Freesurfer December 2022

freesurfer@nmr.mgh.harvard.edu

75 participants
92 discussions

TRACULA tutorial and processing questions
by Tran, Diana 05 Dec '22

05 Dec '22

Dear FreeSurfer TRACULA experts, I am new to FreeSurfer and using TRACULA to process DTI data. From the mail-archive, I understand TRACULA mainly needs the aparc+aseg output from recon_all in order to run. Using the recon_all output information, I was able to complete the 3 steps in TRACULA, but only after switching from the 7.1.1 version to the 6.0.5.1 version of FreeSurfer. I have the following questions about TRACULA: 1. Some of the tutorial files that are needed to run the TRACULA tutorial are not there upon downloading or do not match the tutorial instructions. Is there an updated version of the tutorial instructions that match the current files? 2. Do you have insight as to why TRACULA -prep exits with ERRORS when it's run with version 7.1.1 of FreeSurfer, but exits without errors when it's run with version 6.0.5.1? Reviewing the scripts, it seems the most notable difference are the values for i_ras, j_ras, and k_ras. Version 6.0.5.1 gives varying numbers, while version 7.1.1 gives values of -1, 0, or 1. 3. I came across the webpage introducing version 7.2 with substantial updates for TRACULA after having run my dataset with version 6.0 (https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) It states, "Unless the new features are employed, recon-all will give the same exact result as 7.1.1 and 7.1.0." Is this also true for TRACULA? Would you advise rerunning my dataset with version 7.2 of TRACULA (or even 7.3, but the recent release notes for this version didn't mention TRACULA changes)? 4. Is there another location to find the dwi_motion_byvol.txt output file? Currently the instructions say it should be located in the /subject#/dmri folder but only the dwi_motion.txt can be found there (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaOutputs) 5. For some subjects with visible motion distortions in manual quality check, I ran TRACULA as a second QC measure. However, they are still given a score of 0 and 1 for percent bad slices and average dropout score, respectively, according to the dwi_motion.txt. In fact, for all the subjects I ran, they all received those scores with the exception of one subject, who actually had minimal motion artifacts in manual QC. I'm not sure how to interpret this and was wondering if you could please advise. 6. While combing through the mail-archive to better understand how to use TRACULA, I noticed dt_recon being mentioned with TRACULA processing. Is this a step that needs to be completed before running TRACULA? Or is it part of an older version of processing that is already built into the updated versions 6.0+ of TRACULA? Thank you in advance for your time! Warm regards, Diana

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SynthSR and Apple M1 Incompatability
by Sorby-Adams, Annabel 05 Dec '22

05 Dec '22

Dear FreeSurfers, I have been trying to get SynthSR up and running and have come to the realisation there is a conflict with the current tools and the new apple chips (macOS Monterey, Apple M1 chip, 16GB). I have tried the workaround via this thread on the mailing list to no avail (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg73091.html) I then tried to install homebrew, conda, and run a virtual environment which allowed me to download tensorflow. The steps I followed with comments are attached. However, now there is an issue when calling mri_synth as follows: File "/Applications/freesurfer/dev/python/scripts/mri_synthsr", line 18, in <module> import tensorflow as tf ModuleNotFoundError: No module named 'tensorflow' I am not sure if there is a disconnect in where I have installed tensorflow such that mri_synthsr is unable to locate it. If anyone has found a workaround for this they would be willing to share it would be greatly appreciated! Thanks, Annabel Annabel Sorby-Adams, PhD Fulbright Postdoctoral Research Fellow Department of Neurology Massachusetts General Hospital Lunder 6 55 Fruit Street, Boston MA https://www.massgeneral.org/ Harvard Medical School https://hms.harvard.edu/ E asorby-adams(a)mgh.harvard.edu T +1 617 251 6465

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Are inflated surfaces vertices transformed in Freeview?
by Sarah Lavelle 04 Dec '22

