Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30090 discussions

error in recon-all
by 王康程 15 Aug '17

15 Aug '17

Hello FreeSurfer Developers, I'm attempting to do recon-all for a subject. But it reported error although I try several times. The files for recon-all log and error are attached. CORRECTING DEFECT 1 (vertices=10662, convex hull=4463) normal vector of length zero at vertex 137885 with 0 faces vertex 137885 has 0 face No such file or directory Linux compute-0-106 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s CTRL_011 exited with ERRORS at Tue Aug 15 04:28:55 EDT 2017 I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? -- ------- Kangcheng Wang PhD, Faculty of Psychology, Southwest University, China / Visiting Research Scholor, Massachusetts General Hospital

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Re: [Freesurfer] Help with hippocampal subfield alignment
by Antonin Skoch 15 Aug '17

15 Aug '17

Dear Elizabeth, I would guess that something went seriously wrong in the recon-all with your data. Does Talairach registration and skull strip look reasonable? Antonin Skoch

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Fwd: Call for Nominations - OHBM Student and Postdoc Special Interest Group {Disarmed} {Disarmed}
by Douglas Greve 15 Aug '17

15 Aug '17

FYI -------- Forwarded Message -------- Subject: Call for Nominations - OHBM Student and Postdoc Special Interest Group {Disarmed} Date: Tue, 15 Aug 2017 09:44:19 -0500 From: info(a)humanbrainmapping.org Reply-To: info(a)humanbrainmapping.org To: greve(a)nmr.mgh.harvard.edu *Call for Nominations - OHBM Student and Postdoc Special Interest Group * Dear OHBM Members, The OHBM Student and Postdoc Special Interest Group (SIG) are seeking nominations for our 2017-2018 committee. The SIG provides a community of shared interests for OHBM trainees. The committee aims to provide professional, personal and career development for OHBM trainees as well as social and mentoring opportunities at the annual meeting. Committee members benefit from being an integral part of the SIG, directing its activities, and working with the OHBM Executive and wider community. We are committed to diversity and equality and are seeking representation from trainees across the world. *Eligibility * * Nominees must be current students or postdocs. Students are defined as those working full time towards a graduate degree - M.S., Ph.D. or M.D. degree. Postdocs are individuals who are no more than four years after completing such a degree at the time of next annual meeting. * Nominees must be members of OHBM in good standing at the time of the next annual meeting * Nominees must be planning to attend the next two annual meetings in Seoul 2018 and Rome 2019 (and likely to attend the meeting in 2020). To nominate yourself for a position on the committee please fill out the nomination form and attach your CV:https://goo.gl/forms/iUF7wnMDhbdldGCG2 <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> Email ohbmtrainees(a)gmail.com <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> if you have any questions. *Nominations close on the 16th September 2017. * Kind regards, OHBM Student and Postdoc SIG *Organization for Human Brain Mapping (OHBM)* 5841 Cedar Lake Road, Suite 204 Minneapolis, MN 55416 USA Phone: 1 952-646-2029 | Fax: 1 952-545-6073 info(a)humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> www.humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> To opt out of OHBM emails, contact the OHBM Executive Office at info(a)humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…>. Click here to Unsubscribe <http://www.humanbrainmapping.org/i4a/etrack/unsub.cfm?campaignID=3518&conta…>

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(no subject)
by Silvia Obertino 15 Aug '17

15 Aug '17

Hello, I try to map the surface to the native space, using the following command adjusted for my data: mri_surf2surf --sval-xyz pial --reg register.native.dat rawavg.mgz --tval lh.pial.native --tval-xyz --hemi lh --s subjectname the output is: ERROR: --tval-xyz flag needs 1 argument FYI: --tval-xyz now requires a volume. So in the web-page ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat) the comand is not correct. What kind of volume can I put, to get the surface in the native space? Thank, Silvia

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SPC in surface area
by Maria A Infante 15 Aug '17

15 Aug '17

Hi everyone, I have a questions concerning the SPC values for an individual brain region. I am looking at group differences (3 groups) in SPC in surface and found one region that was significant after correcting for multiple comparisons. I want to follow up with pairwise comparisons. Is there a way to extract the SPC values for that particular region? Are these the same values as the ones on the stack file? Thanks, Alejandra

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use manually defined talairach.xfm
by clemens.schroeder＠uzh.ch 15 Aug '17

15 Aug '17

Hi I got a Talairach Failure Detection Error and therefore did manual registration using tkregister2 following the advice at: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview Again following the advice on the site, I re-ran recon-all just to run into the identical error. When I checked talairach.xfm it was the same as BEFORE I did manual registration in tkregister2. The above site states: Because the talairach transformation affects everything in the stream it is necessary to rerun the whole process using your new talairach, which is a default. However, it seems this is not the default since recon-all comes up with its own talairach.xfm and overwrites my manual version, after which recon-all fails. How can I make recon-all use my manual registration?

