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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. > > >