Hello, I am trying to preprocess couple of dicom images (146 dicom image) and I constantly get this error. "dan% *recon-all -all -i IM-0065-0001.dcm -s fsdir (recon-all script)*
Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /Users/dan/Desktop/paul/01-005-C/AX_FSPGR_3D_3
Actual FREESURFER_HOME /Applications/freesurfer
Darwin opennet-33-172.uhnres.utoronto.ca 14.5.0 Darwin Kernel Version 14.5.0: Thu Apr 21 20:40:54 PDT 2016; root:xnu-2782.50.3~1/RELEASE_X86_64 x86_64
/Users/dan/Desktop/paul/01-005-C/AX_FSPGR_3D_3/fsdir
\n mri_convert /Users/dan/Desktop/paul/01-005-C/AX_FSPGR_3D_3/IM-0065-0001.dcm /Users/dan/Desktop/paul/01-005-C/AX_FSPGR_3D_3/fsdir/mri/orig/001.mgz \n
mri_convert /Users/dan/Desktop/paul/01-005-C/AX_FSPGR_3D_3/IM-0065-0001.dcm /Users/dan/Desktop/paul/01-005-C/AX_FSPGR_3D_3/fsdir/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /Users/dan/Desktop/paul/01-005-C/AX_FSPGR_3D_3/IM-0065-0001.dcm...
Starting DICOMRead2()
dcmfile = /Users/dan/Desktop/paul/01-005-C/AX_FSPGR_3D_3/IM-0065-0001.dcm
dcmdir = /Users/dan/Desktop/paul/01-005-C/AX_FSPGR_3D_3
Ref Series No = 3
Found 150 files, checking for dicoms
Found 146 dicom files in series.
First Sorting
Computing Slice Direction
Vs: 0 0 1
Vs: 0 0 1
Second Sorting
Counting frames
nframes = 1
nslices = 146
ndcmfiles = 146
PE Dir = ROW (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2.4.90--
Loading pixel data
Segmentation fault
Darwin opennet-33-172.uhnres.utoronto.ca 14.5.0 Darwin Kernel Version 14.5.0: Thu Apr 21 20:40:54 PDT 2016; root:xnu-2782.50.3~1/RELEASE_X86_64 x86_64
recon-all -s fsdir exited with ERRORS at Thu Sep 8 20:25:11 EDT 2016
For more details, see the log file /Users/dan/Desktop/paul/01-005-C/AX_FSPGR_3D_3/fsdir/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
[opennet-33-172:paul/01-005-C/AX_FSPGR_3D_3] dan"
Also, I tried "mri_convert" command and i received same error. Here's my script "
setenv SUBJECTS_DIR .......
cd ........
*mri_convert -it dicom -i IM-0065-0001.dcm -ot nii -o 01005C.nii.gz"*
*Please can anyone tell me where it went wrong. thank you. *
*Paul*