Hi Garth,
several questions: are your data in an FA/ directory after running tbss1? Or is it possible that you ran an old version of tbss1 (creating then a FAi/ directory)?
Also, what do you get if you do a ls $FSLDIR/data/standard/ ?
Cheers,
Gwenaelle
--- En date de : Mer 22.4.09, Garth Coombs <[log in to unmask]> a écrit :
> De: Garth Coombs <[log in to unmask]>
> Objet: [FSL] tbss steps 2 and 3 errors
> À: [log in to unmask]
> Date: Mercredi 22 Avril 2009, 16h23
> Hi,
>
> We are just starting to run TBSS for the first time and are
> running into
> some problems that we can't figure out. tbss_1_preproc
> seems to be running
> fine, but when I move onto tbss_2_reg, I get the following
> errors (about 75%
> of the time, and not specific to any particular subjects):
>
> *************
> tbss_2_reg -T
> /bin/cp: cannot create regular file `FA/target.nii.gz':
> No such file or
> directory
> /usr/local/fsl/bin/tbss_2_reg: line 127: cd: FA: No such
> file or directory
> K1013_dti_FA_FA_to_target K1015_dti_FA_FA_to_target
> K1016_dti_FA_FA_to_target
> 9302
> *************
>
> On the few instances in which I don't get those errors,
> when I move on to
> tbss_3_postreg, I get the follwoing errors:
>
> *************
> tbss_3_postreg -S
> using pre-chosen target for registration transforming all
> FA images into
> MNI152 space K1013_dti_FA_FA
> ** ERROR (nifti_image_read): failed to find header file for
> 'K1013_dti_FA_FA_to_target_warp'
> ** ERROR: nifti_image_open(K1013_dti_FA_FA_to_target_warp):
> bad header info
> Error: failed to open file K1013_dti_FA_FA_to_target_warp
> ERROR: Could not open image K1013_dti_FA_FA_to_target_warp
> Image Exception :
> #22 :: Failed to read volume K1013_dti_FA_FA_to_target_warp
> An error occured
> while reading file: K1013_dti_FA_FA_to_target_warp
> K1015_dti_FA_FA
> ** ERROR (nifti_image_read): failed to find header file for
> 'K1015_dti_FA_FA_to_target_warp'
> ** ERROR: nifti_image_open(K1015_dti_FA_FA_to_target_warp):
> bad header info
> Error: failed to open file K1015_dti_FA_FA_to_target_warp
> ERROR: Could not open image K1015_dti_FA_FA_to_target_warp
> Image Exception :
> #22 :: Failed to read volume K1015_dti_FA_FA_to_target_warp
> An error occured
> while reading file: K1015_dti_FA_FA_to_target_warp
> K1016_dti_FA_FA
> ** ERROR (nifti_image_read): failed to find header file for
> 'K1016_dti_FA_FA_to_target_warp'
> ** ERROR: nifti_image_open(K1016_dti_FA_FA_to_target_warp):
> bad header info
> Error: failed to open file K1016_dti_FA_FA_to_target_warp
> ERROR: Could not open image K1016_dti_FA_FA_to_target_warp
> Image Exception :
> #22 :: Failed to read volume K1016_dti_FA_FA_to_target_warp
> An error occured
> while reading file: K1016_dti_FA_FA_to_target_warp 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 : auto-choose: single slices -> volume, volumes
> -> 4D (time series)
> 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!
> skeletonising 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
> ERROR: Could not open image mean_FA
> Image Exception : #22 :: Failed to read volume mean_FA
> terminate called
> after throwing an instance of
> 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/tbss_3_postreg: line 182: 21245 Aborted
>
> $FSLDIR/bin/tbss_skeleton -i mean_FA -o mean_FA_skeleton
> now view mean_FA_skeleton to check whether the default
> threshold of 0.2
> needs changing, when running:
> tbss_4_prestats <threshold>
> *************
>
> If I then try to run fslview on the all_FA, it tells me
> that it could not
> find the hdr or img files.
>
> I have a feeling this is something simple that we're
> missing because we
> haven't run TBSS before, but we just can't figure
> it out and any help would
> be greatly appreciated.
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