Van: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> namens Antonin Skoch <ansk@ikem.cz>
Verzonden: maandag 27 februari 2017 13:27
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] Overestimation of volume in Hippocampus

Dear Michel,

by default in the recon-all the input images are resampled to 1x1x1mm3. To disable this and retain your resolution, you have to add -hires flag (and adapt the mris_inflate -n parameter).

This could improve the segmentation results, however I would not expect that it is the reason of volume overestimation you are refering to. I am not expert at hippocampal anatomy, therefore I cannot comment on your results.

But I am guessing, maybe the hippocampal atlas in FreeSurfer includes some portions which have not been included in the MCI studies you refer to? Maybe you can find answer in the Hippocampal subfields paper:

http://www.nmr.mgh.harvard.edu/~iglesias/pdf/subfieldsNeuroimage2015preprint.pdf

Antonin

Dear Antonin,

I did use the T2 scan for the T2pial refinement during the recon-all however I 
actually already preformed the hippocampal subfields and when i looked at the 
txt file generated from that the results are quite similar.
I used the multispectral segmentation.
I didn't not use the -hires flag but what does this flag exactly do if i may 
ask?

Sincerely,

Michel Hu


________________________________
Van: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> namens Antonin Skoch <a...@ikem.cz>
Verzonden: maandag 27 februari 2017 12:31
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] Overestimation of volume in Hippocampus


Dear Michel,

Given your resolution 0.8x0.8x0.8, did you run recon-all with -hires flag? What 
did you used T2 image for? As a -T2pial refinement? T2 image is not used for 
hippocampal segmentation in standard recon-all stream.
But pay attention that with -hires you also have to alter default value for 
mris_inflate, as specified here
http://freesurfer.net/fswiki/SubmillimeterRecon
In my case -n was not enough, I would recommend -n 50 (more does not do any 
harm).

In any case, I would recommend to try hippocampal subfields module.

https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

This should be more precise than "standard" aseg segmentation and given you 
have also 3D T2, multispectral T1 and T2 segmentation can be used.

Antonin Skoch


Dear Shane,

I have checked the aseg.mgz and in only one I would say the segmentation failed
however the others look fine and I'm taking the measurements from the text file
that is generated from the aseg.stats.
Should I redo the recon-all with a different input? I have always given
freesurfer T1 and a T2 scan to process  both having a resolution of 0.8x0.8x0.8
mm.

Sincerely,
Michel Hu


________________________________
Van: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> namens Shane S
<shane.schofi...@yahoo.com>
Verzonden: maandag 27 februari 2017 11:15
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] Overestimation of volume in Hippocampus

Hi Michel Hu,

Yes, that’s too large for MCI or even controls for that matter I think. Have
you checked the aseg.mgz? I generally find that the hippocampus is well
segmented, even in patients with a lot of atrophy.

Are you taking the measurements with the asegstats2table?

Sincerely,

--
Shane S


On 27 February 2017 at 10:12:09, Michel Hu (a...@live.nl<mailto:a...@live.nl>)
wrote:

Dear Shane,

I apologize for not being clear. The reported value is of only one half of the
hippocampus.
I have only run 4 subjects of the 75 however they all have a reported value of
between 6000 to 10000 mm^3 summed together for the hippocampus.

Sincerely,
Michel Hu


________________________________
Van: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> namens Shane S
<shane.schofi...@yahoo.com>
Verzonden: maandag 27 februari 2017 11:00
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] Overestimation of volume in Hippocampus

Hi Michel Hu,

Is that a summed value of left and right hippocampus? That seems normal to me
since averaged total hippocamppal volumes for MCI have been typically reported
at around 2500-3500mm3.

Thanks,
--
Shane S


On 27 February 2017 at 09:44:27, Michel Hu (a...@live.nl<mailto:a...@live.nl>)
wrote:

Dear Freesurfer experts,

I have run several subjects through the recon-all pipeline including the
hippocampal segmentation with freesurfer 6.0 on Ubuntu 16.04. However when
looking at the text file with the volumes it seems that all the numbers are
bigger than normal as all my subjects have MCI and freesurfer reports them
having all over 5000 mm^3. I was wondering if the problem could lie somewhere
in the recon-all process?
Thank you for your time

Sincerely,
Michel Hu