2.  That path should become the setting for the environment variable FREESURFER_HOME. - R. On Aug 20, 2022, at 17:05, Robb, William Hudson <william.h.robb(a)vanderbilt.edu> wrote:         External Email - Use Caution         Hello,   When is the Freesurfer 7.3.2 docker expected to be released? I see 7.2.0 available here but not 7.3.2 : MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1_zBoU_WD5P-_UVZx_tMLTAeFQjb2dV_qRiZuUZbblu0uB…   Thank you, Hudson Robb _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu

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freesurfer ubuntu pass code
by Noam Khayat 22 Aug '22

22 Aug '22

External Email - Use Caution Hi, My name is Noam and I'm a PhD Student from the Department of Neurobiology At HUJI, Israel. I downloaded "Freesurfer VirtualBox" and I the pass code to unzip the /FS_7_2_0_ubuntu_18_04_06.ova.7z/ file Thank you. Noam

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Docker for Freesurfer 7.3.2
by Robb, William Hudson 20 Aug '22

20 Aug '22

External Email - Use Caution Hello, When is the Freesurfer 7.3.2 docker expected to be released? I see 7.2.0 available here but not 7.3.2 : https://secure-web.cisco.com/1CIGFPTxp-eNfPdsaiYMN6EMjcqI9LQ08AQau2vTMYh9Nv… Thank you, Hudson Robb

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Password for 7.2.0 VM box virtual machine
by Joe Romero 20 Aug '22

20 Aug '22

External Email - Use Caution I require the password to unzip the above named archive.

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TRACULA - preprocessing error
by Liliana Wu 20 Aug '22

20 Aug '22

External Email - Use Caution Hi, I ran the preprocessing command trac-all -prep -c $SUBJECTS_DIR/script and I am getting the following error ERROR: fio_pushd: /home/lwu/Desktop/OIRM02/trc/OIRM02/dlabel/mni I don’t see the mni folder created in my files… I am trying to only reconstruct the following pathways. set pathlist = ( lh.cst_JL rh.cst_JL \ lh.unc_JL rh.unc_JL \ lh.ccg_PP rh.ccg_PP \ lh.cab_PP rh.cab_PP) set ncpts = (6 6 5 5 5 5 4 4) I appreciate any help, Thank you Liliana

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Segment subregion error
by Md. Mamun Al-Amin 19 Aug '22

19 Aug '22

External Email - Use Caution Hi Freesurfer experts, I have been encountering following errors after running segment_subregions command. I am using freesurfer version 7.3.2, Recon -all -all has been done with the option -cm segment_subregions thalamus --cross sub-0049 Step 1: preprocessing inputs for thalamus segmentation Running command: mri_convert /var/folders/dl/1zpqwlt95bnfb3ydwm2mqd1w0000gn/T/tmp8ppe_a7y/tempImage.mgz /var/folders/dl/1zpqwlt95bnfb3ydwm2mqd1w0000gn/T/tmp8ppe_a7y/tempImage.mgz -odt float -rt cubic -vs 0.5 0.5 0.5 Preprocessing took 22 seconds Step 2: aligning atlas to reference segmentation Traceback (most recent call last): File "/Applications/freesurfer/7.3.2/python/scripts/segment_subregions", line 99, in <module> subregions.run_cross_sectional(args.structure, parameters) File "/Applications/freesurfer/7.3.2/python/packages/freesurfer/subregions/process.py", line 52, in run_cross_sectional model.align_atlas_to_seg() File "/Applications/freesurfer/7.3.2/python/packages/freesurfer/subregions/core.py", line 240, in align_atlas_to_seg mask = mask.resize(1, interp='nearest') TypeError: resize() got an unexpected keyword argument 'interp' (base) abdullah@BadaliMac recon-all % Kind regards *Md. Mamun Al-Amin, PhD* *---------------------------* *Postdoctoral Fellow* *Stark Neuroscience Research Institute* *Indiana University School of Medicine* *320 W. 15th Street, NB Bldg Rm 103* *Indianapolis, IN 46202*

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Thalamic nuclei exited with ERRORS
by Yann Quidé 19 Aug '22

