Dear FSL experts,

I have been following carefully all the instructions in http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/tbss/index

I have got mean_FA_skeleton, all_FA, ....

I have generated another folder called AD and inside there are all the AD images but with the name exact as the images that are in origdata folder...

Next, I have run the following command inside the AD folder: tbss_1_preproc -f 1000000 *.nii.gz



Next, I have go back to mytbss directory, which contains origdata, FA, stats, AD...folders

Next I have run tbss_non_FA AD...and  I got the following error:

rosalia@rosalia-PORTEGE-Z930:~$ cd /home/rosalia/Desktop/ESTUDI_AC_PREPROCESSADES/TBSS/mytbss
rosalia@rosalia-PORTEGE-Z930:~/Desktop/ESTUDI_AC_PREPROCESSADES/TBSS/mytbss$ tbss_non_FA AD
using pre-chosen registration target: target
upsampling alternative images into standard space
AC01
Image Exception : #22 :: ERROR: Could not open image ../AD/AC01
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
AC02
Image Exception : #22 :: ERROR: Could not open image ../AD/AC02
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
AC03
Image Exception : #22 :: ERROR: Could not open image ../AD/AC03
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
AC04
Image Exception : #22 :: ERROR: Could not open image ../AD/AC04
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
AC05
Image Exception : #22 :: ERROR: Could not open image ../AD/AC05
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
AC06
Image Exception : #22 :: ERROR: Could not open image ../AD/AC06
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
AC07
Image Exception : #22 :: ERROR: Could not open image ../AD/AC07
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
AC08
Image Exception : #22 :: ERROR: Could not open image ../AD/AC08
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
AC09
Image Exception : #22 :: ERROR: Could not open image ../AD/AC09
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
AC10
Image Exception : #22 :: ERROR: Could not open image ../AD/AC10
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
AC11
Image Exception : #22 :: ERROR: Could not open image ../AD/AC11
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
AC12
Image Exception : #22 :: ERROR: Could not open image ../AD/AC12
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
AC13
Image Exception : #22 :: ERROR: Could not open image ../AD/AC13
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
AC14
Image Exception : #22 :: ERROR: Could not open image ../AD/AC14
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
AC15
Image Exception : #22 :: ERROR: Could not open image ../AD/AC15
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
B01
Image Exception : #22 :: ERROR: Could not open image ../AD/B01
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
B02
Image Exception : #22 :: ERROR: Could not open image ../AD/B02
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
B03
Image Exception : #22 :: ERROR: Could not open image ../AD/B03
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
B04
Image Exception : #22 :: ERROR: Could not open image ../AD/B04
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
B05
Image Exception : #22 :: ERROR: Could not open image ../AD/B05
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
B06
Image Exception : #22 :: ERROR: Could not open image ../AD/B06
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
B07
Image Exception : #22 :: ERROR: Could not open image ../AD/B07
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
B08
Image Exception : #22 :: ERROR: Could not open image ../AD/B08
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
B09
Image Exception : #22 :: ERROR: Could not open image ../AD/B09
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
B10
Image Exception : #22 :: ERROR: Could not open image ../AD/B10
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
B11
Image Exception : #22 :: ERROR: Could not open image ../AD/B11
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
B12
Image Exception : #22 :: ERROR: Could not open image ../AD/B12
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
merging all upsampled AD images into single 4D image

Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds]
     -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 : auto-choose: single slices -> volume, volumes -> 4D (time series)
     -tr : concatenate images in time and set the output image tr to the final option value
Cannot open volume all_AD for reading!
projecting all_AD onto mean FA skeleton
Image Exception : #22 :: ERROR: Could not open image all_AD
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
now run stats - for example:
randomise -i all_AD_skeletonised -o tbss_AD -m mean_FA_skeleton_mask -d design.mat -t design.con -n 500 --T2 -V
(after generating design.mat and design.con)
rosalia@rosalia-PORTEGE-Z930:~/Desktop/ESTUDI_AC_PREPROCESSADES/TBSS/mytbss$