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30086 discussions

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.

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midline to cut the brain stem into Left and Right
by 刘梦醒 02 Sep '20

02 Sep '20

External Email - Use Caution Hi Freesurfer group, For some reason, I have to use the left and right brain stem separately. I wonder if there is one way to have a midline, to cut the brain stem into Left and Right? Many thanks, Mengxing

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Re: [Freesurfer] G_subcallosal region is missing
by Marina Fernández 02 Sep '20

02 Sep '20

External Email - Use Caution Hi Doug, When I load the volume aparc.a2009s+aseg.mgz in a subject without the G_subcallosal region in the lh.aparc.a2009s.stats file, I can see that in the other hemisphere (right in this case) there is G_subcallosal while in the left hemisphere this contralateral region is filled by the lh_S_suborbital region. So, it's covered by another label. What should we do? Best wishes, Marina ---------------------------------------------------------------------------------------------------------------------------- Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Wed, 02 Sep 2020 07:23:58 -0700 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> Does the cortex label cover it? What does the aparc look like in that area? On 9/2/2020 6:09 AM, Marina Fernández wrote: 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 _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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

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

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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