External Email - Use Caution
Thanks Eugenio,
I'll do that.
Much appreciated.
best regards
Erik
Postdoctoral Research Fellow
Dept. Of Psychiatry
Royal College of Surgeons in Ireland
ERC Building
Beaumont Hospital
Dublin
&
Dept. Of Psychiatry
Trinity College Institute of Neuroscience
The Llyod Institute
Trinity College Dublin
D2
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez,
Eugenio <e.igles...@ucl.ac.uk>
Sent: 16 November 2018 15:45:27
To: Freesurfer support list
Subject: Re: [Freesurfer] loading and rendering the Amygdala nuclei only in
Freeview
External Email - Use Caution
Hi Erik,
If you render labels >7000, you shouldn’t see a rendering of the subfields –
but they will indeed remain visible in the orthogonal views. If you want to get
rid of them, you can use mri_threshold:
mri_threshold
lh.hippoAmygLabels-T1-HippoAMYT1andT2FLAIR.v20.FS60.FSvoxelSpace.mgz 6999
onlyAmyg.mgz
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London, and
Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology
http://www.jeiglesias.com
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Erik O'Hanlon
<erikohan...@rcsi.ie>
Erik O'Hanlon
Postdoctoral researcher
[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]
RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont D9 Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/>
Transforming Healthcare Education, Research and Service: RCSI Strategic Plan
2018-2022<http://www.rcsi.ie/strategy2018>
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Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, 16 November 2018 at 08:15
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] loading and rendering the Amygdala nuclei only in Freeview
External Email - Use Caution
Hi FS Experts,
I'm trying to make some images of my amygdala nuclei in freeview and selected
my T1 as background and then loaded up
lh.hippoAmygLabels-T1-HippoAMYT1andT2FLAIR.v20.FS60.FSvoxelSpace.mgz image
which loads up perfectly. I selected the "show existing labels " and the
freesurfer colour LUT but when I select the range for 7001-7015 for amygdala
only, the hippocampal subfields are still there. Is there a way to only load
the amygdala nuclei. I'm sure it's something simple I'm just not doing, but I
can't seem to get it to work.
Any pointers gladly accepted
Thanks
Erik
Erik O'Hanlon
Postdoctoral researcher
[cid:image001.png@01D47D99.7BDC9930]
RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont D9 Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/>
RCSI Homepage - Royal College of Surgeons in Ireland<http://www.rcsi.com/>
www.rcsi.com
RCSI provides extensive education and training in the healthcare professions at
undergraduate and postgraduate level. Learn about our undergraduate courses in
medicine, pharmacy and physiotherapy, our surgical training and our range of
postgraduate opportunities.
Transforming Healthcare Education, Research and Service: RCSI Strategic Plan
2018-2022<http://www.rcsi.ie/strategy2018>
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