Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

error running samseg on cluster
by Ritobrato Datta 12 Aug '21

12 Aug '21

External Email - Use Caution Hi All, I am trying to run samseg as follows on a cluster and am getting a message that I need to install tensorflow (which is already installed). Please see below. Please advise how to fix this. Many thanks Rito ------------------------------------------------------------- run_samseg --input t12t2.nii.gz t2_brain.nii.gz --lesion --lesion-mask-pattern 0 1 --save-posteriors --output t2_lesions error: This tool requires tensorflow, but fspython does not ship with tensorflow by default. You (or a sys admin) can install the CPU version via:fspython -m pip install tensorflow==1.13.1 fspython -m pip install tensorflow==1.13.1 Requirement already satisfied: tensorflow==1.13.1 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (1.13.1) Requirement already satisfied: protobuf>=3.6.1 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (3.17.3) Requirement already satisfied: keras-applications>=1.0.6 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.0.8) Requirement already satisfied: absl-py>=0.1.6 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (0.13.0) Requirement already satisfied: six>=1.10.0 in /home/rito/software/freesurfer7/python/packages (from tensorflow==1.13.1) (1.14.0) Requirement already satisfied: grpcio>=1.8.6 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.39.0) Requirement already satisfied: termcolor>=1.1.0 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.1.0) Requirement already satisfied: astor>=0.6.0 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (0.8.1) Requirement already satisfied: gast>=0.2.0 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (0.5.2) Requirement already satisfied: numpy>=1.13.3 in /home/rito/software/freesurfer7/python/packages (from tensorflow==1.13.1) (1.18.4) Requirement already satisfied: keras-preprocessing>=1.0.5 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.1.2) Requirement already satisfied: wheel>=0.26 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (0.37.0) Requirement already satisfied: tensorboard<1.14.0,>=1.13.0 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.13.1) Requirement already satisfied: tensorflow-estimator<1.14.0rc0,>=1.13.0 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow==1.13.1) (1.13.0) Requirement already satisfied: h5py in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from keras-applications>=1.0.6->tensorflow==1.13.1) (3.1.0) Requirement already satisfied: markdown>=2.6.8 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (3.3.4) Requirement already satisfied: werkzeug>=0.11.15 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (2.0.1) Requirement already satisfied: mock>=2.0.0 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from tensorflow-estimator<1.14.0rc0,>=1.13.0->tensorflow==1.13.1) (4.0.3) Requirement already satisfied: cached-property; python_version < "3.8" in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from h5py->keras-applications>=1.0.6->tensorflow==1.13.1) (1.5.2) Requirement already satisfied: importlib-metadata; python_version < "3.8" in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from markdown>=2.6.8->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (4.6.3) Requirement already satisfied: dataclasses; python_version < "3.7" in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from werkzeug>=0.11.15->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (0.8) Requirement already satisfied: zipp>=0.5 in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from importlib-metadata; python_version < "3.8"->markdown>=2.6.8->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (3.5.0) Requirement already satisfied: typing-extensions>=3.6.4; python_version < "3.8" in /home/rito/software/freesurfer7/python/lib/python3.6/site-packages (from importlib-metadata; python_version < "3.8"->markdown>=2.6.8->tensorboard<1.14.0,>=1.13.0->tensorflow==1.13.1) (3.10.0.0) You are using pip version 18.1, however version 21.2.3 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

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FreeSurfer QA TOOLS errors
by Xin Qi 12 Aug '21

12 Aug '21

External Email - Use Caution Hello FreeSurfer Developers: We would like to use FreeSurfer QA TOOLS. After installing it, I tested it on one subject that finished Freesurfer recon-all processing using the latest FreeSurfer 7.1. but got errors that seem many files are missing in the mri, surf, stat folders created by FreeSurfer 7.1, which are requested by FreeSurfer QA TOOLS I attach the recon_checker summary log and zipped snaps file for your reference. *1) FreeSurfer version: * freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 *2) Platform: *Ubuntu 18.04.5 LTS (Bionic Beaver) *3) uname -a:* Linux ip-10-111-250-7 5.4.0-1039-aws #41~18.04.1-Ubuntu SMP Fri Feb 26 11:20:14 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux *4). recon_checker.ALL.summary.log:* see attached file with zipped snaps folder contains snap shoots Looking forward to hearing from you. Thank you very much. Best regards Xin

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Re: [Freesurfer] Announcing FreeSurfer version 7.2
by fsbuild 12 Aug '21

