In my case, the fMRI data is in LPS orientation, but the MNI152 in FSL are in LAS orientation. To overlay our fMRI results to MNI152 template, I wonder I should reorient the fMRI

data to LAS orientation, am I right?

When I use mri_convert to do the task, it only convert the first volme and discard other volume. Why?

Thanks again

Zonglei Zhen

On Tue, Jan 10, 2012 at 6:44 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Hi Zonglei, it should be fixed for version 5. Note that you should not use --out_orientation unless the orientation information is actually wrong. I think FSL has some tools to re-orient the

doug

Zhen Zonglei wrote:

Hi, Doug;
Is the bug still in FS5.0.

When I used mri_convert to reorient a 4D BOLD volume. All frames except the first frame are discarded.
My command: mri_convert --out_orientaiton LAS f.nii.gz flas.nii.gz
Is there a convenient way to reorient the 4D volume to match the MNI template in FSL ?

fslswapdim in fsl can not adaptively swap to the assigned orientation based on the nii header.

Best

Zonglei Zhen

On Fri, Mar 12, 2010 at 6:40 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

This is a bug in the released version of FS. Our development
version is
fixed. I've put a version here

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert

ythomas wrote:
> Hi,
>
> I am trying to downsample a 4D volume using mri_convert. However, it
> seems to be killing the 4 dimension. For example, if I do
>
> mri_convert -voxsize 4 4 4 tmp.mgz tmp444.mgz
>
> The original volume which is 256 x 256 x 256 x 120 becomes 64 x
64 x 64.
>
> Thanks,
> Thomas
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