Hi Darren,
I just found out that when you save a label in tksurfer, it saves it
using the orig surface coords, which explains the discrepancy. Try
running label2label with --trgsurf orig. Alternatively, you can save
your label in the white surface if you start up tksurfer with -orig
white
doug
Darren Weber wrote:
This is an example of diff output for the test without the --trgsurf option:
endorphin.14> diff --side-by-side DLWeber_rh_ACC.label
DLWeber_surface_rh_ACC.label | head -
#!ascii label , from subject ucsf_wa #!ascii
label , from subject ucsf_wa
660 660
106091 3.122 21.824 57.650 0.000000 | 106091
2.037 22.222 57.359 0.000000
106981 7.056 22.926 59.092 0.000000 | 106981
7.114 22.942 59.024 0.000000
106982 6.147 22.676 59.500 0.000000 | 106982
6.137 22.636 59.159 0.000000
106983 5.178 22.521 58.995 0.000000 | 106983
4.816 22.583 58.765 0.000000
106984 4.149 22.523 58.728 0.000000 | 106984
3.440 22.988 58.509 0.000000
106985 3.138 22.925 58.465 0.000000 | 106985
2.206 23.278 58.150 0.000000
106991 7.153 22.847 58.153 0.000000 | 106991
7.272 22.963 58.219 0.000000
106992 6.603 22.649 58.357 0.000000 | 106992
6.639 22.730 58.329 0.000000
Are these values just from different layers in the rh.<surf> data?
Thanks, Darren
Doug Greve wrote:
I think it should be the same. When the source and target subjs are
the same, there should not be any resampling.
On Tue, 11 Jul 2006, Bruce Fischl wrote:
It probably won't be the same as a cp in any case, as you will go
through some resampling steps.
cheers,
Bruce
On Tue, 11 Jul 2006, Doug Greve wrote:
The label coords as created by tksurfer should be that of the white
surface, so you're really just changing the coords from that of white
to that of pial. Can you try removing --trgsurf pial from your cmd
and see if the labels are the same?
doug
Darren Weber wrote:
Dear Doug et al.,
I'm trying to test mri_label2label because we've observed some strange
results in the download for:
freesurfer-Linux-rh9-stable-pub-v3.0.2
To test the program, I thought it would be sensible to map a label of
one subject onto itself, with a different label filename for the
output.
So I created a large label in a subject rh inflated surface and
saved it
to X.label file. I then tried to run mri_label2label using the same
srcsubject and target subject, with a different name for the target
label, ie:
mri_label2label \
--srclabel $SUBJECTS_DIR/${srcsubject}/label/$label \
--trglabel $SUBJECTS_DIR/${srcsubject}/label/$newlabel \
--srcsubject ${srcsubject} \
--trgsubject ${srcsubject} \
--regmethod surface --hemi $hemi --trgsurf pial
In effect, this should be equivalent to:
cd $SUBJECTS_DIR/${srcsubject}/label/
cp $label $newlabel
That is, the label mapping onto the same subject surface should be
identical. It is not. Can you please try to replicate this result? I
would like to know if it is particular to the setup here. If you
find a
bug in mri_label2label, please forward a fix ASAP, as we are trying to
complete some analysis that depends on mapping labels across subjects.
Thanks, Darren
--
Darren L. Weber, Ph.D.
Postdoctoral Scholar
Dynamic Neuroimaging Laboratory,
UCSF Department of Radiology,
185 Berry Street, Suite 350, Box 0946,
San Francisco, CA 94107, USA.
Tel: +1 415 353-9444
Fax: +1 415 353-9421
www: http://dnl.ucsf.edu/users/dweber
"To explicate the uses of the brain seems as difficult
a task as to paint the soul, of which it is commonly
said, that it understands all things but itself."
Thomas Willis (The Anatomy of the Brain and Nerves, 1664)
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
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In order to help us help you, please follow the steps in:
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