what software package are you using to do the fMRI analysis?
doug

On 1/9/12 9:19 PM, Zhen Zonglei wrote:

Thank you very much, Doug.

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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   Douglas N. Greve, Ph.D.
   MGH-NMR Center

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