12 Aug '21

External Email - Use Caution Hello Kiyotaka, Please try refreshing your copy/install of the Ubuntu 7.2.0 distribution as the packages have been updated to fix the warning below. I think you were using the installer, so you could try the commands below to download and re-install with apt.  (If you were using the tar file then just change the file name in the wget command to be freesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz, expand it in the right location and skip the commands with sum, apt remove, apt install). .... with installer ... $ rm -f  freesurfer_7.2.0_amd64.deb $ wget https://secure-web.cisco.com/1i8WchnZn-ZDMrXexp7WlIVIxgdWjuz06xq1yUvfYcAZHM… $ sum freesurfer_7.2.0_amd64.deb 20191 3199044 $ sudo apt remove freesurfer .... output deleted .... $ apt install ./freesurfer_7.2.0_amd64.deb .... output deleted ... .... check environment ... $ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh .... the output should have no warnings and you can also check ... $ env | grep MINC MINC_BIN_DIR=/usr/local/freesurfer/7.2.0/mni/bin MINC_LIB_DIR=/usr/local/freesurfer/7.2.0/mni/lib $ which nu_correct /usr/local/freesurfer/7.2.0/mni/bin/nu_correct - R. -------- freesurfer-linux-ubuntu18_x86_64-7.2.0-20210714-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      /home/username/freesurfer/7.2.0/subjectsWARNING: MINC_BIN_DIR not defined.         'nu_correct' and other MINC tools         are used by some Freesurfer utilities.         Set NO_MINC to suppress this warning.WARNING: MINC_LIB_DIR not defined.         Some Freesurfer utilities rely on the         MINC toolkit libraries.         Set NO_MINC to suppress this warning.FSL_DIR           /usr/local/fsl =====

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fsaverage file download
by Shruthi Srinivasan 10 Aug '21

10 Aug '21

2 1

bilateral seed to whole brain connectivity analysis
by Nasiriavanaki, Zahra,M.D. 10 Aug '21

10 Aug '21

Dear Experts, I have functional ROIs on the left and right hemispheres, and I’m trying to do a bilateral seed to whole brain connectivity analysis. My question is: in order to make a bilateral seed, shall I manually average the .dat files (output of fcseed-sess) from left hemi and right hemi to make a bilateral seed (see below)? fcseed-config -segid 1 -seg lh.mgz -fcname lh.dat -fsd rest -rlf restruns -mean -cfg lh.config fcseed-sess -s . -d . -cfg lh.config fcseed-config -segid 1 -seg rh.mgz -fcname rh.dat -fsd rest -rlf restruns -mean -cfg rh.config fcseed-sess -s . -d . -cfg rh.config bilateral.dat= (lh.dat+rh.dat)/2 OR should I use the left and right ROIs in fcseed-config at the same time, so the out put of fcseed-sess be the bilateral seed? Please see below commands: fcseed-config -segid 1 -seg lh.mgz -segid 1 -seg rh.mgz -fcname bi.dat -fsd rest -rlf restruns -mean -cfg bi.config fcseed-sess -s . -d . -cfg bi.config I appreciate your responses. Thanks, Mona Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

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Fwd: [Neuroimaging] [Nibabel] Discourse category for Surface API discussions
by Satrajit Ghosh 09 Aug '21

09 Aug '21

External Email - Use Caution fyi ---------- Forwarded message --------- From: Christopher Markiewicz <markiewicz(a)stanford.edu> Date: Mon, Aug 9, 2021 at 5:01 PM Subject: [Neuroimaging] [Nibabel] Discourse category for Surface API discussions To: neuroimaging(a)python.org <neuroimaging(a)python.org> Hi all, I'm starting to work on the Surface API portion of the Nibabel grant. I've created a category on the Discourse here: https://secure-web.cisco.com/1fZyTqmwozZU5Qoa2utEX0kDdW_8B7XIMEFga96aHR-Yct… And I've started some initial notes here mostly laying out the problem: https://secure-web.cisco.com/1qQtCe4EJSW0O7Z_CBMnNittP03bU4FYzr1xy2YZOTw_oa… The next steps are going to be to identify use cases for people working with surface data, which will also involve finding people who I may not know about, so please forward this on to people who might be interested in joining the discussion. -- Christopher J. Markiewicz, PhD Center for Reproducible Neuroscience Stanford University _______________________________________________ Neuroimaging mailing list Neuroimaging(a)python.org https://secure-web.cisco.com/1Zrv7RS4PEvZfb7azKaQbWoX5ysGPT8TngX38S6Ud5LMDA…

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Announcement for Neurodevelopmental Special Issue in Brain Sciences
by Picci, Giorgia 09 Aug '21

