Freesurfer June 2022

freesurfer@nmr.mgh.harvard.edu

84 participants
123 discussions

Unit of the Numbers in cache.th40.neg.y.ocn.dat
by Na, Xiaoxu 17 Feb '24

17 Feb '24

External Email - Use Caution Dear Freesurfer Experts, As I'd like to extract the average value of each subject in the cluster after running group analysis, may I know the unit of these numbers? Since the one I'm running is surface area, and the cluster is 444mm^2, all the numbers in the file cache.th40.neg.y.ocn.dat is in the range of [0.55 1.05], may I know if this is correct and if so, how the unit is for those? Thanks a lot! ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx 1 -4.8321 40067 444.11 -58.1 -16.6 -23.9 0.0002 0 0.0004 670 -2784.11 Regards, Xiaoxu ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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How is cache.th40.pos.sig.voxel.mgh computed, exactly?
by Mark Ebden 04 Aug '23

04 Aug '23

External Email - Use Caution Hi, I was wondering if anyone knows how the numbers in cache.th40.pos.sig.voxel.mgh are computed, or where I'd look to learn this. There is a one-liner in the documentation<https://secure-web.cisco.com/1R2vQZUhHj-zAreoIH8kMlOuUPh5jYx8TyPmfmDzbM1Dl-…> but I'd like the mathematical details of the correction etc. so I can determine what the final numbers (from 0 to 1) represent. I've noticed from browsing the plot in FreeView that significant areas have values close to 1, which is puzzling. Thanks if you could point me in the right direction. Kind regards, Mark Mar [cid:b7c6e65e-f85e-4206-aaa0-1ec00aa2fde2] Mark Ebden, D.Phil (Pronouns: He/Him) Research Analyst The Hospital for Sick Children 555 University Ave, Toronto ON M5G 1X8 P 416.888.0841 [cid:3b077a75-32bb-46ed-b1d2-b74379e6a8d1]<https://secure-web.cisco.com/17-WtJwO2uIWyZ7umzDRCiH0I5Q1NZ-tfYcx_zx9tznEDb…> ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

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Fwd: mri_robust_template - MyMatrix::RotationMean Error
by Andrew Beaudin 07 Feb '23

07 Feb '23

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Extract single time frame
by Rockers, Elijah D. 16 Oct '22

16 Oct '22

Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I did this before, I believe with freesurfer, but I have somehow forgot the name of the command, and I can't seem to find it. I believe it could be used to specify particular regions of the volume, as well as time. I need the entire volume, still, but only one frame. Thanks in advance! Eli Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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aseg.presurf edits are undone or incomplete when brainmask.mgz edits are involved
by Keefe, Sarah 12 Sep '22

12 Sep '22

External Email - Use Caution Hi FreeSurfer Team, Our group is in the process of switching to Freesurfer 7.1.1 from 5.3. We have been taking advantage of Freesurfer 7's aseg.presurf volume to add in correction of unlabeled cerebellum to our standard edit checklist rather than our previous workflow of having a Freesurfer fail our quality control standards and be excluded from analysis if too much cerebellum is unlabeled on aparc+aseg segmentation. We're consistently running into an issue when we have a Freesurfer that requires corrections to both brainmask.mgz and aseg.presurf.mgz. An example of when this happens is if the Freesurfer output labels dura as cerebellum cortex on aparc+aseg (which requires erasing the included dura from brainmask.mgz) and the output also has an exclusion of cerebellum from the aparc+aseg segmentation (which requires correctly labeling the excluded voxels on aseg.presurf.mgz). We have found that if we edit both the aseg.presurf.mgz and brainmask.mgz volumes and then rerun recon-all with both, the cerebellum exclusion segmentation fix does not "take" completely and individual voxels in the cerebellum that were corrected in the edited volume are still left unlabeled. We have 100% confirmed that our labeling edits to aseg.presurf are correct and complete before this happens. To reduce confusion and attempt some consistency across our editing team, we relaunch recon-all with the same flags every time: -autorecon2 -autorecon3 -qcache To work around this issue, we implemented a workflow where editors will make brainmask.mgz corrections, then rerun recon-all (rerun 1), and then make aseg.presurf corrections, and rerun recon-all again (rerun 2). This seems to work although it is frustrating since we are trying to minimize the number of reruns of recon-all and we typically tell people to stop and make a final quality control decision after 3 reruns. What we are finding is if another issue pops up on brainmask.mgz after rerun 2 that then needs corrections (e.g. other areas of dura are incorrectly included in the pial surface or aparc+aseg cerebellum labeling but weren't included before so weren't erased) then after making those edits and rerunning recon-all, the previously corrected aparc+aseg cerebellum segmentation shows "missing" unlabeled voxels, same as if we had run recon-all once with both aseg.presurf and brainmask volumes edited. The attached image shows an example of our process and the issues we're seeing. The end result (F) also happens if we edit both brainmask.mgz and aseg.presurf.mgz edits and rerun recon-all once with both included. screenshot A is the aparc+aseg.mgz of the original recon-all output (run 0) where cerebellum is unlabeled (red arrows). There is also visible dura labeled as cerebellum that we need to fix (yellow arrow). screenshot B is the aparc+aseg.mgz of the recon-all rerun output after just the brainmask.mgz was edited and saved (run 1). Additional segmentation issues have appeared in addition to the original ones (red arrows). This screenshot also shows an example of the type of edit we are doing to brainmask - we have erased dura from brainmask.mgz to correct the cerebellum cortex labeling and the edit worked (yellow arrow). screenshot C is the aseg.presurf.mgz volume after run 1 before editing for the cerebellum exclusion issue. screenshot D is our edited and saved aseg.presurf volume BEFORE we run the second recon-all relaunch. We have corrected the labeling (green arrows). screenshot E is the aparc+aseg.mgz after a recon-all relaunch with only the new edit to aseg.presurf. (run 2). The cerebellum exclusion error has been fixed in aparc+aseg (green arrows). This run 2 of recon-all caused more issues to show up that required more brainmask.mgz edits. screenshot F is what we see if we edit brainmask.mgz again and rerun recon-all (run 3). The output of run 3 shows missing voxels in the cerebellum where we had fixed them before. Unlabeled voxels appear throughout the areas that were edited in C and were corrected in D. We try to minimize edits and maintain consistency across our editing team by asking people to only erase dura from brainmask.mgz that has been erroneously included in the cerebellum labelling or in the pial surface (rather than other dura that also happens to be included in the brainmask.mgz). We also ask people to relaunch recon-all with the same -autorecon2 -autorecon3 -qcache flags each time for consistency across our data. We really really want to be able to cut down the number of times we are relaunching recon-all but we are unable to fix both these issues at once (it ends up like screenshot F after 1 rerun). Is there a way to prevent the aseg.presurf.mgz edits from "undoing" voxels when brainmask.mgz edits are included or done after aseg.presurf? Any assistance or alternative techniques for solving this would be much appreciated. We are primarily using the Freesurfer 7.1.1 Docker container but I have also been able to replicate this issue on CentOS 8 and Ubuntu 20.04 with build stamp freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551. Thanks so much, Sarah ________________________________ 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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Reliability and sensitivity of two whole-brain segmentation approaches − ASEG and SAMSEG
by Donatas Sederevicius 28 Aug '22

