Freesurfer May 2024

freesurfer@nmr.mgh.harvard.edu

56 participants
69 discussions

recon-all process still not finishing properly
by Dong, Yilei 08 May '24

08 May '24

External Email - Use Caution Hi Freesurfer Support, The past few weeks, I've emailed about my recon-all processing stream never completely finishing. We are still encountering the same problem. For context, our recon-all job submission script runs recon-all for 1 image. Given a folder of 100 MRI images, we have another script that calls upon the recon-all script for each image within the folder via a for loop. The result is 100 jobs running in parallel on the cluster. I have attached a screenshot of the parameters we set whenever we submit each recon-all job for each image by SLURM to UCSD's cluster. The maximum time we are allowed for each job is 48 hours. Our jobs are shared-node jobs, which means we run more than 1 job on a single node. This time, we increased RAM from 8GB to 16GB in hopes the entire recon-all processing stream can fully run through for each image, but it still stops at "mri_pretess done" and does not go on to the -fill step. Each job submitted to the cluster took around 4 hours and 20 minutes each to run in our most recent attempt. If increasing the RAM did not change anything for us, how else can we get more verbose error messages? What other reasons could be why our recon-all aborts before finishing? I have attached a recon-all.log from one of our subjects for reference and a screenshot of the parameters we set for submitting jobs in our cluster for reference. Freesurfer version: 7.2.0, but already available as module on UCSD's cluster system Platform: Rocky Linux release 8.8 (Green Obsidian) uname -a: Linux login01 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 28 15:04:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux Recon-all log: see attached Thank you! Sincerely, Yilei

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Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis
by Dan Levitas 08 May '24

08 May '24

External Email - Use Caution Hi Kersten, If that's alright with you then that would be great. I completely accept if my threshold is accurate and leaves no significant findings, I just can't find a comparable threshold on this forum or elsewhere with such an elevated threshold value. I can touch base next week to see what you need from me. Thanks again, Dan On Tue, May 7, 2024 at 3:09 PM Diers, Kersten /DZNE <Kersten.Diers(a)dzne.de> wrote: > Hi Dan, > > I can see no obvious issues at the moment, but am happy to take a closer > look when I am back in office next week. > > The fslmer tool ist just an R Implementation of the Matlab scripts, so I > don't see any need to use them in your case. > > Best, > > Kersten > > Gesendet von Outlook für Android <https://secure-web.cisco.com/1KzII-MfH6rTxaOnzZUTUvJp9x_boMj6aQnEUUoTp8Re7R…> > > ------------------------------ > *Von:* Dan Levitas <djlevitas208(a)gmail.com> > *Gesendet:* Dienstag, Mai 7, 2024 7:11:58 PM > *An:* djlevitas208(a)gmail.com <djlevitas208(a)gmail.com> > *Cc:* Kersten.Diers(a)dzne.de <Kersten.Diers(a)dzne.de>; > MREUTER(a)mgh.harvard.edu <MREUTER(a)mgh.harvard.edu>; > freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> > *Betreff:* Re: [Freesurfer] Lingering questions for Longitudinal > spatiotemporal LME analysis > > CAUTION: This email originated from outside of DZNE. Do not click links > or open attachments unless you recognize the sender and know the content is > safe. > ACHTUNG: Dies ist eine externe E-Mail, bitte seien Sie vorsichtig beim > Anklicken von Links oder Öffnen von Anhängen > > Hi Kersten & Martin, > > I just wanted to ping this thread again, as I'm still unsure about my pcor > value (4.4) that I'm getting. I've seen other posts where the threshold > (thmin) value specified in functions such as *mri_surfcluster* are around > 2 (corresponding to a p-value of 0.01) when threshold *sig.mgh file(s). > Given that I'm interested in both right and left hemispheres, I'm surprised > that my single threshold value to account for both hemispheres is so high > relative to others posts I've come across in the forum. I seem to have > followed the LME approach correctly ( > https://secure-web.cisco.com/1SQ58WEznZe-ibw3QO19omrHSeej1iX-z28jkMlUtsQ61n…) but > I'm unsure if I've done something that has resulted in an elevated pcor > value. > > Martin had recommended the *fslmer* tool ( > https://secure-web.cisco.com/1k8MMiLU-B44BypnewP6obBaoWvRatpcAdkGjbKYO0VGEe…) I'd be happy to use that instead if > it's more current and the preferred tool for this kind of analysis. > > Thanks again, > > Dan > >

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ERROR: cannot find AntsN4BiasFieldCorrectionFs in path
by Christine Farrugia 07 May '24

07 May '24

External Email - Use Caution Hi, I have installed FreeSurfer (freesurfer-linux-centos7_x86_64-7.4.1) into my research group's directory on the University cluster, using the tar archive. I source it with GROUPDIR=<path_to_group_directory> export FREESURFER_HOME=$GROUPDIR/software/freesurfer . $FREESURFER_HOME/SetUpFreeSurfer.sh export PATH=$FREESURFER_HOME/bin:${PATH} and am trying to run recon-all like so: recon-all -s <subj_id> -i <path_to_T1_data> -T2 <path_to_T2_data> -T2pial -autorecon-all However, FreeSurfer keeps giving the error: ERROR: cannot find AntsN4BiasFieldCorrectionFs in path when AntsN4BiasFieldCorrectionFs is definitely in freesurfer/bin Any insight into the matter would be greatly appreciated 🙂 Regards, Christine The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

