Hi,
I'm a little bit confused about how to apply first_roi_slicesdir. Prior to
assessing the segmentations, all possible structures were segmented using
run_first_all.
When I run:
first_roi_slicesdir p1.nii.gz p1_all_fast_firstseg.nii.gz
I get the following output:
total number of image: 2
number of image pairs: 1
Image Exception : #99 :: Out of memory
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
(standard_in) 1: parse error
(standard_in) 1: parse error
(standard_in) 1: parse error
1 p1
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: indexing (in both time and space) starts with 0 not 1!
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: indexing (in both time and space) starts with 0 not 1!
run slicesdir
p1_t1grot1
** ERROR (nifti_image_read): failed to find header file for 'p1_t1grot1'
** ERROR: nifti_image_open(p1_t1grot1): bad header info
Error: failed to open file p1_t1grot1
ERROR: Could not open image p1_t1grot1
Image Exception : #22 :: Failed to read volume p1_t1grot1
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/slicesdir: line 132: 8313 Aborted ${FSLDIR}/bin/slicer
$A $B -s 1 $sliceropts
Cannot open slicesdir/grota.png for reading
/usr/local/fsl/bin/slicesdir: line 132: 8320 Segmentation fault
${FSLDIR}/bin/pngappend $convertopts slicesdir/${Q}.png
Finished. To view, point your web browser at
file:/media/linuxdata/johndata/PSOBIDdata/poor3DT1anon/slicesdir/index.html
removing files...
p1_t1grot1
p1_all_fast_firstseglbgrot1
For Info, I'm running FSL on CentOS 5.3, 64bit, 6Gb RAM.
When I run first_roi_slicesdir on a single structure, ie
first_roi_slicesdir p1.nii.gz p1-R_Hipp_nii.gz
Then it works fine
Is first_roi_slicesdir only supposed to run on single structures?
I'd be interested to know how i might be able to modify first_roi_slicesdir
so that it runs on multiple structures and on multiple subjects, perhaps
someone has solved this problem already?
Best wishes,
John
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