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More information about how are my folders organized.... *Look at the path:* rosalia@rosalia-PORTEGE-Z930:~ $ cd /home/rosalia/Desktop/ESTUDI_AC_PREPROCESSADES/TBSS/mytbss rosalia@rosalia-PORTEGE-Z930:~/Desktop/ESTUDI_AC_PREPROCESSADES/TBSS/mytbss$ ls AD FA origdata stats rosalia@rosalia-PORTEGE-Z930:~/Desktop/ESTUDI_AC_PREPROCESSADES/TBSS/mytbss$ cd /home/rosalia/Desktop/ESTUDI_AC_PREPROCESSADES/TBSS/mytbss/ AD/ FA/ origdata/ stats/ rosalia@rosalia-PORTEGE-Z930:~/Desktop/ESTUDI_AC_PREPROCESSADES/TBSS/mytbss$ cd /home/rosalia/Desktop/ESTUDI_AC_PREPROCESSADES/TBSS/mytbss rosalia@rosalia-PORTEGE-Z930:~/Desktop/ESTUDI_AC_PREPROCESSADES/TBSS/mytbss$ ls AD FA origdata stats rosalia@rosalia-PORTEGE-Z930:~/Desktop/ESTUDI_AC_PREPROCESSADES/TBSS/mytbss$ cd /home/rosalia/Desktop/ESTUDI_AC_PREPROCESSADES/TBSS/mytbss/AD rosalia@rosalia-PORTEGE-Z930:~/Desktop/ESTUDI_AC_PREPROCESSADES/TBSS/mytbss/AD$ ls FA origdata rosalia@rosalia-PORTEGE-Z930:~/Desktop/ESTUDI_AC_PREPROCESSADES/TBSS/mytbss/AD$ cd /home/rosalia/Desktop/ESTUDI_AC_PREPROCESSADES/TBSS/mytbss/AD/FA rosalia@rosalia-PORTEGE-Z930:~/Desktop/ESTUDI_AC_PREPROCESSADES/TBSS/mytbss/AD/FA$ ls AC01_FA_mask.nii.gz AC10_FA.nii.gz B05_FA_mask.nii.gz AC01_FA.nii.gz AC11_FA_mask.nii.gz B05_FA.nii.gz AC02_FA_mask.nii.gz AC11_FA.nii.gz B06_FA_mask.nii.gz AC02_FA.nii.gz AC12_FA_mask.nii.gz B06_FA.nii.gz AC03_FA_mask.nii.gz AC12_FA.nii.gz B07_FA_mask.nii.gz AC03_FA.nii.gz AC13_FA_mask.nii.gz B07_FA.nii.gz AC04_FA_mask.nii.gz AC13_FA.nii.gz B08_FA_mask.nii.gz AC04_FA.nii.gz AC14_FA_mask.nii.gz B08_FA.nii.gz AC05_FA_mask.nii.gz AC14_FA.nii.gz B09_FA_mask.nii.gz AC05_FA.nii.gz AC15_FA_mask.nii.gz B09_FA.nii.gz AC06_FA_mask.nii.gz AC15_FA.nii.gz B10_FA_mask.nii.gz AC06_FA.nii.gz B01_FA_mask.nii.gz B10_FA.nii.gz AC07_FA_mask.nii.gz B01_FA.nii.gz B11_FA_mask.nii.gz AC07_FA.nii.gz B02_FA_mask.nii.gz B11_FA.nii.gz AC08_FA_mask.nii.gz B02_FA.nii.gz B12_FA_mask.nii.gz AC08_FA.nii.gz B03_FA_mask.nii.gz B12_FA.nii.gz AC09_FA_mask.nii.gz B03_FA.nii.gz slicesdir AC09_FA.nii.gz B04_FA_mask.nii.gz AC10_FA_mask.nii.gz B04_FA.nii.gz rosalia@rosalia-PORTEGE-Z930:~/Desktop/ESTUDI_AC_PREPROCESSADES/TBSS/mytbss/AD/FA$ cd /home/rosalia/Desktop/ESTUDI_AC_PREPROCESSADES/TBSS/mytbss/AD/origdata/ rosalia@rosalia-PORTEGE-Z930:~/Desktop/ESTUDI_AC_PREPROCESSADES/TBSS/mytbss/AD/origdata$ ls AC01_FA.nii.gz AC07_FA.nii.gz AC13_FA.nii.gz B04_FA.nii.gz B10_FA.nii.gz AC02_FA.nii.gz AC08_FA.nii.gz AC14_FA.nii.gz B05_FA.nii.gz B11_FA.nii.gz AC03_FA.nii.gz AC09_FA.nii.gz AC15_FA.nii.gz B06_FA.nii.gz B12_FA.nii.gz AC04_FA.nii.gz AC10_FA.nii.gz B01_FA.nii.gz B07_FA.nii.gz AC05_FA.nii.gz AC11_FA.nii.gz B02_FA.nii.gz B08_FA.nii.gz AC06_FA.nii.gz AC12_FA.nii.gz B03_FA.nii.gz B09_FA.nii.gz rosalia@rosalia-PORTEGE-Z930:~/Desktop/ESTUDI_AC_PREPROCESSADES/TBSS/mytbss/AD/origdata$ 2014-08-28 18:40 GMT+02:00 Rosalia Dacosta Aguayo <[log in to unmask]>: > 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$ > >