Freesurfer

freesurfer@nmr.mgh.harvard.edu

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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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brain volumes normalization
by yunus soleymani 02 May '24

02 May '24

External Email - Use Caution Thank you for the help.my next question When I normalize the surface area to the eTV, they are in different units (mm2, mm3). The resulting unit will be 1/m, is that okay? --------------------------------------------------------------------------------Yunus Soleymani Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences soleymani.yunus(a)yahoo.com+98 914 526 9298--------------------------------------------------------------------------------

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Lingering questions for Longitudinal spatiotemporal LME analysis
by Dan Levitas 02 May '24

02 May '24

External Email - Use Caution Hello, I've been following the FreeSurfer longitudinal LME analysis tutorial ( https://secure-web.cisco.com/1UXjrD54pEj2u6JH6Y-Z-dHoSgY6qcbXqPg43uVU2GGyBv…) which has been excellent; however I have a few lingering questions pertaining to my specific analysis. For reference, I am interested in assessing rates of longitudinal atrophy in each of my two groups (0=controls, 1=clinical). Regarding what I've currently done: 1). My Qdec file contains 4 columns: fsid, fsid_base, time(years), group 2). I followed the steps to create the appropriate M matrix, and since my preliminary analysis is simply to create a *group x time* linear model, my design matrix is X = [ones(length(M),1) M M(:,1).*M(:,2)]; and my contrast is CM = [0 0 0 1] 3). I've followed the pipeline for the lme_mass_fit_EMinit, lme_mass_RgGrow, and lme_mass_fit_Rgw functions. 4). I'm skipping the model comparison steps, as I prefer my model with the two random effects (intercept, time). 5). Get stats (F_lhstats = lme_mass_F(lhstats, CM), applied multiple comparison correction ([detvtx,sided_pval,pth] = lme_mass_FDR2(F_lhstats.pval,F_lhstats.sgn,lhcortex,0.05,0); and saved the sided p-values. My questions are: a). Since I'm interested in both hemispheres and the tutorial only assesses the left, do I need to do step #3 with the right hemisphere data? b). Would I need to do the last step in the tutorial to get a single threshold for both hemispheres and then perform the analysis this way? P = [ F_lhstats.pval(lhcortex) F_rhstats.pval(rhcortex) ]; G = [ F_lhstats.sgn(lhcortex) F_rhstats.sgn(rhcortex) ]; [detvtx,sided_pval,pth] = lme_mass_FDR2(P,G,[],0.05,0); pcor = -log10(pth) Thank you for the clarification. Dan

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FW: Infant Freesufer auto-recon failure
by Lemley, Rachel 02 May '24

02 May '24

External Email - Use Caution Good afternoon, We are attempting to run freesurfer on infant data, but are running into an issue with the autorecon-pial code. We corrected the pial surface on the brainmask.mgz in freeview, saved the brainmask.mgz edits, and are trying to run autorecon-pial, but we get the following error that I have attached below. It is looking for a file in surf labeled lh.orig.premesh, but it does not exist. Any suggestions on how to fix this? Am I missing a step? Respectfully, Rachel Lemley The error log is attached below: Subject Stamp: freesurfer-linux-centos7_x86_64-infant-dev-4a14499-20210109-4a14499 Current Stamp: freesurfer-linux-centos7_x86_64-infant-dev-4a14499-20210109-4a14499 INFO: SUBJECTS_DIR is /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects Actual FREESURFER_HOME /n/sw/ncf/apps/infant-freesurfer/4a14499/centos7_x64 Linux holy7c090602.rc.fas.harvard.edu 4.18.0-425.10.1.el8_7.x86_64 #1 SMP Thu Jan 12 16:32:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux '/n/sw/ncf/apps/infant-freesurfer/4a14499/centos7_x64/bin/recon-all' -> '/ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/scripts/recon-all.local-copy' /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/mri/transforms /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02 /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02 #-------------------------------------------- #@# Mask BFS Mon Apr 22 14:06:18 EDT 2024 /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 401939 voxels in mask (pct= 2.40) MRImask(): AllowDiffGeom = 1 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2024:04:22:14:06:19 mri_mask N 5 e 2.09 S 0.01 U 0.76 P 37% M 77200 F 0 R 3233 W 0 c 64 w 51 I 768 O 768 L 2.29 1.57 1.12 @#@FSLOADPOST 2024:04:22:14:06:21 mri_mask N 5 2.29 1.57 1.12 #-------------------------------------------- #@# AutoDetGWStats lh Mon Apr 22 14:06:21 EDT 2024 cd /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh infant-dev-4a14499 cd /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/mri setenv SUBJECTS_DIR /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/lh.orig.premesh error: No such file or directory error: MRISread(../surf/lh.orig.premesh): could not open file Command exited with non-zero status 1 @#@FSTIME 2024:04:22:14:06:21 mris_autodet_gwstats N 8 e 0.73 S 0.00 U 0.28 P 39% M 43208 F 0 R 1873 W 0 c 23 w 20 I 120 O 0 L 2.29 1.57 1.12 @#@FSLOADPOST 2024:04:22:14:06:22 mris_autodet_gwstats N 8 2.29 1.57 1.12 Linux holy7c090602.rc.fas.harvard.edu 4.18.0-425.10.1.el8_7.x86_64 #1 SMP Thu Jan 12 16:32:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux recon-all -s KAN1_02 exited with ERRORS at Mon Apr 22 14:06:23 EDT 2024 For more details, see the log file /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1hDoMTcotBNpi6ZDqlu1xK1AeLrzrk_QC8e4t7bga0WOa9h…

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Re: [Freesurfer] question about infantfreesurfer
by Knut J Bjuland 02 May '24

02 May '24

External Email - Use Caution What I mean is that it's a beta version, so I just wanted to make sure that I can use these results in a publication. Knut Jørgen Bjuland

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