>
> Hi, Everyone,
>
> I was using mri_extract_label command to extract the region that I am
> interested in, what I did was as follow:
>
> mri_extract_labe aparc+aseg.mgz 10 seg.nii
>
> It worked. However, when I tried to see it in the spm8, the intensity is
> 128 (interested region) and 0(dark are
Hello,
I encountered a problem with the command
recon-all -s jan -autorecon-all
which is supposed to be for all the steps. A full reconstruction.
INFO: set hdr.hist.orient to -1
ERROR: failure writing
/usr/local/freesurfer/subjects/jan/mri/tmp-mri_motion_correct.fsl-5574/cor-2.img
So I tried flip
Hi Jan,
is there enough space in /usr/local/freesurfer/subjects/jan? Do you have
write permission?
Bruce
On Thu, 28 Jan 2010, Janani Dhinakaran wrote:
> Hello,
>
> I encountered a problem with the command
> recon-all -s jan -autorecon-all
> which is supposed to be for all the steps. A full reco
the terminal should display the error message that is output by
mri_glmfit. can you send that message? or run the command from the
command line to get the error message.
n.
On Tue, 2010-01-26 at 15:54 -0500, Kevin Head wrote:
> I am having a problem with qdec. My table.dat and levels files are
the qdec tutorial describes how to draw a label on a region, and then
map that label (roi) back to each subject. from there, aparcstats2table
can be used to gather that roi data into a table for import into a stats
program where you perform your analysis.
n.
On Wed, 2010-01-27 at 08:04 +0900, Man
sorry, i meant to say include the --no-aseg flag with
make_average_volume (make_average_subject is just a wrapper script that
calls make_average_volume and make_average_surface).
n.
On Wed, 2010-01-27 at 14:02 +0800, lordowen wrote:
> Hi:
>
> Thank you for your replies. But how I can including
Dear all,
Is there an easy way to resize a volume, as in stretch it? I've gone the
tkregister2 route of making a dat file and applying it with mri_convert
(after converting to xfm) but for some reason it crops my volume, even
when there's no good reason why it should. I'm hoping for a function or
Try using mri_vol2vol. You can't rescale, but it should solve your
cropping problem.
Reza Farivar wrote:
> Dear all,
>
> Is there an easy way to resize a volume, as in stretch it? I've gone the
> tkregister2 route of making a dat file and applying it with mri_convert
> (after converting to xfm) b
We have a large number of scans with excellent, visually inspected and
manually trimmed brain masks, so we would like to use these masks to
assist the FreeSurfer processing. One way we have experimented with to
achieve this is to clip the T1 to remove anything non-brain before
importing it into th
Hi Ron,
we do use the talairach for things like estimating icv, so that would
concern me a bit. I don't think there is a straightforward way to insert
the skull stripped image into our stream though. Maybe Nick has a better
idea?
Bruce
On Thu, 28 Jan 2010,
Pierson, Ronald K wrote:
> We hav
you could break it apart:
recon-all -s subjid -autorecon1 -noskullstrip
cp brainmask.auto.mgz
cp brainmask.auto.mgz brainmask.mgz
recon-all -s subjid -autorecon2 -autorecon3
n.
On Thu, 2010-01-28 at 15:31 -0500, Bruce Fischl wrote:
> Hi Ron,
>
> we do use the talairach for things like esti
i forgot to add: dont use the skull-stripped image as input. your's
just gets inserted after -autorecon1 to replace brainmask..mgz
n.
On Thu, 2010-01-28 at 15:59 -0500, Nick Schmansky wrote:
> you could break it apart:
>
> recon-all -s subjid -autorecon1 -noskullstrip
>
> cp brainmask.auto.mg
Thanks! Yes, that makes perfect sense - looking at:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
Ron
-Original Message-
From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
Sent: Thursday, January 28, 2010 3:04 PM
To: Bruce Fischl
Cc: Pierson, Ronald K; freesurfer@nmr.m
Hello, Bruce,
Thanks for your reply. I still have two questions,
1. Does these gca files also include 9 arrays such as those template files
saved into .tiff file.
Is there any place in the WIKI explain the format of the gca files?
What is the difference between gca#0 and gca#1?
2. I tried th
I have managed to use the mri_extract_label to pull individual ROI's
from the wmparc.mgz file and it works perfectly for my need. I'm
wondering if it is possible to script this command to create individual
ROI images for all non-zero regions in one step? Essentially I would
like to be able to
Hi Guang,
it should be:
mri_convert atlas.gca#0 means.mgz
mri_convert atlas.gca#1 labels.mgz
mri_convert atlas.gca#2 priors.mgz
cheers,
Bruce
p.s. sorry, I don't think the gca format is documented anywhere, but you
are welcome to the code if you want
On Thu, 28 Jan 2010, Guang Zeng wrote:
>
Hi Ben,
I would do it in matlab I guess, although mri_extract_label will take
multiple labels on the commandline and extract each one of them.
cheers
Bruce
On Thu, 28
Jan 2010, Pruce, Benjamin wrote:
> I have managed to use the mri_extract_label to pull individual ROI's
> from the wmparc.mgz
You could also run mri_segstats on the wmparc to generate a stats file
(use --non-empty). This lists all the non-empty segments it find. If you
pass it the FreeSurferLUT.txt as the ctab, then it lists the names as
well as the index number. You could then write a script to loop through
the indic
Hello, Bruce,
Thanks a lot for your quick reply?
Could I ask what is the difference between labels.mgz and priors.mgz (or
atlas.gca#1 and atlas.gca#2).
I load both of them in tkmedit, move the mouse in the image, they all gave me
the same value.
Thanks!
Guang
> Date: Thu, 28 Jan 2010 16:51:5
really? Hmmm, that sounds like a bug. It should be:
labels --> indices of the most likely label at each voxel
priors --> the probability that that label occurs at that voxel
means --> the mean intensity of the most likely label
you can also use -nth $frame instead of #$frame
On Thu, 28
Jan
20
there's a wiki page with a bit of info, including the gca.c/h files:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GcaFormat
On Thu, 2010-01-28 at 17:09 -0500, Bruce Fischl wrote:
> really? Hmmm, that sounds like a bug. It should be:
>
> labels --> indices of the most likely label at eac
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