Re: [Freesurfer] Stats for Yeo and Choi Parcellations

[Thomas Yeo]

Hi Bronwyn,

You can first create a striatum mask in the native subject's space:

>> mri_binarize --i subject/mri/aparc+aseg.mgz --match 11 --match 12
--match 26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz

Then use the resulting mask to mask the striatum parcellation:

>> fslmaths Choi_atlas_AD_subject.nii.gz -mas striatum_mask.nii.gz
Choi_atlas_AD_subject_mask.nii.gz

Regards,
Thomas



On Mon, May 9, 2016 at 11:40 AM, Bronwyn Overs  wrote:

> Hi Thomas,
>
>
> Thanks, I have taken your advise and used the LooseMask for the 7 network
> parcellation in steps 3a and b. How do I now mask it again with
> FreeSurfer's segmentation of striatal regions as you have suggested?
>
> 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 9/05/2016 12:29 pm, Thomas Yeo wrote:
>
> Hi Bronwyn,
>
> I was using that as a placeholder. You can use any of these:
>
> Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
> Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
> Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
> Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
>
> Depending on whether you want the 7 or 17 networks and/or whether you want
> to use the loose or tight mask. My suggestion is to use the LooseMask and
> then after the parcellation has been project to the subject's native space,
> you can mask it again with FreeSurfer's segmentation of striatal regions
> (e.g., caudate, putamen and nucleus accumbens) in your subject's native
> MRI.
>
> For Step 2, you can use FSL_MNI152_FreeSurferConformed_1mm.nii or you can
> use the MNI152 1mm template distributed by FSL.
>
> Regards,
> Thomas
>
> On Mon, May 9, 2016 at 9:37 AM, Bronwyn Overs 
> wrote:
>
>> Hi Thomas,
>>
>> I am not sure which file you are referring to when you say
>> "Choi_atlas1mm.nii.gz". The files I have from the freesurfer wiki are:
>>
>> Choi_JNeurophysiol12_MNI152_README
>> Choi2012_7Networks_ColorLUT.txt
>> Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
>> Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
>>
>> Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
>>
>> Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
>> Choi2012_17Networks_ColorLUT.txt
>> Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
>> Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
>>
>> Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
>>
>> Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
>> FSL_MNI152_FreeSurferConformed_1mm.nii.gz
>>
>> Which if any of these should I designate as the source in step 3a?
>>
>> Also for step 2 I used "FSL_MNI152_FreeSurferConformed_1mm.nii", is this
>> correct?
>>
>> 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 6/05/2016 12:50 am, Thomas Yeo wrote:
>>
>> Hi Doug, the Choi file is a striatal functional connectivity atlas which
>> we distribute. It's under the average directory.
>>
>> Hi Bronwyn,
>>
>> To transform the Choi's striatal atlas to your individual subject, Here's
>> a (non-ideal) suggestion I previously suggested to another user:
>>
>> 1) Assuming you are quite happy with the freesurfer striatal parcellation
>> in your individual subjects, then I am assuming freesurfer nonlinear
>> registration (talairach.m3z) is working quite well. Talairach.m3z warps
>> your subject to an internal freesurfer space (kinda like MNI305, but not
>> quite). Let's say the freesurfer recon-all output is at
>> /SUBJECT_FS/
>>
>> 2) Run the MNI152 1mm template (the one from FSL) through recon-all.
>> Recon-all will give you a Talairach.m3z that allows you to map the
>> MNI152 1mm template to the internal freesurfer space. Let's say the
>> freesurfer recon-all output is at /MNI152_FS/
>>
>> 3) Then do the following:
>>
>> 

Re: [Freesurfer] Stats for Yeo and Choi Parcellations

[Bronwyn Overs]

Hi Thomas,


Thanks, I have taken your advise and used the LooseMask for the 7 
network parcellation in steps 3a and b. How do I now mask it again with 
FreeSurfer's segmentation of striatal regions as you have suggested?


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 9/05/2016 12:29 pm, Thomas Yeo wrote:

Hi Bronwyn,

I was using that as a placeholder. You can use any of these:

Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz

Depending on whether you want the 7 or 17 networks and/or whether you 
want to use the loose or tight mask. My suggestion is to use the 
LooseMask and then after the parcellation has been project to the 
subject's native space, you can mask it again with FreeSurfer's 
segmentation of striatal regions (e.g., caudate, putamen and nucleus 
accumbens) in your subject's native MRI.


