Hi Eugene

 

It is from mice (brain extracted). I think I have correctly read the information (just the question mark left to the selected layer). ;)

 

Cheers

Rafael

 

Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im Auftrag von Eugene Duff
Gesendet: Mittwoch, 27. Mai 2015 19:20
An: [log in to unmask]
Betreff: Re: [FSL] AW: [FSL] AW: [FSL] AW: [FSL] Downsampling of fMRI image

 

 

 

On 27 May 2015 at 18:14, Rafael Wampfler <[log in to unmask]> wrote:

Hi Eugene

I don’t know if field strength was 7T, I have to check that. But I don’t think that there is something wrong with the input or reference image. They both look ok when viewed with FSLview.

 

 

This suggests that the headers are incorrect (or you are not reading the resolution info from the images correctly)?  Is it whole brain data?

 

Cheers

 

 

 

Cheers

 

Rafael

 

Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im Auftrag von Eugene Duff
Gesendet: Mittwoch, 27. Mai 2015 18:53
An: [log in to unmask]
Betreff: Re: [FSL] AW: [FSL] AW: [FSL] Downsampling of fMRI image

 

Hi Rafael - 

 

On 27 May 2015 at 17:46, Rafael Wampfler <[log in to unmask]> wrote:

Hi Eugene

The exact command was:

 

flirt    -in    input_image \
          -ref ref_image \
          -out output_image \
          -applyxfm \
           -init /usr/share/fsl/5.0/etc/flirtsch/ident.mat

 

input_image: 90 x 60 x 12 x 350 with voxel dimension 1 x 1 x 1

ref_image: 80 x 35 x 12 x 350 with voxel dimension 0.2 x 0.2 x 0.5 mm

 

 

There is something wrong with the ref_image I think: if the resolution was indeed, e.g. 5 times higher, it would need 5 times as many voxels in those dimensions to cover a similar sized image.  Actually, both images seem very high resolution for FMRI - unless it's 7T? 

 

Eugene

 

 

 

 

Thank you and cheers

 

Rafael

 

Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im Auftrag von Eugene Duff
Gesendet: Mittwoch, 27. Mai 2015 18:40
An: [log in to unmask]
Betreff: Re: [FSL] AW: [FSL] Downsampling of fMRI image

 

Hi - 

 

On 27 May 2015 at 17:34, Rafael Wampfler <[log in to unmask]> wrote:

Hi Eugene

It does not fail, i.e. there was no error but the resulting image looked very wrong, It was almost black...

 

I used the “identity mask” provided by FSL and I don’t have a structural or anatomical template, I only have functional images. As input to flirt I used the image with dimensionality 90 x 60 x 12, as reference I used the 80 x 35 x 12 image and as mask the identity mask. Vice verca (switching input and ref image) did also not work.

 

 

I'm not sure what you mean by "Identity mask".  What was the exact command you used and dimensions of each image?  If your images have the dimensionalities you describe, there should not be much difference in resolution.

 

Eugene

 

 

Cheers

 

Rafael

 

Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im Auftrag von Eugene Duff
Gesendet: Mittwoch, 27. Mai 2015 16:04
An: [log in to unmask]
Betreff: Re: [FSL] Downsampling of fMRI image

 

Hi Rafael - 

 

On 25 May 2015 at 21:37, Rafael Wampfler <[log in to unmask]> wrote:

Hello

I have a set of fMRI images. One group has a dimensionality of 90 x 60 x 12 x 350 with voxel dimension 1 x 1 x 1 mm (350 volumes). The other group has a dimensionality of 80 x 35 x 12 x 350 with voxel dimension 0.2 x 0.2 x 0.5 mm. I'm using one of the images as reference image for registration. Due to the difference in resolution the registration fails (with flirt).

 

How does it fail?  Differences in registration should not affect flirt.

 

 

So I have to first downsample or upsample. I have tried the following approach:

flirt    -in    input_image \
          -ref good_size_image \
          -out output_image \
          -applyxfm \
           -init /usr/share/fsl/5.0/etc/flirtsch/ident.mat

This does not work, not for downsampling and not for upsampling. 

How should I do correct downsampling / upsampling?

 

 

How does this fail?

 

Cheers

 

Eugene