Hmm, I tried manually realigning along the AC-PC line and it failed in the same way. Just to test things out, I also tried segmenting the single subject T1 template in the spm12 canonical folder thinking that it should work if alignment was the issue. It failed in the same way.

This also doesn't explain why this would work using the conn toolbox (which calls the same spm functions as the batch, correct?) yet fail when using the batch interface. Any thoughts on this?

~Meg

On Wed, May 3, 2017 at 4:19 AM, John Ashburner <[log in to unmask]> wrote:

My guess is that it is the usual problem of not having good starting estimates. Before you do anything with your images, run CheckReg with a selection of the images and one of the MNI-space images released with SPM. If the images are poorly aligned, then things will fail. Orientations should be within about 15-20 degrees, and the positioning should be within 3-4 cm.

Best regards,

-John

On 3 May 2017 at 02:48, Megan Finnegan <[log in to unmask]> wrote:

Hello SPM Experts,

I'm trying to run a segmentation in SPM12 on a structural and am getting some strange results. I tried running a grey and white matter segmentation via the batch editor. This is my first time working with segmentation, so I've just used the default settings. However the segmentation appears to fail. I also tried doing the segmentation in the conn toolbox and it seems to come out as expected.

I've attached a screen shot of the segmenations from both the SPM12 batching GUI (left set of images) and the conn toolbox (right set of images). What could be causing these results?

Thanks!

~Meg