Hi, Bruce,
Do you mean that we can not use freesurfer for hippocampus volume segmentation,
if my data are with the same scanning parameters? We did statitical analysis
for volumes of other sub-cortical areas from freesurfer, found some interesting
results. If you said that the gray matter is too dark in our image, can we
still use it for other sub-cortical areas volume segmentation?
I will be appreciated for your answer.
With my best regards,
Aize
> Date: Mon, 17 Aug 2009 17:01:40 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: caoa...@hotmail.com
> CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] (no subject)
>
> Hi Aize,
>
> I think the hippocampal gray matter is so dark in your images that it is
> very difficult to distinguish from CSF. Do you have a lot of data collected
> with these parameters? If not, we probably could suggest some better ones.
>
> cheers,
> Bruce
>
> On Tue, 18 Aug 2009, caoaize
> wrote:
>
> >
> > Hello Bruce,
> >
> >
> >
> > The sequence we used is called Turbo field Echo, I need to check it again.
> >
> >
> >
> > I checked our scanning protocol, found that we did have marker on the
> > subjects' forehead. I generate the right hippocampus from freesurfer,
> > overlay with orig.nii (from orig.mgz), the overlay shows that the subject's
> > right side is the right side in freesurfer's statistical report. It means
> > that our left side is bigger than the right side. This result consitently
> > appears on our other subjects data.
> >
> >
> >
> > I extract the hippocampus left side mask in this way:
> >
> > mri_binarize --i aseg.mgz --match 17 --o hippo_left.nii
> >
> >
> >
> > The label for right side is 53. Anything wrong for what I used?
> >
> >
> >
> > Also, I used asegstats2table --subject s1 s2... --meas volume --tablefile
> > stats.txt to get the statistical report.
> >
> >
> >
> > If we accept the low corelation between manual and auto segmentation, how
> > can we explain that the left side is bigger than the right side?
> >
> >
> >
> > I hope your help. Thanks a lot.
> >
> >
> >
> > Best Regards,
> >
> >
> >
> > Aize
> >
> >> Date: Mon, 17 Aug 2009 13:51:26 -0400
> >> From: fis...@nmr.mgh.harvard.edu
> >> To: caoa...@hotmail.com
> >> Subject: RE: [Freesurfer] (no subject)
> >>
> >> wow, I don't think I've ever seen a T1-weighted MR with gray matter this
> >> dark. The gray/csf contrast is very low. What kind of sequence is it?
> >>
> >> On Tue, 18 Aug 2009, caoaize wrote:
> >>
> >>>
> >>> Hi, Bruce,
> >>>
> >>>
> >>>
> >>> Here is the aseg.mgz and norm.mgz files. Thanks.
> >>>
> >>>
> >>>
> >>> Aize
> >>>
> >>>> Date: Mon, 17 Aug 2009 13:27:07 -0400
> >>>> From: fis...@nmr.mgh.harvard.edu
> >>>> To: caoa...@hotmail.com
> >>>> Subject: RE: [Freesurfer] (no subject)
> >>>>
> >>>> Hi Aize,
> >>>>
> >>>> I need the aseg.mgz as well (and probably the norm.mgz). Differences in
> >>>> the definitions of what is hippocampus and what isn't will reduce the
> >>>> correlation coefficient. They should still be somewhat correlated, but
> >>>> even
> >>>> a perfect pair of segmentations under each protocol for each subject will
> >>>> not have a perfect correlation, so it's hard to assess what it means,
> >>>> since
> >>>> the protocols are different.
> >>>> Bruce
> >>>>
> >>>>
> >>>> On Tue, 18 Aug 2009, caoaize wrote:
> >>>>
> >>>>>
> >>>>> Our data is 3T, the manual segmentation follow the McConnell protocol
> >>>>> described in "Volumetry of hippocampus and amygdala with
> >>>>> high-resolution MRI and three-dimensional analysis software: minimizing
> >>>>> the discrpancies between laboratories". I do not know what is the
> >>>>> difference between yours and theirs. But, if both method are
> >>>>> consistant, then the correlation coeffienct should be high. Here is one
> >>>>> image that has bad segmention on happocampus.
> >>>>>
> >>>>>
> >>>>>
> >>>>> I am appreciate for your help.
> >>>>>
> >>>>>
> >>>>>
> >>>>> Aize
> >>>>>
> >>>>>
> >>>>>> Date: Mon, 17 Aug 2009 11:52:19 -0400
> >>>>>> From: fis...@nmr.mgh.harvard.edu
> >>>>>> To: caoa...@hotmail.com
> >>>>>> CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
> >>>>>> Subject: RE: [Freesurfer] (no subject)
> >>>>>>
> >>>>>> it lost interior voxels? That doesn't sound right. Can you send us an
> >>>>>> image? If your manual protocol is different than the one we used then
> >>>>>> the
> >>>>>> DICE overlap is somewhat irrelevant.
> >>>>>>
> >>>>>> cheers,
> >>>>>> Bruce
> >>>>>>
> >>>>>> On Mon, 17 Aug 2009, caoaize wrote:
> >>>>>>
> >>>>>>>
> >>>>>>> Hi, Bruce,
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> I am not clear what manual segmentation protocol we are using, it was
> >>>>>>> done by a trained RA. Currently we just calculate the volumes
> >>>>>>> correlation between manual segmentation and the auto one, but not
> >>>>>>> your DICE method. Our aquisitions are: Philips 3D sense, T1TFE, TR
> >>>>>>> 7.9ms.
