Hi Doug,
I tried the tkmedit command and it loaded the volume with the mask, although I
got a message saying:
Error: Parsing command line options
Option -reg not recognized
This option was not recognized and ignored.
Not sure why this occurred, as I loaded it from scratch through the GUI (File
The first thing that you should do is load your mask as an overlay in
tkmedit to make sure that it is actually falling where you think it
is:
tkmedit yoursubject orig -overlay ./mask.img -reg ./register.dat \
-fthresh 0.5
The fthresh is set assuming your mask is 0 or 1. You can even load
the
Sorry, I forgot to mention, I have the mask in analyze format (I traced it in
another program). I ran mri_vol2surf using the register.dat file format that
Doug provided, and got the output below. Although it creates a .w file, nothing
happens when I load it in tksurfer, I'm gessing because the v
Hi Alex,
I think you can just load the label into tksurfer (file->label->load) and
it will sample it onto the surface, assuming that it was drawn on one of
the volumes that the surface was created from (or a coregistered one).
The 1st time you do this it may take a bit, but if you save it agai
It needs a registration matrix that goes from the volume to the surface
space (defined by the orig volume). If you traced your mask on the orig
volume (or something derived from it), then you can create an identity
matrix:
---cut here
yoursubjectname
1
1
1
1 0 0 0
0
Hi,
I'm trying apply ROI masks that I've manually traced in volume space to the
same image's surface using mri_vol2surf. mri_vol2surf seems to requires a
register.dat file, and I'm unsure what needs to be registered, since the volume
that I traced the masks on is exactly the same as the one that
Hello, everybody.
In 2004 FreeSurfer course lecture slides by D Salat, B Fischl
and D Greve there are a couple
of slides I am curious about. These are slides # 65 and #66
named correspondingly
“Thickness maps” and “Thinning from young
to old age”.
Have those images been produced by F
it depends on what kind of labels you want. You can fill activated regions
or just draw them on the surface in tksurfer
On Thu, 30 Jun 2005, Kirk, Gregory wrote:
A while ago Dr. Fischl sent me -
use mris_anotomical_stats -l to get
stats for a region. I have not found how to create
these lab
Title: generate label files
A while ago Dr. Fischl sent me -
use mris_anotomical_stats -l to get
stats for a region. I have not found how to create
these label files. Can somebody give me a starting
hint.
Thankx
Greg.
___
Freesurfer
can you send the exact screen output (with your command)?
On Thu, 30 Jun 2005, David Soscia wrote:
Hey guys,
After some help from Andy Bell, I was able to get one of my images
converted from .dcm format, up and running with the program. For some
reason now, I keep getting the same error messa
Hey guys,
After some help from Andy Bell, I was able to get one of my images
converted from .dcm format, up and running with the program. For some
reason now, I keep getting the same error message when trying to convert
some other files (in a different location to COR format). It keeps
saying "u
Hi,
I encounter the error in processing one of my MPRAGE brain image.
MRInormalize: could not find any valid peaks
I found the previous post suggesting to add the -no1d option, but it
doesn't work, the same error message.
I use the 2004 snapshot version on Fedora Core 3, getting success
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