Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations

[Thomas Yeo]

External Email - Use Caution

Hi Bronwyn,

I know it's been a long time, but my RA recently explored this and we think
that mri_aparc2aseg might be a better option that mri_label2vol. Anyway,
here's the updated process for mapping the Yeo2011 networks from fsaverage5
to individual volumetric space:

1) *Transform from fsaverage to subject's surface*
mri_surf2surf --srcsubject fsaverage5 --trgsubject yoursubject --hemi lh
--sval-annot path_to/lh.Yeo2011_17Networks_N1000.annot –tval
$SUBJECTS_DIR/yoursubject/label/lh.Yeo_17Network_native.annot
(repeat for rh)

2) *Transform from subject's surface into your subject's volume*
Instead of using "mri_label2vol", we now recommend using "mri_aparc2aseg".
This will give you ROIs that fully cover subject's grey matter.

mri_aparc2aseg --s yoursubject --annot Yeo_17Network_native --o
$SUBJECTS_DIR/yoursubject/mri/outputfile.mgz

One thing to note: "mri_aparc2aseg" will automatically add 1000 for left
cerebral cortex voxels and add 2000 for right cerebral cortex voxels.
Therefore, for example, a left hemisphere voxel in network 5 will have a
value of 1005 in your outputfile.mgz. Here is our suggestion:
a) Find the indices of left/right cerebral cortex by extracting the voxels
with a value of 3 or 42 in the subject's aseg.
b) Use those indices to mask out the voxels that are not cerebral cortex in
your outputfile.mgz file (i.e. set non cerebral cortical voxels to be 0).
c) For the cortical voxels, you may subtract 1000 for those between 1000
and 2000; and subtract 2000 for those greater than 2000.

Thanks,
Thomas

On Thu, Jun 23, 2016 at 2:26 PM Bronwyn Overs  wrote:

> Thanks very much Thomas.
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
> [image: Neuroscience Research Australia]
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1883
> neura.edu.au
>
> [image: Follow @neuraustralia on twitter]
> [image: Follow NeuRA on facebook]
> [image: Subscribe
> to the NeuRA Magazine] 
> On 23/06/2016 4:20 pm, Thomas Yeo wrote:
>
> You should be able to use the 5.3 version.
>
> Regards,
> Thomas
>
> On Thu, Jun 23, 2016 at 2:16 PM, Bronwyn Overs 
> wrote:
>
>> Hi Thomas,
>>
>> Thanks for your reply.
>>
>> The fsaverage directory I have for fs v 5.1 does not include the lh and
>> rh Yeo2011_7Networks_N1000.annot files. I only have this in the 5.3 version
>> of fsaverage. Can I still use the 5.3 version annot files or would I need a
>> seperate set processed with version 5.1?
>>
>> Kind regards,
>>
>> Bronwyn Overs
>> Research Assistant
>> [image: Neuroscience Research Australia]
>>
>> Neuroscience Research Australia
>> Margarete Ainsworth Building
>> Barker Street Randwick Sydney NSW 2031 Australia
>> *M* 0411 308 769 *T* +61 2 9399 1883 <%2B61%202%209399%201883>
>> neura.edu.au
>>
>> [image: Follow @neuraustralia on twitter]
>> [image: Follow NeuRA on facebook]
>> [image:
>> Subscribe to the NeuRA Magazine]
>> 
>> On 23/06/2016 3:17 pm, Thomas Yeo wrote:
>>
>> Hi Bronwyn,
>>
>> You raise a good point. You can consider creating a cortical mask using
>> aparc+aseg.mgz and use that to mask the networks.
>>
>> However, another approach (which might be more accurate) is to take
>> cortical networks in fsaverage space and transform to your subject's
>> surface and then transform into your subject's volume:
>>
>> # Transform from fsaverage to subject's surface
>> >> mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi
>> lh --sval-annot *lh.Yeo2011_17Networks_N1000.annot*  --tval
>> $SUBJECTS_DIR/yoursubject/label/*lh.Yeo_17Network_native.annot*
>>
>> # Transform from subject's surface into your subject's volume (I am not
>> super sure about this. You probably want to double check the output is
>> correct)
>> >> *mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot **--o
>> outfile.nii.gz --hemi lh --subject HS_001 **--regheader*
>>
>> --Thomas
>>
>> On Wed, Jun 22, 2016 at 8:25 AM, Bronwyn Overs 
>> wrote:
>>
>>> Hi Mailing List,
>>>
>>> I am attempting to apply the Yeo 2011 7-network fucntional parcellations
>>> to a set of fs MRIs processed with v5.1.0. Below are listed the first three
>>> steps I plan to take and I am seeking advice as to:
>>>
>>> A) Whether this approach is valid.
>>> B) Steps to take next.
>>>
>>>
>>>
>>> * Steps 1-3: *
>>>
>>> *1. Run MNI152 1mm template through recon-all*
>>> recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid
>>> Yeo2011_MNI152_FS
>>> recon-all -all -subjid Yeo2011_MNI152_FS
>>>
>>> *2. Warp the Yeo_atlas1mm.nii.gz to freesurfer nonlinear volumetric
>>> space*
>>> mri_vol2vol --mov
>>> Yeo2011_7Networks_MNI152

Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations

[Bronwyn Overs]

Thanks very much Thomas.

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883

neura.edu.au 

Follow @neuraustralia on twitter 
Follow NeuRA on facebook 
Subscribe to the 
NeuRA Magazine 


On 23/06/2016 4:20 pm, Thomas Yeo wrote:

You should be able to use the 5.3 version.

Regards,
Thomas

On Thu, Jun 23, 2016 at 2:16 PM, Bronwyn Overs > wrote:


Hi Thomas,

Thanks for your reply.

The fsaverage directory I have for fs v 5.1 does not include the
lh and rh Yeo2011_7Networks_N1000.annot files. I only have this in
the 5.3 version of fsaverage. Can I still use the 5.3 version
annot files or would I need a seperate set processed with version 5.1?

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 

neura.edu.au 

Follow @neuraustralia on twitter
Follow NeuRA on facebook
Subscribe
to the NeuRA Magazine


On 23/06/2016 3:17 pm, Thomas Yeo wrote:

Hi Bronwyn,

You raise a good point. You can consider creating a cortical mask
using aparc+aseg.mgz and use that to mask the networks.

However, another approach (which might be more accurate) is to
take cortical networks in fsaverage space and transform to your
subject's surface and then transform into your subject's volume:

# Transform from fsaverage to subject's surface
>> mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject
--hemi lh --sval-annot /lh.Yeo2011_17Networks_N1000.annot/ 
--tval

$SUBJECTS_DIR/yoursubject/label//lh.Yeo_17Network_native.annot/

# Transform from subject's surface into your subject's volume (I
am not super sure about this. You probably want to double check
the output is correct)
>> /mri_label2vol --annot
lh.Yeo2011_17Networks_N1000.HS_001.annot //--o outfile.nii.gz
--hemi lh --subject HS_001 //--regheader/

--Thomas

On Wed, Jun 22, 2016 at 8:25 AM, Bronwyn Overs
mailto:b.ov...@neura.edu.au>> wrote:

Hi Mailing List,

I am attempting to apply the Yeo 2011 7-network fucntional
parcellations to a set of fs MRIs processed with v5.1.0.
Below are listed the first three steps I plan to take and I
am seeking advice as to:

A) Whether this approach is valid.
B) Steps to take next.

*
Steps 1-3:
*

*1. Run MNI152 1mm template through recon-all*
recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid
Yeo2011_MNI152_FS
recon-all -all -subjid Yeo2011_MNI152_FS

*2. Warp the Yeo_atlas1mm.nii.gz to freesurfer nonlinear
volumetric space*
mri_vol2vol --mov
Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii
--s Yeo2011_MNI152_FS --targ
$FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z
--o Yeo2011_atlas_FSI.nii.gz --nearest

*3. warp the Yeo_atlas_freesurfer_internal_space.nii.gz to
each subject:*
mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s
subjID --targ Yeo2011_atlas_FSI.nii.gz --m3z talairach.m3z
--o Yeo2011_atlas_subjID.nii.gz --nearest --inv-morph


When previously mapping the Choi 2012 straital parcellations,
steps 4 and 5 were:

4. *Creating a striatal mask in the native subject's space
from freesurfer segmented Caudate (11 & 50), Putamen (12 &
51), and Accumbens (26 & 58)*:
mri_binarize --i subjID/mri/aparc+aseg.mgz --match 11 --match
12 --match 26 --match 50 --match 51 --match 58 --o
striatum_mask.nii.gz

*5. **Using this mask to mask the choi striatal parcellations*
fslmaths Choi2012_atlas_subjID.nii.gz -mas
striatum_mask_subjID.nii.gz Yeo_atlas_subjID_mask.nii.gz


Do I need to do a similar thing for the Yeo cortical
parcellations and if so what regions should I include in the
cortical mask?