28 Aug '22

External Email - Use Caution A new pre-print paper comparing two FreeSurfer’s whole-brain segmentation methods - ASEG and SAMSEG is now available (see the link below). The study is of great interest to many researchers in the field, providing new insights and guiding the selection of the processing method. https://www.biorxiv.org/content/10.1101/2020.10.13.335737v1

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Problem with longitudinal processing
by Wittayer, Matthias 28 Aug '22

28 Aug '22

External Email - Use Caution Dear community, I tried to process MS- patient's MRIs (mostly same scanner, same settings) Longitudinally over a long period of time. I first processed all timeponits crosssectionally and then initialised the base image by recon- all - base TP1 TP2 TP3 etc. Now I am trying to run label based morphometry and it seems some areas are growing rather than shrinking. Which is highly unlikely. I tried to exclude timepoint of a relapse to rule out perifocal edema interfering with measures but the problem remains. Did anybody have the same problem? Is it a potential bug or just a garbage in garbage out problem (though I don't know what would be wrong with our scans)? Does it make sense to make an intermediate template for two timeponits only? I.e. recon- all -base TP1 TP2; recon -all -base TP2 TP3 ... and use them for longitudinal runs? Thanks for your opinions. Best Matthias

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SAMSEG and statistics
by k3ops＠free.fr 27 Aug '22

27 Aug '22

External Email - Use Caution Hi FreeSurfer community, I recently discovered the SAMSEG application in the FreeSurfer 7.2.0 release and started to give a try on few subjects were FreeSurfer was having a hard time to segment brain structures (due to poor contrast). So I have few questions to harmonize the SAMSEG and FreeSurfer statistical files: 1. "samseg.stats" file is not compliant with the "asegstats2table" application so I was not able to generate a final CSV file with volumetric results Is there another solution? 2. "samseg.stats" file does not provide large brain structures like "BrainSegNotVent" or "SupraTentorialNotVent", is there a way to get them calculated? 3. "samseg.stats" file does not provide left/right or global cortical thickness, is there a command line to execute to get these extra values? Thanks. Best, Florent

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Amygdala Subfields - longitudinal volumes differ a lot from the cross-sectionals
by Andrea Dell'Orco 29 Jul '22

29 Jul '22

External Email - Use Caution Dear all, I have a Cohort of subjects with multiple time points. I have segmented the T1w with the normal recon-all and sub fields and then with the longitudinal pipeline as described in the wiki. When I compare the sub fields Volumes, there is a good agreement, with the expected variability, between longitudinal and not longitudinal for the Whole Hippocampus rh and lh. The Volumes for the amygdala are on the other hand, really different, especially for the left Whole amygdala. Here some plots with the correlation longitudinal vs non-longitudinal pipeline: https://secure-web.cisco.com/14VEQLZEbs96z59Y5ty9CueQKgO9cELG9hY62vKSTRXY_0… Do someone has some idea, what can be the problem? Regards, Andrea Dell'Orco -- Andrea Dell'Orco Wissenschaftlicher Mitarbeiter Charité – Universitätsmedizin Berlin NeuroCure Clinical Research Center NCRC AG Kognitive Neurologie Charitéplatz 1, D-10117 Berlin Tel +49 30 450 560 185 Fax +49 30 450 7 560 280 Interne Besuchsadresse: CCM, Sauerbruchweg 5, E2 http://secure-web.cisco.com/1ePTkJygSqAcb6M2j8DqUJJZTkIxZCuN07o23jJpGzlCGkh…

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TRACULA -bedp parallel processing
by Salar Dini, Elaheh 27 Jul '22

27 Jul '22

External Email - Use Caution Hello, I have tried to create a text file with command lines that can be run in parallel by using trac-all -bedp -c <config file> -jobs Parallel. When I use this command three text files are produced named: pre.Parallel, post.Parallel, and Parallel. Should I just use Parallel as a source for command lines? What are pre.Parallel and post.Parallel for? I am attaching my Configuration file, pre.Parallel, post.Parallel, and Parallel to this message as well. OS: Centos 7, Freesurfer version: 7.2.0 Thank you for your help. Kindly, Ela

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Freesurfer June 2022