Hi, For what it's worth, I have seen a very similar skull-strip failure on at least one of my brains processed with Freesurfer 5.0 but not using the -nuintensitycor-3T flag. Happy to send data, if helpful.
Best. Michael On Wed, Feb 16, 2011 at 2:03 PM, Mehul Sampat <mpsam...@gmail.com> wrote: > Hi Bruce, > > Okay. I will try it out 5.1 in the future and compare it to 4.5. > > I also have a question about comparisons between version 4.5 and 5.0 > > In some cases, I saw that FS 4.5 does a slightly better job at skull > stripping than FS 5.0. > Esentially, FS 5.0 seems to make errors in the back of the brain and cuts > out some tissue. > (Please see attached images). > > The images are the same slice from the same subject processed with FS 4.5 > and 5.0 (This happens across 5-10 slices) > In 5.0, I used the following command: recon-all -s "subj--id" -i > "nifti-file" -all -nuintensitycor-3T > (I have seen this issue in atleast 5 subjects in our data) > > Since 5.0 uses the graph cuts, could the error be due the combination of > (graph cuts + -nuintensitycor-3T) ? > Also, I guess I could run 5.0 and use only graph cuts or -nuintensitycor-3T > to isolate the error ? > > Thanks > Mehul > > > > On Tue, Feb 15, 2011 at 12:05 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> > wrote: >> >> Hi Mehul, >> >> I think 5.1 will work better for large ventricles than 4.5, but I'll be >> interested to hear your experience. >> >> cheers >> Bruce >> On Tue, 15 Feb 2011, Mehul Sampat wrote: >> >>> Hi Bruce, >>> We have two studies being conducted (one cross-sectional and one >>> longitudinal) >>> Some of the subjects in have a lot of atrophy and have large ventircles. >>> >>> For the cross-sectional analysis stream are there many differences >>> between >>> 4.5 and the forthcoming 5.1 ? Or would it be fine to use 4.5 for >>> cross-sectional analysis ? >>> >>> (I understand that for the longitudinal study, I should wait for 5.1 and >>> process all the timepoints with 5.1) >>> >>> >>> Thanks >>> Mehul >>> >>> >>> >>> On Thu, Jan 20, 2011 at 10:36 AM, Bruce Fischl >>> <fis...@nmr.mgh.harvard.edu>wrote: >>> >>>> Hi Derin >>>> >>>> we are tracking down some issues with it and hope to have it out within >>>> a >>>> month >>>> >>>> cheers >>>> Bruce >>>> On Thu, 20 Jan 2011, Derin Cobia wrote: >>>> >>>>> All, >>>>> >>>>> Just curious about the current estimated timeline for version 5.1, >>>>> trying >>>> >>>> to schedule some projects around it. Thanks! >>>>> >>>>> -Derin >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> 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 > > > 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
