Dear FSL experts,
I'm running the TBSS_non_FA script for L1 in FSL 4.1.4. I have performed the full TBSS analyses on my FA data. I have followed the steps for "using non_FA images in TBSS, however when I give the command: tbss_non_FA L1 I receive the following error:
-imac:FA np$ tbss_non_FA l1
using pre-chosen registration target: IUGR_014_dti_FA_FA
upsampling alternative images into standard space
/usr/fsl/bin/tbss_non_FA: line 95: /usr/fsl/bin/imglob: Argument list too long
merging all upsampled l1 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 : auto-choose: single slices -> volume, volumes -> 4D (time series)
** ERROR (nifti_image_read): failed to find header file for 'all_l1'
** ERROR: nifti_image_open(all_l1): bad header info
Error: failed to open file all_l1
Cannot open volume all_l1 for reading!
projecting all_l1 onto mean FA skeleton
** ERROR (nifti_image_read): failed to find header file for 'all_l1'
** ERROR: nifti_image_open(all_l1): bad header info
Error: failed to open file all_l1
ERROR: Could not open image all_l1
Image Exception : #22 :: Failed to read volume all_l1
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/fsl/bin/tbss_non_FA: line 104: 1774 Abort trap ${FSLDIR}/bin/tbss_skeleton -i mean_FA -p $thresh mean_FA_skeleton_mask_dst ${FSLDIR}/data/standard/LowerCingulum_1mm all_FA all_${ALTIM}_skeletonised -a all_$ALTIM
now run stats - for example:
randomise -i all_l1_skeletonised -o tbss_l1 -m mean_FA_skeleton_mask -d design.mat -t design.con -n 500 --T2 -V
(after generating design.mat and design.con)
I found a similar error on the list, but i can't modify the line as Matthew suggest, I used the root user but I receive "su sorry"
${FSLDIR}/bin/fslmerge -t ../stats/all_$ALTIM `$FSLDIR/bin/imglob *_to_target_${ALTIM}.*`
in $FSLDIR/bin/tbss_non_FA
to read:
${FSLDIR}/bin/fslmerge -t ../stats/all_$ALTIM `$FSLDIR/bin/imglob *_to_target_${ALTIM}.nii.gz`
I really appreciate your help,
Regards,
Nelly Padilla. M.D. Phd
Clinical Research
Department of Maternal-Fetal Medicine, ICGON
Fetal and Perinatal Medicine Research Group,IDIBAPS
Hospital Clinic - Universitat de Barcelona
Sabino de Arana 1- Helios III
08028 Barcelona
Spain
|