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30099 discussions

Infinite loop in mri_convert
by Nooshin Zadeh 05 Nov '14

05 Nov '14

Dear FreeSurfer experts, I get a new message when I use "mri_convert" command to convert dicom to mgz. I used to apply this command before and there was no problem. I wonder what is the reason that I get the new message. In addition, it does not create mgz file, and goes to infinite loop. *mri_convert "/M1/t1_se_ax_5/IM-0004-0001.dcm" "/FS/M1/mri/orig/001.mgz"* mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /M1/t1_se_ax_5/IM-0004-0001.dcm... Getting Series No Scanning Directory INFO: Found 39 files in /Users/christine/Raw_Data/M226/t1_se_ax_5 INFO: Scanning for Series Number 5INFO: found 37 files in series INFO: loading series header info. I appreciate if you can advise me. Regards, Nooshin PhD Candidate Departments of Electrical & Computer Engineering University of Miami Email: n.zadeh(a)miami.edu

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Freeview-stable4 error?
by DeCross, Stephanie N. 05 Nov '14

05 Nov '14

Hi, I'm trying to look at 2 connectivity files (saved in SPM) at the same time using Freeview, but how I've been doing it in the past is no longer working and I haven’t changed anything on my end. What I had been doing: 1. cd to the folder with my connectivity files and typing the shortcut command: stable4 (which does the following: setenv USE_STABLE_4_5_0; source /space/freesurfer/nmr-stable4-env) 2. typing the command: freeview ../../../../N12Trio_avg152T1.nii LSHSxAmyg.covBDI_PosCorr_p05_20vox.img LSHSxAmyg.covBDI_NegCorr_p05_20vox.img_blue.nii.gz This command used to work fine, but is now giving me the error: freeview.bin: error while loading shared libraries: libvtkverdict.so.vtk5.2.0: cannot open shared object file: No such file or directory This command DOES work if I don't type the shortcut command stable4 and instead keep using the stable53 environment I was already in (setenv FSL_DIR /usr/pubsw/packages/fsl/4.1.9; source /space/nexus/1/users/avi-tools/enable_avi.csh; setenv SUBJECTS_DIR /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53; source /usr/local/freesurfer/nmr-stable53-env). While I'm not positive it affects anything, I'd rather be consistent with the stable4 way I've been doing it in the past - is there a way to fix it and use Freeview in stable4, or does this freeview.bin error mean that I can no longer use Freeview with stable4? Thanks, Stephanie Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 Phone: 617-724-3283 Fax: 617-726-4078

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freeview fault: PETSC Error ...
by Krieger, Donald N. 04 Nov '14

04 Nov '14

I recently downloaded and installed freesurfer-Linux-centos6_x86_64-table-pub-v5.3.0.tar.gz . I had been running this version previously but had to reload everything due to a disk crash. recon-all -all goes to completion with no errors. freeview starts up fine but fails on loading a volume file with the PETC error listed below. I found several references to this error in the archive but no resolution for my problem. Any thoughts would be welcome - thanks. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si… ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a linux-gnu named BTRC-Server01 by kriegerd Tue Nov 4 06:55:17 2014 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 Regards, Don [Signature0001] Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text

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Create surface Labels of equal size
by Bastian Cheng 04 Nov '14

04 Nov '14

Dear Freesurfers, I would like to mark the brain surface (fsaverage) for an illustration of stimulation areas (TMS). I have calculated coordinates in Vertex RAS and Vertex Talairach. They are correctly located on the fsaverage surface in tksurfer. Is there a way to create labels of equal sizes at those coordinates? Ideally by using a script (since I have to mark them in 50 patients). this is purely for illustrative purposes. All coordinates are in fasaverage space. Any help would be appreciated, Bastian

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Recon-all error on 1.5t GE T1
by Zachary Greenberg 04 Nov '14

04 Nov '14

Hi Freesurfers, I'm trying to recon-all a T1 image acquired on a 1.5T GE scanner. I'm running: recon-all -subjid EC -all -mprage -openmp 8 -use-gpu And the process errors out at: mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz mghRead(/crtx1/zgreenberg/subjects/EC/mri/aseg.auto.mgz, -1): read error Apparently there is some error trying to read aseg.auto.mgz during mri_seg_diff. Has anyone had this problem before? I tried to mdi_info aseg.auto.mgz and I get the same read error. Thanks for any help you can offer. Log and error attached. -zack