-- 


Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883


neura.edu.au 

Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations

[Thomas Yeo]

You should be able to use the 5.3 version.

Regards,
Thomas

On Thu, Jun 23, 2016 at 2:16 PM, Bronwyn Overs  wrote:

> Hi Thomas,
>
> Thanks for your reply.
>
> The fsaverage directory I have for fs v 5.1 does not include the lh and rh
> Yeo2011_7Networks_N1000.annot files. I only have this in the 5.3 version of
> fsaverage. Can I still use the 5.3 version annot files or would I need a
> seperate set processed with version 5.1?
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
> [image: Neuroscience Research Australia]
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1883
> neura.edu.au
>
> [image: Follow @neuraustralia on twitter]
> [image: Follow NeuRA on facebook]
> [image: Subscribe
> to the NeuRA Magazine] 
> On 23/06/2016 3:17 pm, Thomas Yeo wrote:
>
> Hi Bronwyn,
>
> You raise a good point. You can consider creating a cortical mask using
> aparc+aseg.mgz and use that to mask the networks.
>
> However, another approach (which might be more accurate) is to take
> cortical networks in fsaverage space and transform to your subject's
> surface and then transform into your subject's volume:
>
> # Transform from fsaverage to subject's surface
> >> mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh
> --sval-annot *lh.Yeo2011_17Networks_N1000.annot*  --tval
> $SUBJECTS_DIR/yoursubject/label/*lh.Yeo_17Network_native.annot*
>
> # Transform from subject's surface into your subject's volume (I am not
> super sure about this. You probably want to double check the output is
> correct)
> >> *mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot **--o
> outfile.nii.gz --hemi lh --subject HS_001 **--regheader*
>
> --Thomas
>
> On Wed, Jun 22, 2016 at 8:25 AM, Bronwyn Overs 
> wrote:
>
>> Hi Mailing List,
>>
>> I am attempting to apply the Yeo 2011 7-network fucntional parcellations
>> to a set of fs MRIs processed with v5.1.0. Below are listed the first three
>> steps I plan to take and I am seeking advice as to:
>>
>> A) Whether this approach is valid.
>> B) Steps to take next.
>>
>>
>>
>> * Steps 1-3: *
>>
>> *1. Run MNI152 1mm template through recon-all*
>> recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid
>> Yeo2011_MNI152_FS
>> recon-all -all -subjid Yeo2011_MNI152_FS
>>
>> *2. Warp the Yeo_atlas1mm.nii.gz to freesurfer nonlinear volumetric space*
>> mri_vol2vol --mov
>> Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii --s
>> Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z
>> talairach.m3z --o Yeo2011_atlas_FSI.nii.gz --nearest
>>
>> *3. warp the Yeo_atlas_freesurfer_internal_space.nii.gz to each subject:*
>> mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ
>> Yeo2011_atlas_FSI.nii.gz --m3z talairach.m3z --o Yeo2011_atlas_subjID.nii.gz
>> --nearest --inv-morph
>>
>>
>> When previously mapping the Choi 2012 straital parcellations, steps 4 and
>> 5 were:
>>
>> 4. *Creating a striatal mask in the native subject's space from
>> freesurfer segmented Caudate (11 & 50), Putamen (12 & 51), and Accumbens
>> (26 & 58)*:
>> mri_binarize --i subjID/mri/aparc+aseg.mgz --match 11 --match 12 --match
>> 26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz
>>
>> *5. **Using this mask to mask the choi striatal parcellations*
>> fslmaths Choi2012_atlas_subjID.nii.gz -mas striatum_mask_subjID.nii.gz
>> Yeo_atlas_subjID_mask.nii.gz
>>
>>
>> Do I need to do a similar thing for the Yeo cortical parcellations and if
>> so what regions should I include in the cortical mask?
>> --
>>
>> Kind regards,
>>
>> Bronwyn Overs
>> Research Assistant
>> [image: Neuroscience Research Australia]
>>
>> Neuroscience Research Australia
>> Margarete Ainsworth Building
>> Barker Street Randwick Sydney NSW 2031 Australia
>> *M* 0411 308 769 *T* +61 2 9399 1883 <%2B61%202%209399%201883>
>> neura.edu.au
>>
>> [image: Follow @neuraustralia on twitter]
>> [image: Follow NeuRA on facebook]
>> [image:
>> Subscribe to the NeuRA Magazine]
>> 
>>
>> ___
>> 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.
>>
>>

Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations

[Bronwyn Overs]

Hi Thomas,

Thanks for your reply.