For Step 2, you can use FSL_MNI152_FreeSurferConformed_1mm.nii or you 
can use the MNI152 1mm template distributed by FSL.


Regards,
Thomas

On Mon, May 9, 2016 at 9:37 AM, Bronwyn Overs > wrote:


Hi Thomas,

I am not sure which file you are referring to when you say
"Choi_atlas1mm.nii.gz". The files I have from the freesurfer wiki are:

Choi_JNeurophysiol12_MNI152_README
Choi2012_7Networks_ColorLUT.txt
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
Choi2012_17Networks_ColorLUT.txt
Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
FSL_MNI152_FreeSurferConformed_1mm.nii.gz

Which if any of these should I designate as the source in step 3a?

Also for step 2 I used "FSL_MNI152_FreeSurferConformed_1mm.nii",
is this correct?

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 6/05/2016 12:50 am, Thomas Yeo wrote:

Hi Doug, the Choi file is a striatal functional connectivity
atlas which we distribute. It's under the average directory.

Hi Bronwyn,

To transform the Choi's striatal atlas to your individual
subject, Here's a (non-ideal) suggestion I previously suggested
to another user:

1) Assuming you are quite happy with the freesurfer striatal
parcellation in your individual subjects, then I am assuming
freesurfer nonlinear registration (talairach.m3z) is working
quite well. Talairach.m3z warps your subject to an internal
freesurfer space (kinda like MNI305, but not quite). Let's say
the freesurfer recon-all output is at /SUBJECT_FS/

2) Run the MNI152 1mm template (the one from FSL) through
recon-all. Recon-all will give you a Talairach.m3z that allows
you to map the MNI152 1mm template to the internal freesurfer
space. Let's say the freesurfer recon-all output is at
/MNI152_FS/

3) Then do the following:

a) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear
volumetric space:

>> setenv SUBJECTS_DIR 
>> mri_vol2vol_used --mov Choi_atlas1mm.nii.gz --s MNI152_FS
--targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z
talairach.m3z --o Choi_atlas_freesurfer_internal_space.nii.gz
--interp nearest

b) warp the Choi_atlas_freesurfer_internal_space.nii.gz to your
subject:

>> setenv SUBJECTS_DIR 
>> mri_vol2vol --mov $SUBJECTS_DIR/AD_SUBJECT_FS/mri/norm.mgz --s
AD_SUBJECT_FS --targ 

Re: [Freesurfer] Stats for Yeo and Choi Parcellations

[Thomas Yeo]

Hi Bronwyn,

I was using that as a placeholder. You can use any of these:

Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz

Depending on whether you want the 7 or 17 networks and/or whether you want
to use the loose or tight mask. My suggestion is to use the LooseMask and
then after the parcellation has been project to the subject's native space,
you can mask it again with FreeSurfer's segmentation of striatal regions
(e.g., caudate, putamen and nucleus accumbens) in your subject's native
MRI.

For Step 2, you can use FSL_MNI152_FreeSurferConformed_1mm.nii or you can
use the MNI152 1mm template distributed by FSL.

Regards,
Thomas

On Mon, May 9, 2016 at 9:37 AM, Bronwyn Overs  wrote:

