Freesurfer

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12 participants
30081 discussions

Subthalamic nucleus volume
by T. Pansuwan 05 Apr '21

05 Apr '21

External Email - Use Caution Dear Freesurfer experts, As part of my project, I would need to have subthalamic nucleus as one of my ROIs in which this is not available by Freesurfer. I found a probabilistic subthalamic nucleus atlas in FSL atlases (in MNI152 space) and thought I would convert this to fsaverage space. I have attempted: mri_label2vol —reg $FREESURFER_HOME/average/mni152.register.dat —seg STN-maxprob-thr25-0.5mm.nii.gz —temp $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz —o STN_mni152_in_mni305.nii.gz But the location was much more dorsal than original, 1) I was wondering if there are alternative methods I should try and what could have been the problem? At the end, I hope to obtain individual subject’s subthalamic nucleus volume, 2) I was wondering how to convert volume in fsaverage space to labels in fsaverage space so that I can convert the labels to native space? Thank you so much! Tanrada Pansuwan

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ERROR: Cannot find stats file
by atacan zeybek 05 Apr '21

05 Apr '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to create a text file of amygdalar nuclei of given subjects. I use this command: asegstats2table --subjects 8070 8071 8077 --statsfile=amygdalar-nuclei.lh.T1.v21.stats --tablefile=amygdalarnuclei.lh.T1.v21.txt –skip And get an error like this: ERROR: Cannot find stats file /home/atacan/Desktop/freesurfer/subjects/8070/stats/amygdalar-nuclei.lh.T1.v21.stats Unfortunately I can't search the mail archives because I get an another error while loading the page. Freesurfer version: CentOS 7 x86_64 (64b) tar archive Platform: Ubuntu 20.04.2 LTS

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functional to anatomical registration question
by Nasiriavanaki, Zahra 05 Apr '21

05 Apr '21

Dear Freesurferers, I have a question and I appreciate it much if you could please reply. I need to know how to check subcortical functional to anatomical registration. I know for checking the cortical registration I can use the below command: tkregister2 --s $subj --mov template.nii.gz --surf --reg init.register.dof6.dat Could you please tell me what command should I use to check the registration in subcortex? Thanks MOna Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry Massachusetts General Hospital 149 13th Street, 149-2615 Boston, MA, USA, 02129

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Running recon-all with FLAIR
by Edina Szabó 05 Apr '21

05 Apr '21

External Email - Use Caution Dear All, We are running recon-all on the latest version of FreeSurfer (v7.1.1). We are using both T1 and FLAIR images to better define the pial surfaces, but when we run the recommended command line (recon-all -subject subjectname -i /path/to/input_volume -FLAIR /path/to/FLAIR_volume -FLAIRpial -all) the pial surface is very underestimated (?.pial.FLAIR – and the aseg volume is based on these surfaces), and we get better results without the FLAIR. It seems that FreeSurfer mis-registers the FLAIR to the T1 during the process. Is there a separate step we should do to register FLAIR to T1? Thank you, Edina

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mri_vol2surf empty output
by Karan Desai 05 Apr '21

05 Apr '21

External Email - Use Caution Hi FS Forum, I am posting because after using the command mri_vol2surf to downsample my scans to fsaverage4, I ended up with empty files when viewed in Freeview. This is the command that I ran generally: mri_vol2surf --src bold_preproc.nii.gz --out lh.imagename.nii.gz --regheader sub-01 --trgsubject fsaverage4 -hemi lh I am assuming there are some tags that I may be missing which are leading me to output with empty nii.gz files. The input bold preprocessed files are viewed normally in Freeview, but the output is empty. Thank you in advance.

