Freesurfer August 2020

freesurfer@nmr.mgh.harvard.edu

101 participants
152 discussions

Re: [Freesurfer] recon-all exited with errors
by Vinny K 09 Sep '20

09 Sep '20

External Email - Use Caution Hi, I've tried to process a scan but it gets hung up on a particular large defect and then exits with error. I've had large defects with other scans before but recon-all was able to get past it. How can I correct this? I've attached the recon-all log. Thanks, Vinny

2 2

BrainSegNotVent
by Harkey, Thomas Jarrott 08 Sep '20

08 Sep '20

External Email - Use Caution Hello, I am a student learning free surfer. I was able to obtain intracranial volume by running recon-all –i file.dcm –subject bert –autorecon1 and then mri_segstats --subject bert --etiv-only How can I obtain the BrainSegNotVent volume? I have tried mri_segstats --subject bert --brain-vol-from-seg however, “ERROR: must specify a segmentation volume” Can this be calculated using the data from autorecon1, or do I need to run -all? Which segmentation do I need to specify? My contact information is below, Thank you! -- Thomas Harkey University of Arkansas for Medical Sciences College of Medicine, Class of 2022 501-553-6318 TJHarkey(a)uams.edu<mailto:TJHarkey@uams.edu> ---------------------------------------------------------------------- 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.

2 12

recon-all error
by Jie Zhao 08 Sep '20

08 Sep '20

External Email - Use Caution Dear freesurfer developer: I am using Freesurfer 7.1.1 and encounter an error like this when using recon-all : zhao@zhao-VirtualBox:~$ export SUBJECTS_DIR=/usr/local/freesurfer/subjects zhao@zhao-VirtualBox:~$ recon-all -s test4 -i sample-002.nii.gz -autorecon1 Subject Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 Current Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux zhao-VirtualBox 4.15.0-20-generic #21-Ubuntu SMP Tue Apr 24 06:16:15 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Segmentation fault ERROR: Executable 'mri_ca_label -all-info failed! Is it missing from the distribution?' What can I do to fix this? Thanks Best regards Jie Zhao

7 26

Piriform gyrus and other regions of the olfactory pathway
by Diógenes Bispo 08 Sep '20

08 Sep '20

External Email - Use Caution Dear, I would like to know how do I get thickness and cortical volume measurements of the piriform gyrus in Freesurfer version 7, as well as other regions of the olfactory pathway. Thanks. Diógenes Bispo Neuroradiologist diogenesdiego(a)gmail.com

3 3

Extracting hierarchical hippocampal segmentation volumes
by Kelsey Leigh Canada 07 Sep '20

07 Sep '20

External Email - Use Caution Hello, I am newer to Freesurfer and have been unable to find a reference on how to extract the volumes/voxels of the hierarchical segmentations using FS 7.1 (e.g, from rh.hippoAmygLabels-T1-T2.v21.CA.mgz). I am trying to compare manual segmentations to those generated by Freesurfer and the closest hierarchical segmentation is "CA". However, because the volume output (i.e., from quantifyHAsubregions.sh) does not seem specific to a given hierarchical segmentation, I am unsure how the molecular layer is being assigned for the "CA" segmentation given these voxels are assigned to the nearest voxel that isn't the molecular layer or background. Any guidance on how to extract volumes that reflect the "CA" segmentation would be greatly appreciated. Best regards, Kelsey Canada

2 1

tkregister2 deprecated for FS7.1?
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 02 Sep '20

02 Sep '20

Hi FS devs, I am following https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview? as a tutorial to fix the bad talaiarch file I have. I know that tkmedit is deprecated, but I was wondering if tkregister2 is too. If so, I was wondering what software I would use (or commands, I assume using freeview) since that page still refers to tkregister2. Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

3 6

mri_preproc error with FS6.0
by chelseachays＠yahoo.com 01 Sep '20

01 Sep '20

External Email - Use Caution Hello, I am running into an error while running the LGI analyses using FreeSurfer 6.0 following Jove article recommendations ( https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369773/) The error is occuring when I try to run the following command: mris_preproc --fsgd FSGD.txt --target average --hemi lh --meas pial_lgi --out lh.lgi.mgh Here is the error message: nsubjects = 57tmpdir is ./tmp.mris_preproc.174575 /data/EDresearch/AdolAN_All/enigma/output Log file is lh.lgi.mris_preproc.log Mon Aug 31 08:25:13 PDT 2020 setenv SUBJECTS_DIR /data/EDresearch/AdolAN_All/enigma/output cd /data/EDresearch/AdolAN_All/enigma/output /usr/local/freesurfer/bin/mris_preproc --fsgd FSGD.txt --target average --hemi lh --meas pial_lgi --out lh.lgi.mgh Linux induction3.sdsc.edu 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.174575 Src lh average.sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/57 541202132011 Mon Aug 31 08:25:13 PDT 2020 -------------- ----------------------- mri_surf2surf --srcsubject 541202132011 --srchemi lh --srcsurfreg average.sphere.reg --trgsubject average --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.174575/541202132011.1.mgh --sval /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.pial_lgi --sfmt curv --noreshape --cortex MRISread(/data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.average.sphere.reg): could not open file Source registration surface changed to average.sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /data/EDresearch/AdolAN_All/enigma/output cd /data/EDresearch/AdolAN_All/enigma/output mri_surf2surf --srcsubject 541202132011 --srchemi lh --srcsurfreg average.sphere.reg --trgsubject average --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.174575/541202132011.1.mgh --sval /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.pial_lgi --sfmt curv --noreshape --cortex sysname Linux hostname induction3.sdsc.edu machine x86_64 user chays srcsubject = 541202132011 srcval = /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.pial_lgi srctype = curv trgsubject = average trgval = ./tmp.mris_preproc.174575/541202132011.1.mgh trgtype = srcsurfreg = average.sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.average.sphere.reg No such file or directory mri_surf2surf: could not read surface /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.average.sphere.reg No such file or directory Of note, this command works fine when substituting the fsaverage rather than study average template, however this is an adolescent sample so we are not able to use the fsaverage. Any help would be greatly appreciated! Best, Chelsea Chelsea C. Hays, Ph.D. Neuropsychology Postdoctoral Fellow Center of Excellence in Stress and Mental Health UC San Diego|VA San Diego Healthcare Systemchays@ucsd.edu|chelsea.hays2@va.gov

