Hi - I suggest that you take a local copy of tbss_deproject, and
duplicate the applywarp line, putting "echo" before the first copy, so
that you can see what applywarp call is being made - hopefully that
will help work out what's going wrong here.
Cheers.
On 24 Feb 2009, at 00:31, SUBSCRIBE FSL Anonymous wrote:
> Hello, I've been trying to deproject the results of my TBSS analysis
> to
> original native space. From there I was planning on using the ROI
> as a seed
> point for tractography. Unfortunately, the tbss_deproject command is
> not
> working completely with my data. Also, I'm using FSL 4.0 and not
> the latest
> version. Here's what I ran:
>
> tbss_deproject FA_results_095.nii.gz 3
>
> The error message is below. I'm not sure if that message gives you
> all the
> info you need to make sense of the issue. I can tell you that the
> FA_results_095 file does exist, and resides in the stats directory.
> I've
> previously run this command with out error on other analysis with
> this data.
> I figure I'm doing something incorrect. Also, the FAi directory has a
> "subject99-dti_FA_FAi_to_target_nonlinear_inv.nii.gz" that resulted
> from the
> first time I ran this command, but is not rewritten when I rerun the
> command. Any assistance is, as always, greatly appreciated.
>
> ERROR INFORMATION (cut and pasted):
>
> processing subject99-dti_FA_FAi:
> ***************************************************
> The following COMPULSORY options have not been set:
> -w,--warp filename for warp transform (volume)
> -o,--out filename for output (warped) image
> ***************************************************
>
> applywarp (Version 1.2)
> Copyright(c) 2001, University of Oxford (Mark Jenkinson)
>
> Usage:
> applywarp -i invol -o outvol -r refvol -w warpvol
>
> Compulsory arguments (You MUST set one or more of):
> -i,--in filename of input image (to be warped)
> -w,--warp filename for warp transform (volume)
> -o,--out filename for output (warped) image
>
> Optional arguments (You may optionally specify one or more of):
> -r,--ref filename for reference image
> --abs treat warp field as absolute: x' = w(x)
> --rel treat warp field as relative: x' = x + w(x)
> --premat filename for pre-transform (affine matrix)
> --postmat filename for post-transform (affine matrix)
> -m,--mask filename for mask image (in reference space)
> --interp interpolation method {nn,trilinear,sinc}
> -v,--verbose switch on diagnostic messages
> -h,--help display this message
>
>
> Usage: /home/student/fsl4/fsl/bin/imrm <list of image names to remove>
> NB: filenames can be basenames or not
> ** ERROR (nifti_image_read): failed to find header file for
> 'subject99-dti_FA_FAi_FA_results_095'
> ** ERROR: nifti_image_open(subject99-dti_FA_FAi_FA_results_095): bad
> header info
> Error: failed to open file subject99-dti_FA_FAi_FA_results_095
> ERROR: Could not open file
> ** ERROR (nifti_image_read): failed to find header file for
> 'subject99-dti_FA_FAi_FA_results_095'
> ** ERROR: nifti_image_open(subject99-dti_FA_FAi_FA_results_095): bad
> header info
> Error: failed to open file subject99-dti_FA_FAi_FA_results_095
> ERROR: Could not open file
> ** ERROR (nifti_image_read): failed to find header file for
> 'subject99-dti_FA_FAi_FA_results_095'
> ** ERROR: nifti_image_open(subject99-dti_FA_FAi_FA_results_095): bad
> header info
> Error: failed to open file subject99-dti_FA_FAi_FA_results_095
> ERROR: Could not open file
>
> Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin>
> <zsize>
> fslroi <input> <output> <tmin> <tsize>
>
> fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin>
> <zsize>
> <tmin> <tsize>
> Note: counting (in both time and space) starts with 0 not 1!
> ** ERROR (nifti_image_read): failed to find header file for
> 'subject99-dti_FA_orig_FA_results_095_tmpslice'
> ** ERROR: nifti_image_open(subject99-
> dti_FA_orig_FA_results_095_tmpslice):
> bad header info
> Error: failed to open file subject99-
> dti_FA_orig_FA_results_095_tmpslice
> Cannot open volume subject99-dti_FA_orig_FA_results_095_tmpslice for
> reading!
> ** ERROR (nifti_image_read): failed to find header file for
> 'subject99-dti_FA_orig_FA_results_095_tmpslice'
> ** ERROR: nifti_image_open(subject99-
> dti_FA_orig_FA_results_095_tmpslice):
> bad header info
> Error: failed to open file subject99-
> dti_FA_orig_FA_results_095_tmpslice
> Cannot open volume subject99-dti_FA_orig_FA_results_095_tmpslice for
> reading!
> dc: stack empty
>
> Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin>
> <zsize>
> fslroi <input> <output> <tmin> <tsize>
>
> fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin>
> <zsize>
> <tmin> <tsize>
> Note: counting (in both time and space) starts with 0 not 1!
> ** ERROR (nifti_image_read): failed to find header file for
> 'subject99-dti_FA_orig_FA_results_095_tmpslice'
> ** ERROR: nifti_image_open(subject99-
> dti_FA_orig_FA_results_095_tmpslice):
> bad header info
> Error: failed to open file subject99-
> dti_FA_orig_FA_results_095_tmpslice
> Cannot open volume subject99-dti_FA_orig_FA_results_095_tmpslice for
> reading!
> ** ERROR (nifti_image_read): failed to find header file for
> 'subject99-dti_FA_orig_FA_results_095_tmpslice'
> ** ERROR: nifti_image_open(subject99-
> dti_FA_orig_FA_results_095_tmpslice):
> bad header info
> Error: failed to open file subject99-
> dti_FA_orig_FA_results_095_tmpslice
> Cannot open volume subject99-dti_FA_orig_FA_results_095_tmpslice for
> reading!
> dc: stack empty
> ** ERROR (nifti_image_read): failed to find header file for
> 'subject99-dti_FA_orig_FA_results_095'
> ** ERROR: nifti_image_open(subject99-dti_FA_orig_FA_results_095):
> bad header
> info
> Error: failed to open file subject99-dti_FA_orig_FA_results_095
> Cannot open volume subject99-dti_FA_orig_FA_results_095 for reading!
> ** ERROR (nifti_image_read): failed to find header file for
> 'subject99-dti_FA_orig_FA_results_095_tmpslice'
> ** ERROR: nifti_image_open(subject99-
> dti_FA_orig_FA_results_095_tmpslice):
> bad header info
> Error: failed to open file subject99-
> dti_FA_orig_FA_results_095_tmpslice
> Cannot open volume subject99-dti_FA_orig_FA_results_095_tmpslice for
> reading!
> ** ERROR (nifti_image_read): failed to find header file for
> 'subject99-dti_FA_orig_FA_results_095_tmpslice'
> ** ERROR: nifti_image_open(subject99-
> dti_FA_orig_FA_results_095_tmpslice):
> bad header info
> Error: failed to open file subject99-
> dti_FA_orig_FA_results_095_tmpslice
> Cannot open volume subject99-dti_FA_orig_FA_results_095_tmpslice for
> reading!
>
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------
|