[Mne_analysis] mne_flash_bem

Nandita Shetty nandita at nmr.mgh.harvard.edu
Thu Mar 6 16:46:50 EST 2008
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Sarah,
How did you execute the mne_organize_dicom command?

The script expects the <source> to be a relative path to your dicom files
i.e  <source> should be a symbolic link to your dicom files. Matti, please
correct if I am wrong.

~N&ita


> 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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