[Mne_analysis] mne_flash_bem

Sarah Steinvorth ssteinv at nmr.mgh.harvard.edu
Thu Mar 6 16:30:55 EST 2008
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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
--------------------------------------
/autofs/space/theta_001/users/Sarah/Stern/Subjects/SBT_MEG_002/mri/flash/parameter_maps
mri_convert ../../T1.mgz 
./fsl_rigid_register.14376/refvol.fsl_rigid_register.nii
mri_convert ../../T1.mgz 
./fsl_rigid_register.14376/refvol.fsl_rigid_register.nii
$Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $
reading from ../../T1.mgz...
TR=2530.00, TE=1.64, TI=1200.00, flip angle=7.00
i_ras = (-1, 4.55089e-09, -5.01089e-08)
j_ras = (-1.6151e-08, -7.92514e-09, -1)
k_ras = (-4.42652e-08, 1, 9.08367e-09)
writing to ./fsl_rigid_register.14376/refvol.fsl_rigid_register.nii...
--------------------------------------
/autofs/space/theta_001/users/Sarah/Stern/Subjects/SBT_MEG_002/mri/flash/parameter_maps
mri_convert flash5.mgz 
./fsl_rigid_register.14376/invol.fsl_rigid_register.nii
mri_convert flash5.mgz 
./fsl_rigid_register.14376/invol.fsl_rigid_register.nii
$Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $
reading from flash5.mgz...
ERROR: cannot find 
/autofs/space/theta_001/users/Sarah/Stern/Subjects/SBT_MEG_002/mri/flash/parameter_maps/flash5.mgz

Step 5a: Converting flash5 volume into COR format...

mri_convert flash5_reg.mgz ../../flash5
$Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $
reading from flash5_reg.mgz...
ERROR: cannot find 
/autofs/space/theta_001/users/Sarah/Stern/Subjects/SBT_MEG_002/mri/flash/parameter_maps/flash5_reg.mgz
flash5 volume conversion to COR failed

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