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mri_glmfit long_stats_slopes with group
by Kasper Jessen 15 Aug '17

15 Aug '17

Dear Freesurfer, I would like to test if the percentage change (two time points) of cortical thickness is different between two groups. What i have done: FIRST: long_stats_slopes --qdec ./qdec/long.qdec.table.dat --stats lh.aparc.stats --meas thickness --sd $SUBJECTS_DIR --do-spc --generic-time --stack-spc ./qdec/long.lh.aparc.stats.stack.txt SECOND: mri_glmfit --osgm --glmdir lh_thickness.aparc-spc --table long.lh.aparc_thickness.stats.stack.txt THIRD: cat lh_thickness.aparc-spc/sig.table.dat Qesteions: 1. How do i test if there is a significant difference between the two groups? 2. How do i visualise this difference in FreeView? Best regards Kasper Jessen

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recon-all error
by Yeseul Kim 14 Aug '17

14 Aug '17

Hi I'm beginner of freesurfer and have an error while using recon-all. I'm Mac (Sierra) user. My subject's data is under: /Applications/freesurfer/subjects/yeseul_data After open terminal, I put commands like: export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh export SUBJECTS_DIR=/Applications/freesurfer/subjects/yeseul_data/sbj1 recon-all –i $SUBJECTS_DIR/20170720_LHS.MR.HEAD_CNIR_IBS.0017.0001.2017. 07.20.16.26.07.667681.198987303.IMA –subject $SUBJECTS_DIR/sbj1_rec -all (My subjects' data is *.IMA format. Filenames are like "20170720_LHS.MR_HEAR_CNIR_IBS.0017.0001......198987303.IMA". I don't think I need to convert IMA format to another, right? Each subject has 192 IMA files and I want to apply recon-all to all of these files.) When I run these commands, I get a messages like: -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni Yeseului-MacBook-Pro:~ yeseulkim$ Yeseului-MacBook-Pro:~ yeseulkim$ export SUBJECTS_DIR=/Applications/ freesurfer/subjects/yeseul_data/sbj1 Yeseului-MacBook-Pro:~ yeseulkim$ Yeseului-MacBook-Pro:~ yeseulkim$ recon-all –i $SUBJECTS_DIR/20170720_LHS.MR .HEAD_CNIR_IBS.0017.0001.2017.07.20.16.26.07.667681.198987303 –subject $SUBJECTS_DIR/sbj1_rec -all ERROR: Flag i unrecognized. i /Applications/freesurfer/subjects/yeseul_data/sbj1/ 20170720_LHS.MR.HEAD_CNIR_IBS.0017.0001.2017.07.20.16.26.07.667681.198987303 subject /Applications/freesurfer/subjects/yeseul_data/sbj1/sbj1_rec -all Darwin Yeseului-MacBook-Pro.local 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Tue Aug 15 01:08:53 KST 2017 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard. edu/fswiki/BugReporting Does it matter with the format of my data files? Or did I set variables incorrectly? Thank you in advance! Best wishes, Yeseul -- Yeseul Kim Visual Cognitive Neuroscience Lab Department of Psychology Korea University Seoul, Korea

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obtaining the most recent build of FreeSurfer development version
by Antonin Skoch 14 Aug '17

14 Aug '17

Dear experts, I would like to download the most recent build of FreeSurfer development version (linux 64 bit). The origin/dev git repository contains commit up to today (14.8.17), but last change of "daily build" of dev version is 28.7.17. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Linux-c… How is the build of dev version sheduled? Antonin Skoch

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mri_binarize/mri_mask command help
by Yagmur Ozdemir 19 14 Aug '17

14 Aug '17

Dear FreeSurfer experts, I am trying to use the following command to merge the volume file of a template with original T1 orientation*, with a file like rawavg to get the full brain volume, but the following attached image gets produced and I am pretty sure, as a freesurfer novice, I am using a wrong command line. I have tried mri_mask as well but do not think it is the command to go. I also checked if two volumes are in the same orientation using mri_orient. mri_binarize --i rawavg.mgz --o scanner.template_angle.mgz --wm+vcsf * (I have the native oriented version of this volume template as well, and I attached a photo of the template as well) I would deeply appreciate if someone could help me correct my command line. Thank you all for the time and help Idil

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