Freesurfer

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30130 discussions

Re: [Freesurfer] HPC Usage - Moving On from CentOS7
by Horn, Mitchell Jacob 30 Mar '23

30 Mar '23

As an update I’ve tested another run (bert, 7.2.0, no flags, recon-all) on an OS-8 system but set LD_PRELOAD to the 7 system’s libm.so: export LD_PRELOAD=/alma/cos7lib/libm.so recon-all …. And that produced the equivalent results of all my CentOS7 runs: [Table Description automatically generated with low confidence] I believe this is very important information to the general community for stability with the imminent and inevitable switch to OS-8 HPC platforms. Best, Mitch

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Seed-based fcMRI: mean BOLD post nuisance regressor
by Vinke, Louis N.,PHD 30 Mar '23

30 Mar '23

Hello, After running a seed-based connectivity 1st level analysis on an individual subject, is it possible to pull out the mean BOLD activation (across all time-points; all runs) in a way that any “noise” in the time-series has already been regressed out (i.e., motion, ventricle, csf, wm, global mean, high/low pass filter)? I imagine it is one of the outputs in the analysis folder and not found within any particular FC seed sub-folder (containing pcc.nii.gz, etc.). In other words, one may run different seed-based connectivity analyses, but the mean activation estimate will not change so long as the nuisance parameters stay the same. The meanfunc overlay looks to be what I’m interested in, but unclear if this is created after regressing out nuisance parameters. Thanks. -Louis

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(no subject)
by Rachel Wagner 30 Mar '23

30 Mar '23

External Email - Use Caution Please unsubscribe me

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Pass code
by BREUILLY MARINE 30 Mar '23

30 Mar '23

External Email - Use Caution Hello, I have downloaded the FreeSurfer Vitrual VM images for my research project and a pass code is required to open the image. As mentioned in the guidelines https://secure-web.cisco.com/1oZit62PBJoLikTlTdvtgmPiBPc4ThiBZJNpYfu6IvCxQz…, we need to send an email to the help list. Could you please send me the pass code for FS_7_2_0_ubuntu_18_04_06.ova.7z ? Thank you in advance, Best regards, ---- Marine BREUILLY Chercheure postdoctorale Plateforme LyMIC CIQLE, Faculté de médecine Rockefeller, Université Claude Bernard Lyon 1 8 avenue Rockefeller, 69008 LYON tel: +33(0)660033005

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errors with running recon-all -autorecon1
by 张思敏 29 Mar '23

29 Mar '23

External Email - Use Caution Hello FreeSurfer Developers, I'm trying to run the command: recon-all -subjid <subname> -autorecon1. I'm getting the an error message and the error log reads as follows: error: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Then I run the command: recon-all -subjid <subname> -autorecon1. I get the same error as before. Finally, I run the command: tkregister2 --s subjid --fstal. But I am new to Freesurfer so I can't get the meaning of the output after running that command. How do I know if this is true？I‘ve attached the tkregister2.png and the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-darwin-macOS-7.2.0 2) Platform: MacOS release 10.15.7 (Catalina) 3) uname -a: Darwin zsilencedeMacBook-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Mon Aug 31 22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64 x86_644) recon-all.log: see attached 5) tkregister2.png: see attached Thanks!

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Tracula, trac-all, bug in interreg
by Tan Li Kuo 29 Mar '23

29 Mar '23

External Email - Use Caution Hi, I've been trying to configure Tracula to use different inter-subject registration methods. It fails for type #3 (robust cost) and #4 (nonlinear CVS). From the trac-all script (line #1634), it looks like Tracula points to different trctrain templates depending on the registration method used (mni, rob, cvs, syn, fnt). The problem is, the FreeSurfer distribution appears to only include template files for mni and syn. E.g., $FREESURFER_HOME/trctrain/hcp/mgh_1001 Basic info: 1) FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 2) Platform: Ubuntu 22.04.1 LTS 3) uname -a: Linux medphys-rtx 5.15.0-53-generic #59-Ubuntu SMP Mon Oct 17 18:53:30 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Thanks! -- Tan Li Kuo Medical Physics, Dept. Biomedical Imaging Faculty of Medicine Universiti Malaya -- " PENAFIAN: E-mel ini dan apa-apa fail yang dikepilkan bersamanya ("Mesej") adalah ditujukan hanya untuk kegunaan penerima(-penerima) yang termaklum di atas dan mungkin mengandungi maklumat sulit. Anda dengan ini dimaklumkan bahawa mengambil apa jua tindakan bersandarkan kepada, membuat penilaian, mengulang hantar, menghebah, mengedar, mencetak, atau menyalin Mesej ini atau sebahagian daripadanya oleh sesiapa selain daripada penerima(-penerima) yang termaklum di atas adalah dilarang. Jika anda telah menerima Mesej ini kerana kesilapan, anda mesti menghapuskan Mesej ini dengan segera dan memaklumkan kepada penghantar Mesej ini menerusi balasan e-mel. Pendapat-pendapat, rumusan-rumusan, dan sebarang maklumat lain di dalam Mesej ini yang tidak berkait dengan urusan rasmi Universiti Malaya adalah difahami sebagai bukan dikeluar atau diperakui oleh mana-mana pihak yang disebut. DISCLAIMER: This e-mail and any files transmitted with it ("Message") is intended only for the use of the recipient(s) named above and may contain confidential information. You are hereby notified that the taking of any action in reliance upon, or any review, retransmission, dissemination, distribution, printing or copying of this Message or any part thereof by anyone other than the intended recipient(s) is strictly prohibited. If you have received this Message in error, you should delete this Message immediately and advise the sender by return e-mail. Opinions, conclusions and other information in this Message that do not relate to the official business of University of Malaya shall be understood as neither given nor endorsed by any of the forementioned. "

