Dear all,
I tried to run a subject's T1 starting with the dicom convert step (until now, I used .nii volumes as imput, after dicom conversion in spm; I would like to be able to use the dicom convert in freesurfer, since I have a -T2pial step to refine pias afterwards, and it's easier this way).
I get the following mri_convert error about jpeg compression (this is the only dicom output processed at our facility):
recon-all -s subj -i /home/ovl/Desktop/freesurferdicom/subj/T1/51129
Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20131217 Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20131217 INFO: SUBJECTS_DIR is /usr/local/fs5.3/freesurfer/subjects Actual FREESURFER_HOME /usr/local/fs5.3/freesurfer Linux Wild-Dog-Performance 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /usr/local/fs5.3/freesurfer/subjects/subj
mri_convert /home/ovl/Desktop/freesurferdicom/subj/T1/51129 /usr/local/fs5.3/freesurfer/subjects/subj/mri/orig/001.mgz
mri_convert /home/ovl/Desktop/freesurferdicom/subj/T1/51129 /usr/local/fs5.3/freesurfer/subjects/subj/mri/orig/001.mgz $Id: mri_convert.c,v 1.206 2013/11/12 03:15:51 greve Exp $ reading from /home/ovl/Desktop/freesurferdicom/subj/T1/51129... Starting DICOMRead2() dcmfile = /home/ovl/Desktop/freesurferdicom/subj/T1/51129 dcmdir = /home/ovl/Desktop/freesurferdicom/subj/T1 Ref Series No = 302 Found 167 files, checking for dicoms Found 165 dicom files in series. First Sorting Computing Slice Direction Vs: -0.999557 0.0285859 -0.00787544 Vs: -0.99956 0.028586 -0.00787546 Second Sorting Counting frames nframes = 1 nslices = 165 ndcmfiles = 165 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.4.70-- ERROR: the pixel data cannot be loaded as it is JPEG compressed. (Transfer Syntax UID: 1.2.840.10008.1.2.4.70) jpegUID: --1.2.840.10008.1.2.4-- Linux ovl-Wild-Dog-Performance 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s subj exited with ERRORS at Sun Dec 22 21:22:11 CST 2013
For more details, see the log file /usr/local/fs5.3/freesurfer/subjects/subj/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Is there a workaround in freesurfer?
Thank you,
Octavian