Hi Theresa
can you open the inputs to mri_ca_normalize in freeview ok? The nu.mgz
for example? Please send us the recon-all.log so we can examine it.
If all the inputs look fine, then upload your subject and we will have a
look.
cheers
Bruce
On Fri, 9 Mar 2018, Marschall, T.M. wrote:
De
Dear all,
I’m currently running the -reconall command on 40 subjects. One of them exited
the mri_ca_normalize step with an error saying:
Abort (core dumped)
I tried rerunning it, however the error keeps occurring. So I have search the
list, but could not find a solution to my problem. Does
Hello all,
I am experiencing an error during the mri_ca_normalize step of
auto-recon-1 using a non-default atlas (for infant brains). Essentially,
"norm.mgz" and "ctrl_pts.mgz" are both outputting as blank files
(completely black). However, brainmask.mgz looks completely fine, which
leads
-seg
would be the correct flag if you wanted to specify an aseg-type volume to
do the normalizaton based on instead of using a transform and the gca. You
can't give it an intensity volume though (lke the nu.mgz) - it won't know
what to do with it
Bruce
On Tue, 2 Jul 2013, Mark Plantz wrote
Hi Bruce,
Is -seg the correct flag to input an .mgz file instead of a .gca atlas?
After making the recommened changes, the command will not seem to work. My
input is as follows:
mri_ca_normalize -seg
/Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-7549/mri/nu.mgz
/Volumes/Wong_Lab/CochlearImplant
It also looks like you have an extra forward slash at the end of seg.mgz
On 07/02/2013 12:13 PM, Bruce Fischl wrote:
> Hi Mark
>
> for mri_ca_normalize all the optional arguments (prefixed with a dash)
> must come before all the mandatory ones. Also, you shouldn't give it
> the mri directory -
Hi Mark
for mri_ca_normalize all the optional arguments (prefixed with a dash)
must come before all the mandatory ones. Also, you shouldn't give it the
mri directory - give it an input volume (like nu.mgz).
cheers
Bruce
On Tue, 2 Jul 2013, Mark Plantz
wrote:
Hello,
I am currently havi
Hello,
I am currently having some difficulties with the mri_ca_normalize
command. I am attempting to create a normalized volume file using an input
brain with the following command:
mri_ca_normalize
/Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-neo-mgz/mri/ -seg
/Volumes/Wong_Lab/Cochle
could also be something wrong with running zcat
Bruce Fischl wrote:
sounds like un.mgz doesn't exist (or you don't have read permission)
On Mon, 28 Nov 2005, Michele Perry wrote:
Hi,
mri_ca_normalize failed for a subject. Here is the CA normalize portion
of recon-all.log:
sounds like un.mgz doesn't exist (or you don't have read permission)
On Mon,
28 Nov 2005, Michele Perry wrote:
Hi,
mri_ca_normalize failed for a subject. Here is the CA normalize portion
of recon-all.log:
===
CA Normalize Thu Nov 17 17:02:05 PST 2005
$
Hi,
mri_ca_normalize failed for a subject. Here is the CA normalize portion
of recon-all.log:
===
CA Normalize Thu Nov 17 17:02:05 PST 2005
$SUBJECTS_DIR//mri
mri_ca_normalize -mask brain.mgz nu.mgz
/space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64/avera
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