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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu namens Antonin Skoch ansk@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.nlmailto: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.nlmailto: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