See previous postings on this issue. You need to redownload 4.1.5 for a
bugfix.
Peace,
Matt.
_____
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Wayne Su
Sent: Tuesday, February 16, 2010 5:48 PM
To: [log in to unmask]
Subject: [FSL] Inwarp error in new FSL release
Hello,
I got errors while I was running following command after FNIRT (for FSL
4.1.5),
$FSLDIR/bin/invwarp -w nonlinear_transf -o nonlinear_transf_inv -r
struct_bias_brain
***************************************************
The following COMPULSORY options have not been set:
-r,--ref filename for reference volume
***************************************************
Part of FSL (build 415)
fnirtfileutils
Copyright(c) 2007, University of Oxford (Jesper Andersson)
Usage:
fnirtfileutils --in=my_fnirtcoefs --ref=my_refvol --out=my_field
fnirtfileutils --in=my_fnirtcoefs --ref=my_refvol --jac=my_jacobians
fnirtfileutils --in=my_fnirtcoefs --ref=my_refvol --out=my_field --withaff
Compulsory arguments (You MUST set one or more of):
-i,--in filename of input coefficient volume (to be converted)
-r,--ref filename for reference volume
Optional arguments (You may optionally specify one or more of):
-o,--out filename for output (field/coef) volume
-f,--outformat Output format [field spline], default=field
-w,--warpres Warp resolution (mm), only relevant when
--outformat=spline
-k,--knotspace Knot-spacing (voxels), only relevant when
--outformat=spline
-j,--jac filename for output (jacobian map) volume
-a,--withaff If set, the affine transform is included in the
field/jacobian
-v,--verbose switch on diagnostic messages
-h,--help display this message
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/hr2std_field'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/hr2std_field): bad header info
Error: failed to open file /tmp/fsl_vFqsxFA/hr2std_field
Cannot open volume /tmp/fsl_vFqsxFA/hr2std_field for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/hr2std_field'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/hr2std_field): bad header info
Error: failed to open file /tmp/fsl_vFqsxFA/hr2std_field
Cannot open volume /tmp/fsl_vFqsxFA/hr2std_field for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/hr2std_field'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/hr2std_field): bad header info
Error: failed to open file /tmp/fsl_vFqsxFA/hr2std_field
Cannot open volume /tmp/fsl_vFqsxFA/hr2std_field for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/fieldx'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/fieldx): bad header info
Error: failed to open file /tmp/fsl_vFqsxFA/fieldx
Cannot open volume /tmp/fsl_vFqsxFA/fieldx for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/fieldy'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/fieldy): bad header info
Error: failed to open file /tmp/fsl_vFqsxFA/fieldy
Cannot open volume /tmp/fsl_vFqsxFA/fieldy for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/fieldz'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/fieldz): bad header info
Error: failed to open file /tmp/fsl_vFqsxFA/fieldz
Cannot open volume /tmp/fsl_vFqsxFA/fieldz for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/fieldx'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/fieldx): bad header info
Error: failed to open file /tmp/fsl_vFqsxFA/fieldx
Cannot open volume /tmp/fsl_vFqsxFA/fieldx for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/roi2std_field'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/roi2std_field): bad header info
Error: failed to open file /tmp/fsl_vFqsxFA/roi2std_field
ERROR: Could not open image /tmp/fsl_vFqsxFA/roi2std_field
Image Exception : #22 :: Failed to read volume
/tmp/fsl_vFqsxFA/roi2std_field
invwarp: Problem reading warp-file /tmp/fsl_vFqsxFA/roi2std_field
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/standard2highres_warp'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/standard2highres_warp): bad
header info
Error: failed to open file /tmp/fsl_vFqsxFA/standard2highres_warp
Cannot open volume /tmp/fsl_vFqsxFA/standard2highres_warp for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/standard2highres_warp'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/standard2highres_warp): bad
header info
Error: failed to open file /tmp/fsl_vFqsxFA/standard2highres_warp
Cannot open volume /tmp/fsl_vFqsxFA/standard2highres_warp for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/standard2highres_warp'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/standard2highres_warp): bad
header info
Error: failed to open file /tmp/fsl_vFqsxFA/standard2highres_warp
Cannot open volume /tmp/fsl_vFqsxFA/standard2highres_warp for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/fieldx'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/fieldx): bad header info
Error: failed to open file /tmp/fsl_vFqsxFA/fieldx
Cannot open volume /tmp/fsl_vFqsxFA/fieldx for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/fieldy'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/fieldy): bad header info
