I only have one input. The last posting's orig.jpg was 001.mgz, and
motioncor.jpg is orig.mgz. We usually run motioncor because it produces the
orig.mgz which has been conformed.
On Mon, Jun 3, 2013 at 2:41 PM, Bruce Fischl wrote:
> what does the 001.mgz look like? Do you have more than one inpu
what does the 001.mgz look like? Do you have more than one input
(otherwise you wouldn't need motion correction)? If so, you'll need to do
this for each one
On Mon, 3 Jun 2013, Erin Browning wrote:
The orig.mgz is hyerintense (there's a screenshot of it in another post
now). The AFNI file is i
try what I suggested and see if that helps
On Mon, 3 Jun 2013, Erin Browning
wrote:
Here is an example of what AR2 looks like (without playing with niterations
or anything like that to reduce the overall hypterintensity). The white
matter line is much closer to the pial line than it should be.
Here is an example of what AR2 looks like (without playing with niterations
or anything like that to reduce the overall hypterintensity). The white
matter line is much closer to the pial line than it should be.
On Mon, Jun 3, 2013 at 2:00 PM, Bruce Fischl wrote:
> Hi Erin
>
> that can happen i
what is the problemexactly? how do the surfaces look?
doug
On 06/03/2013 02:54 PM, Erin Browning wrote:
>
> It seems like it getting darker messes up the normalization later on;
> could this be the case? Here's what it looks like in AFNI
> (1029-afni.jpg), and here's what it looks like after we
Hi Erin
that can happen if you lose too much dynamic range when "conforming". What
does the orig.mgz look like? What voxel format is the afni file in (uchar?
float?) mri_convert has a -ns 1 flag to turn off intensity scaling ("no
scale"). If the brik was in float you could use something like (
