# mne\_flash\_bem
**URL:** https://mne.discourse.group/t/mne-flash-bem/29
**Category:** Mailing List Archive (read-only)
**Tags:** list-archive
**Created:** [March 6, 2008, 9:30pm UTC](https://mne.discourse.group/t/mne-flash-bem/29 "2008-03-06T21:30:55Z")
**Posts on this page:** 3
**Page:** 1
### Author:  [@system](https://mne.discourse.group/u/system)
#### Post date: [March 6, 2008, 9:30pm UTC](https://mne.discourse.group/t/mne-flash-bem/29/1 "2008-03-06T21:30:55Z")
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
---
### Author:  [@system](https://mne.discourse.group/u/system)
#### Post date: [March 6, 2008, 9:46pm UTC](https://mne.discourse.group/t/mne-flash-bem/29/2 "2008-03-06T21:46:50Z")
Sarah,
How did you execute the mne\_organize\_dicom command?
The script expects the \ to be a relative path to your dicom files
i.e \ should be a symbolic link to your dicom files. Matti, please
correct if I am wrong.
~N&ita
---
### Author:  [@system](https://mne.discourse.group/u/system)
#### Post date: [March 6, 2008, 9:55pm UTC](https://mne.discourse.group/t/mne-flash-bem/29/3 "2008-03-06T21:55:29Z")
You are exactly right. I realize I have not told this in the manual.
- Matti