Dear Antonin,
I believe I figured out what I was doing wrong! I forgot to correct the voxel volumes with the intracranial volumes. After the correction I'm getting the expected values. I was referring to the -cw256 flag and i will check if the T2 is correctly registered to T1 Thanks again!
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 14:12 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] Overestimation of volume in Hippocampus
Dear Michel,
not sure if I understand. Do you mean that you cropped your T2 to FOV 256 mm ?
I think that this should have no effect until you cropped parts of the brain.
Maybe, as a part of quality-check you can check whether your T2 is correctly registered to T1 by inspection
T1_to_<analysisID>.v10.QC.gif
as stated in https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
Antonin
Dear Antonin,
Thank you for the assistance! I really appreciate it. My final goal is to determine the volume of the dentate gyrus however I first wanted to establish if the volume of the whole hippocampus was within expected boundaries before moving on to the dentate gyrus. Do you perhaps know if forcing the field of view to 256 would affect the segmentation because the T2 scans have a FOV of 320?
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 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...http://www.nmr.mgh.harvard.edu/%7Eiglesias/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.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
HippocampalSubfields - Free Surfer Wikihttps://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields surfer.nmr.mgh.harvard.edu Segmentation of hippocampal subfields. This functionality is present in the Development Version of FreeSurfer and will be included in the FreeSurfer 6.0 release
SubmillimeterRecon - Free Surfer Wikihttp://freesurfer.net/fswiki/SubmillimeterRecon freesurfer.net Recon with native submillimeter resolution. See also HighFieldRecon. This page describes how to run the FreeSurfer recon-all for data with voxel sizes less than 1mm3 ...