My name is Flavio, student at Universidade Federal Fluminense. I research image segmentation methods applied to brain cortical structures segmentation.
I've compared against the hippocampal region got from FIRST-FSL to Freesurfer, using the same magnetic resonance (MR) image.
The FSL is a neuroimage analysis tool developed by FMRI group from Oxford. I found out a great volume difference between segmentations. Despite different automated image analysis tool, I was expecting a higher volume overlap index when comparing the same brain structure from the same MR image. I got about 25% volume overlap.
Is there any "recon-all" flag that I can use in conjunction with entire process so as to get better volume overlap? I would appreciate any suggestion.
Thank you in advance,
Flavio.
Hi Flavio,
25% is pretty low. Can you send us an example image of our segmentation?
cheers, Bruce On Mon, 8 Jun 2009, Flavio Seixas wrote:
My name is Flavio, student at Universidade Federal Fluminense. I research image segmentation methods applied to brain cortical structures segmentation.
I've compared against the hippocampal region got from FIRST-FSL to Freesurfer, using the same magnetic resonance (MR) image.
The FSL is a neuroimage analysis tool developed by FMRI group from Oxford. I found out a great volume difference between segmentations. Despite different automated image analysis tool, I was expecting a higher volume overlap index when comparing the same brain structure from the same MR image. I got about 25% volume overlap.
Is there any "recon-all" flag that I can use in conjunction with entire process so as to get better volume overlap? I would appreciate any suggestion.
Thank you in advance,
Flavio.
I think FreeSurfer has more reliability. In houndreds of manually segmented hippocampi we found FreeSurfer measures to be pretty stable.
the manually segmented hippocampi usually has 15% - 20% less volume. However we still don't know which method is more accurate. There's a study right now in USP to try to figure it out using the removed hippocampi.
If you need a local help (I mean in Brazil) you can write to my e-mail
2009/6/8, Flavio Seixas flseixas@yahoo.com.br:
My name is Flavio, student at Universidade Federal Fluminense. I research image segmentation methods applied to brain cortical structures segmentation.
I've compared against the hippocampal region got from FIRST-FSL to Freesurfer, using the same magnetic resonance (MR) image.
The FSL is a neuroimage analysis tool developed by FMRI group from Oxford. I found out a great volume difference between segmentations. Despite different automated image analysis tool, I was expecting a higher volume overlap index when comparing the same brain structure from the same MR image. I got about 25% volume overlap.
Is there any "recon-all" flag that I can use in conjunction with entire process so as to get better volume overlap? I would appreciate any suggestion.
Thank you in advance,
Flavio.
you also have to be careful of differences in definition (e.g. is the fimbria part of the hippocampus?)
cheers, Bruce On Mon, 8 Jun 2009, Pedro Paulo de Magalhães Oliveira Junior wrote:
I think FreeSurfer has more reliability. In houndreds of manually segmented hippocampi we found FreeSurfer measures to be pretty stable.
the manually segmented hippocampi usually has 15% - 20% less volume. However we still don't know which method is more accurate. There's a study right now in USP to try to figure it out using the removed hippocampi.
If you need a local help (I mean in Brazil) you can write to my e-mail
2009/6/8, Flavio Seixas flseixas@yahoo.com.br:
My name is Flavio, student at Universidade Federal Fluminense. I research image segmentation methods applied to brain cortical structures segmentation.
I've compared against the hippocampal region got from FIRST-FSL to Freesurfer, using the same magnetic resonance (MR) image.
The FSL is a neuroimage analysis tool developed by FMRI group from Oxford. I found out a great volume difference between segmentations. Despite different automated image analysis tool, I was expecting a higher volume overlap index when comparing the same brain structure from the same MR image. I got about 25% volume overlap.
Is there any "recon-all" flag that I can use in conjunction with entire process so as to get better volume overlap? I would appreciate any suggestion.
Thank you in advance,
Flavio.
also of note, there are three recent papers comparing manual hippocampal tracing to freesurfer automated segments...
Shen L, Firpi HA, Saykin AJ, West JD. (2009). Parametric surface modeling and registration for comparison of manual and automated segmentation of the hippocampus. Hippocampus. Jun;19(6):588-95.
Cherbuin N, Anstey KJ, Réglade-Meslin C, Sachdev PS. (2009). In vivo hippocampal measurement and memory: a comparison of manual tracing and automated segmentation in a large community-based sample. PLoS ONE. 4(4):e5265. Epub 2009 Apr 16.
Morey RA, Petty CM, Xu Y, Hayes JP, Wagner HR 2nd, Lewis DV, LaBar KS, Styner M, McCarthy G. (2009). A comparison of automated segmentation and manual tracing for quantifying hippocampal and amygdala volumes. Neuroimage. 2009 Apr 15;45(3):855-66. Epub 2008 Dec 30. ***This paper looked at Freesurfer, FSL's FAST, and manual tracings...
Best, jamie.
I think FreeSurfer has more reliability. In houndreds of manually segmented hippocampi we found FreeSurfer measures to be pretty stable.
the manually segmented hippocampi usually has 15% - 20% less volume. However we still don't know which method is more accurate. There's a study right now in USP to try to figure it out using the removed hippocampi.
If you need a local help (I mean in Brazil) you can write to my e-mail
2009/6/8, Flavio Seixas flseixas@yahoo.com.br:
My name is Flavio, student at Universidade Federal Fluminense. I research image segmentation methods applied to brain cortical structures segmentation.
I've compared against the hippocampal region got from FIRST-FSL to Freesurfer, using the same magnetic resonance (MR) image.
The FSL is a neuroimage analysis tool developed by FMRI group from Oxford. I found out a great volume difference between segmentations. Despite different automated image analysis tool, I was expecting a higher volume overlap index when comparing the same brain structure from the same MR image. I got about 25% volume overlap.
Is there any "recon-all" flag that I can use in conjunction with entire process so as to get better volume overlap? I would appreciate any suggestion.
Thank you in advance,
Flavio.
-- Enviado do meu celular
Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Bruce Fischl -
Flavio Seixas -
Jamie Hanson -
Pedro Paulo de Magalhães Oliveira Junior