Hi, just a quick question...

We get this error:

register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=6.0 using (99, 95, 113) as brain centroid... mean wm in atlas = 126, using box (82,71,91) --> (116, 118,134) to find MRI wm before smoothing, mri peak at 0 after smoothing, mri peak at 0, scaling input intensities by inf Darwin mac124901.med.cornell.edu 8.11.1 Darwin Kernel Version 8.11.1: Wed Oct 10 18:23:28 PDT 2007; root:xnu-792.25.20~1/RELEASE_I386 i386 i386

recon-all exited with ERRORS at Mon Apr 6 15:19:36 EDT 2009

How do we scale the nu.mgz images? Our 001.mgz are looking fine...

thanks!

---------- Forwarded message ---------- From: Nurunisa Neyzi nneyzi@gmail.com Date: Mon, Apr 6, 2009 at 3:31 PM Subject: Re: FW: XNAT update: Processing failed for PrenatalMA_13_MR_1 To: Chris Derauf dderauf@hawaii.edu

i think this is what's going on:

we get

"before smoothing, mri peak at 0 after smoothing, mri peak at 0, scaling input intensities by inf" which is wrong.

this is happening because nu.mgz is very dark.

same problem they had here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2008-April/007603.htm...

in our case though I think 001.mgz is looking fine, it is the nu.mgz that's kind of dark.

let's see what's the easiest way fix it.

On Mon, Apr 6, 2009 at 3:25 PM, Nurunisa Neyzi nneyzi@gmail.com wrote:

actually it goes wrong in the first step. even outside the pipeline. so it's not an XNAT issue.

On Mon, Apr 6, 2009 at 3:23 PM, Chris Derauf dderauf@hawaii.edu wrote:

...

Yes, I did specify the BK Pediatric atlas