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 drsampadasinha@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 greve@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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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

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 fischl@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 < drsampadasinha@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 greve@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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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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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.

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 greve@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 < drsampadasinha@gmail.com javascript:_e(%7B%7D,'cvml','drsampadasinha@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 <greve@nmr.mgh.harvard.edu javascript:_e(%7B%7D,'cvml','greve@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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_______________________________________________ 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

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