Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

FreesurferNHP
by Lauro, Peter 12 Jul '16

12 Jul '16

Hello, I'm trying to reconstruct cortical surfaces from non-human primate MRIs. I tried following the instructions/scripts listed here ( https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData) but I was unable to make it work (I'm also running FS 5.3). I noticed on the Washington-Pipelines github FAQ page listed a FreesurferNHP pipeline ( https://github.com/Washington-University/Pipelines/wiki/FAQ#9-what-if-i-wan…) but it hasn't been released yet. Do you know when this pipeline will be available? Alternatively, is there another way I can obtain the pipeline scripts and template volumes? Thank you, Pete Lauro

3 2

ERROR reading /..../label/lh.BA1.label
by Uquillas, Federico D'Oleire 12 Jul '16

12 Jul '16

Dear fellow FreeSurfer users, My jobs fail at the the last mri_label2label step of -autorecon3, and I cannot figure out why. Any help or input would be greatly appreciated. I am attaching a recon-all log for two of these subjects. The error says that it's not possible to read the labels contained in the fsaverage/labels/ folder. These labels/files do exist however if you look in the /labels/ folder. I'm using Centos 6.7 (Final) Kernel Linux 2.6.32-573.22.1.el6.x86_64 GNOME 2.28.2 My username is fdu0. A path to my most recent error fail can be the following: /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 (PBS Job ID: 11918069) another one with this same error fail is /FreeSurferProc/AD08 (PBS Job ID: 11914847). Thank you very much for your time and any help you may be able to provide. Fred

1 0

Fwd: TRACULA stat extraction issue
by Shashwath Meda 12 Jul '16

12 Jul '16

Dear Group - I seem to have run into an issue when attempting to assimilate the averaged pathway information from TRACULA into a group table. I have attached my input list of paths and my output table for one of the tracts. The below is the command that i have used but as you can see the values in my final table are all from one subject (just replicated) despite my input list having paths from different subjects, Has anyone encountered a similar situation? tractstats2table --load-pathstats-from-file fmajor_PP_avg33_mni_bbr.txt --overall --tablefile fmajor_PP_avg33_mni_bbr.table -- Best, Shashwath

2 3

Freeview question
by pfotiad＠nmr.mgh.harvard.edu 12 Jul '16

12 Jul '16

Hello FS Community, Lately, whenever I am trying to use freeview I get the following error message: freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directory Exit 127 The error started showing up after the cluster went down. I was wondering whether there was a way to fix this since I don't have admin privileges (and hence can't sudo). Thanks in advance, Panos

2 2

Slight rotation when viewing brainmask.mgz in Freeview - why and is this a cause for concern?
by Reema Jayakar 12 Jul '16

12 Jul '16

Hello FS developers/users, When viewing brainmask.mgz in Freeview, for some subjects the brain is slightly (~10-20 degrees) rotated. By looking at the raw data, I see that their head position in the scanner was slightly skewed. I thought that brainmask.mgz is created after Talairach transformation and normalization has been completed. I took this to mean that the brainmask.mgz file has been registered to an atlas. If so, shouldn't the brainmask.mgz files for all subjects appear with 0 rotation in freeview? Should I be concerned that this is not the case for my dataset? Thanks for your help! Reema -- *Reema Jayakar, M.A.* Doctoral Candidate - Clinical Neuropsychology Health Resources and Services Administration (HRSA) Fellow Department of Psychology Georgia State University Email: rjayakar1(a)student.gsu.edu

1 0

Visually inspecting subcortical segmentations + what command should be run to apply manual fixes to aseg.mgz voxels?
by Reema Jayakar 12 Jul '16

12 Jul '16

Hello FS developers/users, I have a two part question regarding subcortical segmentation: 1) To visually inspect if segmentation accurately captures structure boundaries (e.g., amygdala) I am using the norm.mgz file and overlaying it with the aseg.mgz file in Freeview. Is this correct? Or should I be using brainmask.mgz (instead of norm.mgz)? Also, Freeview gives me some options - "Resample to standard RAS space" and "Apply registration file". Where can I find information about whether or not to use these options? 2) If I manually edit the boundaries of the amygdala (either by erasing voxels or using the color brush to add voxels), what command should I use to re-run such that the corrections are applied to my aseg.stats output? The command I found on the wiki page says to use recon-all -autorecon-2-noaseg -subjid <Subj_ID>. My understanding was that the -noaseg flag will skip all the subcortical segmentation steps and that is not what I want. What I want is for FS to re-run subcortical segmentation such that it reflects the voxel editing I did in Freeview. This is the first time I am doing something like this so any help you can provide or pointing me to the right resource would be great! Thank you! Reema -- *Reema Jayakar, M.A.* Doctoral Candidate - Clinical Neuropsychology Health Resources and Services Administration (HRSA) Fellow Department of Psychology Georgia State University Email: rjayakar1(a)student.gsu.edu

