I used mri_binarize to get a mask of the hippocampus from aseg.mgz and then used mri_mask to mask the norm.mgz to get a volume of intensities. After this process, I noticed that hippocampus do not seem aligned in terms of the z (axial) axis. Of note, the hippocampus center of mass seem to fluctuate over a wider range of values than I was expecting- one hippocampus might exist in the 85 to 108 axial slices, while another hippocampus might exist in the 120 to 142 slices. I am intending to perform voxelwise analysis over a dataset.
Is there an additional step/flag that aligns MRI in terms of the axial dimension? I used the recon all with the hippocampus flags. > On May 8, 2015, at 3:21 PM, Chester Dolph <cdolp...@odu.edu> wrote: > > Thanks! >> On May 8, 2015, at 3:15 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> >> wrote: >> >> 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 >>>> >>>> -- >>>> >>> >>> _______________________________________________ >>> 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 03OpvftiG) is spam: >> Spam: >> https://www.spamtrap.odu.edu/canit/b.php?i=03OpvftiG&m=86ae69949657&t=20150508&c=s >> Not spam: >> https://www.spamtrap.odu.edu/canit/b.php?i=03OpvftiG&m=86ae69949657&t=20150508&c=n >> Forget vote: >> https://www.spamtrap.odu.edu/canit/b.php?i=03OpvftiG&m=86ae69949657&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