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mri_watershed -brain_atlas undocumented?
by tvg[fs] 04 Nov '14

04 Nov '14

- This is a repost. It seems it did not come trough yesterday. Apologies if this becomes a double post - Hi all, I noticed that during skull stripping the standard recon-all pipeline uses option "-brain_atlas" in the routine "mri_watershed". However documentation of this argument cannot be found in the help section or on the website. mri_watershed --help | less -p atlas https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed?highlight=(atlas) Is this an undocumented flag or simply a synonym for "-atlas"? Does the "-brain_atlas" flag take an extra argument to specify the atlas? Thanks, Tom Specs: Mac OS X 10.8.5 freesurfer-Darwin-lion-stable-pub-v5.3.0 $ mri_watershed --version stable5

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mri_label2label
by Roberta Santoro 04 Nov '14

04 Nov '14

Dear all, I would like to draw a ROI on a group average surface (template) and map it back to the surface of individual subjects. For this, I would like to create the template based on my subjects, rather than using fsaverage. As far as I understood, I should first create the template by using: make_average_subject –out myAvg –subjects s1 s2 … Then, I should register each subject to the template with: mris_register --curv s1/surf/lh.sphere SUBJECTS_DIR/myAvg/lh.reg.template.tif s1/surf/lh.sphere.reg.myAvg. At this point, I can map the ROI to a given subject by using the command mri_label2label: mri_label2label --srclabel labelName --srcsubject myAvg --trgsubject s1 trglabel OutputLabelName --hemi lh --regmethod surface. There is one thing I don’t understand: how can I tell the command mri_label2label that it should use the registration file that I have created in the previous step (namely lh.sphere.reg.myAvg)? If I don't specify anything, is the function going to use the sphere.reg file that refers to the registration between subject s1 and fsaverage? In general, is the pipeline I described correct? Thanks a lot for your help. Best Roberta

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Quality of surface-based alignment
by Caspar M. Schwiedrzik 04 Nov '14

04 Nov '14

Hi Freesurfers, I was wondering whether there is a good way to assess post-hoc how well the alignment between two surfaces was. I wouldn't like to run the alignment again, but I could, if necessary. I would like to compare this alignment to a bunch of other alignments to see whether it was worse than the others. Thanks, Caspar

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Fsaverage for ROI analysis of children
by Smith, Michael 04 Nov '14

04 Nov '14

Hello all, I have been conducting an ROI analysis and following the cortical thickness ROI tutorial found here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness. After going through this tutorial with a few of my subjects I’ve noticed the ROI when registered to the fsaverage template is not in the correct position. I’m guessing this is due to the nature of my subjects (children ranging from 8months-11 years old). Is there a better template I should use for this analysis? Also, when I run mri_segstats to get the cortical thickness for my ROI, will these numbers be inaccurate too? Thanks in advance! It is worth noting I am running Darwin-lion-stable-pub-v5.3.0 Best, Michael S.

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Re: [Freesurfer] Before recon-all, is it necessary to set origin of the image?
by Bruce Fischl 04 Nov '14

04 Nov '14

Hi Ngoaka no, you don't need to set the origin of the image. Just point recon-all at a single slice from the correct dicom series (of a highres T1-weighted scan) with the -i <full path and file name of dicom slice> -all -s <subject id that you pick> and you should be good to go cheers Bruce On Tue, 4 Nov 2014, CHONNIKAN JONGKREANGKRAI wrote: > > Dear all, > > > I'm new on FreeSurfer. > I want to calculate cortical thickness, hippocampus volume from MRI images > (obtained from ADNI). > > After installation, I tried recon-all. >> Only this process, can I obtain > cortical thickness and hippocampus volume? > > And someone told me that I have to set origin of the image of each case > using SPM program. > > I want to know that is it necessary? > > > Thank you for your kind attention > > > Best Regards, > > Ngoak > > > >

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