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Fw:errors with running recon-all -autorecon1
by 张思敏 29 Mar '23

29 Mar '23

External Email - Use Caution TO: freesurfer(a)nmr.mgh.harvard.edu FROM: 1913191(a)mail.nankai.edu.cn SUBJECT: recon-all -autorecon1 error: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Hello FreeSurfer Developers, I'm trying to run the command: recon-all -subjid <subname> -autorecon1. I'm getting the an error message and the error log reads as follows: error: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Then I run the command: recon-all -subjid <subname> -autorecon1. I get the same error as before. Finally, I run the command: tkregister2 --s subjid --fstal. But I am new to Freesurfer so I can't get the meaning of the output after running that command. How do I know if this is true？I‘ve attached the tkregister2.png and the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-darwin-macOS-7.2.0 2) Platform: MacOS release 10.15.7 (Catalina) 3) uname -a: Darwin zsilencedeMacBook-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Mon Aug 31 22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64 x86_644) recon-all.log: see attached 5) tkregister2.png: see attached Thanks.

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Autrecon-pial command
by Carlos Alcocer 29 Mar '23

29 Mar '23

External Email - Use Caution Hello all, Does -autorecon-pial flag also recreate the statistics tables with the new surfaces? or do you have to run autorecon3 after to recalculate stats files? Tks, Carlos

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Longitudinal processing of single time point data
by Hemond, Christopher 29 Mar '23

29 Mar '23

External Email - Use Caution Dear Freesurfer experts, I am processing longitudinal data from subjects participating in a pre-post analysis; a few subjects do not have follow-up data. I'd like to still include these subjects and plan on using mixed effects analysis methods given the unbalanced data. I am following the wiki tutorials in this regard (specifically https://secure-web.cisco.com/1YHlXw74PCpQ3T6qawqkxxMCM_VcHyTlbf-HZnuBTtb68u…) which suggests that subjects having a single time point should be processed in the longitudinal pipeline to reduce bias (from Bernal-Rusiel 2013). From the webpage: "Single time-point subjects: Because of drop-outs it can happen that some individuals were scanned only at a single time point. Instead of removing this valuable information, it is possible (e.g. in the linear mixed effects models LME) to include this data. For that it, however, becomes necessary to run the single time points through the longitudinal stream, to ensure that also those images undergo the same processing steps. This can be done by simply passing a single time point in the base creation step" On a single-timepoint subject I ran: "recon-all -base <subject_base> -tp <baseline_timepoint> -all However I get the following error: ERROR: It appears that the -base templateID that you passed: -base <subject_base> is an existing regular (cross sectional) run! Please make sure you pass a new name (not one of the time points) for the template with -base. I've searched the archive but didn't find anything with this. Maybe I am doing something obviously wrong! Any help you could provide would be greatly appreciated. I'm running freesurfer-darwin-macOS-7.3.2-20220804-6354275. Many thanks, Chris <https://secure-web.cisco.com/1YHlXw74PCpQ3T6qawqkxxMCM_VcHyTlbf-HZnuBTtb68u…> The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, transmission, re-transmission, dissemination or other use of, or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer.

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How to extract hippocampus from nu.mgz using lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz
by Hoang Gia Minh 29 Mar '23

29 Mar '23

External Email - Use Caution Dear experts, I am doing a Hippocampus segmentation task using Freesurfer. After I run the command: recon-all -i sub-ADNI002S0295_ses-M00_T1w.nii.gz -s S1 -hippocampal-subfields-T1 -all -openmp 80 in which sub-ADNI002S0295_ses-M00_T1w.nii.gz is my input MRI scan I received an MRI folder that included "nu.mgz, aseg.mgz, etc." However, file "lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz" is just a mask or label file of the hippocampus. I want to extract the hippocampus from the original scan (nu.mgz or orig.mgz) using lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz. Is there any command or step that I can do? Thank you so much Best regards Minh -- *Hoang Gia Minh, MSc* *Research Assistant* Department of Biomedical Science and Engineering Gwangju Institute of Science and Technology (GIST) TEL: (+84)-38-521-3040 EMAIL: hoanggiaminh1996(a)gmail.com

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