Freesurfer July 2021

freesurfer@nmr.mgh.harvard.edu

91 participants
121 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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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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Reliability and sensitivity of two whole-brain segmentation approaches − ASEG and SAMSEG
by Donatas Sederevicius 28 Aug '22

28 Aug '22

External Email - Use Caution A new pre-print paper comparing two FreeSurfer’s whole-brain segmentation methods - ASEG and SAMSEG is now available (see the link below). The study is of great interest to many researchers in the field, providing new insights and guiding the selection of the processing method. https://www.biorxiv.org/content/10.1101/2020.10.13.335737v1

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WM or Pial edits to correct surfaces
by Alexopoulos, Dimitrios 27 Sep '21

27 Sep '21

External Email - Use Caution Hi users, We're having some issues with running some of our 2-3yo data (0.8mm isotropic) through FS7 with and without the -hires flag. There are persistent issues with the frontal lobe regions where the pial has not extended to outer surface as illustrated below. The WM surface contour look reasonable but the pial has underestimated the outer cortex resulting in an incorrect surface (below). I don't think control points will work (low intensity values in the 50-60s), and no WM to add to the WM.mgz. Any suggestion on how to push the pial surface out to capture the cortical surface?? Thx. Jim [cid:image004.png@01D752FB.04011E10] [cid:image005.jpg@01D752FB.04011E10] [cid:image001.png@01D752F8.E6507AC0] [cid:image002.png@01D752F8.E6507AC0] [cid:image006.png@01D752FB.04011E10][cid:image007.jpg@01D752FB.04011E10] ________________________________ 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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lme_mass_F error
by Emmanuel Nwosu 24 Sep '21

24 Sep '21

External Email - Use Caution Dear All I am running the longitudinal post processing statistical analysis and this error comes up each time I run the lme_mass_F. Does anyone have an idea of why this is happening and how to resolve it. Any help will be appreciated *************************************************************************************************** F_lstats = lme_mass_F(tlstats,CM); Computing F statistics, degrees of freedom and P-values ... Error using lme_mass_F (line 92) The source code (/matlab filepath/lme_mass_F.m) for the parfor-loop that is trying to execute on the worker could not be found. Caused by: Undefined function 'fcdf' for input arguments of type 'double'. Error using remoteParallelFunction (line 84) Worker unable to find file. Undefined function 'fcdf' for input arguments of type 'double' **************************************************************************************************** Kind regards Emmanuel

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Announcing FreeSurfer version 7.2
by Douglas N. Greve 23 Sep '21

23 Sep '21

We are please to announce version 7.2. Mostly bug fixes and behind-the-scenes enhancements. But there are a few new goodies and one new "known issue" about defacing. Check out https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes doug

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Re: [Freesurfer] Announcing FreeSurfer version 7.2
by fsbuild 12 Aug '21

12 Aug '21

External Email - Use Caution Hello Kiyotaka, Please try refreshing your copy/install of the Ubuntu 7.2.0 distribution as the packages have been updated to fix the warning below. I think you were using the installer, so you could try the commands below to download and re-install with apt.  (If you were using the tar file then just change the file name in the wget command to be freesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz, expand it in the right location and skip the commands with sum, apt remove, apt install). .... with installer ... $ rm -f  freesurfer_7.2.0_amd64.deb $ wget https://secure-web.cisco.com/1i8WchnZn-ZDMrXexp7WlIVIxgdWjuz06xq1yUvfYcAZHM… $ sum freesurfer_7.2.0_amd64.deb 20191 3199044 $ sudo apt remove freesurfer .... output deleted .... $ apt install ./freesurfer_7.2.0_amd64.deb .... output deleted ... .... check environment ... $ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh .... the output should have no warnings and you can also check ... $ env | grep MINC MINC_BIN_DIR=/usr/local/freesurfer/7.2.0/mni/bin MINC_LIB_DIR=/usr/local/freesurfer/7.2.0/mni/lib $ which nu_correct /usr/local/freesurfer/7.2.0/mni/bin/nu_correct - R. -------- freesurfer-linux-ubuntu18_x86_64-7.2.0-20210714-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurfer/7.2.0FSFAST_HOME       /usr/local/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /home/username/freesurfer/7.2.0/subjectsWARNING: MINC_BIN_DIR not defined.         'nu_correct' and other MINC tools         are used by some Freesurfer utilities.         Set NO_MINC to suppress this warning.WARNING: MINC_LIB_DIR not defined.         Some Freesurfer utilities rely on the         MINC toolkit libraries.         Set NO_MINC to suppress this warning.FSL_DIR           /usr/local/fsl =====

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fsaverage file download
by Shruthi Srinivasan 10 Aug '21

10 Aug '21

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mri_glmfit-sim ERROR
by Boa Sorte Silva, Narlon 03 Aug '21

