Freesurfer

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30076 discussions

Medial prefrontal cortex mPFC in Destrieux Atlas
by Christophe Destrieux 14 Nov '18

14 Nov '18

External Email - Use Caution Hi Daiana It’s impossible to tell since the anatomical classes of this atlas are limited by the sulco-gyral pattern ; for instance the mPFC includes only part of the superior frontal gyrus (its medial aspect) but the superior frontal gyrus also include the SMA and pre SMA It's easier for the lateral parietal cortex which contains : G_pariet_inf-Angular G_pariet_inf-Supramar G_parietal_sup best > > Hi all, > > I am trying to find out which regions in Destrieux atlas would correspond to mPFC? > > Any ideas ? > > Also for lateral parietal cortex .. > > Than you, > Daiana Christophe Destrieux, Unité iBrain UMRS INSERM U1253, Université de Tours https://ibrain.univ-tours.fr/ <https://ibrain.univ-tours.fr/> Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé - 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07

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2 PhD & 1 post-doc open positions in Lausanne - Quantitative fetal brain MR imaging
by Yasser Alemán 14 Nov '18

14 Nov '18

External Email - Use Caution Dear colleagues, 2PhD and 1 post-doc positions are available at my group, University of Lausanne, Switzerland. The positions are funded for 4 years (with annual contract renew) by the Swiss National Science Foundation grant. Ideally starting on January 2019 but this can be adapted. Briefly we look for the following profiles: 1 post-doc: versatile both in MRI physics/sequence programming and image processing, dedicated to the development of MR sequences aimed at quantitative T1 and T2 mapping of the fetal brain. 2 PhD thesis: (i) the development machine learning segmentation methods for the fetal brain analysis and their integration to a joint segmentation-super-resolution reconstruction of T2-weighted and T2 quantitative images of the fetal brain. (ii) the development of an image processing pipeline for the super-resolution reconstruction of diffusion fetal brain MRI, including the exploration of new acquisition schemes on phantom data. Details of the project and profiles are attached. For more information please contact Dr. Meritxell Bach Cuadra (meritxell.bachcuadra(a)unil.ch) Best regards, Meritxell Bach Cuadra

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Improving skull stripping - Need help
by Rosalia Dacosta Aguayo 14 Nov '18

14 Nov '18

External Email - Use Caution Dear FreeSurfer team, In order to improve the skull stripping for some of the participants of the sample, I replaced the brainmask.mgz generated in FreeSurfer by the betted image generated from FSL, and I run recon-all again. The problem is that, again, FreeSurfer generated again another brainmask without saving my brainmask and now, I have, again, a bad skull stripped image. Any help with this would be greatly appreciated. Best regards, Rosalia

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freeview crash when launch in ubuntu 18.04
by Knut J Bjuland 14 Nov '18

14 Nov '18

External Email - Use Caution Dear Freesurfer exports, I am unable to launch freeview. I have uncommented qt_setup to be able to start freeview but now it does not start at all. I am sending output from a session where I started it using gdb. Please look below. I am using the latest version of freeview download from http://www.freesurfer.net/fswiki/UpdateFreeview Best regards Knut Jørgen Bjuland PhD knutjb-HP-Z640-Workstation:~/abel/data/tracula> source $FREESURFER_HOME/bin/tcl_setup knutjb-HP-Z640-Workstation:~/abel/data/tracula> source $FREESURFER_HOME/bin/vtk_setup knutjb-HP-Z640-Workstation:~/abel/data/tracula> #source $FREESURFER_HOME/bin/qt_setup #source: Command not found. knutjb-HP-Z640-Workstation:~/abel/mci_data/tracula> gdb freeview.bin GNU gdb (Ubuntu 8.1-0ubuntu3) 8.1.0.20180409-git Copyright (C) 2018 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "x86_64-linux-gnu". Type "show configuration" for configuration details. For bug reporting instructions, please see: <http://www.gnu.org/software/gdb/bugs/>. Find the GDB manual and other documentation resources online at: <http://www.gnu.org/software/gdb/documentation/>. For help, type "help". Type "apropos word" to search for commands related to "word"... Reading symbols from freeview.bin...(no debugging symbols found)...done. (gdb) run Starting program: /usr/local/freesurfer/bin/freeview.bin [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1". [New Thread 0x7fffe6839700 (LWP 515411)] [New Thread 0x7fffdc539700 (LWP 515412)] [New Thread 0x7fffdbd38700 (LWP 515413)] [New Thread 0x7fffda2a1700 (LWP 515414)] [New Thread 0x7fffca424700 (LWP 515418)] Thread 1 "freeview.bin" received signal SIGABRT, Aborted. __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:51 51 ../sysdeps/unix/sysv/linux/raise.c: No such file or directory.

