Re: [Freesurfer] Regarding_ Midbrain_misalignment

[Dr Sampada Sinha]

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  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
> > 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 > > 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 
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>> ___ Freesurfer mailing list
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>>> 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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> 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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Re: [Freesurfer] Regarding_ Midbrain_misalignment

[Douglas Greve]

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 
> 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
> 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

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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Re: [Freesurfer] Regarding_ Midbrain_misalignment

[Dr Sampada Sinha]

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 
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 
>> 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 

Re: [Freesurfer] Regarding_ Midbrain_misalignment

[Bruce Fischl]

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  
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  
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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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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Re: [Freesurfer] Regarding_ Midbrain_misalignment

[Dr Sampada Sinha]

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 
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 
> 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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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Regarding_ Midbrain_misalignment

[Dr Sampada Sinha]

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 
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
>
>
>
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> 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
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Re: [Freesurfer] Regarding_ Midbrain_misalignment

[Douglas Greve]

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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.