3 3

Error using FsPalm
by 정현우 01 Sep '20

01 Sep '20

External Email - Use Caution Hello Freesurfer Developers, I'm trying to do permutation simulation on 50 subjects to find brain region clusters of which cortical thicknesses have significant association with clinical parameters while controlling for age and sex. I tried this via 'mri_glmfit-sim' but it seems that permutation analysis could not be done with non-orthogonal variables in Freesurfer. I copied the command I used and the error output below. mri_glmfit-sim --glmdir NK_IES_avoidance_correlation.rh.glmdir --perm 1000 1.3 abs --cwp 0.05 --2spaces ERROR: design matrix is not orthogonal, cannot be used with permutation. If this something you really want to do, run with --perm-force So I tried using PALM, which allows permutation analysis with non-orthogonal variables according to a post in the Freesurfer Archive. I installed PALM, FsPalm and Octave on my computer and ran the command below, but I ran into another error output (copied below) that I do not quite understand. fspalm --glmdir NK_IES_avoidance_correlation.rh.glmdir --cft 1.3 --twotail --name perm.NK_IES_avoidance_correlation.rh --iters 1000 --2spaces --cwp .05 --octave preparing a palm subdirectory in /media/sjkim/hd2/subject_data/glm/NK_IES_avoidance_correlation.rh.glmdir/perm.NK_IES_avoidance_correlation.rh found NK_IES_avoidance_correlation.rh.glmdir/surface file - this is a surface-based analysis using the glmfit input file /media/sjkim/hd2/subject_data/glm/NK_IES_avoidance_correlation.rh.10.mgh using area file /media/sjkim/hd2/subject_data/fsaverage/surf/rh.white.avg.area.mgh palm prep complete - running the generated matlab script... error: 'fast_p2z' undefined near line 1 column 11 error: cannot find expected palm output "fsp_clustere_tstat_fwep.mgz" - check for run_palm.m failures I copied the matlab script 'run_palm.m' below. hemi = 'rh'; input = '/media/sjkim/hd2/subject_data/glm/NK_IES_avoidance_correlation.rh.10.mgh'; maskfile = '/media/sjkim/hd2/subject_data/glm/NK_IES_avoidance_correlation.rh.glmdir/mask.mgh'; surffile = '/media/sjkim/hd2/subject_data/fsaverage/surf/rh.white'; areafile = '/media/sjkim/hd2/subject_data/fsaverage/surf/rh.white.avg.area.mgh'; %% Changing threshold for two-tailed test cft = 1.3 + 0.301; pthresh = 10^-cft; zthresh = fast_p2z(pthresh); iters = 1000; zthreshstr = sprintf('%f',zthresh); itersstr = sprintf('%d',iters); palm('-i',input,'-m',maskfile,'-d','design.mat','-t','design.con','-logp',... '-n',itersstr,'-C',zthreshstr,'-o','fsp','-twotail','-s',surffile, areafile); return; Do you have any suggestions on how I could figure out this problem? Of note, I am using Freesurfer v6.0 and Ubuntu 18.04.4 LTS platform. Thanks in advance, Hyunwoo Jeong

2 7

intersubject longitudinal analysis
by KennethSPrice 01 Sep '20

01 Sep '20

External Email - Use Caution Hello Freesurfers! I am working through the longitudinal tutorial found here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial To keep it simple, I ran longitudinal processing on 2 timepoints for one subject. My qdec file had only two entries. I would like to look at pct difference in thickness for one subject. I ran long_mris_slopes --qdec qdec.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR When I run the overlay I get an error saying that "the overlay cannot be loaded", although the file exists. freeview -f $FREESURFER_HOME/subjects/fsaverage/surf/lh.pial:overlay=$SUBJECTS_DIR/OAS2_0001/surf/lh.long.thickness-spc.fwhm15.fsaverage.mgh:overlay_threshold=2,5 First of all, is this method sound in order to visualize pct change in thickness for one subject? If so, why is the overlay not loading? Best, Ken Sent with [ProtonMail](https://protonmail.com) Secure Email.

2 1

remark regarding tcsh with bad locale
by Rovai Antonin 01 Sep '20

01 Sep '20

External Email - Use Caution Hi, this is not really a question but rather a comment that, hopefully, will help those running into the issue I ran into today. I was using mri_glm-sim with --mczsim 2 option, and got an error saying that "2,0 must be 1.3, 2.0 ...". The issue is that printf (used in the mri_glm-sim script) refers to the LC_NUMERIC locale which, in my unfortunate case, has instructed printf %2.1f to replace the dot by a comma. You can check this by typing locale in a terminal. If, like me, you live in an undercivilized part of the world, then you may update your locale using e.g. sudo update-locale LC_NUMERIC=en_US.UTF-8 Log in and out and you'll be back on the right side of the force. It would be great if a future release of FS could include a locale check :-) Hope this help someone, someday. Best AR Hôpital Erasme - ULB Cliniques universitaires de Bruxelles Route de Lennik 808 - B - 1070 Bruxelles S www.erasme.ulb.ac.be Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer

2 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 August 2020