09 Aug '21

External Email - Use Caution Dear all, It is our pleasure to invite manuscript submissions for publication in our special issue entitled "Neurodevelopmental Correlates of Substance Use and Abuse in Adolescence" in Brain Sciences (IF: 3.33; ISSN 2076-3425; CODEN: BSRCCS). For this special issue, we are soliciting original research papers, brief reports, reviews, perspectives, and meta-analyses regarding the neural antecedents and consequences of adolescent substance use. We particularly encourage submissions that focus on cutting-edge methodological approaches and imaging methods (e.g., brain-predicted age, multimodal approaches, leveraging large datasets, dynamic/brain state & functional connectivity). Manuscripts are due November 25th, 2021 and will be peer-reviewed and published online as they are accepted. Further details regarding this special issue can be found here<https://secure-web.cisco.com/1gLIbySUMZ9_BPqko-w2QqJO5OhNNe2MASV8liqYOJ4ySQ…>. If you have any questions, please feel free to reach out to the guest editors or managing editor (Emma Paintain, emma.paintain(a)mdpi.com<mailto:emma.paintain@mdpi.com>). Kind regards, Dr. Emma Rose (Penn State University) Dr. Giorgia Picci (Boys Town National Research Hospital & PSU) ______________________________________ Giorgia Picci, PhD (she/her) Postdoctoral Research Fellow * DICoN Lab<https://secure-web.cisco.com/1x2Ljh6i4aAkfI4hxBBOh8XoGqaNEM2kgNwjnks9OV8A-R…> Institute for Human Neuroscience Boys Town National Research Hospital

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dwi_orig_las issue trac-all -prep in FS 7.2
by juergen.haenggi＠upd.unibe.ch 09 Aug '21

09 Aug '21

External Email - Use Caution Dear TRACULA experts I use the newest version of TRACULA (FS 7.2, official release) and face the same problem as already reported by another user https://secure-web.cisco.com/1X5AHUcHXClyJtmxIDuq0cEQ7oR9Y81XGrojDN0ZsSnvYn… As suggested by the answer to the above link, this other user did not use an official release of FS, and no explicit solution was mentioned in this link. I used an official version, but got the same error. BTW, if using TRACULA in FS 7.1.1, this error did not occur. The error that occurs is the following (log and config file attached): error: niiRead(): error opening file /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/01_TRACULA_Results_NIFTI_FS720/IPS_CO_007/dmri/dwi_orig_las.nii.gz As described by the other user, the file is initially created, but then renamed to dwi.nii.gz and therefore not present in the dmri directory. BTW, my data is already in LAS orientation. The error only occurs if using NIFTI files but not if using the DICOM files. Actually, I could use DICOMs, but I faced the problem that dTE could not be found in the DICOM header and/or b0info.dat file, respectively, (see error below) because only one TE is present in the DICOM header of the phase image as suggested by the meta data in the OSIRIX DICOM viewer, and therefore I would rather use NIFTI files and define dTE in the config file as it has been suggested that this is possible in TRACULA in FS 7.2. writing to /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/b0pha.nii.gz... mri_probedicom --i /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/00_TRACULA_Prepared_DICOMs_FS720/IPS_CO_007/Phase/33163229.dcm > /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/b0info.dat ERROR: Need dTE for field map /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/00_TRACULA_Prepared_DICOMs_FS720/IPS_CO_007/Phase/33163229.dcm However, if I try to use DICOM files and "set dTE = 2.46“ in the config file, the same error occurred as when not setting dTE in the config file. Thanks in advance for any advice Best regards Jürgen

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Ubuntu image developer password
by John Hayes 07 Aug '21

07 Aug '21

External Email - Use Caution Hi, I installed the Ubuntu image in virtual box to run free surfer on windows, but it is requiring a password to log into the developer user. Is it possible to get this password? Thanks, John

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Diffusion MRI postdoc position
by Corinna Bauer 06 Aug '21

06 Aug '21

External Email - Use Caution We are seeking a full-time postdoctoral fellow with experience in diffusion analysis with an emphasis on network-based approaches, NODDI, DKI, and tract-specific analysis. The NIH-funded project employs structural, diffusion, and relaxometry based MRI methods to target thalamo-cortical changes in morphometry, neural networks, and MRI-based markers of myelin in youths with perinatal brain injury. We are seeking a candidate with the following qualifications: • Doctoral degree in computer science, neuroscience, or related field • Advanced skills in the processing and analysis of diffusion (including connectivity, DKI, and NODDI approaches) data, particularly focusing on network-based approaches are required • Strong coding skills in python, MATLAB, bash, etc. • Experience with fMRI design and analysis is a plus Interested candidates should send a cover letter including, a brief summary of their research interests and career goals, their C.V., and the names and phone numbers of three references to Corinna Bauer ( Corinna_Bauer(a)meei.harvard.edu) Additional details can be found at: https://secure-web.cisco.com/1PRcDuRd4mfRf2yIwKkDZ9B-oKmLA-2p68m-jCGxuMCJA8…

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