03 Aug '21

External Email - Use Caution Dear experts, I am running this command to apply correction for multiple comparisons on my data: mri_glmfit-sim --glmdir a_glm_results/lh.thickness.velocity.10.glmdir \ --cache 1.3 abs \ --cwp 0.05 \ --2spaces However, I receive the following error: INFO: unrecognized mri_glmfit cmd option doss ... probably not a problem SURFACE: fsaverage lh log file is a_glm_results/lh.thickness.velocity.10.glmdir/cache.mri_glmfit-sim.log cd /Users/narlonsilva/Desktop/freesufer_subjects /Applications/freesurfer/7.1.1/bin/mri_glmfit-sim --glmdir a_glm_results/lh.thickness.velocity.10.glmdir --cache 1.3 abs --cwp 0.05 FreeSurferEnv.csh 7.1.1 Mon Jul 26 10:02:49 EDT 2021 Darwin Narlons-MacBook-Pro.local 20.4.0 Darwin Kernel Version 20.4.0: Thu Apr 22 21:46:47 PDT 2021; root:xnu-7195.101.2~1/RELEASE_X86_64 x86_64 narlonsilva setenv SUBJECTS_DIR /Users/narlonsilva/Desktop/freesufer_subjects FREESURFER_HOME /Applications/freesurfer/7.1.1 Original mri_glmfit command line: cmdline mri_glmfit --y a_cat_data/lh.thickness.velocity.10.mgh --fsgd a_fsgd/velocity.fsgd doss --C a_contrasts/velocity_sex_age.mtx --surf fsaverage lh --cortex --glmdir a_glm_results/lh.thickness.velocity.10.glmdir DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = doss fwhm = 1240.684619 ERROR: cannot find /Applications/freesurfer/7.1.1/average/mult-comp-cor/fsaverage/lh/cortex/fwhm1241/abs/th13/mc-z.csd I was wondering how to fix the error? Thank you! I have a MacBook Pro: macOS Big Sur version 11.3.1. Best regards, Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSFHR/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon

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Contrast for continuous-by-continuous interactions
by Avi Gharehgazlou 03 Aug '21

03 Aug '21

External Email - Use Caution Hi experts, I am using the command line stream on Freesurfer for my analyses. Although I have successfully designed all my contrasts, I wanted confirmation from you regarding one contrast that I am unsure about. Will you please check if the below contrast appropriately investigates age-by-IQ interaction effects across my two groups (TD and NDDs)? I am also copying here information regarding my regressors and the first few lines of my FSGD file for further detail. *Contrast:* To examine age-by-IQ interaction effects across groups (TD and NDDs): agexIQinteraction_acrossgroups.mtx 0 0 0 0 0.5 0.5 0.5 0.5 0 0 0 0 -0.5 -0.5 -0.5 -0.5 My regressors: · 2 discrete factors: Diagnosis, sex · 4 groups/levels/classes: TD M, TD F, NDD M, NDD F · 3 continuous covariates: age, SA, IQ · Number of classes: 4 · Number of variables: 3 · NregressorsDODS= Nclasses*(Nvariables+1)= 4*(3+1)= 16 · Regressor 1: ones for TDM subjects, 0 otherwise. Codes intercept for TDM · Regressor 2: ones for TDF subjects, 0 otherwise. Codes intercept for TDF · Regressor 3: ones for NDDM subjects, 0 otherwise. Codes intercept for NDDM · Regressor 4: ones for NDDF subjects, 0 otherwise. Codes intercept for NDDF · Regressor 5: age for TDM subjects, 0 otherwise. Codes for TDM · Regressor 6: age for TDF subjects, 0 otherwise. Codes for TDF · Regressor 7: age for NDDM subjects, 0 otherwise. Codes for NDDM · Regressor 8: age for NDDF subjects, 0 otherwise. Codes for NDDF · Regressor 9: SA for TDM subjects, 0 otherwise. Codes for TDM · Regressor 10: SA for TDF subjects, 0 otherwise. Codes for TDF · Regressor 11: SA for NDDM subjects, 0 otherwise. Codes for NDDM · Regressor 12: SA for NDDF subjects, 0 otherwise. Codes for NDDF · Regressor 13: IQ for TDM subjects, 0 otherwise. Codes for TDM · Regressor 14: IQ for TDF subjects, 0 otherwise. Codes for TDF · Regressor 15: IQ for NDDM subjects, 0 otherwise. Codes for NDDM · Regressor 16: IQ for NDDF subjects, 0 otherwise. Codes for NDDF My FSGD file: GroupDescriptorFile 1 Title TD_vs_NDDs_sex_age_SA_IQ Class TDM Class TDF Class NDDM Class NDDF Variables age SA IQ Input 100092_01 TDM 0.060861784 1.747581397 0.386693428 … I'd really appreciate your confirmation of my contrast, Thanks so much, Avi

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Freesurfer July 2021