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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. JIGLESIASGONZALEZ@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)
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ioana cracana iioana.cracana@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
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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,
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