thanks, Doug! sorry, I had misinterpreted the --surf argument when I had
originally checked --help. Got the proper label created AND got the
overlay.mgz to work as well. All my labels are there in the overlay.mgz
created using mri_vol2surf once I change the thresholds of the overlay - I
can then is
nope, you need to give it just the name of the subject and the
hemisphere. Run it with --help for more info
On 04/20/2016 11:35 AM, Trisanna Sprung-Much wrote:
> Hi Doug
>
> I had run mri_cor2label using the --surf option. Is what I did below
> correct?
>
>
> trisanna@kaplan:~$ mri_cor2label --i
Hi Doug
I had run mri_cor2label using the --surf option. Is what I did below
correct?
trisanna@kaplan:~$ mri_cor2label --i
/data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --id 1 --l
/data-01/trisanna/freesurfer/icbm-102/label/labeltest --surf lh.pial
$Id: mri_cor2label.c,v 1.12 2011/03/
I think the problem is that this is being interpreted as a volume label.
The first column is the surface vertex number which you can see is all
-1s indicating no vertex. To create a surface label, run mri_cor2label
with the --surf subject hemi option. Ruopeng, can you add something to
freeview
Hi Doug and Bruce
*This what I get when I run the head command on the label:*
trisanna@kaplan:~$ head
/data-01/trisanna/freesurfer/icbm-102/label/labeltest.label
#!ascii label , from subject lh.pial vox2ras=TkReg
1651
-1 -29437.500 -0.500 0.500 0.00
-1 -30660.500 -0.500 0.500 0.000
Can you load another label, eg, lh.cortex.label? Also, I noticed that
there is a space between "label=" and "/data/..." in the command line
below. That space should not be there, so if it was there when you ran
the command try again without the space.
On 4/19/16 9:19 PM, Trisanna Sprung-Much w
Hi Trisanna
can you run:
head /data-01/trisanna/freesurfer/icbm-102/label/labeltest.label
and send us the output?
cheers
Bruce
On Tue, 19
Apr 2016, Trisanna Sprung-Much wrote:
Hi Doug
I tried again in the terminal and got this:
trisanna@kaplan:~$ freeview -f
/data-01/trisanna/freesurfer
Hi Trisanna
your output is a .mgz file, which is *not* a label. Try loading it as an
overlay. The label format is different (ascii for one thing, and only part
of the surface for another).
cheers
Bruce
On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote:
Hi Doug
I thought this was the case as
Hi Doug
I tried again in the terminal and got this:
*trisanna@kaplan:~$ freeview -f
/data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=
/data-01/trisanna/freesurfer/icbm-102/label/labeltest.label *
[0]PETSC ERROR:
[0]P
Hi Doug
I thought this was the case as well but when I try manually in Freeview and
select the correct label, Freeview crashes and gives this error in the
terminal:
trisanna@kaplan:~$ freeview
*** Error in `freeview.bin': double free or corruption (out):
0x29080920 ***
Abort (core dumped)
I don't think that is the problem. The problem is that it cannot find
the file. Try giving it the whole path
On 04/19/2016 05:45 PM, Bruce Fischl wrote:
> Hi Trisanna
>
> if your output is .mgz it isn't a label file. Labels are stored in
> .label names and are text files. The .mgz is a scalar fi
Hi Trisanna
if your output is .mgz it isn't a label file. Labels are stored in .label
names and are text files. The .mgz is a scalar field over the surface (that
is, a vector with a single value at each surface location). In freeview you
can view it as:
freeview -f lh.inflated:overlay=surfac
Hi Doug
So I ran mri_vol2surf and generated my .mgz surface overlay using
--regheader as you suggested. I than ran mri_cor2label using that .mgz
file. This also completed successfully. *However, when I then try to open
the pial surface and the corresponding new label in freeview, it says it
cannot
many thanks - will give this a go!
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve
wrote:
> yes, but the surface overlay is in mgz (or nii.gz) format
>
> On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote:
> >
yes, but the surface overlay is in mgz (or nii.gz) format
On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote:
> Hi Doug
>
> below is the email I had written last Friday. I thought it got lost in
> the mix. I was told by Bruce to use identity.nofile as the
> transformation since my labels and T1s
sorry for the confusion. Some of our tools use identity.nofile, but these
use --regheader
cheers
Bruce
On Tue, 19 Apr 2016, Trisanna
Sprung-Much wrote:
Hi Doug
below is the email I had written last Friday. I thought it got lost in the
mix. I was told by Bruce to use identity.nofile as the
Hi Doug
below is the email I had written last Friday. I thought it got lost in the
mix. I was told by Bruce to use identity.nofile as the transformation since
my labels and T1s are already in the same space and I just want to resample
my labels to the surfaces.
*I will try, as you suggest, --regh
I'm not sure what identity.nofile is or what you are trying to do (no
previous info in the email). If whatever you are trying to map to the
surface is already in anatomical space (so no registration necessary),
then you can use --regheader with mri_vol2surf. mri_cor2label will take
a volume for
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