you can just create a label file I guess. What input does SUMA take?
On Tue,
5 May 2015, Francesca Strappini wrote:
Sorry, just to be clear, I meant how can I create a mask on the surface in
which at each vertex is assigned a value, 0 or 1.
I need to create this mask for exporting the freesurfer labels into SUMA and
ultimately to extract the time series from each vertex.
Thanks
Francesca
2015-05-05 16:06 GMT+03:00 Francesca Strappini
<francescastrapp...@gmail.com>:
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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The information in this e-mail is intended only for the person
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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
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
--
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
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
dispose of the e-mail.
