Hello,
Are you using su to do the changes as root? You should be able to make the changes by starting the process with sudo instead.
Many Regards
Matthew
> 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
>
|