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

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