Freesurfer April 2021

freesurfer@nmr.mgh.harvard.edu

104 participants
144 discussions

Freeview does not open files through the Freeview window (Terminal only)
by Max Korbmacher 14 Apr '21

14 Apr '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to open files through Freeview v.2.0 (I’m using freesurfer-i386-apple-darwin11.4.2-stable6-20170119), but cannot do it “manually” but only through scripting / the terminal. The operating system is macOS BigSur 11.2.3 (20D91). The latest attempt to open files this way have led the program to crashes or freeze. Please find attached an error report from the program crashing. Best, Max

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perl version needed for FS5.3
by Saemann, Philipp 14 Apr '21

14 Apr '21

External Email - Use Caution Hi all, we have problems in launching the recon-all command of FS5.3 (needed for a reconstruction of old results): during the nu_correct command various perl commands are called with a fix #!/usr/bin/perl -w The primary error is some "Can't used 'define(@Array)'. A bit of search showed that this seems perl version issue. Up to versio 5.18 this only seems to produce a warning, but no fatal error. On the respective node of our cluster we have installed another perl and call this module before, so the "which perl" correctly points to that perl main function. Still, errors appear, e. g. cannot locate MNI/Startup.pm, so obviously some packages are not correctly linked. What is the Installation recommendation on a Linux 64 Bit System to maFS5.3 compatible with the local perl? Best, Philipp

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Re: [Freesurfer] striatal parcellation
by Marques Ana-raquel 14 Apr '21

14 Apr '21

External Email - Use Caution ? Dear Freesurfer Team, we would like to perform a volumetric analysis in Parkinson's disease using freesurfer, and we have previously used recon all to perform tha surface based analysis and automate segmentation. We would also like to extract the different volumes of striatal parcellation using the Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz. However, we can't find how to perform this parcellation, and how to add it to the recon all steps? Thank you very much for your help! ? Ana Marques MD, PhD Service de Neurologie Hopital Gabriel-Montpied CHRU Clermont-Ferrand ar_marques(a)chu-clermontferrand.fr<mailto:ar_marques@chu-clermontferrand.fr> TEL: 04 73 751 600 FAX: 04 73 751 596

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mris_label2annot - make all command exiting with errors
by Marion DURTESTE 14 Apr '21

14 Apr '21

External Email - Use Caution Dear FreeSurfer developers, When running RECON-ALL -MAKE ALL after correcting a few errors from the recon-all output, it exits with an error. This occurs when the mris_label2annot command is called. > Loading /Users/mariondurteste/Documents/PhD/FreeSurfer/ReconstructedAfterQC/ToDo/ALA076_1/surf/lh.orig > 1 1376057 FG1 > 2 16711935 FG2 > ERROR: lh.FG2.mpm.vpnl.label, n=580, vertex 119494 out of range If we rerun the -make all command a second time it then finishes without errors. Do you know why this is ? * FREESURFER version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 * Platform: macOS BigSur 11.2.2 Thanks for your help ! Marion D

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make_average_subject error
by Jordan Mullins 14 Apr '21

14 Apr '21

External Email - Use Caution Hello, I am trying to create an average subject from a set of subjects, but keep getting an error that says "mghRead(mri/norm.mgz, -1): could not open file". I've read that several others have solved this issue by installing the patch available at http://secure-web.cisco.com/1holHARxUGo27ZLvlj5vX0sbezsRgmRaNdE1T-Z728EASqG…. I did this, but continue to get the same error. I'm working with Freesurver Version 6.0.0 and MacOS Big Sur Version 11.2.3. I've attached the recon-all.log below, but please let me know if you need additional information. Any insight on this would be appreciated! Thank you! Jordan -- *Jordan L. Mullins, B.A.* Doctoral Student, Department of Psychology University of California, Riverside http://secure-web.cisco.com/1mshZJHsrG2WjtWWNRNV7vunyA6LicMMo4DqXl-CgSaJWwH…

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recon-all transformations: raw nii to T1.mgz
by Peled, Noam 14 Apr '21

14 Apr '21

Hello, I was running recon-all on a raw T1 image with the following properties: dimensions: 126 x 144 x 88 voxel sizes: 1.777778, 1.777778, 1.780000 Orientation: PSL Besides the raw T1, I have other nii files with the same dimensions and orientation that I want to visualize on top of the recon-all output T1.mgz. How can I run the same transformations (and reslicing) that were used in recon-all (from my raw nii file to T1.mgz) on the other nii files? Thanks! Noam