19 Aug '22

External Email - Use Caution Hi team, I am trying to run the thalamic nuclei pipeline with FS7.3.2, on scans processed with recon-all from FS5.3 (mac OSX10.13). However, I receive the below error. Any idea how I could solve this? Thanks in advance. Yann ------------------------------ USER yann HOST Ians-Mac-Pro.local PROCESSID 86082 PROCESSOR x86_64 OS Darwin ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 Darwin Ians-Mac-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64 ------------------------------ freesurfer-darwin-macOS-7.3.2-20220804-6354275 setenv SUBJECTS_DIR /Volumes/MacintoshHD2/mridata/IGP/ENIGMA_SZ_Thalamic_nuclei/Subjects cd /Volumes/MacintoshHD2/mridata/IGP/ENIGMA_SZ_Thalamic_nuclei/ENIGMA_BARI /Applications/freesurfer/7.3.2/bin/segmentThalamicNuclei.sh sub-BA_IGP001 #-------------------------------------------- #@# Thalamic Nuclei processing Fri 19 Aug 2022 20:10:24 AEST ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/7.3.2/MCRv97//runtime/maci64:/Applications/freesurfer/7.3.2/MCRv97//bin/maci64:/Applications/freesurfer/7.3.2/MCRv97//sys/os/maci64:/Applications/freesurfer/7.3.2/lib/gcc/lib: Invalid MEX-file '/private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64': dlopen(/private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64, 6): Symbol not found: ____chkstk_darwin Referenced from: /private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64 (which was built for Mac OS X 10.15) Expected in: /usr/lib/libSystem.B.dylib in /private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64 Error in kvlClear (line 11) Error in SegmentThalamicNuclei (line 139) MATLAB:mex:ErrInvalidMEXFile Darwin Ians-Mac-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64 Thalamic nuclei exited with ERRORS at Fri 19 Aug 2022 20:11:24 AEST

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lesions number and lesion volume of MS with samseg
by Dilek Özkan 19 Aug '22

19 Aug '22

External Email - Use Caution Hello dear all, I want to use Freesurfer-Samseg for MS lesion segmentation(cross-sectional). I have ground truth values(binary mask), lesions number and lesion volume. I will compare these with the output of freesurfer-samseg. I am confused about the usage of mri_binarize and mri_segstats. Could you explain in detail the steps I need to follow for my purpose? Best, Wish

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samseg lesions labels and values
by Cerri, Stefano 18 Aug '22

18 Aug '22

Hi Dilek, Yes, "--save-posteriors Lesions" will save a probability map with path *yourOutputDir*/posteriors/Lesions.mgz 1 and 2) Lesions are labeled as 99 in seg.mgz. A value of 0.04 in the stats file indicate that the lesion volume is 0.04 mm^3, so it makes sense that seg.mgz has no voxels labeled as 99. However, it means that something went wrong with the segmentation. What was the command you used to segment these DIR images? I'd probably use --lesion-mask-pattern 1 for them (although I've never tried to run SAMSEG on DIR images). Do you have a T1w scan to add for better whole-brain segmentation and consequently better lesion segmentation? 3) You can use the lesion probability map obtained with the --save-posteriors Lesions flag and use mri_binarize and mri_segstats to obtain binary segmentation and corresponding volumes at different thresholds. Note that you don't need to use the same threshold of run_samseg. Hope it helps, Stefano ------------------------------ Message: 2 Date: Thu, 18 Aug 2022 19:45:14 +0300 From: Dilek ?zkan <dozkan521(a)gmail.com> Subject: [Freesurfer] samseg lesions labels and values To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAPQSyvKJBirH9oOdKXeg=k8BUfdohYvMMoaLnscy-5X0GOMZ7w(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello dear all, I want to use Freesurfer-Samseg for MS lesion segmentation(cross-sectional). I have read that I need to add "--save-posteriors Lesions" to run_samseg to obtain lesion probabilities. 1)In the stats file I can see the value of "Lesions" (0.04) But when I try to see on freeview, it says label=99 (lesion label) has no value. So, I can't see the lesions. 2)There are a few labels related to lesions. For example wm lesions; (498: wmsa, 499: other_wmsa) I have no volume related to these labels neither in my stats file nor on freeview. Should I get only the "Lesions label" for the MS lesion mask? 3)As input, I am using only DIR ?mages. I w?ill try different thresholds. I have read that by playing mri_binarize and mri_segstats, we can try different thresholds without re-running anything. So, the threshold value required for mri_binarize command refers to the same threshold input in the initial the command of *run_samseg*? Best, Wish

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Freesurfer August 2022