yes, you can use a label for this (we use the ?h.cortex.label for this
purpose routinely to remove non-cortical stuff)
On Tue, 5 May 2015,
Francesca Strappini wrote:
Thank you so much! I understand what's the problem and I will make my custom
ctab file.
Last question, about the annot files, is it possible with freesurfer to
create a mask with the annot or the label files in which the value 1 is
assigned to the region and 0 to the rest of the brain?
Thanks again!
Best
Francesca
2015-05-05 4:20 GMT+03:00 Nick Schmansky, MGH <ni...@nmr.mgh.harvard.edu>:
Francesca,
I looked at the files you sent and replicated the problem. It
is due to
creating your lh.EKppa.annot file using FreeSurferColorLUT.txt
as the
colortable file. You should create your own colortable file,
which is
simple to do, and create a new .annot file using that colortable
(ie,
the --ctab option in mris_label2annot).
Here is a simple colortable.txt file (just a text file) with
four
entries, which in this example, means that you have three
annotations.
The first entry must be as it is shown, ie, 'unknown', as this
is used
to automatically 'label' all the vertices which do not have a
.label
file.
0 unknown 25 5 25 0
1 mylabel1 0 92 23 0
2 mylabel2 131 148 255 0
3 mylabel3 0 0 255 0
I fixed the code locally so that it doesn't segfault, and you
can get
the new mris_convert here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Lin
ux-centos6_x86_64-stable-pub-v5.3.0/bin/
but note this does not fix your core problem, it only allows
mris_convert to run to completion and create a valid .annot.gii
file.
It will still have strange label names for your annotations
(like
"Left_Hippocampus") taken from the embedded FreeSurferColorLUT.
Nick
On Thu, 2015-04-30 at 14:17 +0300, Francesca Strappini wrote:
> Hi, sorry to bother, I'm re-posting this question just in case
it got
> lost. Thanks.
>
> Hi,
>
> I have a question about mris_convert. I've created some
regions on the
> surface and now I would like to make them directly readable
into SUMA. I
> ran this command but it ended with an error message.
> mris_convert --annot lh.EKppa.annot
> /usr/local/freesurfer/subjects/EK/surf/lh.white
lh.EKppa.annot.gii
>
> reading colortable from annotation file...
> colortable with 14176 entries read (originally
> /usr/local/freesurfer/FreeSurferColorLUT.txt)
> Segmentation fault (core dumped)
>
> I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
running on
> Ubuntu 14.04.2 LTS.
>
> Thanks in advance for the help!
>
> Best
> Francesca
>
>
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--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
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E-mail: francesca.strapp...@weizmann.ac.il
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