04 Dec '22

External Email - Use Caution Dear freesurfer, I am trying to import surface files into MATLAB and highlight a selected vertex on it. I am getting the coordinates from FreeView and then trying to find the same position in my matlab plot using the RAS surface coordinates. My code works perfectly for lh.pial but not for lh.inflated. Is lh.inflated transformed in FreeView? Why doesn't my method work the same for the inflated surface? How can I fix this? HIGHLIGHT vertex '80609' on INFLATED SURFACE in matlab %Vertex 80609 on /subject/bert/surf/lh.inflated; % FROM FREEVIEW : %lh.pial = [-39.45, 8.55, 50.40] = Surface RAS %lh.inflated = [-37.02, 8.26, 48.41] = Surface RAS [vertices, faces] = freesurfer_read_surf( '/Applications/freesurfer/7.3.2/subjects/bert/surf/lh.inflated'); % Plot the rotated surface data patch('Faces', faces, 'Vertices', vertices, 'FaceColor', [0.5 0.5 0.5], 'EdgeColor', 'none'); % Hp = patch('vertices',vertices,'faces',faces(:,[1 3 2])); camlight('headlight','infinite'); title('Left hemisphere of the cortex (file = lh.pial) with a point overlayed in FreeSurfer Surface RAS Coordinate System') xlabel('R') ylabel('A') zlabel('S') hold on; str=sprintf('Vertex A'); label1=str; vertexA=[-37.02, 8.26, 48.41]; plot3(vertexA(1), vertexA(2), vertexA(3), '*r'); text(vertexA(1),vertexA(2), vertexA(3),label1,'Color','r', 'FontSize',20, 'VerticalAlignment','bottom','HorizontalAlignment','left'); Any help would be greatly appreciated, Thanks! Sarah

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Application portal open for 2023 session of Training in Advanced Statistical Methods in Neuroimaging and Genetics
by ROBERT CARY WELSH 04 Dec '22

04 Dec '22

External Email - Use Caution Hi folks, We are pleased to announce that the application portal is open for the NIH funded 2023 session of the course, “Training in Advanced Statistical Methods in Neuroimaging and Genetics”. The course will start on Monday, April 3, 2023 and finish on April 14, 2023. We are happy to announce that the course is to be held in person, in Salt Lake City, Utah, United States at the University Guest House Conference Center. The course is an intensive 2-weeks, about 8 hours per day of a mix of lectures and hands-on computer labs. https://secure-web.cisco.com/1JJFCdzRClJM2Xqll0c8NLjKWqD4YoOYoDg4SgxaTCGUF-… For those staying on site the course cost is $3000, which includes hotel accommodations at the Guest House (arrival on April 2 with departure on April 15), breakfast, lunch, day time snacks, and the planned evening activities. There is also a commuter course tuition for those that might be local to the SLC metropolitan area or are fine with finding their own accommodations. The commuter cost is $850, which will include lunch, day time snacks, and the planned evening activities. More details on the website. All course attendees will arrange for their own transportation to Salt Lake City. The course cost does include a daily pass to the Salt Lake City Trax light rail/commuter system. (Please note that the course instructors effort is supported by the NIH grant thus avoiding that cost be passed on to the course attendees). Because of the limited size and advanced nature of the course, attendance is by application only – please make sure to fully read the website instructions. In general, applicants must be a US citizen or permanent resident, though we do have the ability to accommodate 2 to 5 individuals that do not meet this criteria. We anticipate the total class size to be between 18 and 25 students. There are opportunities for scholarships which can partially offset hotel accommodations. These are based on true financial need and you will be instructed how to apply if you are admitted to the course. We look forward to seeing you in SLC in 2023! Robert Welsh ------------------------------ Robert Welsh, PhD Course Director, Training in Advanced Statistical Methods in Neuroimaging and Genetics Anna Docherty, PhD Associate Course Director, Training in Advanced Statistical Methods in Neuroimaging and Genetics Huntsman Mental Health Institute Department of Psychiatry University of Utah

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Autorecon-pial with T1w and T2w images
by Steve Petersen 04 Dec '22

04 Dec '22

External Email - Use Caution Dear FreeSurfer experts, After reviewing and manually editing the recon-all outputs in freeview, I'm going to re-run the recon-all command with the autorecon-pial flag. My question is, does the autorecon-pial also take into account the T2w image or does it only consider the T1w image?. In case of not considering both images (T1w and T2w), is there a way to run the autorecon-pial with both images in order to get a more accurate pial surface segmentation? Thank you very much in advance. Best regards,

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unzip the FS_7_2_0_Ubuntu_18_04_06.ova.7z file
by Zeyu Chang 03 Dec '22

03 Dec '22

External Email - Use Caution Hi, I am writing to request the pass code to unzip the FS_7_2_0_Ubuntu_18_04_06.ova.7z file. Thanks, Zeyu

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LGI label statistics
by Luke K Harper 02 Dec '22

