Hi,
I am having a problem running men_flash_bem. It seems that the
convertion to mgz files does not work and that there might be a problem
with the directory structure.
I did run mne_organize_dicom; it's output is in
/space/theta/1/users/Sarah/Stern/Subjects/SBT_MEG_002/flash_organized ;
links to flash05 and flash30 were created.
Please, see below for a full error description.
Any help with what I am doing wrong is greatly appreciated.
thanks, Sarah
[theta:flash_organized] (nmr-std-env) mne_flash_bem &
[1] 14294
[theta:flash_organized] (nmr-std-env)
Processing the flash MRI data for subject SBT_MEG_002 to produce
BEM meshes under
/space/theta/1/users/Sarah/Stern/Subjects/SBT_MEG_002/bem/flash
Step 1 : Converting images...
mri_convert flash05/002/550000-000008-000001.dcm
/space/theta/1/users/Sarah/Stern/Subjects/SBT_MEG_002/mri/flash/mef05_002.mgz
file not found or unknown file type for file
flash05/002/550000-000008-000001.dcm
mri_convert flash05/003/550000-000008-000177.dcm
/space/theta/1/users/Sarah/Stern/Subjects/SBT_MEG_002/mri/flash/mef05_003.mgz
file not found or unknown file type for file
flash05/003/550000-000008-000177.dcm
mri_convert flash05/004/550000-000008-000353.dcm
/space/theta/1/users/Sarah/Stern/Subjects/SBT_MEG_002/mri/flash/mef05_004.mgz
file not found or unknown file type for file
flash05/004/550000-000008-000353.dcm
mri_convert flash05/005/550000-000008-000529.dcm
/space/theta/1/users/Sarah/Stern/Subjects/SBT_MEG_002/mri/flash/mef05_005.mgz
file not found or unknown file type for file
flash05/005/550000-000008-000529.dcm
mri_convert flash05/006/550000-000008-000705.dcm
/space/theta/1/users/Sarah/Stern/Subjects/SBT_MEG_002/mri/flash/mef05_006.mgz
file not found or unknown file type for file
flash05/006/550000-000008-000705.dcm
mri_convert flash05/007/550000-000008-000881.dcm
/space/theta/1/users/Sarah/Stern/Subjects/SBT_MEG_002/mri/flash/mef05_007.mgz
file not found or unknown file type for file
flash05/007/550000-000008-000881.dcm
mri_convert flash05/008/550000-000008-001057.dcm
/space/theta/1/users/Sarah/Stern/Subjects/SBT_MEG_002/mri/flash/mef05_008.mgz
file not found or unknown file type for file
flash05/008/550000-000008-001057.dcm
mri_convert flash05/009/550000-000008-001233.dcm
/space/theta/1/users/Sarah/Stern/Subjects/SBT_MEG_002/mri/flash/mef05_009.mgz
file not found or unknown file type for file
flash05/009/550000-000008-001233.dcm
mri_convert flash30/002/550000-000006-000001.dcm
/space/theta/1/users/Sarah/Stern/Subjects/SBT_MEG_002/mri/flash/mef30_002.mgz
file not found or unknown file type for file
flash30/002/550000-000006-000001.dcm
mri_convert flash30/003/550000-000006-000177.dcm
/space/theta/1/users/Sarah/Stern/Subjects/SBT_MEG_002/mri/flash/mef30_003.mgz
file not found or unknown file type for file
flash30/003/550000-000006-000177.dcm
mri_convert flash30/004/550000-000006-000353.dcm
/space/theta/1/users/Sarah/Stern/Subjects/SBT_MEG_002/mri/flash/mef30_004.mgz
file not found or unknown file type for file
flash30/004/550000-000006-000353.dcm
mri_convert flash30/005/550000-000006-000529.dcm
/space/theta/1/users/Sarah/Stern/Subjects/SBT_MEG_002/mri/flash/mef30_005.mgz
file not found or unknown file type for file
flash30/005/550000-000006-000529.dcm
mri_convert flash30/006/550000-000006-000705.dcm
/space/theta/1/users/Sarah/Stern/Subjects/SBT_MEG_002/mri/flash/mef30_006.mgz
file not found or unknown file type for file
flash30/006/550000-000006-000705.dcm
mri_convert flash30/007/550000-000006-000881.dcm
/space/theta/1/users/Sarah/Stern/Subjects/SBT_MEG_002/mri/flash/mef30_007.mgz
file not found or unknown file type for file
flash30/007/550000-000006-000881.dcm
mri_convert flash30/008/550000-000006-001057.dcm
/space/theta/1/users/Sarah/Stern/Subjects/SBT_MEG_002/mri/flash/mef30_008.mgz
file not found or unknown file type for file
flash30/008/550000-000006-001057.dcm
mri_convert flash30/009/550000-000006-001233.dcm
/space/theta/1/users/Sarah/Stern/Subjects/SBT_MEG_002/mri/flash/mef30_009.mgz
file not found or unknown file type for file
flash30/009/550000-000006-001233.dcm
Step 2 : Creating the parameter maps...
Parameter maps directory cleared
reading mef*.mgz...ERROR: cannot find
/autofs/space/theta_001/users/Sarah/Stern/Subjects/SBT_MEG_002/mri/flash/mef*.mgz
mri_ms_fitparms: could not read volume mef*.mgz
No such file or directory
Step 3 : Synthesizing flash 5...
reading T1 volume from T1.mgz...
ERROR: cannot find
/autofs/space/theta_001/users/Sarah/Stern/Subjects/SBT_MEG_002/mri/flash/parameter_maps/T1.mgz
mri_synthesize: could not read T1 volume T1.mgz
No such file or directory
Step 4 : Registering flash 5 with MPRAGE...
$Id: fsl_rigid_register,v 1.26 2007/06/12 15:11:07 greve Exp $
Thu Mar 6 16:24:59 EST 2008
flash5_reg.mgz