External Email - Use Caution        

Hi Iglesias,

I would like to learn the  two ways for estimating volumes mentioned in
another post, see below. Please send me the codes in Freesurfer to do this.

Thank you,

Kate


---------- Forwarded message ---------
From: Iglesias Gonzalez, Juan E. <jiglesiasgonza...@mgh.harvard.edu>
Date: Wed, Apr 8, 2020, 10:43 AM
Subject: Re: [Freesurfer] Hippocampal subfields
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>


Dear Ioana,

This is tricky because the volumes are computed from soft segmentations,
which are not the ones you’re editing. In general, editing outputs is a bad
idea; it may be better to simply discard the cases for which quality
control fails.

Having said that: if you want to use corrected cases, you could compute
volumes by simply summing the number of voxels with each label, and
multiplying by the volume of a voxel (which is 1/27=0.03703703703 cubic
mm). But if you do this, then you need to compute the volume this way for
all cases, including the ones you didn’t edit (you don’t want to mix 2 ways
of estimating volumes).

Cheers,

/Eugenio





Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com







*From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of ioana cracana
<iioana.crac...@gmail.com>
*Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Date: *Wednesday, April 8, 2020 at 04:59
*To: *"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
*Subject: *[Freesurfer] Hippocampal subfields



*        External Email - Use Caution        *

Hello,

I'm doing a study about hippocampal atrophy and I'm using the Segmentation
of Hippocampal subfields tool. There were some minor errors and I edited
them using Freeview, voxel edit tool.  I would like to generate a new
[lr]h.hippoSfVolumes-T1.v10.txt
file using the edited [lr]h.hippoSfLabels-T1.v10.mgz in order to see the
new results. What command do i have to use? Is there another way to edit
the hippocampal subfields?And how do i see the results?

I'm using Freesurfer v6.0.0. on macOS Mojave.



Thanks,

Ioana
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