Hello FSL Users,
I am interested in using tbss_deproject to invert or "pull back" a small mask of voxels in MNI152
space into the native space using
fslmaths example_mask -thr 0.95 grot
followed by:
tbss_deproject grot 3 (all from the stats directory)
I have successfully done this for tbss_maxc_tstat1 (as in the tbss_deproject documentation) in the
past but now am having trouble inverting the mask. I get the following messages. Any
suggestions would be greatly appreciated!!
Thank you,
Marc
~/Data/sumit31/statsRD> tbss_deproject grot 3
de-projecting <skeleton-space-image> into all_FA (nonlinearly aligned) subject space
output will be grot_to_all_FA
de-projection done
now creating inverse warp fields...
list of original images = total15910_FA_FAi total15911_FA_FAi total16176_FA_FAi
total16810_FA_FAi total17479_FA_FAi total17483_FA_FAi total17977_FA_FAi total17978_FA_FAi
total18261_FA_FAi total18263_FA_FAi total18643_FA_FAi total18868_FA_FAi total19520_FA_FAi
total19770_FA_FAi total19868_FA_FAi total19871_FA_FAi total20271_FA_FAi total20525_FA_FAi
total20572_FA_FAi total20574_FA_FAi total20677_FA_FAi total20994_FA_FAi total20995_FA_FAi
total21001_FA_FAi total21002_FA_FAi total21003_FA_FAi total21950_FA_FAi total22256_FA_FAi
total22262_FA_FAi total22534_FA_FAi total22540_FA_FAi
original target = target
processing total15910_FA_FAi:
***************************************************
The following COMPULSORY options have not been set:
-w,--warp filename for warp transform (volume)
-o,--out filename for output (warped) image
***************************************************
applywarp (Version 1.2)
Copyright(c) 2001, University of Oxford (Mark Jenkinson)
Usage:
applywarp -i invol -o outvol -r refvol -w warpvol
Compulsory arguments (You MUST set one or more of):
-i,--in filename of input image (to be warped)
-w,--warp filename for warp transform (volume)
-o,--out filename for output (warped) image
Optional arguments (You may optionally specify one or more of):
-r,--ref filename for reference image
--abs treat warp field as absolute: x' = w(x)
--rel treat warp field as relative: x' = x + w(x)
--premat filename for pre-transform (affine matrix)
--postmat filename for post-transform (affine matrix)
-m,--mask filename for mask image (in reference space)
--interp interpolation method {nn,trilinear,sinc}
-v,--verbose switch on diagnostic messages
-h,--help display this message
Usage: /usr/local/fsl/bin/imrm <list of image names to remove>
NB: filenames can be basenames or not
** ERROR (nifti_image_read): failed to find header file for 'total15910_FA_FAi_grot'
** ERROR: nifti_image_open(total15910_FA_FAi_grot): bad header info
Error: failed to open file total15910_FA_FAi_grot
ERROR: Could not open file
** ERROR (nifti_image_read): failed to find header file for 'total15910_FA_FAi_grot'
** ERROR: nifti_image_open(total15910_FA_FAi_grot): bad header info
Error: failed to open file total15910_FA_FAi_grot
ERROR: Could not open file
** ERROR (nifti_image_read): failed to find header file for 'total15910_FA_FAi_grot'
** ERROR: nifti_image_open(total15910_FA_FAi_grot): bad header info
Error: failed to open file total15910_FA_FAi_grot
ERROR: Could not open file
Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize>
fslroi <input> <output> <tmin> <tsize>
fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin>
<tsize>
Note: counting (in both time and space) starts with 0 not 1!
** ERROR (nifti_image_read): failed to find header file for 'total15910_FA_orig_grot_tmpslice'
** ERROR: nifti_image_open(total15910_FA_orig_grot_tmpslice): bad header info
Error: failed to open file total15910_FA_orig_grot_tmpslice
Cannot open volume total15910_FA_orig_grot_tmpslice for reading!
** ERROR (nifti_image_read): failed to find header file for 'total15910_FA_orig_grot_tmpslice'
** ERROR: nifti_image_open(total15910_FA_orig_grot_tmpslice): bad header info
Error: failed to open file total15910_FA_orig_grot_tmpslice
Cannot open volume total15910_FA_orig_grot_tmpslice for reading!
dc: stack empty
Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize>
fslroi <input> <output> <tmin> <tsize>
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