what are you trying to mask?
On Tue, 5 May 2015, Francesca Strappini wrote:
Thank you! Do you know which function should I use?
Best
Francesca
2015-05-05 15:30 GMT+03:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>:
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
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il
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HelpLine at
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in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.
--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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