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Surface failure in centos7 dev freesurfer
by Baxter P. Rogers 13 Nov '18

13 Nov '18

External Email - Use Caution Hi all - I'm having a problem with recon-all in the current dev version of Freesurfer. It is failing somewhere in the surface creation steps. I get an error during mris_extract_main_component: ERROR: MRISalloc: nvertices=-1879047998 < 0 No such file or directory The filled left and right white matter images look reasonable but I can't load the lh.orig.nofix surface in Freeview. More info below. Thanks much for any help, Baxter ----------------------------------------------------------------------------- FREESURFER VERSION: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-linux… Downloaded 2018-11-12 SHA256 792a0e90ec6b4cfd3a530c3e5b4c9aead575dbb45217756e66931bb5d118e89d ----------------------------------------------------------------------------- SYSTEM INFORMATION: CentOS 7.5.1804 Running in Docker on OS X El Capitan with 1 CPU, 6.5 GB RAM # df -h Filesystem Size Used Avail Use% Mounted on overlay 74G 30G 40G 43% / tmpfs 64M 0 64M 0% /dev tmpfs 3.2G 0 3.2G 0% /sys/fs/cgroup osxfs 465G 438G 27G 95% /wkdir /dev/sda1 74G 30G 40G 43% /etc/hosts shm 3.0G 0 3.0G 0% /dev/shm # cat /proc/meminfo MemTotal: 6616764 kB MemFree: 4934288 kB MemAvailable: 6134084 kB ... ----------------------------------------------------------------------------- ATTEMPT TO VIEW SURFACE IN FREEVIEW: Failed to load Surface .../surf/lh.orig.nofix # ls -l lh.orig.nofix -rw-rw-r-- 1 root root 4320024 Nov 11 23:02 lh.orig.nofix ----------------------------------------------------------------------------- LATER PORTIONS OF recon-all.log mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 49 found - 49 modified | TOTAL: 49 ... pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 1264 (out of 703656: 0.179633) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... ... Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 ... pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 15 (out of 347364: 0.004318) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.39 2016/07/20 21:05:04 zkaufman Exp $ $Id$ slice 30: 1553 vertices, 1720 faces ... slice 250: 179904 vertices, 180024 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix ERROR: MRISalloc: nvertices=-1879047998 < 0 No such file or directory

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QA_tools do not find v.mgz
by Simon Jones 13 Nov '18

13 Nov '18

External Email - Use Caution I have run some Freesurfer 6 recon-all processed data through the Freesurfer QA analysis QA_tools_v1.2. The output looks mostly good but I repeatedly see these errors. ERROR: Subject a1 missing output file ../mri/v.mgz ERROR: Subject a1 missing output file ../stats/wmsnr.e3.dat I do actually find 100% of wmsnr.e3.dat files so that may not be a problem. But only 41% of my subjects have a file called v.mgz. This looks like ventricles prior to aseg processing. I do not find the file v.mgz referenced in any of the recon-all log files or help pages. I don’t think I have been aware of this file previously. Why are many subjects missing this file and should I worry about it. Thanks for your help, Simon

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From .nii.gz
by Rosalia Dacosta Aguayo 13 Nov '18

13 Nov '18

External Email - Use Caution Dear Free Surfer team, I wonder how I could pass from .nii.gz format to .mgz format in order to change the brainmask.mgz generated by FreeSurfer for my bet image from FSL. I have noticed that lot of brainmask images have optic radiations and part of the skull. Best regards, Rosalia

2 1

Medial prefrontal cortex mPFC in Destrieux Atlas
by Daya P 13 Nov '18

13 Nov '18

External Email - Use Caution Hi all, I am trying to find out which regions in Destrieux atlas would correspond to mPFC? Any ideas ? Also for lateral parietal cortex .. Than you, Daiana

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Fwd: Manually fix FreeSurder ICV value when talairach.xfm registration is incorrect
by Gamaliz 13 Nov '18

13 Nov '18

External Email - Use Caution I have a few T1 scans that have obvious incorrect registration to mni_average_305. I opened tkregister2 --s subjid --fstal --surfs and I am able to fix the registration, but I wonder how to use the ew registration to recalculate the new ICV. I am interested in doing it with Freesurfer (as I know I could get the matrix and calculate the determinant. I guess I will have to save the transform and rerun some of Freesurfer command to overwrite the old icv value? Thanks Gabriel

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Editing errors
by Rosalia Dacosta Aguayo 13 Nov '18

13 Nov '18

External Email - Use Caution Dear Free Surfer team, I am visually checking for errors in every step of the recon-all process. In the skull stripping stage, some participants have left skull behind, but the grey matter (gm) and white matter (wm) separation is right. Should I edit the brainmask image in order to make that no skull is left behind even when the gm and wm are fine? Best regards, Rosalia

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