sure. You can look at the papers by Kennedy, Caviness and Makris On Wed, 18 Jul 2012, John Drozd wrote:
> Hi Bruce, > > Thank you very much for your clarifications. I will ask ADNI for their > permission and I will consult CMA for their definitions. > > Thank you, > Have a great day, > John > > Sent from my iPhone 4S > > > On 2012-07-18, at 6:42 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > >> Hi John >> >> we follow the conventions of the Center for Morphometric Analysis (CMA) here >> at MGH. I'm not actually sure what landmarks they use to separate what they >> call "inferior lateral ventricle" from the main one, but you can check with >> them. >> >> As for ADNI, we might have that data but I'm not sure we are allowed to >> distribute it. If you check with them about it and let us know we'll give >> you what we have. >> >> cheers >> Bruce >> >> >> On Tue, 17 Jul 2012, John Drozd wrote: >> >>> Hi Bruce, >>> >>> I apologize for my detailist nature. >>> I found the csv files on the ADNI web site containing the numerical values >>> of volume in mm^3 numbers. Do you mean that there should also be the >>> corresponding label maps on the ADNI web site, particularly of the third >>> and lateral ventricles? I know when I ran recon-all it gave all the label >>> maps of each parcellation of the brain and I could overlay these labels on >>> the grey scale images and render 3D surface models in Slicer. If this is >>> the case, could you confirm this. Then I'll email ADNI to see if they have >>> the label maps corresponding to the csv files that they have in the ADNI >>> Study Data -> MRI Images -> Image Analysis link. >>> >>> I am particularly interested in where Freesurfer separates the lateral >>> ventricles from the third ventricle at the foramina, or at the connection >>> between the posterior horns and the third ventricle. If you have any >>> insight in this, that would be helpful. I am glad that Freesurfer includes >>> the isolated horn pieces, as you explained. I particularly found that >>> accurate segmentation of the horns was very important for the significance >>> statistics in comparing AD, MCI and NEC groups. The next step for me will >>> be sub-regional ventricle volumes, not only left and right but separate >>> volumes of horns. I am curious how you defined the division of left from >>> right for the ventricles? Was it special landmarks on the atlas? >>> >>> Thank you, >>> John >>> >>> Sent from my iPhone 4S >>> >>> >>> On 2012-07-17, at 2:13 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: >>> >>>> Hi John >>>> >>>> have you checked with the ADNI folks? I think they have FreeSurfer >>>> segmentation on many if not most of their subjects. We place no >>>> connectivity constraints on the ventricular segmentations because they get >>>> so thin that indeed sometimes 1mm data cannot resolve the connections. So >>>> sometimes the temporal or occipital horn are disconnected, and sometimes >>>> not. >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> On Tue, 17 Jul 2012, John Drozd wrote: >>>> >>>>> Hello, >>>>> >>>>> I have successfully developed an automated algorithm combining pixel >>>>> intensity-based and shape based approaches to segment the lateral >>>>> ventricles. I have applied my algorithm to a small data set of 1.5 T1 >>>>> ADNI images consisting of 24 AD (subjects with Alzheimer Disease) 19 MCI >>>>> (subjects with Mild Cognitive Impairment) and 24 NEC (elderly controls). >>>>> In my cases, particularly AD cases, I noticed that the segmentation of >>>>> the lateral ventricles is connected to the third ventricle with foramina >>>>> (usually 1 on a side or on both sides). Also, sometimes I find a >>>>> connection with the posterior horn and third ventricle. I have >>>>> researched CSF flow and from the literature, and all of these are real >>>>> connections. I am near completion of developing an automated cropping >>>>> scheme with a colleague to crop the third ventricle at these junctions. >>>>> >>>>> Our implementation is a combination of C++ code that we have developed >>>>> and modified ITK classes. We have been viewing our segmented label maps >>>>> in Slicer3 and generated 3D renderings using Slicer3's Model Maker module >>>>> which is based on Marching Cubes. >>>>> >>>>> I have viewed a Freesurfer segmentation in Slicer3 based on a tutorial on >>>>> the Slicer web site. >>>>> >>>>> I presented a poster of our results at the AIC and AAIC conference which >>>>> I am at now in Vancouver, and a few people have asked me to compare my >>>>> volumes with other methods. They were particularly interested in >>>>> comparing my volumes with Freesurfer ventricle volumes and >>>>> cross-sectional and longitudinal data. I was told and found csv files on >>>>> the ADNI web site of Freesurfer analysis. I plan to correlate my values >>>>> with Freesurfer's values, but I would be interested if Freesurfer also >>>>> finds these connections between the third ventricle and lateral >>>>> ventricles and also if it includes isolated temporal horn pieces when the >>>>> horns are discontinuous due to the MRI not being able to resolve a very >>>>> thin portion of the temporal horn. >>>>> >>>>> So, would it be possible, if I gave you a list of my ADNI subjects, for >>>>> you to provide me the freesurfer label maps that correspond to the >>>>> volumes in the csv files that are on the ADNI web site please? I could >>>>> run Freesurfer but I would prefer having the label maps that exactly >>>>> correspond to the Freesurfer ventricle volumes that are on the ADNI >>>>> website. These would be from the two versions of Freesurfer noted on the >>>>> ADNI web site in the ADNI Study Data/MRI image analysis link. >>>>> >>>>> Thank you, >>>>> John >>>>> >>>>> Sent from my iPhone 4S >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom it >>>> is >>>> addressed. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>> error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>> >>> >>> > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