1 0

mri_glmfit-sim
by Lauri Tuominen 12 Jul '16

12 Jul '16

Dear Freesurfers, As freesurfer mri_glmfit-sim is based on AlphaSim & FSL randomise, I would like to know if the results I’m getting are affected by recently found bugs/violations in RFT assumptions, e.g. http://www.pnas.org/content/early/2016/06/27/1602413113.full.pdf. Thank you in advance! Lauri Tuominen

2 1

tcsh update
by shi yao wang 12 Jul '16

12 Jul '16

Dear FS experts: I am running FS in local computer and showing following error message and program stopped at recon-all WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! Do I need to update tcsh? and how can I do it. thanks Lawrence

2 1

R: Re: Recon-all error after El Capitain update
by stdp82＠virgilio.it 12 Jul '16

12 Jul '16

This is the command and the error line. Thanks. Stefano recon-all -all -i $SUBJECTS_DIR/T1_STRUCT.nii.gz -subject SUBJECTS_DIR #-------------------------------------------- INFO: fsaverage subject does not have perirhinal labels! \n cd /Applications/freesurfer/subjects/subject_prova/Control89; rm -Rf fsaverage; cd - \n INFO: Creating symlink to fsaverage subject... \n cd /Applications/freesurfer/subjects/subject_prova/Control89; ln -s /Applications/freesurfer/subjects/fsaverage; cd - \n \n mri_label2label --srcsubject fsaverage --srclabel /Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh. BA1.label --trgsubject SUBJECTS_DIR --trglabel ./lh.BA1.label --hemi lh -- regmethod surface \n No such file or directory mri_label2label: could not open label file /Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh. BA1.label srclabel = /Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh. BA1.label srcsubject = fsaverage trgsubject = SUBJECTS_DIR trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova/Control89 FREESURFER_HOME /Applications/freesurfer Loading source label. No such file or directory ERROR reading /Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh. BA1.label Darwin iMac-di-Stefano.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s SUBJECTS_DIR exited with ERRORS at Sat Jul 9 17:20:34 CEST 2016 For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Control89/SUBJECTS_DIR/scripts/recon- all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >----Messaggio originale---- >Da: "dgw" <dgwakeman(a)gmail.com> >Data: 7-lug-2016 15.58 >A: <stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard. edu> >Ogg: Re: [Freesurfer] Recon-all error after El Capitain update > >It's hard to fully diagnose, without the command you called, but it >looks like you have your SUBJECTS_DIR and SUBJECT variable wrong, and >perhaps command syntax. Take another look at your command. > >hth >d > >On Thu, Jul 7, 2016 at 2:59 AM, <stdp82(a)virgilio.it> wrote: >> Hi list, >> >> after update with El Capitain, recon-all -all produce the error reported >> below. >> >> >> Thanks >> >> srclabel = >> /Applications/freesurfer/subjects/subject_prova/subj/fsaverage/label/lh.BA1. label >> >> srcsubject = fsaverage >> >> trgsubject = SUBJECTS_DIR >> >> trglabel = ./lh.BA1.label >> >> regmethod = surface >> >> >> srchemi = lh >> >> trghemi = lh >> >> trgsurface = white >> >> srcsurfreg = sphere.reg >> >> trgsurfreg = sphere.reg >> >> usehash = 1 >> >> Use ProjAbs = 0, 0 >> >> Use ProjFrac = 0, 0 >> >> DoPaint 0 >> >> >> SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova/subj >> >> FREESURFER_HOME /Applications/freesurfer >> >> Loading source label. >> >> No such file or directory >> >> ERROR reading >> /Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh. BA1.label >> >> Darwin iMac-di-Stefano.local 15.5.0 Darwin Kernel Version 15.5.0: >> root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 >> >> >> recon-all -s SUBJECTS_DIR exited with ERRORS >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >

1 0

V3A ROI?
by Anders Hougaard 11 Jul '16

11 Jul '16

Dear experts, I am trying to find a probabilistic map of the visual cortical area V3A. I have not been able to find this particular area in the standard atlases in FSL or FreeSurfer. The Jülich Histological atlas contains a V3V ROI but not V3A. Do any of you know have this ROI as a file or do you know of an atlas which contains it? An estimation based on an experiment, e.g. an average from retinotopic maps of healthy subjects would also be very helpful. All the best, Anders

3 4

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