Thanks Dr Fischl, I will surely try that. Appreciate all your help at the busy time of this year!
Thanks and regards, Sam On Sun, Jun 25, 2017 at 8:12 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Sampada > > it's the eve of HBM and a lot of people are traveling or preparing to > travel, so our response time may be longer! > > As for your problem, you might try mri_vol2vol instead of mri_convert. If > you run it with --help and search for 'talairach' you will find a lot of > useful stuff, including this example: > > mri_vol2vol --help > . > . > . > 3. Apply an MNI transform to data by resampling the anatomical orig.mgz > into talairach space using bert/mri/transforms/talairach.xfm: > > First, check that the talairach.xfm is correct (this is basically the same > thing as 'tkregister2 --s bert --fstal' in Example 2: > > cd bert/mri > tkregister2 --targ orig.mgz \ > --mov $FREESURFER_HOME/average/mni305.cor.mgz \ > --xfm transforms/talairach.xfm --reg /tmp/reg > > Now resample > mri_vol2vol --mov orig.mgz \ > --targ $FREESURFER_HOME/average/mni305.cor.mgz \ > --xfm transforms/talairach.xfm \ > --o orig-in-mni305.mgz > > Now test the resampling: > tkregister2 --mov orig-in-mni305.mgz \ > --targ $FREESURFER_HOME/average/mni305.cor.mgz \ > --reg /tmp/reg --regheader > > > > note that you can just specify the output file as > mdd_brainstem.mni305.nii.gz and it will be saved in nifti. No need for an > additional step > > cheers > Bruce > > > > > On Sun, 25 Jun 2017, 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> 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 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 >> >> >> 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 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
_______________________________________________ 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.
