Dear Prof. Smith
I am taking part of a research about DTI images with the subsequent use of TBSS method.
I have realized FA images and I have use the tbss_1_preproc tool, but during the evaluation of non linear transformation with tbss_2_reg (with any options, template or most suitable target) I have had problems,as shown below. I've realized FA images with MRIConvert,is it the right format?
Thank in advance for your attention
With best regards
Donatella Giuliani
My output:
[giuliani@localhost TBSS_NEW]$ tbss_1_preproc *
Using multiplicative factor of 10000
processing C117_GB_dti_FA
processing C119_PL_dti_FA
Now running "slicesdir" to generate report of all converted images
Finished. To view, point your web browser at
file:/home/giuliani/Desktop/TBSS/TBSS_NEW/FAi/slicesdir/index.html
[giuliani@localhost TBSS_NEW]$ slicesdir S
Finished. To view, point your web browser at
file:/home/giuliani/Desktop/TBSS/TBSS_NEW/slicesdir/index.html
[giuliani@localhost TBSS_NEW]$ ls
FAi origdata slicesdir
[giuliani@localhost TBSS_NEW]$ tbss_2_reg -T
C117_GB_dti_FA_FAi_to_target
C119_PL_dti_FA_FAi_to_target
4409
[giuliani@localhost TBSS_NEW]$ tbss_3_postreg -T
using prechosen
target for registration
transforming all FA images into MNI152 space
C117_GB_dti_FA_FAi
** ERROR (nifti_image_read): failed to find header file
for 'C117_GB_dti_FA_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(C117_GB_dti_FA_FAi_to_target_nonlinear): bad
header info
Error: failed to open file C117_GB_dti_FA_FAi_to_target_nonlinear
ERROR: Could not open image C117_GB_dti_FA_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
C117_GB_dti_FA_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/tbss_3_postreg: line 148: 4952 Aborted
$FSLDIR/bin/applywarp i
$f o
${f}_to_target_nonlinear_hr r
target w
${f}_to_target_nonlinear rel
C119_PL_dti_FA_FAi
** ERROR (nifti_image_read): failed to find header file
for 'C119_PL_dti_FA_FAi_to_target_nonlinear'
** ERROR: nifti_image_open(C119_PL_dti_FA_FAi_to_target_nonlinear): bad
header info
Error: failed to open file C119_PL_dti_FA_FAi_to_target_nonlinear
ERROR: Could not open image C119_PL_dti_FA_FAi_to_target_nonlinear
Image Exception : #22 :: Failed to read volume
C119_PL_dti_FA_FAi_to_target_nonlinear
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/tbss_3_postreg: line 148: 4953 Aborted
$FSLDIR/bin/applywarp i
$f o
${f}_to_target_nonlinear_hr r
target w
${f}_to_target_nonlinear rel
merging all upsampled FA images into single 4D image
Usage: fslmerge <x/
y/z/t/a> <output> <file1 file2 .......>
t
: concatenate images in time
x
: concatenate images in the x direction
y
: concatenate images in the y direction
z
: concatenate images in the z direction
a
: autochoose:
single slices >
volume, volumes >
4D (time series)
** ERROR (nifti_image_read): failed to find header file for 'all_FA'
** ERROR: nifti_image_open(all_FA): bad header info
Error: failed to open file all_FA
Error:: FslCloneHeader: Null pointer passed for FSLIO
creating valid mask and mean FA
** ERROR (nifti_image_read): failed to find header file for 'all_FA'
** ERROR: nifti_image_open(all_FA): bad header info
Error: failed to open file all_FA
Cannot open volume all_FA for reading!
** ERROR (nifti_image_read): failed to find header file for 'all_FA'
** ERROR: nifti_image_open(all_FA): bad header info
Error: failed to open file all_FA
Cannot open volume all_FA for reading!
** ERROR (nifti_image_read): failed to find header file for 'all_FA'
** ERROR: nifti_image_open(all_FA): bad header info
Error: failed to open file all_FA
Cannot open volume all_FA for reading!
** ERROR (nifti_image_read): failed to find header file for 'mean_FA_mask'
** ERROR: nifti_image_open(mean_FA_mask): bad header info
Error: failed to open file mean_FA_mask
ERROR: Could not open image mean_FA_mask
Image Exception : #22 :: Failed to read volume mean_FA_mask
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/tbss_3_postreg: line 190: 4988 Aborted
$FSLDIR/bin/fslmaths
$FSLDIR/data/standard/FMRIB58_FA_1mm mas
mean_FA_mask mean_FA
** ERROR (nifti_image_read): failed to find header file for 'mean_FA'
** ERROR: nifti_image_open(mean_FA): bad header info
Error: failed to open file mean_FA
Cannot open volume mean_FA for reading!
** ERROR (nifti_image_read): failed to find header file for 'all_FA'
** ERROR: nifti_image_open(all_FA): bad header info
Error: failed to open file all_FA
Cannot open volume all_FA for reading!
now view mean_FA_skeleton to check whether the default threshold of 2000
needs changing, when
running:
tbss_4_prestats [threshold]
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