Hi, Bruce,
I have two quick question,
1. After auto-segmentation, we are using 3D slicer to edit hippocampus. Are
there any other researchers who did the same way, auto + manual editing?
2. Since we have a lot of data for related studies that needs hippocampus
volume, we still prefer to use auto one (without editing). What can we do if I
provide you one original data with edited hippocampus label map? What kind of
other information is required?
Please let me know then, thanks.
Aize
> Date: Tue, 18 Aug 2009 09:33:49 -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 hippocampus will probably be the hardest since it shares so much
> of a border with dark things that will be low contrast in your images. I
> didn't really look at other structures - did they appear accurate? One
> thing you can try is to manually correct a single image, then there are
> some switches I can dig up that will take the intensity distribution
> parameters from it instead of from the atlas, that should help.
>
> cheers
> Bruce
>
> On Tue, 18 Aug 2009, caoaize wrote:
>
> >
> > 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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