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Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis
by Dan Levitas 07 May '24

07 May '24

External Email - Use Caution Hi Kersten & Martin, I just wanted to ping this thread again, as I'm still unsure about my pcor value (4.4) that I'm getting. I've seen other posts where the threshold (thmin) value specified in functions such as mri_surfcluster are around 2 (corresponding to a p-value of 0.01) when threshold *sig.mgh file(s). Given that I'm interested in both right and left hemispheres, I'm surprised that my single threshold value to account for both hemispheres is so high relative to others posts I've come across in the forum. I seem to have followed the LME approach correctly (https://secure-web.cisco.com/1P1DqCgATuRJ8Gb_Cv23uM_tkjhG63bDl2SmrFrqCZVQtv… <https://secure-web.cisco.com/1P1DqCgATuRJ8Gb_Cv23uM_tkjhG63bDl2SmrFrqCZVQtv…>) but I'm unsure if I've done something that has resulted in an elevated pcor value. Martin had recommended the fslmer tool (https://secure-web.cisco.com/1f2ZYTXcSbFY4HqsjtbVZ5WFtQdhPr_P5UgrBHbi4cv6tX… <https://secure-web.cisco.com/1f2ZYTXcSbFY4HqsjtbVZ5WFtQdhPr_P5UgrBHbi4cv6tX…>), I'd be happy to use that instead if it's more current and the preferred tool for this kind of analysis. Thanks again, Dan

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mris_label2annot Error: FG1.mpm.vpnl not found in CTAB colortable_vpnl.txt
by LYU, TIANXIANG 07 May '24

07 May '24

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to process recon-all commands, but in mris_label2annot command: ERROR: FG1.mpm.vpnl not found in CTAB /vol0004/hp200139/data/u12257/freesurfer/average/colortable_vpnl.txt Command exited with non-zero status 1 @#@FSTIME 2024:05:07:07:05:22 mris_label2annot N 26 e 4.35 S 0.34 U 2.65 P 68% M 203264 F 4 R 3608 W 0 c 0 w 1728 I 18304 O 0 L 0.92 0.91 0.96 I've checked the directory, but find nothing strange. (file colortable_vpnl.txt exists) I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. Sincerely, Tianxiang Lyu Graduate School of Medicine, Juntendo University

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INTERNATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE IN HEALTHCARE (AIiH)
by Jiaxiang ZHANG 07 May '24

07 May '24

External Email - Use Caution INTERNATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE IN HEALTHCARE (AIiH) 4 - 6 September 2024, Swansea, UK https://secure-web.cisco.com/1ppWAnsYjYnhHxEnKoibtNl4Qu4560BMrard8EPkGQFkgm… (1st CALL FOR ABSTRACT) [ apologies for cross-postings] Submission deadline: Monday 1 July (FIRM) *1. INTRODUCTION * https://secure-web.cisco.com/1kMB0QYwXtTy8ESTcm5TslUdGzHjRontlKUqT_0F6qSbIx… AIiH 2024 welcomes late-breaking short abstract submissions to be included as poster or short spot-light presentation at the conference. This is to both enable fast dissemination of promising preliminary findings and encourage attendance by a broader audience of early career researchers (including research students), healthcare professionals, and industrial practitioners. AIiH 2024 is a single track conference with oral and poster presentations and will include 5 keynote presentations. The conference will also feature a plenary session, which consists of 3 invited speakers who have extensive experiences in related areas. AIiH aims to provide a prominent platform for researchers and practitioners who are devoted to improving healthcare using modern artificial intelligence. We recognise that healthcare applications present complex and sometimes unique challenges across a wide spectrum, from ethics to technical developments, that generic AI methods are often inadequate. By creating this dedicated forum, we encourage discussions and disseminations of efficient and effective AI solutions and technologies for healthcare, and in turn we hope to influence the research, technology adoption, and decision making in healthcare. *2. KEYNOTE SPEAKERS* https://secure-web.cisco.com/1xSHdJFsDbvhgkCBoJWdwm1K821Lxq2yKqNEYDfRAd8VVQ… Prof. Hao Ni University College London Dr. Timothy Rittman Cambridge University Dr. Konstantinos Kamnitsas Oxford University Prof. Jacques Fleuriot Edinburgh University Prof. Eiichiro Tanaka Waseda University, Japan *3. PLENARY SESSION ON TRANSLATING AI RESEARCH INTO PRACTICE* https://secure-web.cisco.com/154XWGvVMO2AcjTRNWbGBh-Cdh9jPWq8MlSYUd4FIqXlkR… Dr. Alba Di Pardo IRCCS Istituto Neurologico Mediterraneo Neuromed Dr. Noura Al Moubayed Durham University & Evergreen Life Dr. Haoda Fu Eli Lilly and Company *4. ABSTRACT SUBMISSION* Submission instructions are available at the conference website: https://secure-web.cisco.com/1kMB0QYwXtTy8ESTcm5TslUdGzHjRontlKUqT_0F6qSbIx… *5. IMPORTANT DATES* Abstract deadline: Monday 1 July (FIRM) Abstract notification: Monday 8 July (FIRM) Abstract registration: Monday 15 July Late registration: Monday 12 August Main conference: Wednesday 4 – Friday 6 September 2024 *5. ORGANISERS* CONFERENCE GENERAL CHAIRS Xianghua Xie, Swansea University, UK Iain Styles, Queen’s University Belfast, UK PROGRAMME CHAIRS Gibin Powathil, Swansea University, UK Marco Ceccarelli, University of Rome Tor Vergata, Italy SPECIAL SESSION CHAIRS Jiaxiang Zhang, Swansea University, UK Rex Ying, Yale University, USA SPONSORSHIP CHAIRS Daniele Cafolla, Swansea University, UK Raoul van Loon, Swansea University, UK PUBLICITY CHAIRS Lu Zhang, Swansea University, UK Beiyu Lin, University of Nevada, USA PUBLICATION CHAIR Jingjing Deng, Durham University, UK *6. SPONSORS* Gold: - Technis Blu - Infordata Silver: - Amicus Therapeutics Bronze: - Zienkiewicz Institute for Modelling, Data and AI - IET Institution of Engineering and Technology Your Researcher Sponsor: - Elsevier Journal of Theoretical Biology Best Paper Award Sponsor: - Springer *7. CONTACT* contact(a)aiih.cc

