On 27 Mar 2017, at 14:59, Dev vasu <[log in to unmask]> wrote:

Dear Sir,

The labels come up MNI_template152_template  and each label indicates one subfield Hippocampus , I am trying to perform VBM analysis for the different subfields labels by using these labels as ROI mask, the only problem is Dimensions of my GM_mask and ROI labels doesn't match .

Following journal details how subfield labels were extracted https://www.ncbi.nlm.nih.gov/pubmed/26594378
 

Thanks

Vasudev 

On 23 March 2017 at 15:36, Dev vasu <[log in to unmask]> wrote:

Dear Sir,

Yes, the labels come from the atlas of Cobra Labs  ( they are made with MaGEt Brain ), I would like to use the labels that i have got as a ROI mask for my analysis , In order to do that i have used fslmaths to use label as ROI mask, but since dimensions/orientation doesn't match , i am incurring an error, also when i resample the labels , i am losing much of the information that i need from those labels.

If there is any way that i can resolve this issue it would be great for me. I am willing to provide further information incase you need

Thanks

Vasudev

On 23 March 2017 at 13:56, Mark Jenkinson <[log in to unmask]> wrote:

Hi,

I don't really understand what you are trying to do.

The screenshot you sent clear show that there is a problem in the labelled image, but I'm not sure where that is from and what it looks like on its own.

Is the problem that you have some labelled images and a brain image and that they don't line up?  If so, it would be helpful to know where the different images come from and how you are viewing them.  It seems that you are using connectome workbench and that the labels come from some sort of atlas.  More information would help us to help you better.

All the best,

Mark

On 21 Mar 2017, at 23:11, Dev vasu <vasudevamurthy.devulapally@gmail.com> wrote:

Dear Sir,

How can i check the orientation of my image if its RAS = +x+y+z  or not, i have checked fslorient and that does not provide much information pertaining to orientation of my image .

Thanks

vasudev

On 21 March 2017 at 23:53, Dev vasu <vasudevamurthy.devulapally@gmail.com> wrote:

Dear Sir,

I am annexing the picture of my image with labels ( Hippocampus ROI ) superimposed  as you can see the orientation of hippocampus is inaccurate , I have checked the same labels in RAS = +x +y +z orientation and they match exactly with hippocampus anatomy , only in case my image it was flipped upside down

Thanks

Vasudev

On 21 March 2017 at 22:43, Mark Jenkinson <[log in to unmask]> wrote:

Hi,

I'm not sure if your labels need to be changed (i.e. they are currently not correct with respect to the anatomy) or if you just want to view the image in a different orientation.

If the labels are correct then do the following:
  fslswapdim imagename.nii.gz -x -y z newimagename.nii.gz

If the labels are incorrect then do:
  fslswapdim imagename.nii.gz -x -y z newimagename.nii.gz
  fslcpgeom imagename.nii.gz newimagename.nii.gz

You may also need to use x instead of -x in the first command if the labels are incorrect - it all depends on whether the original left and right labels were correct or if they need changing too.

All the best,
        Mark

> On 21 Mar 2017, at 20:06, Dev vasu <vasudevamurthy.devulapally@GMAIL.COM> wrote:
>
> Dear all,
>
> I would like to if there is any procedure to reorient the image ( flip ) from AP axis to PA , I have around 50 scans all of which are scanned in A/P axis and i would like to reorient them , kindly please let me know if there is any procedure.
>
> I tried mri_convert and orient_mri is freesurfer but i could not see any changes
>
>
> Thanks
> Vasudev