The fsaverage directory I have for fs v 5.1 does not include the lh and 
rh Yeo2011_7Networks_N1000.annot files. I only have this in the 5.3 
version of fsaverage. Can I still use the 5.3 version annot files or 
would I need a seperate set processed with version 5.1?


Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883

neura.edu.au 

Follow @neuraustralia on twitter 
Follow NeuRA on facebook 
Subscribe to the 
NeuRA Magazine 


On 23/06/2016 3:17 pm, Thomas Yeo wrote:

Hi Bronwyn,

You raise a good point. You can consider creating a cortical mask 
using aparc+aseg.mgz and use that to mask the networks.


However, another approach (which might be more accurate) is to take 
cortical networks in fsaverage space and transform to your subject's 
surface and then transform into your subject's volume:


# Transform from fsaverage to subject's surface
>> mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject 
--hemi lh --sval-annot /lh.Yeo2011_17Networks_N1000.annot/ --tval 
$SUBJECTS_DIR/yoursubject/label//lh.Yeo_17Network_native.annot/


# Transform from subject's surface into your subject's volume (I am 
not super sure about this. You probably want to double check the 
output is correct)
>> /mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot 
//--o outfile.nii.gz --hemi lh --subject HS_001 //--regheader/


--Thomas

On Wed, Jun 22, 2016 at 8:25 AM, Bronwyn Overs > wrote:


Hi Mailing List,

I am attempting to apply the Yeo 2011 7-network fucntional
parcellations to a set of fs MRIs processed with v5.1.0. Below are
listed the first three steps I plan to take and I am seeking
advice as to:

A) Whether this approach is valid.
B) Steps to take next.

*
Steps 1-3:
*

*1. Run MNI152 1mm template through recon-all*
recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid
Yeo2011_MNI152_FS
recon-all -all -subjid Yeo2011_MNI152_FS

*2. Warp the Yeo_atlas1mm.nii.gz to freesurfer nonlinear
volumetric space*
mri_vol2vol --mov
Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii
--s Yeo2011_MNI152_FS --targ
$FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
Yeo2011_atlas_FSI.nii.gz --nearest

*3. warp the Yeo_atlas_freesurfer_internal_space.nii.gz to each
subject:*
mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID
--targ Yeo2011_atlas_FSI.nii.gz --m3z talairach.m3z --o
Yeo2011_atlas_subjID.nii.gz --nearest --inv-morph


When previously mapping the Choi 2012 straital parcellations,
steps 4 and 5 were:

4. *Creating a striatal mask in the native subject's space from
freesurfer segmented Caudate (11 & 50), Putamen (12 & 51), and
Accumbens (26 & 58)*:
mri_binarize --i subjID/mri/aparc+aseg.mgz --match 11 --match 12
--match 26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz

*5. **Using this mask to mask the choi striatal parcellations*
fslmaths Choi2012_atlas_subjID.nii.gz -mas
striatum_mask_subjID.nii.gz Yeo_atlas_subjID_mask.nii.gz


Do I need to do a similar thing for the Yeo cortical parcellations
and if so what regions should I include in the cortical mask?

-- 


Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 

neura.edu.au 

Follow @neuraustralia on twitter
Follow NeuRA on facebook
Subscribe
to the NeuRA Magazine



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Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations

[Thomas Yeo]

Hi Bronwyn,

You raise a good point. You can consider creating a cortical mask using
aparc+aseg.mgz and use that to mask the networks.

