Urgh - thanks for looking into this Jeanette. We'll delve deeper.Cheers.On 18 Aug 2010, at 22:05, Jeanette Mumford wrote:Hi,
I don't know if it would be a computer problem (this error has occurred on two machines), but we used the -B option previously with no error and the problem popped up with fsl 4.1.1. Here is what happens when I ran bet with -m -B -d
Here is the error message again:
/Applications/fsl/bin/bet: line 383: 8794 Segmentation fault ${FSLDIR}/bin/fast -oba 100 ${OUT}_tmp_premask 1>&/dev/null
** ERROR (nifti_image_read): failed to find header file for 'mprage_defaced_brain_tmp_premask_abias'
** ERROR: nifti_image_open(mprage_defaced_brain_tmp_premask_abias): bad header info
Error: failed to open file mprage_defaced_brain_tmp_premask_abias
ERROR: Could not open image mprage_defaced_brain_tmp_premask_abias
Image Exception : #22 :: Failed to read volume mprage_defaced_brain_tmp_premask_abias
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/Applications/fsl/bin/bet: line 383: 8802 Abort trap ${FSLDIR}/bin/fslmaths $IN -mul ${OUT}_tmp_premask_abias ${OUT}_tmp_unbiased
Input image mprage_defaced_brain_tmp_unbiased not valid
Error: input image mprage_defaced_brain_tmp_unbiased_premask not valid
and here is the list of files that were created:
mprage_defaced_brain.nii.gz
mprage_defaced_brain_mask.nii.gz
mprage_defaced_brain_skull.nii.gz
mprage_defaced_brain_tmp_premask.nii.gz
mprage_defaced_brain_tmp_premask_tmp_masked.nii.gz
mprage_defaced_brain_tmp_premask_tmp_standard_mask.nii.gz
mprage_defaced_brain_tmp_premask_tmp_standard_mask_to_in.nii.gz
mprage_defaced_brain_tmp_premask_tmp_to_std.mat
mprage_defaced_brain_tmp_premask_tmp_to_std.nii.gz
mprage_defaced_brain_tmp_premask_tmp_to_std_inv.mat
So, I went through the bet script and I think it is hung up when it calls fast, so I ran that line of code (line 371 in our version of bet, but of course I omitted ">& /dev/null")
fast -oba 100 mprage_defaced_brain_tmp_premask
Here is the error message
Could not open matrix file mprage_defaced_brain_tmp_premask
Could not open matrix file mprage_defaced_brain_tmp_premask
Could not open matrix file mprage_defaced_brain_tmp_premask
csf prior image not transformed correctly! priors are not used!
Segmentation fault
Is it looking for a mat file to pair up with the -a flag? I'm not sure what the 100 does.
Thanks for the help!
JeanetteOn Wed, Aug 18, 2010 at 3:45 AM, Stephen Smith <[log in to unmask]> wrote:
Hi - this means that FAST has not run successfully - maybe the image is too large for FAST to run on your computer?If you use the -d flag it should leave behind as many of the intermediate steps as do complete, which should make it easier to test what's going on.Cheers.On 17 Aug 2010, at 20:29, Jeanette Mumford wrote:Hi,
When I run bet with the -B flag I get the following error message:
/Applications/fsl/bin/bet: line 383: 18901 Segmentation fault ${FSLDIR}/bin/fast -oba 100 ${OUT}_tmp_premask 1>&/dev/null
** ERROR (nifti_image_read): failed to find header file for 'mprage_defaced_brain3_tmp_premask_abias'
** ERROR: nifti_image_open(mprage_defaced_brain3_tmp_premask_abias): bad header info
Error: failed to open file mprage_defaced_brain3_tmp_premask_abias
ERROR: Could not open image mprage_defaced_brain3_tmp_premask_abias
Image Exception : #22 :: Failed to read volume mprage_defaced_brain3_tmp_premask_abias
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/Applications/fsl/bin/bet: line 383: 18909 Abort trap ${FSLDIR}/bin/fslmaths $IN -mul ${OUT}_tmp_premask_abias ${OUT}_tmp_unbiased
Input image mprage_defaced_brain3_tmp_unbiased not valid
Error: input image mprage_defaced_brain3_tmp_unbiased_premask not valid
The results I'm getting seem okay (image seems to have had bias field correction and the mask is much better than without the -B flag). I was just wondering what the error was about and if there would be anything wrong with using the resulting images.
Thanks,
Jeanette
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------