Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30081 discussions

error installing tensorflow
by AJ 21 Apr '21

21 Apr '21

External Email - Use Caution Hi, I am having trouble installing: fspython -m pip install tensorflow==1.13.1 Not sure what the issue is. Any help would be greatly appreciated. best AJ Error message while installing: dyld: lazy symbol binding failed: Symbol not found: _utimensat Referenced from: /Applications/freesurfer/7.1.0//python/bin/python3 Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: _utimensat Referenced from: /Applications/freesurfer/7.1.0//python/bin/python3 Expected in: /usr/lib/libSystem.B.dylib

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Freeview - manjaro
by Vishnu S 21 Apr '21

21 Apr '21

External Email - Use Caution I'm getting a repeated error with libjpeg.so.62. is there any known fix?

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MGH/Harvard: Postdoc in brainstem diffusion and PET imaging in aging/dementia
by Jacobs, H (NP) 21 Apr '21

21 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@01D736D8.2A770D00]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> Or go to: https://secure-web.cisco.com/1CVgdVGKSr9D3ATbyst3zG4_gz-77rYgEGs9ReQqA4IVg9… , job nr 3153522

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Re: [Freesurfer] Hipppocampal segmentation on freesurfer
by Iglesias Gonzalez, Juan E. 21 Apr '21

21 Apr '21

Dear Saurabh, Is this recon-all (aseg.mgz), or the hippocampal subfield module? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Jindal, Saurabh" <jindals(a)wustl.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, April 20, 2021 at 11:30 To: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Hipppocampal segmentation on freesurfer External Email - Use Caution External Email - Use Caution Hi experts, I am working on freesurfer 7.1 now and my ROI is hippocampus, but it seems that there is some non-hippocampal inclusion in the form of choroid plexus and adjacent peri-ventricular white matter. Do we have a standard cutoff criterion for hippocampal inclusion? Like how many voxels for how many slices is okay to let it pass? Saurabh ________________________________ 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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question about mapping fsaverage surface atlas to subject's native volume space
by Ren, Xueying 21 Apr '21

21 Apr '21

External Email - Use Caution Dear experts, I am trying to convert an atlas which is in fsaverage surface space to each subject's native volume space. However, the alignment seems off (e.g., in the parietal lobe, see attached screenshot). I am not sure where the problem is. Here is the code that I used: tkregister2 --mov ${subj_dir}/${subj_id}/mri/rawavg.mgz --targ ${subj_dir}/${subj_id}/mri/orig.mgz --reg register.native.dat --noedit --regheader mri_surf2vol --surfval lh.Wang2015.mgz --hemi lh --subject fsaverage --fillribbon --reg register.native.dat --template ${subj_dir}/${subj_id}/mri/001.mgz --o lh.Wang2015.native.nii.gz Any help would be highly appreciated! Thank you! Caroline

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docker pull freesurfer: manifest error
by Chr. Roßmanith 20 Apr '21

20 Apr '21

External Email - Use Caution Hi, I'd like to use FS 7 in a docker container. When pulling freesurfer I get the following error message: docker pull freesurfer/freesurfer Using default tag: latest Error response from daemon: manifest for freesurfer/freesurfer:latest not found: manifest unknown: manifest unknown Any hint what I'm doing wrong? Regards, Christina Roßmanith

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-nofix topology command
by Stephan Wunderlich 20 Apr '21

20 Apr '21

External Email - Use Caution Dear all, I want to run recon-all with the -nofix command, so that no fix of the topology is done, because it takes too much time or never finishes. Especially these commands in the recon-all.log file never finish. PIDs (232383 232386)… But sometimes when I run recon-all with -nofix the surf/xh.orig files are not created since this is done by the fix topology command. Is there way to still create these files without fixing the topology of the brain so that recon-all finished successfully? I remember that in older version of freesurfer there was not fix topology and it worked as well. Best, Stephan

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FLAIR image analysis
by Jindal, Saurabh 20 Apr '21

20 Apr '21

External Email - Use Caution Hi experts, Could we analyze FLAIR images using freesurfer without having T1 images? Saurabh ________________________________ 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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problem running last step longitudinal analysis
by Zeng, Qi 20 Apr '21

20 Apr '21

External Email - Use Caution Hi Experts, I am running the last step (-long) for a longitudinal analysis, However, encountering an error message saying: "error: ERROR: number of asegs and norm volumes do not match" for all the subjects I run this time. A similar problem has been reported before as the following link. The answer to the question is 'Freesufer version too old'. I have been following the exact same steps two months ago for my last cohort and it was fine. However, this time all the subjects reporting error messages (attaching error.log). Re: [Freesurfer] mri_fuse_segmentations error in longitudinal stream (mail-archive.com) <https://secure-web.cisco.com/1xcCNPG6jeY7R3XZUuavTvtod8U5a5tYZLLrz9Kuekmq6u…> My system: x86_64 GNU/Linux Freesufer version: freesurfer/6.0.0 attached the error.log Best, Qi

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recon_all subcortical volume adjuested eTIV
by Jaime Gomez 20 Apr '21

20 Apr '21

External Email - Use Caution Hi, Does the asegs.stats produced by recon_all have the volume estimates of subcortical structures adjusted by the eTIV? I want to understand the effect of sex in the segmented structures. Should normalize the volumes of aseg.stats (Vol/eTIV) or is already done in recon_all? Thank you!

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