Hi Markus
I'mm not very familiar with the labels extraction , I can just answer
you in anatomical terms ; the anatomical labelling sounds correct to me.
Soory not to be more helpfull
cheers
Hi
for the purpose of illustration I change to
3136 wm-lh-G_temp_sup-Planum_tempolare
The corresponding gray matter part (1136) can seen in cortex.tiff. It is
labeled green and can be found quite in the middle of the picture right from
the red labeled S_temporal_transverse. The successful extraction of the 1136
ctx-lh-G_temp_sup-Planum_tempolare is shown in success.png.
The corresponding white matter of this landmark (3136
wm-lh-G_temp_sup-Planum_tempolare) can also be seen on the right side of
WM.tiff as a green labeled area superior of the pink labeled lateral aspect
of G_temp_sup. (the 3181 wm-lh-S_temporal_transverse is also present as a
very very small red labeled area between the small blue and green areas in
the middle of WM.tiff).
I am not able to extract 3136 and I think this seems to hold also for the
other 3XXX or 4XXX wm-labels from aparc.a2005s+aseg.mgz.
I extracted 2034 ctx-rh-transversetemporal from "aparc+aseg.mgz" and analog
4034 wm-lh-transversetemporal from "wmparc.mgz". I assumed that there must
be a corresponding file of "aparc.a2005s+aseg.mgz" like
"wmparc.a2005s+aseg.mgz" to extract white matter labels.
"aparc.a2005s+aseg.mgz" seems to work only for ctx- but not for wm-labels,
and I don't found something else. The problem is not subject-related.
Regards,
Markus
-----Ursprüngliche Nachricht-----
Von: Christophe Destrieux [mailto:[EMAIL PROTECTED]
Gesendet: Mittwoch, 10. Dezember 2008 14:24
An: Bruce Fischl
Cc: Markus Röhl; freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] mri_extract_label 4181
Hi Bruce and Markus
S_temporal_transverse is constant and should be present on the surface ;
cheers
HI Markus,
that's one of Christophe's labels, so would only be in the
aparc.a2005s+aseg.mgz. Have you cheched the aparc.a2005s.annot on the
surface to verify that it is present there? There are also some labels
that don't appear on every subject, Christophe would know if this is
one of them.
cheers,
Bruce
On Wed, 10 Dec 2008, Markus Röhl wrote:
Dear all,
I used mri_extract_label recently to get NIfTI -binary maps for certain
anatomical landmarks, e.g. the Gyrus temporalis inferior of the left
hemisphere (cortex) which index is listed in FreeSurferColotLUT.txt:
mri_extract_label $FREESURFER_HOME/subjects/VP1/mri/aparc+aseg.mgz 1009
$FREESURFER_HOME/subjects/ROI/VP1/CL_IT.nii.gz
This works fine. Now I want to extract the labels of anatomical
landmarks
like
4181 wm-rh-S_temporal_transverse
I tried every segmentation file I found (aparc+aseg.mgz, wmparc.mgz,
aparc.a2005s+aseg.mgz), but only ended up with empty maps. Where I
can find
or how can I create the necessary segmentation volume?
Regards,
Markus
--
Christophe Destrieux
Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé
37032 Tours - France
tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07
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