Hi Ziad, yes, it's related to that. Thank you for the help!
Best
Francesca
2015-05-06 16:25 GMT+03:00 Ziad Saad sa...@mail.nih.gov:
Hello folks,
I am ccing all those on the thread because I am not sure my reply to the
support list will get through.
GIFTI is the way to go as Matt suggested
Hi Matt, I can answer only partially to your question. SUMA/afni in
general supports GIFTI format but I don't know if is it possible to
directly convert from GIFTI to .dset.
Usually I convert my annot file to .niml.roi with FSread_annot and
.niml.roi to .1D.dset with ROI2dataset.
Best
Francesca
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,
Does SUMA support GIFTI and provide a utility to convert between its
formats and GIFTI? I was also wondering what a .dset was and how to get
it into GIFTI so it could be easily used across software platforms.
Thanks,
Matt.
On 5/5/15, 5:30 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
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
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
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
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
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
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,
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.
Francesca,
How was lh.EKppa.annot created? Is it a custom list of annotations?
Does it include an embedded colortable appropriate for those
annotations?
Can you send me the files 'lh.EKppa.annot' and 'lh.white'? I can try to
replicate the problem.
Also, can you run this:
mris_info
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