Freesurfer November 2018

freesurfer@nmr.mgh.harvard.edu

121 participants
189 discussions

Re: [Freesurfer] freeview crash when launch in ubuntu 18.04 {Disarmed}
by fsbuild 14 Nov '18

14 Nov '18

External Email - Use Caution Hello Knut, You might be better off using the gcc 4.8 compilers on Ubuntu 18 which you can install with$ sudo apt-get install gcc-4..8 g++-4.8 gfortran-4.8 Then on your cmake command line you could set those before the actual cmake command.  I've listed some other options you could try as well after the cmake command (apart from whatever other options you may be using). $ CC=/usr/bin/gcc-4.8  CXX=/usr/bin/g++-4.8  FC=/usr/bin/gfortran-4.8  cmake  -DFS_PACKAGES_DIR=/path_to_the_3rd_packages_after downloading_them  -DCMAKE_INSTALL_PREFIX=/path_to_install_location  -DCMAKE_EXE_LINKER_FLAGS=-Wl,--disable-new-dtags -L/usr/lib/x86_64-linux-gnu -L/usr/local/lib -lz  -DGFORTRAN_LIBRARIES=/usr/lib/gcc/x86_64-linux-gnu/4..8/libgfortran.so - R.On Nov 14, 2018, at 04:08, Knut J Bjuland <knutjorgen(a)outlook.com> wrote:        External Email - Use Caution        Dear Freesurfer… source $FREESURFER_HOME/bin/tcl_setupknutjb-HP-Z640-Workstation:~/abel/data/tracula> source $FREESURFER_HOME/bin/vtk_setupknutjb-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.binGNU gdb (Ubuntu 8.1-0ubuntu3) 8.1.0.20180409-gitCopyright (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) runStarting 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:5151 .../sysdeps/unix/sysv/linux/raise.c: No such file or directory._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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aparc table multiple comparisons
by Ralf Veit 14 Nov '18

14 Nov '18

External Email - Use Caution Dear list members, I run mri_glmfit using the aparc stats tables as input and I got a sig.table.dat file with -log10(p-values) for each ROI and contrast. Are the p-values already corrected for multiple comparisons? If not, what do I have to do in order to get corrected p-values (using aparc stats file as input). Best Ralf Ralf Veit PhD Institute of Medical Psychology and Behavioral Neurobiology Otfried-Müller str. 47 72076 Tübingen phone: +49-7071-2987703 fax: +49-7071-295706

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co-registration between slab of DTI image
by Yixin Ma 14 Nov '18

14 Nov '18

External Email - Use Caution Hi Freesurfer experts, I'm writing to ask about coregistration between a thin oblique coronal slab of DTI image ( only 15 slices) and a cubic 1x1x1 voxel size anatomical image (volume size is 256x256x256), with additional whole brain low-resolution DTI to assist registration. The codes I use are as attached: I have few concerns: 1) the input oblique coronal slab of DWI image does not have header information, should it be better if I input the DWI slab in RAS coordinates (axial volume)? 2) Should I zero-fill the DWI slab to match the volume of T1.mgz? I already did that because it won't start to calculate the cost function between the thin DWI slab and anatomical image if I don't zero-fill. However, I feel like the cost function cannot make sense of the fact that the zeros are already outside the region of interest. 3) Should I use --init-fsl /--init-spm in this case? Neither of these two worked. Is there a better optimization function recommended? I have been using fsl flirt function 2 step registration (from DWI slab to whole brain DWI; From whole brain DWI to whole brain anatomical image) to do the registration. But I don't think it's the best way. For freesurfer bbregister, I have been trying to change things here and there, but the co-registration does not work well. Do you suggest to look at any parameter particularly based on this scenario? Thank you for your help, Yixin Note that isoDWI111_256_axial.nii is the slab of DWI image EPI_iso111_256_axial.nii is the whole brain DWI image [The freesurfer reconstruction is performed before all these] bbregister --s 30426 --mov isoDWI111_256_axial.nii --*int* EPI_iso111_256_axial.nii --init-fsl --reg xform_freesurfer.dat --dti tkregister2 --reg xform_freesurfer.dat --mov isoDWI111_axial.nii mri_vol2vol --reg xform_freesurfer.dat --mov isoDWI111_axial.nii --fstarg --o isoDWI111-*in*-anat.mgh mri_convert isoDWI111-*in*-anat.mgh isoDWI111_reg.nii

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MRISalloc
by Chris Petty 14 Nov '18

14 Nov '18

External Email - Use Caution I’ve tried processing a healthy brain through v6.0.0 and _dev versions only to get hung at this step in each of the versions. The brain looks normal. I’ve tried adjusting the skull strip and using control points in a location that the brain was not found correctly, but it always stops at this exact step. I’ve tried processing with the RAW data as well has HCP preprocessed anatomicals. Any insight into this error? Is this some sort of convoluted memory error? ERROR: MRISalloc: nfaces=-1392508735 < 0 2714 using vox2ras matrix: 2715 -1.00000 0.00000 0.00000 128.00000; 2716 0.00000 0.00000 1.00000 -128.00000; 2717 0.00000 -1.00000 0.00000 128.00000; 2718 0.00000 0.00000 0.00000 1.00000; 2719 2720 rm -f ../mri/filled-pretess255.mgz 2721 2722 2723 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 2724 2725 ERROR: MRISalloc: nfaces=-1392508735 < 0 2726 2727 Linux blade21.dhe.duke.edu<http://blade21.dhe.duke.edu/> 3.10.0-862.2.3.el7.x86_64 #1 SMP Tue May 8 14:55:36 CDT 2018 x86_64 x86_64 x86_64 GNU/Linux 2728 2729 recon-all -s sub-00001 exited with ERRORS at Tue Nov 13 14:13:07 EST 2018 2730 2731 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Questions on ApplyMorph of electrodes coordinates to a common template
by Liu, Feng 14 Nov '18

14 Nov '18

Dear freesurfer users, I have a problem regarding to how to map the electrode coordinates to a common template. After running mri_cvs_register, I got a cvs subfolder, and then I run applyMorph --template /autofs/cluster/freesurfer/centos7_x86_64/dev/subjects/cvs_avg35_inMNI152/mri/orig.mgz --transform $SUBJECTS_DIR/$subid/cvs/combined_tocvs_avg35_inMNI152_elreg_aseg.tm3d point_list $SUBJECTS_DIR/$subid/cvs/coord_xyz.txt $SUBJECTS_DIR/$subid/cvs/transformed_coord.txt linear where coord_xyz.txt contains all the original coordinates information, but after that I did a visualization using freeview, and the transformed coordinates looks outside of the brain. Anyone knows how to fix this problem? Or what is the cause of this problem. The original RAS coordinates align well for the brain of each subject. I searched a lot of email archives, but didn't find a good answer. Thanks. Best regards, Feng [cid:1b19e3e7-51a7-4abb-afdb-c81cb9adc99e]

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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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Freesurfer November 2018