Freesurfer September 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
165 discussions

Re: [Freesurfer] Freesurfer hippocampal error
by Emily K Clarke 02 Sep '20

02 Sep '20

External Email - Use Caution Hi Douglas, Could you point me to the documentation about creating hippocampal files outside of recon-all? I’m not familiar with running this method outside of recon-all since I’ve typically followed the ENIGMA hippocampal pipeline. Best, Emily

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G_subcallosal region is missing
by Marina Fernández 02 Sep '20

02 Sep '20

External Email - Use Caution Dear experts, I have noticed that some subjects don't show the G_subcallosal region in the *h.aparc.a2009s.stats file. Do you know why is this happening? Is there a way to fix it? Thank you in advance. Best regards, Marina

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Dockerfile for official docker image?
by Andrew J. Worth 01 Sep '20

01 Sep '20

External Email - Use Caution Hello, I’m very happy that there is an official Freesurfer Docker image! But it doesn’t match the Dockerfile in the Github repo. I’d really like to take a look at that Dockerfile. Would it be appropriate to add it to the Github repo? Thanks, Andy.

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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

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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

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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.

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Open research assistant position at Ohio State University
by Osher, David E. 01 Sep '20

01 Sep '20

External Email - Use Caution The Cognition and Brain Circuitry Laboratory at the Ohio State University is recruiting a research assistant. Primary duties include: conducting neuroscience research on the functional and structural architecture of the human brain, and its role in cognition; programming, running, and analyzing behavioral and brain-imaging experiments using functional magnetic resonance imaging (fMRI), diffusion weighted imaging (DWI), functional connectivity, and behavioral assessments; scoring and coding data; performing statistical analyses using programs such as, MATLAB, Python, and shell scripting; recruiting research participants; maintaining participant databases; developing outreach letters. The position is available for one year with the possibility of extension based on satisfactory performance and availability of funds. Required qualifications include: Bachelor's degree in psychology, neuroscience, cognitive science, computer science, data science, engineering, physics, or math; conduct of social science research is required; experience in a social science research capacity. Highly desired: strong mathematical, statistical, and coding skills (e.g., MATLAB, Python, shell scripting); strong interpersonal skills for interacting with a diverse group of people; strong organizational skills. This position is an excellent opportunity for individuals considering future graduate studies in cognitive and computational neuroscience. We are seeking an aspiring, self-motivated researcher with strong coding/programming skills who is excited about the brain, cognitive neuroscience, and/or clinical disorders and demonstrates evidence of a serious interest in a career in the field. If you are interested in being considered for these positions, please apply online at https://www.jobsatosu.com/postings/103123 and submit a current CV and names of three references. If you have questions about the position or the lab, please contact Dr. David Osher at osher.6(a)osu.edu<mailto:osher.6@osu.edu> The Ohio State University is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation or identity, national origin, disability status, or protected veteran status. _____________________________________ David E. Osher, Ph.D. Assistant Professor of Psychology The Ohio State University davidosher.com<https://www.davidosher.com/>

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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

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Re: [Freesurfer] Cannot disable the topology correction
by k3ops＠free.fr 01 Sep '20

01 Sep '20

External Email - Use Caution Hi Douglas, thanks for your answer. I agree that desabling the topology correction is not recommended but I am dealing with subjects having many lacunar infarcts that impact this step (running for more than 2 days sometimes and leading to segmentation errors like removing gyri from cerebral cortex). Is there a way to configure the behavior of the topology correction (like number of iterations, ...) from the "recon-all" command line? Thanks, Florent On 8/25/2020 11:24 AM, dgreve(a)mgh.harvard.edu wrote: > Date: Tue, 25 Aug 2020 11:24:28 -0400 > From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Cannot disable the topology correction > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <5284d1e1-011c-2e25-9d22-e222bd9e5989(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8"; format=flowed > > If the topology correction has not been done, then the stream cannot > proceed. If you really want to skip the topofix, then just copy > lh.orig.nofix to lh.orig and run with -nofix, but this is not recommeneded > > On 8/25/2020 11:04 AM, k3ops(a)free.fr wrote: > > External Email - Use Caution > > > > Hi FS team, > > > > I am having an error when disabling (-nofix) the topology correction with the recon-all command. > > The "-nofix" option is skipping the topology correction as expected but then the next step is failing because "?h.orig" file does not exist. > > > > When reading the recon-all table here: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0 > > it looks like "-fix" step (topology correction) is first copying the following file: "cp ?h.orig.nofix ?h.orig" > > So if this step is ignored with the "-nofix" option then "?h.orig" files are not created, which is causing a failure with next step (cannot read ?h.orig). > > > > Do you have any solution to that? > > My goal is to run FreeSurfer without topology correction because for some cases it is running in an infinite loop (more than 2 days of processing). > > > > Thanks, > > Florent > > > > FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 > > Platform: Ubuntu 18.04 > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mris_anatomical_stats
by Palin, Tara 01 Sep '20

01 Sep '20

External Email - Use Caution When using the following command line: mris_anatomical_stats -th3 -mgz- cortex ../label/?h.cortex.label -f ../stats/?h.aparc.pial.stats -b -a ../label/?h.aparc.annot -c ../label/aparc.annot.ctab subject ?h pial do we generate a pial surface area (for each hemisphere) that excludes the medial wall? Thank you, Tara ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Freesurfer September 2020