Error: failed to open file /tmp/fsl_vFqsxFA/fieldy
Cannot open volume /tmp/fsl_vFqsxFA/fieldy for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/fieldz'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/fieldz): bad header info
Error: failed to open file /tmp/fsl_vFqsxFA/fieldz
Cannot open volume /tmp/fsl_vFqsxFA/fieldz for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/fieldx'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/fieldx): bad header info
Error: failed to open file /tmp/fsl_vFqsxFA/fieldx
Cannot open volume /tmp/fsl_vFqsxFA/fieldx for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/standard2highres_full_warp'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/standard2highres_full_warp): bad
header info
Error: failed to open file /tmp/fsl_vFqsxFA/standard2highres_full_warp
ERROR: Could not open file
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/standard2highres_full_warp'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/standard2highres_full_warp): bad
header info
Error: failed to open file /tmp/fsl_vFqsxFA/standard2highres_full_warp
ERROR: Could not open file
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/standard2highres_full_warp'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/standard2highres_full_warp): bad
header info
Error: failed to open file /tmp/fsl_vFqsxFA/standard2highres_full_warp
ERROR: Could not open file
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/standard2highres_full_warp'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/standard2highres_full_warp): bad
header info
Error: failed to open file /tmp/fsl_vFqsxFA/standard2highres_full_warp
Cannot open volume /tmp/fsl_vFqsxFA/standard2highres_full_warp for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/standard2highres_full_warp'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/standard2highres_full_warp): bad
header info
Error: failed to open file /tmp/fsl_vFqsxFA/standard2highres_full_warp
Cannot open volume /tmp/fsl_vFqsxFA/standard2highres_full_warp for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/standard2highres_full_warp'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/standard2highres_full_warp): bad
header info
Error: failed to open file /tmp/fsl_vFqsxFA/standard2highres_full_warp
Cannot open volume /tmp/fsl_vFqsxFA/standard2highres_full_warp for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/standard2highres_full_warp'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/standard2highres_full_warp): bad
header info
Error: failed to open file /tmp/fsl_vFqsxFA/standard2highres_full_warp
ERROR: Could not open file
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/standard2highres_full_warp'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/standard2highres_full_warp): bad
header info
Error: failed to open file /tmp/fsl_vFqsxFA/standard2highres_full_warp
Cannot open volume /tmp/fsl_vFqsxFA/standard2highres_full_warp for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/standard2highres_full_warp'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/standard2highres_full_warp): bad
header info
Error: failed to open file /tmp/fsl_vFqsxFA/standard2highres_full_warp
Cannot open volume /tmp/fsl_vFqsxFA/standard2highres_full_warp for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/back_slice'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/back_slice): bad header info
Error: failed to open file /tmp/fsl_vFqsxFA/back_slice
Cannot open volume /tmp/fsl_vFqsxFA/back_slice for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/standard2highres_full_warp'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/standard2highres_full_warp): bad
header info
Error: failed to open file /tmp/fsl_vFqsxFA/standard2highres_full_warp
ERROR: Could not open file
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/standard2highres_full_warp'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/standard2highres_full_warp): bad
header info
Error: failed to open file /tmp/fsl_vFqsxFA/standard2highres_full_warp
Cannot open volume /tmp/fsl_vFqsxFA/standard2highres_full_warp for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/standard2highres_full_warp'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/standard2highres_full_warp): bad
header info
Error: failed to open file /tmp/fsl_vFqsxFA/standard2highres_full_warp
Cannot open volume /tmp/fsl_vFqsxFA/standard2highres_full_warp for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/left_slice'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/left_slice): bad header info
Error: failed to open file /tmp/fsl_vFqsxFA/left_slice
Cannot open volume /tmp/fsl_vFqsxFA/left_slice for reading!
** ERROR (nifti_image_read): failed to find header file for
'/tmp/fsl_vFqsxFA/standard2highres_full_warp'
** ERROR: nifti_image_open(/tmp/fsl_vFqsxFA/standard2highres_full_warp): bad
header info
Error: failed to open file /tmp/fsl_vFqsxFA/standard2highres_full_warp
ERROR: Could not open file
It's no problem for the earlier FSL version.
Any clue what's wrong?
Wayne