> Hi Thomas,
>
> I am not sure which file you are referring to when you say
> "Choi_atlas1mm.nii.gz". The files I have from the freesurfer wiki are:
>
> Choi_JNeurophysiol12_MNI152_README
> Choi2012_7Networks_ColorLUT.txt
> Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
> Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
>
> Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
>
> Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
> Choi2012_17Networks_ColorLUT.txt
> Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
> Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
>
> Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
>
> Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
> FSL_MNI152_FreeSurferConformed_1mm.nii.gz
>
> Which if any of these should I designate as the source in step 3a?
>
> Also for step 2 I used "FSL_MNI152_FreeSurferConformed_1mm.nii", is this
> correct?
>
> 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 6/05/2016 12:50 am, Thomas Yeo wrote:
>
> Hi Doug, the Choi file is a striatal functional connectivity atlas which
> we distribute. It's under the average directory.
>
> Hi Bronwyn,
>
> To transform the Choi's striatal atlas to your individual subject, Here's
> a (non-ideal) suggestion I previously suggested to another user:
>
> 1) Assuming you are quite happy with the freesurfer striatal parcellation
> in your individual subjects, then I am assuming freesurfer nonlinear
> registration (talairach.m3z) is working quite well. Talairach.m3z warps
> your subject to an internal freesurfer space (kinda like MNI305, but not
> quite). Let's say the freesurfer recon-all output is at
> /SUBJECT_FS/
>
> 2) Run the MNI152 1mm template (the one from FSL) through recon-all.
> Recon-all will give you a Talairach.m3z that allows you to map the MNI152
> 1mm template to the internal freesurfer space. Let's say the freesurfer
> recon-all output is at /MNI152_FS/
>
> 3) Then do the following:
>
> a) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:
>
> >> setenv SUBJECTS_DIR 
> >> mri_vol2vol_used --mov Choi_atlas1mm.nii.gz --s MNI152_FS --targ
> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
> Choi_atlas_freesurfer_internal_space.nii.gz --interp nearest
>
> b) warp the Choi_atlas_freesurfer_internal_space.nii.gz to your subject:
>
> >> setenv SUBJECTS_DIR 
> >> mri_vol2vol --mov $SUBJECTS_DIR/AD_SUBJECT_FS/mri/norm.mgz --s
> AD_SUBJECT_FS --targ Choi_atlas_freesurfer_internal_space.nii.gz --m3z
> talairach.m3z --o Choi_atlas_AD_subject.nii.gz --interp nearest
> --inv-morph
>
> This is not optimal because of the double interpolation. You might want to
> use the MNI template instead of the Choi_atlas to test the above, so you
> can check the goodness of the warp. The final warped MNI template should
> hopefully look identical to your subject. If that works, then use the
> Choi_atlas. Note that mri_vol2vol does not work properly for talairach.m3z 
> below
> version 5, so you should use version 5x mri_vol2vol.
>
> Regards,
>
> Thomas
>
> On Thu, May 5, 2016 at 10:24 PM, Douglas Greve 
> wrote:
>
>>
>>
>> On 5/4/16 11:40 PM, Bronwyn Overs wrote:
>>
>> Hi Freesurfer Mailing List,
>>
>> I wish to extract stats for my sample for the Yeo 2011 cortical
>> parcellations and the Choi 2012 striatal parcellations (7 networks) that
>> are provided for 

Re: [Freesurfer] Stats for Yeo and Choi Parcellations

[Bronwyn Overs]

Hi Thomas,

I am not sure which file you are referring to when you say 
"Choi_atlas1mm.nii.gz". The files I have from the freesurfer wiki are:


Choi_JNeurophysiol12_MNI152_README
Choi2012_7Networks_ColorLUT.txt
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
Choi2012_17Networks_ColorLUT.txt
Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
FSL_MNI152_FreeSurferConformed_1mm.nii.gz

Which if any of these should I designate as the source in step 3a?

Also for step 2 I used "FSL_MNI152_FreeSurferConformed_1mm.nii", is this 
correct?


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 6/05/2016 12:50 am, Thomas Yeo wrote:
Hi Doug, the Choi file is a striatal functional connectivity atlas 
which we distribute. It's under the average directory.


Hi Bronwyn,

To transform the Choi's striatal atlas to your individual subject, 
Here's a (non-ideal) suggestion I previously suggested to another user:


1) Assuming you are quite happy with the freesurfer striatal 
parcellation in your individual subjects, then I am assuming 
freesurfer nonlinear registration (talairach.m3z) is working quite 
well. Talairach.m3z warps your subject to an internal freesurfer space 
(kinda like MNI305, but not quite). Let's say the freesurfer recon-all 
output is at /SUBJECT_FS/


2) Run the MNI152 1mm template (the one from FSL) through recon-all. 
Recon-all will give you a Talairach.m3z that allows you to map the 
MNI152 1mm template to the internal freesurfer space. Let's say the 
freesurfer recon-all output is at /MNI152_FS/


3) Then do the following:

a) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:

>> setenv SUBJECTS_DIR 
>> mri_vol2vol_used --mov Choi_atlas1mm.nii.gz --s MNI152_FS --targ 
$FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o 
Choi_atlas_freesurfer_internal_space.nii.gz --interp nearest


b) warp the Choi_atlas_freesurfer_internal_space.nii.gz to your subject:

