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
I think 2, but it ignores the GCA if you give it a segmentation.
cheers
Bruce
On Thu, 18
Jul 2013, Mark Plantz wrote:
Hello freesurfers,
I am currently trying to create a normalized .mgz file using the
mri_ca_normalize command. Instead of using a .gca atlas, I am using a
manually segmente
Hello freesurfers,
I am currently trying to create a normalized .mgz file using the
mri_ca_normalize command. Instead of using a .gca atlas, I am using a
manually segmented image.
I have tried using the -seg flag. However, I keep getting an error that
I am not inputting the correct argumen
-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
Hi Diandra,
can you try running it with the current dev version and see if the
problem goes away? Krish can get you a binary.
cheers
Bruce
On Thu, 15 Jul 2010, Diandra
Lucia wrote:
> Hi there,
>
> We're processing some new 3T cases in FreeSurfer, and one case has
> been hanging just after it b
Hi there,
We're processing some new 3T cases in FreeSurfer, and one case has
been hanging just after it begins mri_ca_normalize:
#...@# CA Normalize Wed Jul 14 17:16:05 EDT 2010
/home/pnlstaff/freesurfer/subjects/case01264/mri
mri_ca_normalize -mask brainmask.mgz nu.mgz
/share/apps/freesurfer/
Hi Mishkin
if you put the subject on our site we'll take a look.
cheers,
Bruce
On Thu, 4 Dec 2008,
Mishkin Derakhshan wrote:
Hi,
I have one subject which seems to cause mri_ca_normalize to hang.
I've checked and the registration to tal is okay, as is the brainmask.
The subject in question do
Nurunisa,
For mri_ca_normalize, the flags must be the first args, like this:
mri_ca_normalize -noatlas -noxform -mask ...
otherwise the flags will be ignored if they are at the end of the
command (which is bad, but thats the way this works for this bin).
Nick
On Tue, 2008-11-04 at 15:58 -0500
Hi Nurunisa,
for mri_ca_normalize all the options have to come before the mandatory
parameters.
cheers,
Bruce
On Tue, 4 Nov 2008, Nurunisa Neyzi wrote:
Hi, I am getting an error with the command:
mri_ca_normalize -mask
/Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/brain.mgz -seg
/
Hi, I am getting an error with the command:
mri_ca_normalize -mask
/Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/brain.mgz -seg
/Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/cma_seg_noAA.mgz
/Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/nu.mgz -noatlas
-noxform /Users/N
Acutally, the autorecon flags require that the subcortical segmentation
be done (ie, you can't use -nosubcortseg with -autorecon)
Nick Schmansky wrote:
Margo,
In looking at the directory:
/autofs/space/lucy_002/users/margo/subjects/avm004/mri/
it appears the file norm.mgz does not exis
Margo,
In looking at the directory:
/autofs/space/lucy_002/users/margo/subjects/avm004/mri/
it appears the file norm.mgz does not exist, which accounts for the
error running autorecon2.
Normally, the file norm.mgz is created in the autorecon1 stage, so I'm
not sure why it wasn't created, but
Hi, I'm following up on an earlier email about the mri_ca_normalize step
of autorecon2. I am getting an error while running autorecon2 in the
developmental freesurfer version on tkmeg at the nmr center.
The command I ran was:
margo>
and the output error is below. My directory is
/space/lucy/2
Hi Margo,
you should be using the talairach.lta file created by mri_em_register
(not the talairach.xfm that you have in your command line).
cheers,
Bruce
On Thu, 22 Dec 2005, Margo McKenna Benoit wrote:
Hello,
I am having a problem with the mri_ca_normalize step in autorecon2. When I
run
Hello,
I am having a problem with the mri_ca_normalize step in autorecon2.
When I run autorecon2 (in the dev version: recon-all-nmr -subjid avm004
-autorecon2 -nosubcortseg -hemi lh), it gives me a message that norm.mgz
is missing, and it seems that the files are not being created (either in
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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