I processed the T1-weighted data without T2. Therefore, we do not have T2.norm.mgz in the mri folder of each subject. Only for the HP-subfields segmentation, we added additional high-resolution T2-weighted data to increase the accuracy of HP-subfields segmentation.
Thanks! Alireza > On Feb 27, 2017, at 12:53 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> > wrote: > > There is usually a T2.norm.mgz file in the mri folder. If that is there, > then you should use that rather than the raw data that is not bias field > corrected > > >> On 02/27/2017 12:30 PM, ali reza mohammadi nejad wrote: >> Thank you so much Dr. Doug! I just have one more question: >> >> Now I want to compute the same information for our second modality (i.e., >> mean and std intensity of different HP_subfields for our additional scan, >> e,g., T2 or FLAIR). >> My question is that how could I use <analysisID>.FSspace.mgz (in mri folder) >> and T1_to_<analysisID>.v10.Ita (in transform folder) files in mri_segstats >> command? >> >> Thank you in advance for any help. >> Best regards, >> Alireza >> >> >>> On Feb 24, 2017, at 10:51 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> >>> wrote: >>> >>> The basic command is >>> >>> mri_segstats --seg seg.mgz --default-ctab --sum sum.dat --i input.mgz >>> >>> where seg is the hippo sub field seg and input is the input where you >>> want to get the intensities from (probably norm.mgz). Note that you need >>> to use the hipp sub field output that is 1mm (not the high res one) >>> >>> >>>> On 02/24/2017 09:53 AM, ali reza mohammadi nejad wrote: >>>> Dear FreeSurfer Experts, >>>> I want to compute some intensity information (e.g., mean and std) of each >>>> Hippocampal subfields (similar to aseg.stats file). >>>> I think one option could be mri_segstats command, but I am not sure. >>>> If it works, what are the inputs of this command? >>>> >>>> Thank you in advance for any help. >>>> Alireza >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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