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SynthSR Changes Dimension
by AmirHussein Abdolalizadeh 07 May '24

07 May '24

External Email - Use Caution Hi, I'm using SynthSR on a sample of high-resolution T1 scans, however, I noticed the dimensions are changed in between. For example, the original T1 is 176x256x256, but the SynthSRed version has a dimension of 176x257x257. Can we resample this to the original raw scan? I noticed that the SynthSRed version of the T1 scans is smoother and stretched in the Z-axis. Best, Amir

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Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis
by Dan Levitas 05 May '24

05 May '24

External Email - Use Caution Hi Kersten, Thanks for this helpful summary. It seems then that it’s best to apply the threshold to the *sig.mgh file and visualize its results since it contains the sign that specifies the direction of the interaction effect. Assuming this is the case, would an appropriate visualization of the results in Freeview be the following? freeview \ -f $SUBJECTS_DIR/fsaverage/surf/lh.pial:overlay=lh_sig.mgh:overlay_threshold=4.4,10 \ -f $SUBJECTS_DIR/fsaverage/surf/rh.pial:overlay=rh_sig.mgh:overlay_threshold=4.4,10 \ --viewport 3d Where the pcor value is 4.4 (pth = 0.000038474), based on the LME spatiotemporal tutorial, including both hemispheres. This appears overly strict; if I go to the Configure Overlay panel in Freeview and adjust the min Threshold value to 97.5 % (Use percentile), I get some results. I want to ensure that I’m applying the correction properly. Thanks, Dan

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Understanding registration with mri_synthmorph
by Antoine Royer 05 May '24

05 May '24

External Email - Use Caution Hi all! I am working on implementing some freesurfer synth tools into a larger diffusion processing pipeline. Doing so, I would like to use mri_synthmorph to generate a transform and then pass it downstream. FIrstly, I use the dockerized synthmorph version, which seems to present discrepancies in its behaviour vs local testing: 1. Can someone explain the expected output format of freesurfer transforms? When used within docker, I must define affine transforms as .lta and deform transforms as .mgz, otherwise: "ValueError: cannot determine file format from extension for test__init_warp.txt"; while when using mri_synthform from my local freesurfer installation, it doesn't seem like an issue. While I expected .m3z to be the expected output. 2. Here is the sequence of functions I use. My objective is to pass down the resulting transform (affine initialization + deform warp) downstream my pipeline for further registration using ANTs (antsApplyTransforms). I tested and it seems to work, but i would appreciate an opinion. Does the --insrcgeom parameter fixes everything for me? * Initialization + registration (freesurfer): * mri_synthmorph -m affine -t <init.lta> [moving] [fixed] mri_synthmorph -m deform -t <freesurfer_warp.mgz> -o <warped.nii.gz> -i <init.txt> [moving] [fixed] Convert warp from freesurfer (RAS) to ANTs (LPS) using freesurfer warp_convert: mri_warp_convert -g [moving] --inras <freesurfer_warp.mgz> --outlps <ants_warp.nii.gz> Thank you very much!

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Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis
by Dan Levitas 03 May '24

03 May '24

External Email - Use Caution Hi Martin, Thanks for the response! After my original post I went through things more carefully based on my two original two questions and made a follow-up post here (https://secure-web.cisco.com/19ziz4OS6HL3HuOwgHLcrspNdIovd6NTUuIdpJ-mDFOvCA…) with two final questions. The gist of these is that I’m unsure how to apply my multiple comparisons (for both hemispheres) to the analysis and subsequent visualization. Do you have any guidance on how I should proceed. Much appreciated, Dan

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