Re: [Freesurfer] ?Sequence for Hippo_subfields

2014-06-12 Thread Kev 
Much appreciated Eugenio.

I had read a paper where authors report using a ultra high field scanner (7T - 
Cho Z-H, et al. J Psychiatr Res 2010; 44: 881–886), and I notice the reference 
you kindly provided uses a 4T scanner...

I presume using a 3T might be stretching things a bit, and I wonder whether 
future FS releases using T2-weighted images will accept 3T scans?

Best regards and thanks again for great support you guys provide,

Kev


On Jun 12, 2014, at 3:49 AM, Eugenio Iglesias wrote:

 Dear Kev,
 for the subfields, people have been acquiring T2 scans with high in-plane 
 (coronal) resolution like the ones in this paper:
 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820772/
 The subfield atlas in FreeSurfer cannot handle such scans, but we will 
 (hopefully soon) release a version that can.
 Kind regards,
 /Eugenio
 
 Juan Eugenio Iglesias
 Postdoctoral researcher BCBL
 www.jeiglesias.com
 www.bcbl.eu
 
 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
 
 
 - Original Message -
 From: Kev schumm...@gmail.com
 To: Freesurfer support list Freesurfer@nmr.mgh.harvard.edu
 Sent: Wednesday, June 11, 2014 8:32:33 PM
 Subject: [Freesurfer] ?Sequence for Hippo_subfields
 
 Dear FS experts,
 
 I'm in the designing stage of a neuroimaging project on a 3T scanner, and I'm 
 interested in looking at structural information on hippocampus (including 
 subfields).
 
 In addition to the MPRAGE or IR-SPGR, is it worth running a specific 
 acquisition sequence geared to get the most out of all the hippocampus 
 structural measures? 
 
 Thanks and regards,
 
 Kev
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[Freesurfer] ?Sequence for Hippo_subfields

2014-06-11 Thread Kev 
Dear FS experts,

I'm in the designing stage of a neuroimaging project on a 3T scanner, and I'm 
interested in looking at structural information on hippocampus (including 
subfields).

In addition to the MPRAGE or IR-SPGR, is it worth running a specific 
acquisition sequence geared to get the most out of all the hippocampus 
structural measures? 

Thanks and regards,

Kev
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] ?need to edit pial surf in med temp lobe

2014-06-05 Thread Kev 
Thanks!
The aseg tells me it is hippocampus; so just to be sure, when you say freeze 
you mean that this hippocampus is NOT going to be computed as cortical 
thickness?
Cheers,
Kev


On Jun 5, 2014, at 4:07 PM, Bruce Fischl wrote:

 Hi Kev
 
 I'm not sure from the snapshots, but it looks like the region you are 
 talking about is non-cortical. Check the aseg and see what the labels are 
 adjacent to the white/pial surface there. It looks like it is part of the 
 surface that we freeze because it is not cortex.
 
 cheers
 Bruce
 On Thu, 5 Jun 2014, Kev 
 wrote:
 
 Dear freesurfers,
 
 Basic question that arose when reviewing the attached screenshots (salmon 
 rectangles: axial and coronal view of same location).
 
 How much editing would require this subject in terms on pial surface?
 
 Is the highlighted area computed in lobar cortical thickness?
 
 Thanks and regards,
 
 Kev
 
 
 
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