Freesurfer February 2017

freesurfer@nmr.mgh.harvard.edu

162 participants
277 discussions

recon-all error (6.0)
by Trisanna Sprung-Much 24 Feb '17

24 Feb '17

Hi All I am trying to run a subject in 6.0 (it ran perfectly well in 5.3) and it stops when trying to transform to the "conformed" space. I get the following error after about a minute. I have not seen this error before. mri_convert ./tmp.mri_nu_correct.mni.2860/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.2860/nu1.mnc orig_nu.mgz --like orig.mgz --conform ncopen: filename "./tmp.mri_nu_correct.mni.2860/nu1.mnc": Not a netCDF file miopen: MINC package entry point Error opening ./tmp.mri_nu_correct.mni.2860/nu1.mnc mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.2860/nu1.mnc $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.2860/nu1.mnc... Linux kaplan 3.13.0-105-generic #152-Ubuntu SMP Fri Dec 2 15:37:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s icbm-131 exited with ERRORS at Thu Feb 23 11:40:53 EST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any ideas? Best Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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Mindboggle official software release and publication!
by Arno Klein 24 Feb '17

24 Feb '17

Announcing the official release of Mindboggle (http://mindboggle.info) open source software <http://mindboggle.info/software.html> and data <https://osf.io/ydyxu/> for analyzing the shapes of brain structures from human MRI data (processed through FreeSurfer and optionally through ANTs). The release coincides with a publication in PLoS Computational Biology that documents and evaluates the software: Klein A, Ghosh SS, Bao FS, Giard J, Hame Y, Stavsky E, Lee N, Rossa B, Reuter M, Neto EC, Keshavan A. (2017) Mindboggling morphometry of human brains. PLoS Computational Biology 13(3): e1005350. doi:10.1371/journal.pcbi.1005350 <http://doi.org/10.1371/journal.pcbi.1005350> Cheers, @rno

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mri_segstats
by John Anderson 24 Feb '17

24 Feb '17

Dear Freesurfer experts, I have used the following commandline to generate the final statistics in my analysis: mri_segstats --seg aseg.mgz --ctab-default --i suvr.nii --mask mask.nii --sum stats.dat The final output of this command is (attached). Depedning on the anatomical location of the mask, I expect that I will get two structures in the stats file. What is the "unknown" label means? is it CSF? Do I need to include it in my next statistcal analses? I highly appreciate your input! Best, John Sent with [ProtonMail](https://protonmail.com) Secure Email.

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Segmentation question
by yusif Al-kheder 24 Feb '17

24 Feb '17

Hello, I was wondering how does Freesurfer segment the white matter from the grey matter.

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help error RB_ALL_2008-03-26
by Flavia Arduini 24 Feb '17

24 Feb '17

Hi, I try tu run this code: recon-all -s CAROFILO -i /home/matlab/Scrivania/SEGMENTAZIONE/CAROFILO/T2/Phase2/c2scCAROFILO.nii -autorecon2-wm but compare this error ERROR: cannot find /usr/local/freesurfer/average/RB_all_2008-03-26.gca How can I fix this problem? Thanks Flavia Arduini

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Virtualbox for FS v6.0 ?
by Randolph Andrews 24 Feb '17

24 Feb '17

In past releases of FreeSurfer, there had been a version of the software suite contained in a VirtualBox (alongside the MacOS and Linux versions). Currently, I only see Mac & Linux. Is there a plan to release a VirtualBox edition of 6.0 ?

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mri_binarize --gm
by Jinsong Tang 24 Feb '17

24 Feb '17

Dear all, I am trying to run a mri_binarize command on FS 5.3 mri_binarize --i aparc+aseg.mgz --gm --o gmmask.mgz I obtain this: ERROR: Option –gm unknown I found there was a previous post suggest to use the new mri_binarize from https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize I download this one, and replace the old one with this new one. however, I obtian this: mri_binarize : command not found. How to fix this? Thanks and best, Jinsong

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Re: [Freesurfer] LGI data for each region?
by Antonin Skoch 24 Feb '17

24 Feb '17

Dear Shane, use this command: mri_segstats --annot my_subject_id lh aparc --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats Look at the info on FreeSurfer wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/LGI Antonin Skoch Hi Freesurfer, How can I get the LGI measurements for each brain region in Desikan atlas? Instead of getting thickness with aparcstats2table, I want the gyrification instead.Thank you. Cheers, Shane

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LGI data for each region?
by Shane Schofield 24 Feb '17

24 Feb '17

Hi Freesurfer, How can I get the LGI measurements for each brain region in Desikan atlas? Instead of getting thickness with aparcstats2table, I want the gyrification instead. Thank you. Cheers, Shane -- Shane Schofield

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Freeview 3D brush
by Chris Adamson 24 Feb '17

24 Feb '17

Freesurfer devs, I attempted a modification of freeview to insert a 3D brush. I have got it working. If you want to review it to put it in the main version it is there a way to submit the diff with the changes? Cheers, Chris. Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Children’s Hospital Flemington Road, Parkville, Victoria 3052, Australia www.mcri.edu.au<http://www.mcri.edu.au/> E chris.adamson(a)mcri.edu.au T 03 9936 6780 ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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Freesurfer February 2017