Freesurfer March 2021

freesurfer@nmr.mgh.harvard.edu

106 participants
144 discussions

Research Assistant Positions at Washington University School of Medicine
by Dincer, Aylin 22 Mar '21

22 Mar '21

External Email - Use Caution The Benzinger Imaging Core Laboratory<https://sites.wustl.edu/benzinger/> at Washington University School of Medicine is looking for full-time Research Assistants (multiple openings available!) to work with us on magnetic resonance imaging and positron emission tomography studies of Alzheimer disease. Your responsibilities will include: 1. Processing of imaging data using neuroimaging software toolkits (FreeSurfer, MATLAB, R, SAS, SPSS) 2. Performing QC / QA on imaging data and preliminary analyses 3. Opportunities to work on your own research projects and perform statistical analyses. 4. Assisting with research studies, collection of data, set-up and maintenance of equipment. The ideal candidate will be able to work independently, communicate with laboratory staff and investigators, and maintain complete and organized records/reports. They'll have working knowledge of computer software and a familiarity with command line interface computer processing (Linux). They are interested in psychology and/or neuroscience. Apply with one of the links below interested! RTII Posting 50550<https://jobs.wustl.edu/psc/APPLHRMS/EMPLOYEE/HRMS/c/HRS_HRAM.HRS_APP_SCHJOB…> RTII Posting 50947<https://jobs.wustl.edu/psc/APPLHRMS/EMPLOYEE/HRMS/c/HRS_HRAM.HRS_APP_SCHJOB…> All the best, Aylin Aylin Dincer, Neuroimaging Engineer Benzinger Lab | Mallinckrodt Institute of Radiology | Neuroimaging Laboratory Pronouns: she/her/hers Washington University School of Medicine 4525 Scott Ave. St. Louis, MO 63110 aylin.dincer(a)wustl.edu<mailto:aylin.dincer@wustl.edu> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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License Agreement for re-distribution
by Ezequiel Mikulan 22 Mar '21

22 Mar '21

External Email - Use Caution Hi All, I've developed an open-source software for MRI pseudonymization that uses Freesurfer so I wanted to check that I'm correctly handling the licenses. In Freesurfer's License Agreement it says that: "If you distribute Software (as defined below) downloaded from FreeSurfer, all of the paragraphs of Part B of this Agreement must be included with and apply to such Software". It is not clear to me if we should copy the relevant part into our license or if it is ok if we add a text file in the software with Freesurfer's license. In other words, should Part B be included inside our license or inside the software as a file? How should I proceed? Thanks, Ezequiel

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Some brain area missing after running recon-all
by Stef Meliss 22 Mar '21

22 Mar '21

External Email - Use Caution Dear FreeSurfer Experts I am using FreeSurfer on my anatomical data to use segmentations and parcellations in my fMRI analyses in AFNI. After reviewing the output from recon-all -all (FreeSurfer version 6.0.0), I noticed that one subject is missing some occipital areas in the output (e.g. aparc+aseg.mgz). Please see attached for a screenshot of the output from freeview -v mri/brainmask.mgz \ mri/wm.mgz:colormap=heat:opacity=0.4 \ -f surf/lh.white:edgecolor=yellow \ surf/lh.pial:edgecolor=red \ surf/rh.white:edgecolor=yellow \ surf/rh.pial:edgecolor=red \ surf/rh.inflated:visible=0 \ surf/lh.inflated:visible=0 From what I read in the information on troubleshooting the output, I understand that manual editing is necessary to fix this – is this correct? I have verified that the missing areas are included in the brainmask as well as aseg.presurf. I am not sure though how to determine whether I am dealing with a segmentation error or a normalization error or maybe even a combination of both. If you could give me some pointers on which steps to take, that would be highly appreciated. Many thanks in advance for your help. Best regards, Stef

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Freesurfer 6.0.0 Container & MCR
by Ursula Tooley 22 Mar '21

22 Mar '21

External Email - Use Caution Hi Freesurfer experts, I’m trying to use the official FS 6.0.0 container from Dockerhub on a new HPC (for consistency with previous pipelines), and got the error below about not finding the Matlab Compiler Runtime in the container. I have worked around it by explicitly binding the mcr on the HPC to the container with “-B /cbica/software/external/matlab/mcr/v711/:/opt/freesurfer/MCRv80”, but is this the expected behavior? Or is there some issue? My understanding was that one of the advantages of mcr was that you could include it in containers and distribute compiled code, so was surprised to find this come up. Thanks in advance, Ursula --- Ursula Tooley Ph.D. Candidate Neuroscience Graduate Group University of Pennsylvania she/her/hers utooley(a)gmail.com 202.413.5627

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Freesurfer 7.1 recon-all -long exits with erros
by Yakupov, Renat /DZNE 22 Mar '21