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Unusual left-right discrepancy of exvivo annot volumes in perirhinal and entorhinal cortices
by Yi Leng Fung 04 Apr '21

04 Apr '21

External Email - Use Caution Dear FreeSurfer Developers, I was examining the perirhinal and entorhinal annot stats from BA_exvivo_thresh.stats when I noted a significant discrepancy between the left and right hemispheres, particularly obvious on the perirhinal volumes. On a set of 40 scans from normal participants, the means of the perirhinal volumes, in mm3, was 79 on the right hemisphere and 738 on the left hemisphere. Further visual inspection of the BA annot files, along with a visual examination of the label files, suggests to me that when both the entorhinal and perirhinal cortices encounter the same vertex, the shared vertex would be assigned to the entorhinal cortex in the right hemisphere. This allocation results in an unusually small perirhinal cortex in the right hemisphere for the annotation files, and consequently a much larger right entorhinal cortex. I did not notice this unusual allocation in the left hemisphere. I am rather unclear on why this should be the case. I am currently using the stable FreeSurfer 7.1 from May 2020 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b). The release notes for version 7.1.1 do not suggest that this specific issue had been addressed, but apologies in advance if it actually had been. I look forward to hearing back from your team. Thank you. Best regards, Yi-Leng

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Postdoctoral fellowship at MGH in Brainstem PET and DTI
by Jacobs, H (NP) 04 Apr '21

04 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@01D72924.24694840] 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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Re: [Freesurfer] recon-all bug
by fsbuild 01 Apr '21

01 Apr '21

External Email - Use Caution Hello Kody, One thing you could try to get more information printed about what is going on is to edit the very first line in the recon-all script to be: #! /bin/tcsh -xf … instead of #! /bin/tcsh -f Adding the x option will echo each line in the script as it’s run with the variable values expanded, and seeing that output could help with debugging. - R. On Apr 1, 2021, at 20:29, zalewk <zalewk(a)uw.edu> wrote:        External Email - Use Caution        Hi Freesurfer team, My lab recently switched over from FS6 to FS7 and I think I've encountered a bug with recon-all.. I'm running subjects stepwise and editing them, running recon-all with the -autorecon2 and -autorecon3 flags initially are no problem, they run fine.  Trying to re-run them or use the -autorecon2-wm, -autorecon-pial etc. flags lead to crashing at certain parts of the program. The error message I get is "if: expression syntax". Digging into the code, it seems to crash when it hits a line of code "if($ud || $ForceUpdate)". The syntax superficially looks right (I don't know tcsh), checking the variables it seems like $ForceUpdate is never set, but removing it from recon-all doesn't fix the problem.  It seems the $ud variable is for checking if updates are needed for a set of volumes passed to the program. I don't know why that would be a problematic argument, removing that part seems to fix it, but this also seems like an important variable and I don't know enough about tcsh to understand why it works after removing it. Can one of the folks who wrote the recon-all script help me out? I'm running the commands step-wise as a work-around, but that is much less convenient. Best, Kody Zalewski_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] quantification of volume of perivascular spaces
by Antonín Škoch 01 Apr '21

01 Apr '21

External Email - Use Caution Dear experts, elaborating on the topics: As I read the samseg paper, I see that the flag --lesion wouldn't probably work well, since the imposed shape model, tuned for MS lesions, is not appropriate for perivascular spaces which have different shape. Is here a way for user to redefine the shape prior for samseg to tune it for perivascular spaces segmentation? Thank you in advance for any help, Antonin Dear experts,We would like to quantify volume of brain perivascular spaces. Ideally longitudinally - i.e. to study the dynamics of perivascular spaces in multiple measurement of the same subject. Is it possible to use samseg for this? Do you think, that --lesion flag in samseg would work estimation of perivascular spaces? Or other setting of samseg will be better option? Or, would you rather recommend other tools? Any idea/comment will be greatly appreciated. Regards, Antonin Skoch

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Re: [Freesurfer] Left-Right labeled brain MRI
by Arman Avesta 01 Apr '21

01 Apr '21

External Email - Use Caution Oh wow you're brilliant as always, Anastasia! Thank you :) Yendiki, Anastasia Wed, 31 Mar 2021 14:30:26 -0700 How about an aseg volume? The left and right are labeled with different numbers 🙂 ________________________________ From: freesurfer-boun...(a)nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of Arman Avesta <avesta.ar...(a)yahoo.com> Sent: Wednesday, March 31, 2021 5:24 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Left-Right labeled brain MRI External Email - Use Caution Hi, Thank you again for responding to my previous questions! I'm writing a python class to show MR images, and I need to have one brain MRI volume (e.g. nifti or mgz) in which left and right are labeled in some way. FSL website used to provide a test MRI volume that was labeled: [Inline image] Unfortunately I can't find this volume on the internet anymore! So I need help :) Thank you, Arman

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