>> setenv SUBJECTS_DIR 
>> mri_vol2vol --mov $SUBJECTS_DIR/AD_SUBJECT_FS/mri/norm.mgz --s 
AD_SUBJECT_FS --targ Choi_atlas_freesurfer_internal_space.nii.gz --m3z 
talairach.m3z --o Choi_atlas_AD_subject.nii.gz --interp nearest 
--inv-morph


This is not optimal because of the double interpolation. You might 
want to use the MNI template instead of the Choi_atlas to test the 
above, so you can check the goodness of the warp. The final warped MNI 
template should hopefully look identical to your subject. If that 
works, then use the Choi_atlas. Note that mri_vol2vol does not work 
properly for talairach.m3z below version 5, so you should use version 
5x mri_vol2vol.


Regards,

Thomas


On Thu, May 5, 2016 at 10:24 PM, Douglas Greve 
> wrote:




On 5/4/16 11:40 PM, Bronwyn Overs wrote:

Hi Freesurfer Mailing List,

I wish to extract stats for my sample for the Yeo 2011 cortical
parcellations and the Choi 2012 striatal parcellations (7
networks) that are provided for download on the freesurfer wiki.
My questions are as follows:

1. I noticed that the Yeo 2011 annot files are already available
in fsaverage/label. How do I map these annot file to each of my
subjects so that I can extract stats?

Use mri_surf2surf with the --save-annot option

2. For the Choi 2012 files I wish to use
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
. How do I map this file to each of my subjects so that I can
extract stats for the 7Network parcellation?

I don't know about this file. Where is it? Is it something we
distribute?
doug

-- 


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
   

Re: [Freesurfer] Stats for Yeo and Choi Parcellations

[Bronwyn Overs]

Hi Doug,

I tried to run the mri_surf2surf command as follows and got this error:

[b.overs~]$ mri_surf2surf --srcsubject fsaverage --srcsurfval 
lh.Yeo2011_7Networks_N1000.annot --trgsubject testsubj --trgsurfval 
lh.Yeo2011_7Networks_N1000.annot --hemi lh --save-annot

ERROR: Option --save-annot unknown
[b.overs~]$

I could not see any --save annot option in the help file. I am running 
this correctly? Should I be suing the .mgz file as the input or is the 
annotation file ok as this is what I want to resample?


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 6/05/2016 12:24 am, Douglas Greve wrote:



On 5/4/16 11:40 PM, Bronwyn Overs wrote:

Hi Freesurfer Mailing List,

I wish to extract stats for my sample for the Yeo 2011 cortical 
parcellations and the Choi 2012 striatal parcellations (7 networks) 
that are provided for download on the freesurfer wiki. My questions 
are as follows:


1. I noticed that the Yeo 2011 annot files are already available in 
fsaverage/label. How do I map these annot file to each of my subjects 
so that I can extract stats?

Use mri_surf2surf with the --save-annot option
2. For the Choi 2012 files I wish to use 
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz . 
How do I map this file to each of my subjects so that I can extract 
stats for the 7Network parcellation?

I don't know about this file. Where is it? Is it something we distribute?
doug


--

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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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] Stats for Yeo and Choi Parcellations

[Thomas Yeo]

Hi Doug, the Choi file is a striatal functional connectivity atlas which we
distribute. It's under the average directory.

Hi Bronwyn,

To transform the Choi's striatal atlas to your individual subject, Here's a
(non-ideal) suggestion I previously suggested to another user:

1) Assuming you are quite happy with the freesurfer striatal parcellation
in your individual subjects, then I am assuming freesurfer nonlinear
registration (talairach.m3z) is working quite well. Talairach.m3z warps
your subject to an internal freesurfer space (kinda like MNI305, but not
quite). Let's say the freesurfer recon-all output is at
/SUBJECT_FS/

2) Run the MNI152 1mm template (the one from FSL) through recon-all.
Recon-all will give you a Talairach.m3z that allows you to map the MNI152
1mm template to the internal freesurfer space. Let's say the freesurfer
recon-all output is at /MNI152_FS/

3) Then do the following:

a) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:

>> setenv SUBJECTS_DIR 
>> mri_vol2vol_used --mov Choi_atlas1mm.nii.gz --s MNI152_FS --targ
$FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
Choi_atlas_freesurfer_internal_space.nii.gz --interp nearest

b) warp the Choi_atlas_freesurfer_internal_space.nii.gz to your subject:

