Yes, I'm glad that Bruce confirmed this. Good. The majority had deviations that were in the range of 20-40 voxels which seems intuitively in the right range. The ones that concerned me were those that inexplicably deviated in the range of 600 to 1000 voxels out of 4000 or so voxels in the hippocampus. Notably, the large deviations occurred in subjects with some motion artifacts says my colleague, although the hippocampal segmentation itself seemed fairly representative of Freesurfer.
However this last point seems different that the one raised in my first post, since we are getting deviations with the exact same voxels after relabeling. I hope Doug gets a chance to chime in; our lab is somewhat concerned about this right now because we are in the middle of a revision for a journal submission. Best, and thank you, Joshua - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805 Joshua On Thu, May 17, 2012 at 2:05 PM, Joshua . <nimzodisas...@gmail.com> wrote: > Yes. Good. The majority had deviations that were in the range of 20-40 > voxels which seems intuitively in the right range. The ones that concerned > me were those that inexplicably deviated in the range of 600 to 1000 voxels > out of 4000 or so voxels in the hippocampus. Notably, the large deviations > occurred in subjects with some motion artifacts says my colleague, although > the hippocampal segmentation itself seemed fairly representative of > Freesurfer. > > However this last point seems different that the one raised in my first > post, since we are getting deviations with the exact same voxels after > relabeling. I hope Doug gets a chance to chime; our lab is somewhat > concerned about this right now because we are in the middle of a revision > for a journal submission. > > Best, and thank you, > > Joshua > > > On Thu, May 17, 2012 at 12:39 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> > wrote: >> >> yes, that is a consequence of partial volume correction. If you have a 3 >> class boundary (two of which are hippocampal subdivisions), we will compute >> different partial volume fractions than if you have a 2 class boundary. I >> wouldn't expect it to be a huge effect, but they definitely won't be >> identical >> >> >> >> On Thu, 17 May 2012, Joshua Lee wrote: >> >>> We discovered this while subdividing the hippocampus into several >>> subregions using tkmedit to relabel voxels, and finding that these >>> subregions were not adding up to the original volume. I expected some >>> differences, but many deviated more than I had expected. This led me to the >>> test I discussed at the beginning of the thread. >>> >>> >>> Joshua >>> >>> >>> >>> >>> >>> >>> On May 16, 2012, at 1:55 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >>> wrote: >>> >>>> hmmm, that is convincing. I don't think there's anything in mri_segstats >>>> that knows about the meaning of any of the indices, but maybe Doug can >>>> correct me? >>>> >>>> On Wed, 16 May 2012, Joshua Lee wrote: >>>> >>>>> Hi Bruce, >>>>> First, let me add that if I run the mri_segstats without the --pv flag, >>>>> the >>>>> two will have identical volumes. This indicates to me that we captured >>>>> all >>>>> the voxels into the new label. >>>>> Joshua >>>>> - >>>>> Joshua Lee >>>>> Graduate Student >>>>> Center for Mind and Brain & >>>>> Department of Psychology >>>>> University of California, Davis >>>>> 530.747.3805 >>>>> On Wed, May 16, 2012 at 1:38 PM, Bruce Fischl >>>>> <fis...@nmr.mgh.harvard.edu> >>>>> wrote: >>>>> Hi Joshua >>>>> >>>>> probabilities are computed internally, but not stored nor used >>>>> in volume calcualtions. Are you actually doing a 3D fill? I >>>>> don't think the hippocampus label is guaranteed to be connected. >>>>> Can you try instead replacing every voxel in matlab with the >>>>> hippocampus index to your new one? That I think should give you >>>>> the same results. >>>>> >>>>> cheers >>>>> Bruce >>>>> >>>>> On Wed, 16 May 2012, Joshua Lee wrote: >>>>> >>>>> Suppose I were to open a subject aseg.mgz in >>>>> tkmedit, and use the 3D fill >>>>> tool to relabel the entire left hippocampus >>>>> segmentation to >>>>> 'MyNewImaginaryLabel'. If I then re-run the aseg >>>>> stats, should the left >>>>> hippocampus volume from the original aseg.stats be >>>>> identical to the volume >>>>> of MyImaginaryLabel in the newly generated >>>>> aseg.stats? >>>>> >>>>> Every voxel from the prior label is now assigned to >>>>> the new label; yet, I >>>>> am getting different results (by about 100 voxels in >>>>> the ones I've tried). >>>>> >>>>> The command Im using to recalculate: >>>>> mri_segstats --seg >>>>> /usr/local/freesurfer/subjects/s02/new_MRI/new/aseg.auto.mgz >>>>> --sum >>>>> >>>>> /usr/local/freesurfer/subjects/s02/stats/NEWmethod1aseg_Hipp.stats >>>>> --pv >>>>> /usr/local/freesurfer/subjects/s02/mri/norm.mgz >>>>> --excludeid 0 >>>>> --brain-vol-from-seg --brainmask >>>>> /usr/local/freesurfer/subjects/s02/mri/brainmask.mgz >>>>> --in >>>>> /usr/local/freesurfer/subjects/s02/mri/norm.mgz >>>>> --in-intensity-name norm >>>>> --in-intensity-units MR --etiv --surf-wm-vol --ctab >>>>> /usr/local/freesurfer/8regions.txt --subject s02; >>>>> >>>>> Now if I were to relabel 'MyNewImaginaryLabel' to >>>>> 'AthirdLabel', and again >>>>> changing every voxel in 'MyNewImaginaryLabel' to the >>>>> new label, the computed >>>>> volumes do not change. This led me to suspect that >>>>> aseg.mgz contains >>>>> probability estimates at each voxel that are then >>>>> subsequently overwritten >>>>> by my tkmedits. However, per a previous conversation >>>>> from a year ago or so >>>>> with Bruce and also the relevant Freesurfer >>>>> documentation this does not seem >>>>> to be the case. Partial volume information is not >>>>> contained within the >>>>> aseg.mgz (right!?), but is computed by mri_segstats >>>>> by comparing border >>>>> voxels with intensities in the norm.mgz. So I am at >>>>> a loss on why these >>>>> should be different. >>>>> >>>>> This has been replicated in version 4.5 and 5.1 >>>>> - >>>>> Joshua Lee >>>>> Graduate Student >>>>> Center for Mind and Brain & >>>>> Department of Psychology >>>>> University of California, Davis >>>>> 530.747.3805 >>>>> 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
