Hi,
It sounds like it hasn't worked unfortunately.
The errors in fslview are simply because the images are in an incomplete
feat directory. If you change the name of the directory (so it
doesn't end in
.feat) or move the files outside of the feat directory. However, the
static
movies and lack of difference between distorted and undistorted is a
much
worse problem.
What files are in your unwarp directory (within the feat directory)?
And what images are you passing into the FEAT GUI?
As for the rescaling - that is simply something that FEAT does
automatically (and unfortunately can't be turned off) but it won't
affect any processing, as the diffusion fitting process will remove
any global scaling.
Let me know about the unwarp directory and GUI setup and
hopefully we can sort out the problem.
All the best,
Mark
On 1 May 2009, at 19:55, Siewmin Gan wrote:
> Hi,
> I have a couple of questions regarding the output data when I
> used the FEAT Gui to do
> distortion correction of DTI data. The movie section comparing
> distorted and undistorted
> example_func data (third last rows) showed a stationary row of
> images ( i.e there is no
> flipping between one image to another). When I tried to fslview the
> example_func.nii.gz,
> filtered_func_data.nii.gz or the example_func_orig_distorted.nii.gz,
> i could only view the
> first two and not able to view the last image. Also in all cases,
> there would be error
> messages as below for all three:
>
> ERROR (nifti_image_read): failed to find header file for
> '/Users/siewmingan/Desktop/DATASET/patient_1/tryfieldmap_y.feat/
> stats/pe1'
> ** ERROR:
> nifti_image_open(/Users/siewmingan/Desktop/DATASET/patient_1/
> tryfieldmap_y.feat/stat
> s/pe1): bad header info
> Error: failed to open file
> /Users/siewmingan/Desktop/DATASET/patient_1/tryfieldmap_y.feat/stats/
> pe1.
>
> Why does the error message occurs and how I can resolve it?
>
> Because the movie section did not display the contrast between the
> distorted and
> undistorted images, and the 4th row displaying the original
> distorted images looks
> similiar to the 5th row displaying the undistorted images , and I
> couldn't view the
> example_func.nii with the example_func_orig_distorted.nii.gz, I then
> tried to compare the
> example_func.nii.gz with my original 4D data file. I noticed the
> intensity in the
> example_func.nii.gz file is around 2-3 times lower than the original
> 4D data. May I ask
> why that would be so and would that be a problem? Also, if both the
> example_func.nii.gz
> file and the filtered_func_data.nii.gz are both the undistorted 4D
> DTI data from running
> FEAT, why do they have different intensity with the former in 100s
> and the latter in
> 10000s?
>
> Apart from the difference in the intensity in the original 4D data
> and the
> example_func.nii.gz, it was quite hard to detect differences due to
> the different intensity
> of the brain on display ( I've tried both distortion correction with
> the "y" and "-y" option.)
> Is there any way to resolve the previous error messages so I can
> directly compare the
> distorted and undistorted images with the same intensity, and check
> if I have done the
> distortion correction step correctly?
>
>
> Many Thanks
>
> Siewmin
>
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