>> setenv SUBJECTS_DIR 
>> mri_vol2vol --mov $SUBJECTS_DIR/AD_SUBJECT_FS/mri/norm.mgz --s
AD_SUBJECT_FS --targ Choi_atlas_freesurfer_internal_space.nii.gz --m3z
talairach.m3z --o Choi_atlas_AD_subject.nii.gz --interp nearest --inv-morph

This is not optimal because of the double interpolation. You might want to
use the MNI template instead of the Choi_atlas to test the above, so you
can check the goodness of the warp. The final warped MNI template should
hopefully look identical to your subject. If that works, then use the
Choi_atlas. Note that mri_vol2vol does not work properly for
talairach.m3z below
version 5, so you should use version 5x mri_vol2vol.

Regards,

Thomas

On Thu, May 5, 2016 at 10:24 PM, Douglas Greve 
wrote:

>
>
> On 5/4/16 11:40 PM, Bronwyn Overs wrote:
>
> Hi Freesurfer Mailing List,
>
> I wish to extract stats for my sample for the Yeo 2011 cortical
> parcellations and the Choi 2012 striatal parcellations (7 networks) that
> are provided for download on the freesurfer wiki. My questions are as
> follows:
>
> 1. I noticed that the Yeo 2011 annot files are already available in
> fsaverage/label. How do I map these annot file to each of my subjects so
> that I can extract stats?
>
> Use mri_surf2surf with the --save-annot option
>
> 2. For the Choi 2012 files I wish to use
> Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz . How do
> I map this file to each of my subjects so that I can extract stats for the
> 7Network parcellation?
>
> I don't know about this file. Where is it? Is it something we distribute?
> doug
>
> --
>
> 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] 
>
>
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Re: [Freesurfer] Stats for Yeo and Choi Parcellations

[Douglas Greve]

On 5/4/16 11:40 PM, Bronwyn Overs wrote:

Hi Freesurfer Mailing List,

I wish to extract stats for my sample for the Yeo 2011 cortical 
parcellations and the Choi 2012 striatal parcellations (7 networks) 
that are provided for download on the freesurfer wiki. My questions 
are as follows:


1. I noticed that the Yeo 2011 annot files are already available in 
fsaverage/label. How do I map these annot file to each of my subjects 
so that I can extract stats?

Use mri_surf2surf with the --save-annot option
2. For the Choi 2012 files I wish to use 
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz . 
How do I map this file to each of my subjects so that I can extract 
stats for the 7Network parcellation?

I don't know about this file. Where is it? Is it something we distribute?
doug


--

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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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] Stats for Yeo and Choi Parcellations

[Bruce Fischl]

Hi Bronwyn

it depends on the type of stats, but you would either map the Yeo 
annotations to your subjects, or map the stats from your subjects to 
fsaverage.

cheers
Bruce


On Thu, 5 May 2016, Bronwyn Overs wrote:

> Hi Freesurfer Mailing List,
>
> I wish to extract stats for my sample for the Yeo 2011 cortical parcellations 
> and the Choi 2012 striatal parcellations (7 networks) that are provided for 
> download on the freesurfer wiki. My questions are as follows:
>
> 1. I noticed that the Yeo 2011 annot files are already available in 
> fsaverage/label. How do I map these annot file to each of my subjects so that 
> I can extract stats?
> 2. For the Choi 2012 files I wish to use 
> Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz . How do I 
> map this file to each of my subjects so that I can extract stats for the 
> 7Network parcellation?
>
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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[Freesurfer] Stats for Yeo and Choi Parcellations

[Bronwyn Overs]

Hi Freesurfer Mailing List,

I wish to extract stats for my sample for the Yeo 2011 cortical 
parcellations and the Choi 2012 striatal parcellations (7 networks) that 
are provided for download on the freesurfer wiki. My questions are as 
follows:


1. I noticed that the Yeo 2011 annot files are already available in 
fsaverage/label. How do I map these annot file to each of my subjects so 
that I can extract stats?
2. For the Choi 2012 files I wish to use 
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz . How 
do I map this file to each of my subjects so that I can extract stats 
for the 7Network parcellation?

--

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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