You can use mri_binarize with the match option to get a mask of hippocampus from aseg.mgz (use 17 or left hippo and 53 for right, see $FREESURFER_HOME/FreeSurferColorLUT.txt). Then use mri_mask to mask the norm.mgz to get a volume of the intensities doug
On 05/08/2015 03:11 PM, Chester Dolph wrote: > In the last post I meant “using": Would the correct way of extracting the > intensities using the segmentation look something like this? > > I would like to use raw intensity values of a ROI for texture analysis. I > would prefer to have all of the extracted ROI in the same coordinate space so > comparisons may be made between MRI scans. > > By “extract”, I mean isolate the ROI and ignore all other volumes. > >> On May 8, 2015, at 2:54 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> >> wrote: >> >> when you say "extract" what do you mean exactly? >> >> On 05/08/2015 02:36 PM, Chester Dolph wrote: >>> So I looked up the aseg file and the taliarch.label_intensities.txt. Would >>> the correct way of extracting the intensities from the segmentation look >>> something like this? >>> >>> if( aseg.mgz voxel == my taliarch label intensity of interest (e.g., >>> Right_hippocampus values 1.49 0.0 94) >>> >>> my extracted mri voxel = brain.mgz voxel >>> else >>> my extracted mri voxel = 0 >>> end >>> >>> (if there’s a nice script or command that does this, please let me know). >>> >>> Thanks, >>> Chester >>> >>> >>>> On May 8, 2015, at 1:28 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> >>>> wrote: >>>> >>>> do you mean the hippocampus in aseg.mgz or the hippocampal subfields? >>>> >>>> On 05/08/2015 01:26 PM, Chester Dolph wrote: >>>>> Hello, >>>>> >>>>> Rewording to clarify in case the wording was confusing. What is the best >>>>> way to use the segmented hippocampus outputs as a masks on the registered >>>>> MRI to extract the hippocampus intensities? I would like to use >>>>> FreeSurfer to extract the hippocampus and then perform analysis on the >>>>> raw intensities (meaning the processed, ‘recon-all’ MRI ). I noticed >>>>> that the segmented hippocampus outputs have different dimensisons that >>>>> the brain.mgz files and thus I am unsure how align the hippocampus >>>>> outputs for using them as masks. >>>>> >>>>> Thanks, >>>>> Chester >>>>>> On Apr 29, 2015, at 2:17 PM, Chester Dolph <cdolp...@odu.edu> wrote: >>>>>> >>>>>> Hi, >>>>>> >>>>>> I would like to export the processed *.mgz of the Freesurfer pipeline >>>>>> and segmentation of hippocampal subfields *.mgz to *.nii files. I would >>>>>> like to later use the segmentation of the hippocampal subfields as masks >>>>>> on the registered (and best processed) *.mgz. >>>>>> >>>>>> Should I use the brain.mgz file for the fully processed *.mgz file? >>>>>> Sorry if these are naive questions, I am having a hard time >>>>>> understanding what is the best *.mgz file to use in conjunction with the >>>>>> segmented hippocampus outputs. I would like to apply a texture script to >>>>>> these regions of interests. >>>>>> >>>>>> Thank you, >>>>>> Chester >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> gr...@nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> BEGIN-ANTISPAM-VOTING-LINKS >> ------------------------------------------------------ >> >> Teach CanIt if this mail (ID 01OpuTnR3) is spam: >> Spam: >> https://www.spamtrap.odu.edu/canit/b.php?i=01OpuTnR3&m=cd20831f56b5&t=20150508&c=s >> Not spam: >> https://www.spamtrap.odu.edu/canit/b.php?i=01OpuTnR3&m=cd20831f56b5&t=20150508&c=n >> Forget vote: >> https://www.spamtrap.odu.edu/canit/b.php?i=01OpuTnR3&m=cd20831f56b5&t=20150508&c=f >> ------------------------------------------------------ >> END-ANTISPAM-VOTING-LINKS >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
