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
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_______________________________________________
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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.