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mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter
by Camerino, I.L. (Ileana) 14 Apr '21

14 Apr '21

External Email - Use Caution Dear Freesurfer experts, I am running recon all as part of the tractography pipeline on a group of stroke patients. This is are the first lines of my log file: /opt/freesurfer/6.0/bin/recon-all -s sub-056 -i /project/3015068.01/ilecam/Reolang/Data/sub-056/MP2RAGE_denoised_roi.nii.gz -all -sd /project/3015068.01/ilecam/Reolang/Freesurfer/ -qcache subjid sub-056 setenv SUBJECTS_DIR /project/3015068.01/ilecam/Reolang/Freesurfer FREESURFER_HOME /opt/freesurfer/6.0 Actual FREESURFER_HOME /opt/freesurfer/6.0 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Recon all did not finished successfully because a watershed error: Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all. I added many wm control-points to nu.mgz and to T1.mgz but when I re-run recon-all I still get the same error. Please can you help me to solve this problem? Thank you in advance Best regards, Ileana Camerino PhD candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognition Spinozabuilding Room B02.25 Montessorilaan 3, 6525 HR Nijmegen The Netherlands Tel. +31-24 3612618

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MGH/Harvard: Postdoc position in 7T brainstem fMRI and non-invasive vagus nerve stimulation
by Jacobs, H (NP) 14 Apr '21

14 Apr '21

External Email - Use Caution Postdoc Position in the Department of Radiology, Massachusetts General Hospital / Harvard Medical School The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) in Boston, Massachusetts, has an opening for highly qualified individuals at the post-doctoral level to work with Dr. Heidi Jacobs. The Jacobs lab is part of the Gordon Center for Medical Imaging at MGH and focused on improving the early detection and early treatment of Alzheimer’s disease. The lab focuses on the neuromodulatory subcortical nuclei, in particular the locus coeruleus, using a variety of approaches, including 7T MRI, PET imaging, pupil measurements, physiological recording, blood-based markers and cognitive assessments. This postdoc will be involved in a new NIA-funded R01 project using 7T imaging and non-invasive stimulation of the vagus nerve to modulate cognitive performance and locus coeruleus activity in older individuals at risk for Alzheimer’s disease. Our team and this project are closely affiliated with the Harvard Aging Brain Study (HABS). The position is available from June 2021. Most of the work in this project will be performed at the Athinoula A. Martinos Center for Biomedical Imaging, Charlestown Navy Yard. The candidate will be part of ongoing collaborations and be able to work in a stimulating and inspiring environment. The Department of Radiology at MGH is equipped with the first mobile PET/CT, the first brain PET/MRI, the first whole-body PET/MRI in the USA and several MRI scanners, including two 7T ultra-high-field scanner. It is equipped with a large-scale shared memory computing facility for parametric image analysis, tomographic reconstruction, Monte Carlo simulation, and other computationally intensive research applications. Our research group values open communication, motivation, optimism, mutual respect, teamwork, and innovative thinking. Dr. Jacobs is highly committed to individualized mentoring to help trainees achieve the most out of their postdoctoral candidature and to move forward in their career. At a minimum, the training environment will include professional development, one-on-one meetings, group lab meetings, frequent seminars and journal clubs, opportunities to present their work at national and international scientific conferences (i.e. Human Amyloid Imaging, Alzheimer’s Association International Conference, OHBM), and manuscript preparation for publication in high impact journals. In addition, Dr. Jacobs has a strong funding record and will strongly encourage and provide mentorship in grant applications. Requirements: Candidates should have a Ph.D. in Cognitive Neuroscience, Computational Neuroscience, Medical Physics, Computer Science, Biomedical Engineering or related disciplines. Strong analytical, quantitative and programming skills are essential (e.g., fMRI-physiological data analyses, data modeling, simulations). Prior experience in fMRI, non-invasive neurostimulation methods and physiological investigation is advantageous. The candidate should be highly motivated, a strong communicator, possess internal drive to learn independently, but also be comfortable with working as part of a larger collaborative team. A real necessity is a passion for science, strong scientific writing and organizational skills, and a positive attitude. Experience in Alzheimer’s disease dementia or aging would be beneficial. MGH & HMS are equal-opportunity, affirmative action employers. Women and minority candidates are encouraged to apply. [cid:image001.png@01D730FB.C114F660]Apply: The successful candidate will have joint appointments at MGH and HMS. If interested, please send your CV, letter describing interests, background, major achievements, skills, goals and contact information for three professional references. Please send application materials to Dr. Heidi Jacobs, Assistant Professor of Radiology, at hjacobs(a)mgh.harvard.edu<mailto:hjacobs@mgh.harvard.edu>