02 Dec '22

External Email - Use Caution Dear freesurfer, I am attempting to extract LGI statistical data from a label running the mri_segstats command Here is the script I am attempting to run: mri_segstats --slabel A152 rh rh.c1.label --i $SUBJECTS_DIR/A152/surf/rh.pial_lgi --sum rh.aparc.pial_lgi.stats This returns an error: error: mri_segstats: could not open label file rh.c1.label I created the label using freeview - make closed path - then filling the closed path. The label projects on pial and inflated surfaces Furthermore the label is able to be identified and used in the following command mris_anatomical_stats \ -l /Users/lu8342ha/Desktop/subjects/A152/label/rh.c1.label \ -f /Users/lu8342ha/Desktop/subjects/A152/stats/rh.c1.stats \ A152 \ rh Please could you advise me on where I am going wrong here? Many thanks, Luke

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Change made in the release of FSL 6.0.6 may affect Freesurfer
by Aaron Tanenbaum 02 Dec '22

02 Dec '22

External Email - Use Caution I have noticed a change made in the release of FSL 6.0.6 that may affect FreeSurfer. FSL executables now lie in ${FSLDIR}/share/fsl/bin not ${FSLDIR}/bin. The Freesurfer set up script adds ${FSLDIR}/bin to the PATH. Not sure if this causes any trouble.

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FreeView cannot open any images
by Greta Tuckute 01 Dec '22

01 Dec '22

Hello, I am attempting to use FreeView (have used it successfully for a few years, but suddenly it stopped working — cannot identify any cause. Have not updated operating system or similar). The problem is that nothing is loaded or shown. I cannot load e.g., an inflated LH surface from fsaverage. Running: ❯ freeview -f /Applications/freesurfer/subjects/fsaverage/surf/lh.inflated Only opens FreeView and shows the background. lh.inflated is shown under “Surfaces” in the upper left corner, but nothing is shown. Nothing changes with “Reset view”. I tried: - Updating FreeView (did not help) - Reinstalled FreeSurfer (did not help either) Any idea what is going on? No error message. Other FreeSurfer commands work fine. FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg (FreeView: freesurfer-darwin-macOS-dev-freeview.tar.gz from Operating system: macOS Catalina, version 10.15.7 (19H1824) Thanks so much, Greta External Email - Use Caution

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[Tracula] ERRORS when using trac-all -prep
by h21ms-utsumi＠jikei.ac.jp 01 Dec '22

01 Dec '22

External Email - Use Caution Dear Freesurfer experts I'm attempting to running TRACULA in a two subjects(one visit per subject and multiple deffusion scans per visit), as described on the TRACULA tutorial (https://secure-web.cisco.com/1YZplCc8ElxyKpvsfXb9OH_SNhToXmmPHixjCRlcZ51VHS…, https://secure-web.cisco.com/1nYtHW48eZdU7uUKv6TSjlFm9HP9CHGRmfSeoCOA7uunK3…, and https://secure-web.cisco.com/1i1x3WraESWH3k6zfmnPSieIq0qc66z7vq-nTTa6dKs81Q…) but for my subjects I get the following error when I run the trac-all - prep: cp dwi.nii.gz /media/sf_share\freesurfer\7.3.2/subjects/diffusion_ tutorial/trc/subject1/dmri/data.nii.gz cp: cannot stat 'dwi.nii.gz': No such file or directory. I checked the "dmri" directory and found that "data.nii.gz" was missing and "dwi.nii.gz " was there. I've searched the archive list and I found the following two things; the dwi.nii.gz file is the DWI after all corrections have been made and the data.nii.gz file is a symbolic link to the other, so they should be the exact same file. (https://secure-web.cisco.com/1qq_o3GFIoLx7Luv5Fgj2ZN5KBHCJCZzPPrZqzLzT3BdzI…) the data.nii.gz file is necessary for the process of "trac-all -bedp", not "trac-all -prep." (https://secure-web.cisco.com/1pjKE3HFIeU-FqIoHgU1xkoI3rom-BBboaeTQQ7MDiNVT7…) However, no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the dmrirc. tutorial, trac-all.log, pre-diffusion_tutorial_tree.text, and post- diffusion_tutorial_tree.text in case it's of any use. Best regards, Tomohiro Utsumi. ------------------------------------------------------------------------ -------- Tomohiro Utsumi, PhD Student. Department of Psychiatry, The Jikei University School of Medicine, Tokyo, Japan. ------------------------------------------------------------------------ --------

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Freesurfer December 2022