Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

TRACULA - OrientLAS issue for a subject
by Daniel Callow 23 Aug '19

23 Aug '19

External Email - Use Caution For reference, I think the issue had to do with the orientation of these two subjects. I added tome code to use 3dwarp -deoblique to the dwi_orig.nii.gz and then ran orientLAS and it worked this time. The only thing I am unsure about is if this will nulify the bvals and bvecs I have and ruin later preprocessing steps? This is the only solution to the problem I have found thus far though. *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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recon_all hires
by Nasiriavanaki, Zahra 23 Aug '19

23 Aug '19

Dear Freesurfer experts I am doing recon-all on one of my subjects and it seems that it's stuck for days and not going through. I even re-run it and it's still stuck at the same spot as before. I attached the log file and here is my command: recon-all -all -s $subj -i /$subj/anat/$run/mT1v2.nii -expert expertopts/expert.opts -hires -mail zn025 -parallel I appreciate any help. Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Help with using family as random effect in sibling study
by Hopkinson, Casey E 23 Aug '19

23 Aug '19

Hello! I am trying to generate significance maps for a paired-difference analysis of cortical thickness using multiple pairs of siblings, and was wondering if there is a way to incorporate the family ID as a random effect/covariate in Freesurfer. Is it possible for the family ID for each sibling pair to be used as a categorical/discrete variable to then see the effect of family on cortical thickness in addition to the main effects we are looking at? Any guidance would be greatly appreciated! Best, Casey -- Casey Hopkinson Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street, Charlestown, MA, 02129 (p) 617.643.3215

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Converting surface coordinates to MNI coordinates
by Avi Gharehgazlou 23 Aug '19

23 Aug '19

External Email - Use Caution Hi, I am conducting a meta-analysis on papers that have looked at local gyrification index (lGI) in Autism Spectrum Disorder (ASD) relative to typically developing (TD) peers. All lGI papers have used the FreeSurfer software and have reported x,y,z coordinates for their significant clusters (in which lGI in ASD is different from TD). Please help me with the below 2 questions: 1. My understanding is that these coordinates reported in lGI papers are "surface coordinates" (of fsaverage). Is this correct? 2. How can I convert these x,y,z surface coordinates to MNI space coordinates? I'd really appreciate your reply, Thanks so much, Avi

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Gender and age based reconstruction
by Carissa Liana Grijalva 23 Aug '19

23 Aug '19

External Email - Use Caution Hello FreeSurfer Support, I reached out the other day about if there was a way to specify the data is from a specific gender or age during the recon all code, such as a tag at the end. I was told that there is not way to tell recon-all about demographics/subject meta data, and not to worry about this during recon-all, but instead add age and gender as covariates in the model later. Does this mean FreeSurfer automatically finds the right regions regardless of age or gender? Does this work based on gray/white matter thresholds or something similar, so regardless of the demographics of the brain, it find the right regions? Thank you for your time. Best, Carissa Grijalva -- *Carissa Grijalva* *University of Arizona * *Biomedical Engineering PhD Program* *Undergraduate Research Opportunities Consortium Scholar* *NSF WAESO Research Fellow* *Society of Hispanic Professional Engineers*

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Call for Nominations – OHBM Student and Postdoc Special Interest Group
by Heidi Emmanuel Foo 22 Aug '19

22 Aug '19

External Email - Use Caution Dear All, The OHBM Student and Postdoc Special Interest Group (SIG) is seeking nominations for open seats on the 2019-2020 SIG 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 community, directing its activities, and working with the OHBM Executive Office 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.A., 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 the next Annual Meeting. • Nominees must be members of OHBM in good standing at the time of the next Annual Meeting. • Nominees must be attendance at the next two Annual Meetings in Montreal 2020 and Seoul 2021, and be likely to attend the meeting in 2022, and preferably have secured funding to support conference travel. To nominate yourself for election to the SIG Committee please complete this nomination form and attach your CV: https://docs.google.com/forms/d/e/1FAIpQLSeJRKKLi8FmcKdjw3PbT7BLjQyZ3ZmU4yr… no later than September 9th, 2019. Visit our website (https://www.ohbmtrainees.com/terms-of-reference) or email ohbmtrainees(a)gmail.com if you have any questions. Nominations close on the 9th September, 2019. Kind Regards, OHBM Student and Postdoc SIG

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mris_convert segmentation fault on R hemisphere aparc.a2009s only?
by Damion V Demeter 22 Aug '19

