Print

Print
Hi,

Just to add to this, you might be interested in the tool aff2rigid, as this takes an affine registration matrix to standard space and creates a rigid-body registration matrix from it such that it aligns the AC-PC line and mid-sagittal plane.  So to use this you need to perform a 12 DOF registration to standard space, run aff2rigid on the result, and then apply this matrix to transform the original image.

Note that this is not necessary for running VBM, so the above is only needed if you are interested in having rigid-body AC-PC aligned images, but these results will not be used in VBM.

All the best,
Mark


On 17 Jun 2014, at 09:45, paul mccarthy <[log in to unmask]> wrote:

Hi Shahrzad,

If the images are already nearly aligned to each other, you should just be able to apply a rigid body transformation (6 degrees of freedom) with FLIRT. Just choose any one of your images as the reference, and align all of the other images to that reference.

Make sure to look at the results afterwards, to make sure the registration was successful.

Cheers,

Paul


On Mon, Jun 16, 2014 at 7:49 PM, shahrzad kharabian <[log in to unmask]> wrote:
Thanks dear mohamad, this does not solve the issue unfortunately. 




On Monday, June 16, 2014 8:35 PM, "Alshikho, Mohamad J." <[log in to unmask]> wrote:


Hi,
you can use <fslreorient2std input.nii output.nii > to reorient your images to match the orientation of the standard template images (MNI152), but this only rotated to 90, 180 or 270 degree and can't substitute coregistration.

I hope this is helpfull
Cheers, 
mohamad
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of shahrzad kharabian [[log in to unmask]]
Sent: Monday, June 16, 2014 2:09 PM
To: [log in to unmask]
Subject: [FSL] AC-PC

Dear Group, Can anyone help me by suggesting me a way of automatic AC-PC reorientation? 
I have a round 100 T1 weighted scans which need to be checked for AC-PC alignment before entering subsequent steps (VBM) . 


bests, 

-- 
Shahrzad

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.