Hi,
On 1 May 2008, at 06:52, [log in to unmask] wrote:
> Dear Prof. Smith
>
> I am taking part of a research about DTI images with the subsequent
> use of TBSS method.
> I have realized FA images and I have use the tbss_1_preproc tool,
> but during the evaluation of non linear transformation with
> tbss_2_reg (with any options, template or most suitable target) I
> have had problems,as shown below. I've realized FA images with
> MRIConvert,is it the right format?
>
> Thank in advance for your attention
>
> With best regards
>
> Donatella Giuliani
>
> My output:
>
> [giuliani@localhost TBSS_NEW]$ tbss_1_preproc *
>
> Using multiplicative factor of 10000
> processing C117_GB_dti_FA
> processing C119_PL_dti_FA
> Now running "slicesdir" to generate report of all converted images
> Finished. To view, point your web browser at
> file:/home/giuliani/Desktop/TBSS/TBSS_NEW/FAi/slicesdir/index.html
> [giuliani@localhost TBSS_NEW]$ slicesdir S
> Finished. To view, point your web browser at
> file:/home/giuliani/Desktop/TBSS/TBSS_NEW/slicesdir/index.html
When you viewed this page in a local web browser, did the images look
ok?
> [giuliani@localhost TBSS_NEW]$ ls
> FAi origdata slicesdir
>
> [giuliani@localhost TBSS_NEW]$ tbss_2_reg -T
> C117_GB_dti_FA_FAi_to_target
> C119_PL_dti_FA_FAi_to_target
> 4409
>
> [giuliani@localhost TBSS_NEW]$ tbss_3_postreg -T
Did you wait for tbss_2_reg to finish before running this?
What does the following give:
cd FAi
ls -lart
Cheers.
>
> using prechosen
> target for registration
> transforming all FA images into MNI152 space
> C117_GB_dti_FA_FAi
> ** ERROR (nifti_image_read): failed to find header file
> for 'C117_GB_dti_FA_FAi_to_target_nonlinear'
> ** ERROR: nifti_image_open(C117_GB_dti_FA_FAi_to_target_nonlinear):
> bad
> header info
> Error: failed to open file C117_GB_dti_FA_FAi_to_target_nonlinear
> ERROR: Could not open image C117_GB_dti_FA_FAi_to_target_nonlinear
> Image Exception : #22 :: Failed to read volume
> C117_GB_dti_FA_FAi_to_target_nonlinear
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/tbss_3_postreg: line 148: 4952 Aborted
> $FSLDIR/bin/applywarp i
> $f o
> ${f}_to_target_nonlinear_hr r
> target w
> ${f}_to_target_nonlinear rel
> C119_PL_dti_FA_FAi
> ** ERROR (nifti_image_read): failed to find header file
> for 'C119_PL_dti_FA_FAi_to_target_nonlinear'
> ** ERROR: nifti_image_open(C119_PL_dti_FA_FAi_to_target_nonlinear):
> bad
> header info
> Error: failed to open file C119_PL_dti_FA_FAi_to_target_nonlinear
> ERROR: Could not open image C119_PL_dti_FA_FAi_to_target_nonlinear
> Image Exception : #22 :: Failed to read volume
> C119_PL_dti_FA_FAi_to_target_nonlinear
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/tbss_3_postreg: line 148: 4953 Aborted
> $FSLDIR/bin/applywarp i
> $f o
> ${f}_to_target_nonlinear_hr r
> target w
> ${f}_to_target_nonlinear rel
> 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
> : autochoose:
> single slices >
> volume, volumes >
> 4D (time series)
> ** 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
> Error:: FslCloneHeader: Null pointer passed for FSLIO
> 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!
> ** ERROR (nifti_image_read): failed to find header file for
> 'mean_FA_mask'
> ** ERROR: nifti_image_open(mean_FA_mask): bad header info
> Error: failed to open file mean_FA_mask
> ERROR: Could not open image mean_FA_mask
> Image Exception : #22 :: Failed to read volume mean_FA_mask
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/tbss_3_postreg: line 190: 4988 Aborted
> $FSLDIR/bin/fslmaths
> $FSLDIR/data/standard/FMRIB58_FA_1mm mas
> mean_FA_mask 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
> Cannot open volume mean_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!
> now view mean_FA_skeleton to check whether the default threshold of
> 2000
> needs changing, when
> running:
> tbss_4_prestats [threshold]
>
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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
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