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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio e.iglesias@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

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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-bounces@nmr.mgh.harvard.edu on behalf of Erik O'Hanlon erikohanlon@rcsi.ie

Erik O'Hanlon Postdoctoral researcher

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RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022http://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

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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

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RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/

RCSI Homepage - Royal College of Surgeons in Irelandhttp://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 2018-2022http://www.rcsi.ie/strategy2018

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