Thanks Dr Douglas for bringing that out. If I remember correctly these structures did align when I viewed it using freeview. Will send the pictures later to confirm. Also these images had a good overlay with fsaverage image using tkmedit tool. Only that the resolution was not good with fsaverage that I used Colin atlas. Thanks much for your valuable suggestions I will double check and confirm with pics later.
Kind regards, Sampada On Friday, July 7, 2017, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > And the same process worked for thalamus and amygdala? If so, then I don't > know what is going wrong. Try doing the visualization in freeview. Also see > if the amyg/thal seem to be in the right place relative to brainstem when > you visualize all of them together. > > On 6/25/17 9:31 AM, Dr Sampada Sinha wrote: > > 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 > <javascript:_e(%7B%7D,'cvml','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 >> <javascript:_e(%7B%7D,'cvml','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.edu >>> <javascript:_e(%7B%7D,'cvml','Freesurfer@nmr.mgh.harvard.edu');>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> <javascript:_e(%7B%7D,'cvml','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 > > _______________________________________________ > Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu > <javascript:_e(%7B%7D,'cvml','Freesurfer@nmr.mgh.harvard.edu');>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- 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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