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
