Freesurfer

freesurfer@nmr.mgh.harvard.edu

7 participants
30057 discussions

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

1 0

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!

3 6

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

3 2

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--------------------------------------------------------------------------------

1 0

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

2 1

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…

2 2

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

2 1

brain volumes normalization
by yunus soleymani 02 May '24

02 May '24

External Email - Use Caution Hello freesurfers, I have some questions about the output variables of Freesurfer: 1. In the case of brain volume normalization, do I need to normalize all the volumetric results to the eTIV or just the subcortical volumes? 2. Are there any formulas other than simple division in order to normalize the volumes? 3. How are the .ThckStd values (like FS_R_Insula_ThckStd) calculated? What does the "std" mean here? 4. I believe that the surface area outputs are also affected by brain size differences in the population. Are there any reference values in the Freesurfer outputs to which surface areas can be normalized? Thank you in advance for your help. Best regards,Yunus --------------------------------------------------------------------------------Yunus Soleymani Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences soleymani.yunus(a)yahoo.com+98 914 526 9298--------------------------------------------------------------------------------

2 1

Figures for publication
by Asuka Toyofuku 02 May '24

02 May '24

External Email - Use Caution Dear Freesurfer experts, Thanks to all the help from this community, we're finally done with GLM analysis(mri_glimfit) and the cluster-wise correction (mri_glmfit_sim), and now I'm making figures for publication. My question is 1. Which output mgh files are commonly used for making figures for publication? Do people use, for example, cache.th40.abs.sig.cluster.mgh (cluster-wise corrected map: overlay) or cache.th40.abs.sig.masked.mgh (uncorrected sig values masked by the clusters that survive correction) or even uncorrected ones, such as sig.mgh file in the contrast directory before running the correction? From my impression, not many people use e.g., cache.th40.abs.sig.cluster.mgh (which shows no colour gradation inside the clusters)... 2. How do you select the colour-bar cut-off and max values? Most publications I saw use min cut-off value: -log10(p) = 2.00 and max: -log10(p) = 5.00, but some uses min: p=0.05 and max: p=0.01. Obviously, if you set the max value (with the configure section) very low (e.g., 2.0), the size of the cluster gets bigger and looks more significant. Are there any suggestions for setting the configure/threshold for the figures? Many thanks, Asuka

2 1

[FreeSurfer] recon-all exited with error - watershed error
by Krystal Xiwing Yau 01 May '24

01 May '24

External Email - Use Caution Dear FS experts, I am encountering an error when running recon-all. I followed the FAQ <https://secure-web.cisco.com/1UCt6p3edZmVlY3vv2VBSKmRgX9p8Xmur_qX9QMrgPbk8p…> page to rerun the command but still not running through. Would you please kindly advise? The log file is attached to this email. Thank you. Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

1 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer