Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

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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Re: [Freesurfer] Freesurfer Version
by fsbuild 30 Nov '22

30 Nov '22

External Email - Use Caution Hello Jacob, It looks like some digits at the end of "devel-2019128” are missing, but I read that to be a development build from December of 2019. If you look at the dates on the 7.X releases under https://secure-web.cisco.com/1UnwnrVRzttVZt3syMWUb0DaKV1piu03ood…, then a 2019 development build would pre-date the 7.X releases listed there, i.e.,7.1.1 in 7/20207..2.0 in 7/20217.3.2 in 8/2022 We don’t in general recommend use of development builds unless there is a feature or bug fix you need that is in a development build newer than the current release.  Release builds are preferable because they have gone through more testing compared to development builds. We also note the following on the page above when considering upgrading to a new release, Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions). There is a link to the release notes on that page.  Since you have 7.3.1 you could try that, but I suspect recon-all results won’t be exactly the same.  Maybe first try it out on just 1 subject.  Hope this helps. - R. On Nov 30, 2022, at 19:23, Jacob Bunyamin <jacob.bunyamin(a)monash.edu> wrote:        External Email - Use Caution        Good afternoon, I have run recon-all for my subjects,  however I just realised I am using the ver devel-2019128, I wonder which version is this?Is it recommended to re-run the recon-all using the newer updates? (At present we have the option of Freesurfer 7.3.1, 7..2.0, and 7.1.0 in our HPC) Thank you, Kind regards, Jacob --Department of Neuroscience Central Clinical School, Monash University99 Commercial RoadMelbourne VIC 3004E: jacob.bunyamin@monash.edu _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer Version
by Jacob Bunyamin 30 Nov '22

30 Nov '22

External Email - Use Caution Good afternoon, I have run recon-all for my subjects, however I just realised I am using the ver devel-2019128, I wonder which version is this? Is it recommended to re-run the recon-all using the newer updates? (At present we have the option of Freesurfer 7.3.1, 7.2.0, and 7.1.0 in our HPC) Thank you, Kind regards, Jacob -- *Department of Neuroscience* Central Clinical School, Monash University 99 Commercial Road Melbourne VIC 3004 *E:* jacob.bunyamin(a)monash.edu

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passcode
by Eckhart Schulz 30 Nov '22

30 Nov '22

Hello. I'm trying to expand the 7Zip archive for FreeSurfer on the VirtualBox. Please can I get the passcode for FS_7_2_0_ubuntu_18_04_06.ova.7z Sincerely, Eckhart Schulz Dipl.Ing.(FH) Eckhart Schulz Technische Universität Dresden Fakultät Psychologie External Email - Use Caution

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