Freesurfer August 2022

freesurfer@nmr.mgh.harvard.edu

85 participants
120 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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Tracula - Preproc
by Alan Francis 18 Oct '22

18 Oct '22

External Email - Use Caution Hi Anastasia, King Wei: I did as you suggested with the config file and the preprocessing ran for a bit but then an error occurred. I have attached the run script. It says BET not found. Is this the Brain Extraction tool? Could you please shed some light on this? thanks so much, Alan -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine* *Rio Grande Valley* *Texas.*

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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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Unable to run trac-all -prep : cannot file bvals bvecs file
by Ashwati Vipin (Dr) 20 Sep '22

20 Sep '22

External Email - Use Caution Dear Freesurfer developers, I am running the trac-all -prep for my DWI data on Freesurfer version 7.2.0. The configuration file seems to be alright but when I start running the -prep step it gives me the error: writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz... /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula//Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/bvecs.txt: No such file or directory. Darwin DRCSs-iMac.local 21.5.0 Darwin Kernel Version 21.5.0: Tue Apr 26 21:08:22 PDT 2022; root:xnu-8020.121.3~4/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Mon Aug 15 11:32:11 +08 2022 I have attached the log file, error file, bvals and bvecs and the configuration file and as the screenshot below shows: the directory does have the bvals.txt and bvecs.txt files, so I’m not sure why it’s giving me this error? I thought the error was because the bvals and bvecs were given in rows, so I transposed them so they are now in columns but it still doesn’t work. [cid:image001.png@01D8B09D.94718010] I have run tracula before with no issues so I’m really lost here. Could you please help? Thank you so much! Best, Ashwati ________________________________ CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its contents. Towards a sustainable earth: Print only when necessary. 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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Group Analysis - glmfit results
by rstein03＠student.ubc.ca 06 Sep '22

06 Sep '22

External Email - Use Caution Hello Freesurfer Team, I recently ran analysis to compare change in cortical thickness between an Intervention and Control group longitudinally. The contrast is set up as INT-CON, and therefore I would interpret a positive change as the intervention having a greater increase in cortical thickness or less atrophy than the control group. The cluster that survived the Monte-Carlo simulation showed a positive difference in the LH superior parietal region when running both an ‘abs’ and ‘pos’ simulation (these showed the same cluster.summary outputs). There was not a significant cluster when running the ‘neg’ simulation. When I compared the mean change in thickness between groups (cache.th13.abs.y.ocn.dat file), it showed that the control group experienced less atrophy than the intervention despite having a positive cluster output. One possible solution I considered is accounting for baseline differences between groups when looking at mean change. Does glmfit control for baseline cortical thickness in the cluster analysis that is not accounted for in the mean change values from the cache.th13.abs.y.ocn.dat file? Is there another possible explanation for this discrepancy? Thank you in advance, Ryan S Ryan G. Stein MSc Student, Rehabilitation Sciences Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health University of British Columbia | Vancouver Campus | Musqueam Traditional Territory

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Stepwise recon-all to get volumes
by Ruifeng Dong 01 Sep '22

01 Sep '22

External Email - Use Caution Hi all, I am computing volumetry using freesurfer using two different runs. 1. I just use recon-all -all, and then look at the aseg.stats file. 2. I ran recon-all only to the 12th step where gca labeling is done. It doesn't generate the aseg.mgz file but only aseg.auto.mgz. I assumed that they are the same and ran the -asegstats step to get the output in aseg.stats. I noticed there are differences between the above two runs on the same image. Firstly, the volumes of WM, GM and ICV are not there from the 2nd run. How does this happen? In which step does Freesurfer compute these? Secondly, the volumes of some subcortical structures are also different between the two runs. Does Freesurfer make corrections to the volume segmentations after step 12? Thank you! Ruifeng

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Re: [Freesurfer] Thalamic nuclei exited with ERRORS
by fsbuild 31 Aug '22

31 Aug '22

External Email - Use Caution It’s possible something in 7.2.0 still requires MCRv84.  If so, it is probably not going to work to use a soft link to fake out the name, and using a different version of Matlab run time could explain the crashes..  Please send along the output showing MCRv84 is required. - R.

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Freesurfer August 2022