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Hello Moises,

Thanks alot. I tried the way you suggested and now it works! Before i opened it from the fsl GUI window and it gave me the mask in ANALYZE format and now it gave me in .nii.gz format. I ran probtractx and am getting the tracts which I was looking for.

Thank you once again for your valuable time and precious efforts.

Wish you lots of success and happiness!

Best,
Wu

On 29 July 2015 at 16:52, Moises Hernandez <[log in to unmask]> wrote:
And... can you try to initialise fslview from that terminal ?
I mean:

1. open the terminal
2. check that 'echo $FSLOUTPUTTYPE' returns NIFTI_GZ
3. type: fslview
4. Try to create a new 3D mask

What version of FSL are you using ?

Moises.



On 29 July 2015 at 15:39, Wu chen <[log in to unmask]> wrote:
Hello Moises,

Yes when I echo $FSLOUTPUTTYPE I get NIFTI_GZ

Do I need to change something??

Best,
Wu

On 29 July 2015 at 15:51, Moises Hernandez <[log in to unmask]> wrote:
If you open a terminal and type :

echo $FSLOUTPUTTYPE

, what do you get ?
it should be NIFTI_GZ

Moises.

On 29 July 2015 at 14:22, Wu chen <[log in to unmask]> wrote:
Dear Moises,

Thank you for your prompt reply. I even tried it with 3D volume and I get the same message. When I save the mask, fslview saves it in Analyze format (hdr,img). FDT accepts only NIFTI and so I have to convert .hdr and img to nii format using dcm2nii.

Could this saving and conversion be a source of problem? Does fslview also saves the mask in hdr,img format on your computer? ??

previously it use to save in .nii format but now it pops up a window and ask whether we want 4D or 3D mask and after choosing the appropriate volume, it saves the mask automatically in .hdr and img files.

Do you know how to overcome this error message?
Many thanks in advance

Best wishes,
Wu


On 29 July 2015 at 14:23, Moises Hernandez <[log in to unmask]> wrote:
Hi Wu,

Why are you using a 4D mask ? 
You should use a 3D volume.

Best,
Moises.

On 29 July 2015 at 13:17, Wu chen <[log in to unmask]> wrote:
Dear FSL Experts,

I am new to FSL FDT and I am trying to run the probtrackx on a single subject.I have already done ecc, dtifit and bedpostx. Now, I have created a mask in putamen and use seed mask(4D mask) apporach to get the tracts associated with putamen. I get the error message that its invalid NIFTI file. Please see the attached .jpg for the exact error message.

Can someone help me out ? any pointers or suggestions to overcome the problem and I would be very grateful to you.


Best,
Wu