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MGH/Harvard: Brainstem PET and DTI postdoc position
by Jacobs, H (NP) 14 Apr '21

14 Apr '21

External Email - Use Caution Postdoc Position in the Department of Radiology, Massachusetts General Hospital / Harvard Medical School The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) in Boston, Massachusetts, has an opening for highly qualified individuals at the post-doctoral level to work with Dr. Heidi Jacobs. The Jacobs lab is part of the Gordon Center for Medical Imaging at MGH and focused on improving the early detection and early treatment of Alzheimer’s disease. The lab focuses on the neuromodulatory subcortical nuclei, in particular the locus coeruleus, using a variety of approaches, including 7T MRI, PET imaging, pupil measurements, physiological recording, blood-based markers and cognitive assessments. This postdoc will be involved in a new NIA-funded project working on new methods in PET and diffusion imaging to examine tau propagation in aging and Alzheimer’s disease. Our team and this project is embedded within the Harvard Aging Brain Study (HABS). Ideal start date is around July/August 2021. Most of the work in this project will be performed at the Athinoula A. Martinos Center for Biomedical Imaging, Charlestown Navy Yard. The candidate will be part of ongoing collaborations and be able to work in a stimulating and inspiring environment. The Department of Radiology at MGH is equipped with the first mobile PET/CT, the first brain PET/MRI, the first whole-body PET/MRI in the USA and several MRI scanners, including two 7T ultra-high-field scanner. It is equipped with a large-scale shared memory computing facility for parametric image analysis, tomographic reconstruction, Monte Carlo simulation, and other computationally intensive research applications. Our research group values open communication, motivation, optimism, mutual respect, teamwork, and innovative thinking. Dr. Jacobs is highly committed to individualized mentoring to help trainees achieve the most out of their postdoctoral candidature and to move forward in their career. At a minimum, the training environment will include professional development, one-on-one meetings, group lab meetings, frequent seminars and journal clubs, opportunities to present their work at national and international scientific conferences (i.e. Human Amyloid Imaging, Alzheimer’s Association International Conference, OHBM), and manuscript preparation for publication in high impact journals. In addition, Dr. Jacobs has a strong funding record and will strongly encourage and provide mentorship in grant applications. Requirements: Candidates should have a Ph.D. in Cognitive Neuroscience, Computational Neuroscience, Medical Physics, Computer Science, Biomedical Engineering or related disciplines. Strong analytical, quantitative and programming skills as well as expertise in diffusion imaging are essential. Prior experience in PET is advantageous. The candidate should be highly motivated, a strong communicator, possess internal drive to learn independently, but also be comfortable with working as part of a larger collaborative team. A real necessity is a passion for science, strong scientific writing and organizational skills, and a positive attitude. Experience in Alzheimer’s disease dementia or aging would be beneficial. MGH & HMS are equal-opportunity, affirmative action employers. Women and minority candidates are encouraged to apply. [cid:image001.png@01D730FB.32A4E1B0]Apply: The successful candidate will have joint appointments at MGH and HMS. If interested, please send your CV, letter describing interests, background, major achievements, skills, goals and contact information for three professional references. Please send application materials to Dr. Heidi Jacobs, Assistant Professor of Radiology, at hjacobs(a)mgh.harvard.edu<mailto:hjacobs@mgh.harvard.edu>

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preproc-sess
by Manenti, Giorgio 13 Apr '21

13 Apr '21

External Email - Use Caution Dear Experts, I’m encountering a problem when running the preproc-sess on my functional data. When using the flag -surface subject hemi i am getting ":ERROR: source volume is neither source nor target of the registration”. There is any alternative way to get the surfaces? Many thanks for your help Best Giorgio

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Freesurfer April 2021