Hello Dr Greve, Will you please let me know if the above said process I did to overlay brainstorm mask on colin atlas is correct?
Thanks and regards, Sam On Tue, Jun 20, 2017 at 8:47 PM, Dr Sampada Sinha <drsampadasi...@gmail.com> wrote: > Thanks Dr Douglas for your reply. Following is the list of command I used > to generate brainstem mask. > > - I first created from average subject directory, mask of brainstem > using mri_binarize command: > > mri_binarize --match 16 --i aseg.mgz --o hc_brainstem.mgz > > - Then converted to mni305 space using mri_convert command: > > mri_convert mdd_brainstem.mgz mdd_brainstem.mni305.mgz --apply_transform > transforms/talairach.xfm -oc 0 0 0 --conform > > - Converted the .mgz to nii.gz with command: > > mri_convert mdd_brainstem.mni305.mgz mdd_brainstem.mni305.nii.gz > > Finally overlaid it on the mni_colin_t1hires atlas using mango. > > Thanks and regards, > > Sam > > > On Tue, Jun 20, 2017 at 7:59 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> > wrote: > >> how was it created? >> >> On 6/20/17 9:41 AM, Dr Sampada Sinha wrote: >> >> Dear freesurfer experts, >> >> I am trying to over brainstem mask of my patients' group on >> mmi_colin_t1hires atlas. I had no problems in overlaying thalamus or >> amygdala mask, but somehow the midbrain mask is shifted from the actual >> place (please see attachment). Can you please let me know how do I correct >> this error? >> >> Thanks for all your help. >> >> Kind regards, >> >> Sam >> >> -- >> Dr Sampada Sinha >> Research medical scientist (B) >> Department of Geriatric Mental Health (DGMH) >> King George Medical University >> Lucknow-226003 >> , Uttar Pradesh >> India >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://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 >> >> >> 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. >> >> > > > -- > Dr Sampada Sinha > Research medical scientist (B) > Department of Geriatric Mental Health (DGMH) > King George Medical University > Lucknow-226003 > , Uttar Pradesh > India > > > > > > > > > -- Dr Sampada Sinha Research medical scientist (B) Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 , Uttar Pradesh India
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