I've noticed that an error is consistently reported in the unpack log file when I unpack dti scans for any subject:
INFO: this run has an error, but trying anyway
For example, if I try to unpack the dti scan for subject RMCON032, whose data is in /space/archive/216/siemens/TrioTim-35006-20090508-140454-440000, the dcmdir-info output is:
PatientName RMCON032 StudyDate 20090508 StudyTime 140454.440000 <snip> 000024 ep_b0#1 DIFFUSION_HighRes 440000-000024-000001.dcm 000025 ep_b0_700 DIFFUSION_HighRes 440000-000025-000001.dcm 000026 ep_b700t DIFFUSION_HighRes 440000-000026-000001.dcm 000027 ep_b0_700 DIFFUSION_HighRes 440000-000027-000001.dcm 000028 ep_b700 DIFFUSION_HighRes 440000-000028-000001.dcm 000029 ep_b0_700 DIFFUSION_HighRes 440000-000029-000001.dcm 000030 DIFFUSION_HighRes 440000-000030-000001.dcm <snip>
And I enter the command: unpacksdcmdir -src . -targ $SUBJECTS_DIR/RMCON032 -run 24 dti_test nii f.nii -fsfast -log dti_test.log
The unpack.log file contained the warnings and errors below (Also: I expected the log filed to be named dti_test.log so it wouldn't overwrite the unpack.log file I already had for the subject, but instead it was saved as unpack.log, overwriting the preexisting unpack.log)
WARNING: Run 24 appears to be truncated Files Found: 70, Files Expected (lRep+1): 120 FileName ./440000-000024-000001.dcm
Run 24 ----------------------------------------- Thu May 21 10:37:42 EDT 2009 24 dti_test nii f.nii INFO: this run has an error, but trying anyway
RunNo = 23 WARNING: Run 1 appears to be truncated Files Found: 70, Files Expected (lRep+1): 120 FileName ./440000-000024-000001.dcm
Are the dti scans I unpacked usable, or do I need to change my unpack command?
Thanks, Jesse
FREESURFER_HOME: /usr/local/freesurfer/stable4
Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.3.1-20090521
RedHat release: CentOS release 5.3 (Final)
Kernel info: Linux 2.6.18-128.1.6.el5 x86_64
NMR Center info (/space/freesurfer exists):
machine: vantz
SUBJECTS_DIR: /space/ventzl/36/users/RespMon12C/subjects
PWD: /space/archive/216/siemens/TrioTim-35006-20090508-140454-440000
ssh vantz setenv SUBJECTS_DIR /space/ventzl/36/users/RespMon12C/subjects cd /space/archive/216/siemens/TrioTim-35006-20090508-140454-440000