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> In 27 subjects, we have two hippocampus volumes from Freesurfer auto
> >>>>>>> segmentation around 1700, it keeps the edge, but lost lots of inside
> >>>>>>> voxels. I am thinking to manual edit these two volumes, but do not
> >>>>>>> know what happened.
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> Aize
> >>>>>>>
> >>>>>>>> Date: Sat, 15 Aug 2009 09:14:30 -0400
> >>>>>>>> From: fis...@nmr.mgh.harvard.edu
> >>>>>>>> To: caoa...@hotmail.com
> >>>>>>>> CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
> >>>>>>>> Subject: RE: [Freesurfer] (no subject)
> >>>>>>>>
> >>>>>>>> Hi Aize,
> >>>>>>>>
> >>>>>>>> you are using the CMA manual segmentation protocol? We have not
> >>>>>>>> found a
> >>>>>>>> bias in volumes, and our DICE is usually close to .9 for hippocampus.
> >>>>>>>> What acquisitions are you using?
> >>>>>>>>
> >>>>>>>> cheers,
> >>>>>>>> Bruce
> >>>>>>>> On Sat, 15 Aug 2009, caoaize wrote:
> >>>>>>>>
> >>>>>>>>>
> >>>>>>>>> Hi, Bruce,
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> Our segmentation protocol is the same one as Freesurfer's auto
> >>>>>>>>> segmentation, I used recon-all -s subject -all, command. I do not
> >>>>>>>>> know in this protocol, whether fimbria and alveus are included. We
> >>>>>>>>> do not have skin fiducial to tell right or left side. The
> >>>>>>>>> interesting thing the mean volume for auto is less than manual
> >>>>>>>>> segmentation.
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> Aize
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>> Subject: Re: [Freesurfer] (no subject)
> >>>>>>>>>> From: ni...@nmr.mgh.harvard.edu
> >>>>>>>>>> To: fis...@nmr.mgh.harvard.edu
> >>>>>>>>>> CC: caoa...@hotmail.com; freesurfer@nmr.mgh.harvard.edu
> >>>>>>>>>> Date: Fri, 14 Aug 2009 18:53:41 -0400
> >>>>>>>>>>
> >>>>>>>>>> just to add a factoid, from the ADNI data set, 793 subjects
> >>>>>>>>>> processed by
> >>>>>>>>>> freesurfer:
> >>>>>>>>>> Volume Mean: StdDev:
> >>>>>>>>>> ------------------- ----- -------
> >>>>>>>>>> Left-Hippocampus 3184.335 604.930
> >>>>>>>>>> Right-Hippocampus 3233.753 621.896
> >>>>>>>>>>
> >>>>>>>>>> seems pretty symmetric, with the right being slightly larger (but
> >>>>>>>>>> within
> >>>>>>>>>> std). this subject set is a mix of controls, MCI and AD patients.
> >>>>>>>>>>
> >>>>>>>>>> n.
> >>>>>>>>>>
> >>>>>>>>>> On Fri, 2009-08-14 at 17:53 -0400, Bruce Fischl wrote:
> >>>>>>>>>>> is your segmentation protocol the same as the one we base our
> >>>>>>>>>>> automated
> >>>>>>>>>>> segmentation on? For example, are fimbria and alveus considered
> >>>>>>>>>>> part of
> >>>>>>>>>>> the hippocampus?
> >>>>>>>>>>>
> >>>>>>>>>>> As far as left/right switches go, do you have any fiducial
> >>>>>>>>>>> markers (e.g.
> >>>>>>>>>>> vitamin E tablets) in the images?
> >>>>>>>>>>>
> >>>>>>>>>>> cheers
> >>>>>>>>>>> Bruce
> >>>>>>>>>>> On Sat, 15 Aug 2009, caoaize wrote:
> >>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>> Hi, there,
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>> I have some problem for the hippocampus segmentation results.
> >>>>>>>>>>>>
> >>>>>>>>>>>> 1. My structural data are originally in par-rec file. I used
> >>>>>>>>>>>> r2agui to
> >>>>>>>>>>>> convert them into .nii format, then use recon-all -i to convert
> >>>>>>>>>>>> the .nii
> >>>>>>>>>>>> data into freesurfer .mgz format. Based on these operations, I
> >>>>>>>>>>>> run
> >>>>>>>>>>>> recon-all -all on all my data, the statistical report show that
> >>>>>>>>>>>> the mean
> >>>>>>>>>>>> left hippocampus volume is bigger than the right one, while
> >>>>>>>>>>>> literature
> >>>>>>>>>>>> shows that the right one should be bigger. This problem
> >>>>>>>>>>>> continuously
> >>>>>>>>>>>> appeared in our different studies. I am not sure whether it is
> >>>>>>>>>>>> r2agui's
> >>>>>>>>>>>> problem, which changed the oritation of the structural data. Do
> >>>>>>>>>>>> you have
> >>>>>>>>>>>> any idea?
> >>>>>>>>>>>>
> >>>>>>>>>>>> 2. After autosegmentation, we did a statistical comparison
> >>>>>>>>>>>> analysis
> >>>>>>>>>>>> between automatic segmentation and manual segmentation, and the
> >>>>>>>>>>>> correlation is quite low, less than 80%, which is not acceptable
> >>>>>>>>>>>> for us.
> >>>>>>>>>>>>
> >>>>>>>>>>>> 3. Can I edit the auto segmentation results in Freesurfer if we
> >>>>>>>>>>>> think the
> >>>>>>>>>>>> auto segmentation is not good enough in some area?
> >>>>>>>>>>>>
> >>>>>>>>>>>> I will be really appreciated for your help.
> >>>>>>>>>>>>
> >>>>>>>>>>>> Aize
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>> _________________________________________________________________
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