Hi Eugenio, Thanks, the script worked.
Actually I only edited the medulla segmentation in 3 out of the 49 subjects that I have. I suppose the original volumetric estimates for midbrain and pons are still valid and I can just calculate and compare the new medulla volumes for all subjects. Is that correct? Jacky 2016-05-12 12:05 GMT+02:00 Eugenio Iglesias <e.igles...@bcbl.eu>: > My email client is replacing the combination colon + right parenthesis by > a smiley! If the same thing happened to you, please replace the smiley by a > colon and a right parenthesis... > Next time I'll just attach the code. > Sorry for the inconvenience > > Juan Eugenio Iglesias > Postdoctoral researcher BCBL > www.jeiglesias.com > www.bcbl.eu > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > ------------------------------ > *From: *"Eugenio Iglesias" <e.igles...@bcbl.eu> > *To: *"Jacky Lee" <cyle...@gmail.com> > *Cc: *"Freesurfer support list" <Freesurfer@nmr.mgh.harvard.edu> > *Sent: *Thursday, May 12, 2016 5:59:33 AM > > *Subject: *Re: [Freesurfer] Manual correction for brainstem module > > Of course! I haven't tested the code below, but I think it should work > right away. > > Let's assume that FreeSurfer is installed in /usr/local/freesurfer/ (if > not, replace the location in the code below). Also, you'd need to replace > the name of your subject directory. > Finally, I have assumed that brainstemSsLabels.v10.mgz was modified and > saved as brainstemSsLabels.v10.edited.mgz (again, replace as needed). > > > subjectdir='/mysubjectdir/'; > editedFileName='brainstemSsLabels.v10.edited.mgz'; > > addpath /usr/local/freesurfer/matlab > > d=dir(subjectdir); > > for i=1:length(d) > > tentativeSegFile=[subjectdir '/' d(i).name '/mri/' editedFileName]; > > if d(i).isdir && exist(tentativeSegFile,'file') > > A=MRIread(tentativeSegFile); > MidbrainVol=8*sum(A.vol(:)==173); % the eight is because each voxel > of the segmentation has a volume equal to 0.125 cubic mm > PonsVol=8*sum(A.vol(:)==174); > MedullaVol=8*sum(A.vol(:)==175); > SCPvol=8*sum(A.vol(:)==178); > > disp(['Subject ' d(i).name ', midbrain = ' num2str(MidbrainVol) ', > pons = ' num2str(PonsVol) ', medulla = ' num2str(MedullaVol) ', SCP = ' > num2str(SCPvol)]); > > end > > end > > One more thing: if you haven't edited anything around the SCP, I would use > the original estimate for this structure. The reason is that, because the > SCP is very thing, the voxel count is a much poorer approximation for the > volume as computed by the code (i.e., using soft segmentations). > > Cheers, > > Eugenio > > > Juan Eugenio Iglesias > Postdoctoral researcher BCBL > www.jeiglesias.com > www.bcbl.eu > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > ------------------------------ > *From: *"Jacky Lee" <cyle...@gmail.com> > *To: *"Freesurfer support list" <Freesurfer@nmr.mgh.harvard.edu> > *Cc: *"Eugenio Iglesias" <e.igles...@bcbl.eu> > *Sent: *Thursday, May 12, 2016 10:32:24 AM > *Subject: *Re: [Freesurfer] Manual correction for brainstem module > > Hi Eugenio, > > Yes please give me some advice on the matlab commands for this since I am not > very familiar with matlab... > > Cheers, > > Jacky > > > Hi Jacky, > this is a good question, and unfortunately there isn't a great answer to it. > The volume is computed upong a probabilitic segmentation of the voxels that is > not written to disk (this is very similar to what happens with aseg.mgz and > aseg.stats). In order to properly update the volume estimates, you would have > to know the probability that the inpainted voxels belong to the brainstem as > estimated by the algorithm, which we don't currently write to disk. > Another option would be to toss the volumes given by the algorithm, and > compute > new volumes for all cases and brainstem structures using the hard > segmentations. You would simply have to count the number of voxels labeled as > midbrain, pons, SCP and medulla for each subject. You can easily do this e.g. > with Matlab (let me know if you need help with this). > Cheers, > Eugenio > > Juan Eugenio Iglesias > Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > > From: "Jacky Lee" <cyle...@gmail.com> > To: "Freesurfer support list" <Freesurfer@nmr.mgh.harvard.edu> > Sent: Monday, May 9, 2016 2:01:53 AM > Subject: [Freesurfer] Manual correction for brainstem module > > Hi freesurfer experts, > > I have successfully run the brainstem module for some subjects. On visual > checking, I can see there are voxels with T1 hypointense lesions mislabelled > as > non-brainstem tissue. I manually corrected them on the > brainstemSsLabels.v10.mgz on Freeview. Then how do I obtain this new corrected > volume of the brainstem substructures? > > Thanks. > > Regards, > > Jacky > > > > _______________________________________________ > 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. >
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