However, another approach (which might be more accurate) is to take
cortical networks in fsaverage space and transform to your subject's
surface and then transform into your subject's volume:

# Transform from fsaverage to subject's surface
>> mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh
--sval-annot *lh.Yeo2011_17Networks_N1000.annot*  --tval
$SUBJECTS_DIR/yoursubject/label/*lh.Yeo_17Network_native.annot*

# Transform from subject's surface into your subject's volume (I am not
super sure about this. You probably want to double check the output is
correct)
>> *mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot **--o
outfile.nii.gz --hemi lh --subject HS_001 **--regheader*

--Thomas

On Wed, Jun 22, 2016 at 8:25 AM, Bronwyn Overs  wrote:

> Hi Mailing List,
>
> I am attempting to apply the Yeo 2011 7-network fucntional parcellations
> to a set of fs MRIs processed with v5.1.0. Below are listed the first three
> steps I plan to take and I am seeking advice as to:
>
> A) Whether this approach is valid.
> B) Steps to take next.
>
>
>
> * Steps 1-3: *
>
> *1. Run MNI152 1mm template through recon-all*
> recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid
> Yeo2011_MNI152_FS
> recon-all -all -subjid Yeo2011_MNI152_FS
>
> *2. Warp the Yeo_atlas1mm.nii.gz to freesurfer nonlinear volumetric space*
> mri_vol2vol --mov
> Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii --s
> Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z
> talairach.m3z --o Yeo2011_atlas_FSI.nii.gz --nearest
>
> *3. warp the Yeo_atlas_freesurfer_internal_space.nii.gz to each subject:*
> mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ
> Yeo2011_atlas_FSI.nii.gz --m3z talairach.m3z --o Yeo2011_atlas_subjID.nii.gz
> --nearest --inv-morph
>
>
> When previously mapping the Choi 2012 straital parcellations, steps 4 and
> 5 were:
>
> 4. *Creating a striatal mask in the native subject's space from
> freesurfer segmented Caudate (11 & 50), Putamen (12 & 51), and Accumbens
> (26 & 58)*:
> mri_binarize --i subjID/mri/aparc+aseg.mgz --match 11 --match 12 --match
> 26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz
>
> *5. **Using this mask to mask the choi striatal parcellations*
> fslmaths Choi2012_atlas_subjID.nii.gz -mas striatum_mask_subjID.nii.gz
> Yeo_atlas_subjID_mask.nii.gz
>
>
> Do I need to do a similar thing for the Yeo cortical parcellations and if
> so what regions should I include in the cortical mask?
> --
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
> [image: Neuroscience Research Australia]
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1883
> neura.edu.au
>
> [image: Follow @neuraustralia on twitter]
> [image: Follow NeuRA on facebook]
> [image: Subscribe
> to the NeuRA Magazine] 
>
> ___
> 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.
>
>
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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.

[Freesurfer] Yeo 2011 Functional Cortical Parcellations

[Bronwyn Overs]

Hi Mailing List,

I am attempting to apply the Yeo 2011 7-network fucntional parcellations 
to a set of fs MRIs processed with v5.1.0. Below are listed the first 
three steps I plan to take and I am seeking advice as to:


A) Whether this approach is valid.
B) Steps to take next.

*
Steps 1-3:
*

*1. Run MNI152 1mm template through recon-all*
recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid 
Yeo2011_MNI152_FS

recon-all -all -subjid Yeo2011_MNI152_FS

*2. Warp the Yeo_atlas1mm.nii.gz to freesurfer nonlinear volumetric space*
mri_vol2vol --mov 
Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii --s 
Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z 
talairach.m3z --o Yeo2011_atlas_FSI.nii.gz --nearest


*3. warp the Yeo_atlas_freesurfer_internal_space.nii.gz to each subject:*
mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ 
Yeo2011_atlas_FSI.nii.gz --m3z talairach.m3z --o 
Yeo2011_atlas_subjID.nii.gz --nearest --inv-morph



When previously mapping the Choi 2012 straital parcellations, steps 4 
and 5 were:


4. *Creating a striatal mask in the native subject's space from 
freesurfer segmented Caudate (11 & 50), Putamen (12 & 51), and Accumbens 
(26 & 58)*:
mri_binarize --i subjID/mri/aparc+aseg.mgz --match 11 --match 12 --match 
26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz


*5. **Using this mask to mask the choi striatal parcellations*
fslmaths Choi2012_atlas_subjID.nii.gz -mas striatum_mask_subjID.nii.gz 
Yeo_atlas_subjID_mask.nii.gz



Do I need to do a similar thing for the Yeo cortical parcellations and 
if so what regions should I include in the cortical mask?


--

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883

neura.edu.au 

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