sorry, I think this may be a question for the SUMA people - I don't know
what .dset format is. Are you going to do the masking within SUMA? I'll cc
Ziad so he can chime in.
cheers
Bruce
On Tue, 5 May 2015, Francesca Strappini wrote:
I'm trying to mask a time series dataset that I mapped to the surface in
SUMA (surface created with freesurfer and imported into SUMA). I think the
input should be in the .dset fomat (region mapped to the surface). The
problem is that when I save my label the annotation file has only a list of
vertexes related to the region and not all the surface vertexes.
Thanks for the help!
Francesca
2015-05-05 23:04 GMT+02:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>:
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
>
>
>
_______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
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.
--
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.
--
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.
--
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.
