that is certainly wrong. What does it look like on the surface? You can
upload the subject if you want and we will take a look
On Mon, 28 Sep 2015,
Jacobs H (NP) wrote:
Dear Doug,
By looking at it in Freeview. Anatomically, I would expect that the entorhinal
cortex would not be localized so laterally? And some voxels are not in the
temporal lobe.
Best
Heidi
________________________________________
Van: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Verzonden: maandag 28 september 2015 23:00
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] warping surface label to volume space
how are you determining that it is not in the right place? When I run
this it works.
On 09/28/2015 04:54 PM, Jacobs H (NP) wrote:
Hi,
Bringing this to the FS list:
I am trying to warp the entorhinal cortex label (ex vivo) to volume
space, so that I can see and use the full ROI. Using the command
stated below doesn’t seem to work, as it is not in the right location
of the subject’s brain. Any thoughts?
I used this command:
mri_label2vol --label S_3RSPPP/label/lh.entorhinal_exvivo.label
--regheader $SUBJECTS_DIR/S_3RSPPP/mri/orig.mgz --o
lh.entorhinal_exvivo_vol.mgz --fill-ribbon --subject S_3RSPPP --hemi l
This was the output on the terminal:
subject S_3RSPPP --hemi lh
INFO: subject not needed, igorning.
Number of labels: 1
S_3RSPPP/label/lh.entorhinal_exvivo.label
Annot File: (null)
Template Volume: (null)
Outut Volume: lh.entorhinal_exvivo_vol.mgz
Registration File: (null)
Fill Threshold: 0
Label Vox Vol: 1
ProjType: (null)
ProjTypeId: 0
ProjStart: 0
ProjStop: 0
ProjDelta: 0.1
Subject: S_3RSPPP
Hemi: lh
UseNewASeg2Vol: 0
DoLabelStatVol 0
LabelCodeOffset 0
setenv SUBJECTS_DIR /autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS
$Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $
INFO: loading
surface
/autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/surf/lh.white
nvertices = 120130
Reading thickness
/autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/surf/lh.thickness
nlabels = 1
Loading
/autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/mri/ribbon.mgz
Loading S_3RSPPP/label/lh.entorhinal_exvivo.label
Mapping
Any suggestions how I can improve this?
Thanks
Heidi
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