Re: [Freesurfer] Manual correction for brainstem module
Just a short note for other people who may use the matlab script to get volumes from the corrected hard segmentations. The volume in cubic mm should be total voxels divided by 8 instead of multiplying by 8. Cheers, Jacky 2016-05-12 17:44 GMT+02:00 Eugenio Iglesias <e.igles...@bcbl.eu>: > Yes! But take all the medulla volumes from the script. In other words: do > not use the script to compute the medulla volumes of the cases you edited, > and take the medulla volumes from the text file for all other cases. If you > do that, you'd be introducing a fairly ugly bias in the study. > Cheers, > /E > > > 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: *"Eugenio Iglesias" <e.igles...@bcbl.eu> > *Cc: *"Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > *Sent: *Thursday, May 12, 2016 4:11:20 PM > > *Subject: *Re: [Freesurfer] Manual correction for brainstem module > > 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 >> *Subje
Re: [Freesurfer] Manual correction for brainstem module
Yes! But take all the medulla volumes from the script. In other words: do not use the script to compute the medulla volumes of the cases you edited, and take the medulla volumes from the text file for all other cases. If you do that, you'd be introducing a fairly ugly bias in the study. Cheers, /E 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: "Eugenio Iglesias" <e.igles...@bcbl.eu> Cc: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Thursday, May 12, 2016 4:11:20 PM Subject: Re: [Freesurfer] Manual correction for brainstem module 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"
Re: [Freesurfer] Manual correction for brainstem module
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 proper
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.
[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.