22 Aug '19

External Email - Use Caution Hi Bruce, My apologizes, I just saw this reply because I didn't realize I had the list on digest mode. I would very much appreciate your help! How/where should I upload the files? Thank you! Damion Hi Damion if you upload the relevant files so that we can replicate this we will fix it cheers Bruce On Wed, 14 Aug 2019, Damion V Demeter wrote: > >* External Email - Use Caution *> >* I am having an issue processing some of my subjects through the HCP pipeline *>* and have no idea what this error means. If anyone could help out, I'd *>* appreciate it! Here is all the info: *> >* 1. Some (not all) of my subjects are getting a segmentation fault error *>* during the post-freesurfer step of the HCP pipeline. Previous subjects were *>* fully processed fine without error (over 100 of them) and are from the same *>* group (all scanner and acquisition settings identical). Here is the *>* segmentation fault error line: *> >* FreeSurfer2CaretConvertAndRegisterNonlinear.sh: line 294: 46979 Segmentation *>* fault mris_convert --annot *>* "$FreeSurferFolder"/label/"$hemisphere"h."$Map".annot *>* "$FreeSurferFolder"/surf/"$hemisphere"h.white"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native. *>* label.gii *> >* 2. I have narrowed down this error further and have found that it only *>* happens on the right hemisphere aparc.a2009s file. I have manually run the *>* command above for the left and right hemisphere files separately as a test, *>* and the L hemisphere files complete without fail. The R hemisphere, however, *>* always gets this segmentation fault. *> >* This only occurs on certain subjects, but all the files this command is *>* using look good and error free. All previous steps appeared to finish *>* without fail and all expected files were written and can be opened (I'm 99% *>* sure...I might have missed something). I am at a complete loss at how to *>* troubleshoot this further or fix this error. Does anyone have any ideas or *>* solutions? *> >* Thank you! *> > ----- Damion Demeter, MA Doctoral Student UT Austin | Cognitive Neuroscience DCN Lab <https://labs.la.utexas.edu/church-lang/>

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FreeSurfer development version masks
by Hurtado, Aura Maria 22 Aug '19

22 Aug '19

Hello, I am trying to freeze the development freesurfer version for today and I am denied access to copy the following files: /usr/local/freesurfer/dev.backup/average/mult-comp-cor/fsaverage/rh/cortex/mask.mgh /usr/local/freesurfer/dev.backup/average/mult-comp-cor/fsaverage/lh/cortex/mask.mgh /usr/local/freesurfer/dev.backup/subjects/fsaverage6 /usr/local/freesurfer/dev.backup/subjects/fsaverage/scripts/fix-surf7.log /usr/local/freesurfer/dev.backup/subjects/fsaverage3 /usr/local/freesurfer/dev.backup/subjects/fsaverage_sym/scripts/fix-surf7.log /usr/local/freesurfer/dev.backup/subjects/fsaverage4 Are they instrumental? Are they the same as stable6? How can I have access to these? (I am in the Martinos cluster) Thank you, Aura M.

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ERROR reading /<my data path>/fsaverage/label/lh.BA1_exvivo.label
by liuxingze1993 21 Aug '19

21 Aug '19

External Email - Use Caution Hello，Dear FreeSurfer Developers, I’m a doctoral student from Xiangya 2nd Hospital of Central South University, and also a beginner to FreeSurfer. I'm attempting to follow the steps descripted on ‘Practice Working with Data’ (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice) with our own data, but I’ve met the same problem several times when I programing the command ‘recon-all -all -i 61492283 -s Sub219’: (**ps: 61492283 is the T1 file I found after programing the command 'dcmunpack -src . -scanonly.log') SUBJECTS_DIR /media/dell/AA32E/Data_prac/219/20181211/19470000 (**PS: 19470000 is the folder where the T1 located) FREESURFER_HOME /usr/local/freesurfer Loading source label Invalid argument ERROR reading /media/dell/AA32E/Data_prac/219/20181211/19470000/fsaverage/label/lh.BA1_exvivo.label recon-all -s Sub219 exited with ERRORS at <local time here> I've searched the ‘lh.BA1_exvivo.label’ file in the related path and no such file here. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu14.04 LTS 3) uname -a: Linux dell 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thank u for viewing, and I will be waiting here for your professional advice !

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mris_pmake on the inflated surface
by Lee, Jeungchan 21 Aug '19

21 Aug '19

Hi, I’m trying to calculate Dijkstra distance between startVertex and endVertex on the inflated surface (fsaverage, lh.inflated) using mris_pmake. I see several options: --surface0, --surface1, --curv0, --curv1 I think I can use ‘--surface0 inflated’, but not sure about other options e.g., --surface1, --curv0, and --curv1. I read the instruction (curv0 for curvature, curv1 for height parameter…) but was not able to understand what those mean exactly and what to use. Would you explain what the meaning is and what to use? Here is the command line that I have: Mris_pmake --subject fsaverage --hemi lh --surface0 inflated --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs `more ./input_D.txt` (where input_D.txt says startVertex:8762,endVertex:1, for example) Thanks in advance, jeungchan

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