22 Mar '21

External Email - Use Caution Dear Freesurfer developers, I am trying to run the longitudinal processing pipeline of our data on our HPC cluster (SGE based) and it crashes at the 3rd step - generating the longitudinal runs. The exact command is 'recon-all -long tp1dir basedir -all'. There is no error message on the screen, it just says that it exited with errors. The recon-all.log file has no error information either, other than the statement that it exited with errors. It seems to have stopped after mri_nu_correct.mni step and looking further it looks like it crashed at the beginning of orig_nu step, since orig_nu.log has this error message: /usr/bin/time: /dev/stdout: Not a directory Please see attached log files. Additional information: Freesurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 uname -a: Linux compute-0-2.local 2.6.32-504.16.2.el6.x86_64 #1 SMP Wed Apr 22 06:48:29 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux lsb_release -a: LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch Distributor ID: CentOS Description: CentOS release 6.6 (Final) Release: 6.6 Codename: Final What is interesting is that running it on the headnode directly without qsub works fine. The headnode has the same OS and tcsh versions. In my rather poorly informed opinion, it looks like fs_time is the culprit. For a quick fix, is it safe to assume that using fs_time from Freesurfer 6 wont affect the processing pipeline in any way? Thank you! Best regards, Renat.

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-hires vs -conf2hires in 7.1.1.
by Alexopoulos, Dimitrios 21 Mar '21

21 Mar '21

External Email - Use Caution Does the hires flag still generate segs at the native hi resolution and place surfaces on the 1mm volumes, whereas conf2hires generates volumes at 1mm but places surfaces on the hires images? Which option is recommended and why? Jim Get Outlook for Android<https://aka.ms/ghei36> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Freesurfer mailing list
by Burcu Tutuk 21 Mar '21

21 Mar '21

External Email - Use Caution

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Postdoctoral position
by neuroimage analyst 20 Mar '21

20 Mar '21

External Email - Use Caution Hi. We are looking for a postdoc to work with us on multimodal MRI and machine learning to predict Parkinson's disease dementia. An ideal candidate should be well versed and understand multi-shell diffusion MRI analysis and processing and have an interest in developing models for fusing across different MRI and non MRI modalities via deep learning or machine learning models. Contact me directly for more information or Apply here https://secure-web.cisco.com/1esZWcZk9kteVZxe-rcxz8vEdu1K9larHO-dBsWZn3e4QK… Apologies for cross posting. Thank you.

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equivolumetric surfaces
by バキット・ムダシル 20 Mar '21

20 Mar '21

External Email - Use Caution Dear freesurfer experts, I want to create an equivolumetric surfaces (using the tool from: https://secure-web.cisco.com/1RxQBNBh7QLlgBP46WWIONAGLCrtuooPBalXpNMTOlsF1e… <https://secure-web.cisco.com/1RxQBNBh7QLlgBP46WWIONAGLCrtuooPBalXpNMTOlsF1e…>) and to sample the intensities of the T1wDividedByT2w volume at all the depths. I created the surfaces and after running the mri_vol2surf command I faced the error below. I don’t know why the path to the surface is not correct. I tried it in different devices with different versions of freesurfer but the results were the same. Any idea what I did wrong? Thanks Mudathir ################################################# -------- freesurfer-darwin-macOS-7.1.1-20200811-8b40551 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/7.1.1 FSFAST_HOME /Applications/freesurfer/7.1.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/7.1.1/subjects MNI_DIR /Applications/freesurfer/7.1.1/mni FSL_DIR /usr/local/fsl mudathir% mri_vol2surf --src $SUBJECTS_DIR/spl_01/mri/T1wDividedByT2w.nii.gz --out $SUBJECTS_DIR/spl_01/lh.equi_intensity_1.0.mgh --hemi lh --surf $SUBJECTS_DIR/spl_01/surf/lh.equi1.0.pial --out_type mgh --regheader spl_01 srcvol = /Applications/freesurfer/7.1.1/subjects/spl_01/mri/T1wDividedByT2w.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /Applications/freesurfer/7.1.1/subjects/spl_01/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.35001; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Reading surface /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial error: No such file or directory error: MRISread(/Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial): could not open file error: No such file or directory error: mri_vol2surf: could not read surface /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial mudathirbakhit% #################################################

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mri_extract_label mgz to nii ， maximum grayvalue of amygdala subnucleis is zero.
by 况况 19 Mar '21

19 Mar '21

External Email - Use Caution TO: freesurfer(a)nmr.mgh.harvard.edu SUBJECT: mri_segstats error: mri_extract_label mgz to nii Hello FreeSurfer Developers, I'm want to study the volume and function of amygdala subnucleis, so i need to acquire the mask of amygdala subnucleis in MNI space. mri_extract_label subject_001/mri/lh.hippoAmygLabels-T1.v21.mgz 7001 lateral_nucleus_001.nii i total 77 subjects,including left and right amygdala subnucleis , totally acquired 77*18=1332 nii files. Reading the maximum grayvalue of 1332 nii files , and 5 nii files maximum grayvalue is zero. |'lh.Anterior-amygdaloid-area-126.nii'| |'lh.Medial-nucleus-111.nii'| |'lh.Medial-nucleus-319.nii'| |'rh.Anterior-amygdaloid-area-417.nii'| |'rh.Anterior-amygdaloid-area-428.nii'| I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0 2) Platform: CentOS release 6

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Freesurfer March 2021