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 <[email protected]> >> 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 <[email protected]> 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 >>> [email protected] >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> [email protected] >> 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 >> [email protected] >> 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. >> >> >> -- >> BEGIN-ANTISPAM-VOTING-LINKS >> ------------------------------------------------------ >> >> NOTE: This message was trained as non-spam. If this is wrong, >> please correct the training as soon as possible. >> >> Teach CanIt if this mail (ID 03Optt94s) is spam: >> Spam: >> https://www.spamtrap.odu.edu/canit/b.php?i=03Optt94s&m=664b1eae3462&t=20150508&c=s >> Not spam: >> https://www.spamtrap.odu.edu/canit/b.php?i=03Optt94s&m=664b1eae3462&t=20150508&c=n >> Forget vote: >> https://www.spamtrap.odu.edu/canit/b.php?i=03Optt94s&m=664b1eae3462&t=20150508&c=f >> ------------------------------------------------------ >> END-ANTISPAM-VOTING-LINKS >> > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] 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 [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
