Re: [HCP-Users] ROI parcellation

2015-12-17 Thread Joelle Zimmermann 
Hi Michael and all,

My goal is to use the aparc+aseg (in MNI from the standard Structural
package 100307/MNINonLinear/aparc+aseg.nii.gz)as a parcellation for the
volumetric 4D FIX extended clean data that's in MNI
(100307/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000_clean.nii.gz).
However, the aparc+aseg and the fMRI volumetric 4D data are of different
dimensions and resolution.

I'm assuming that the warp was really done in the same (MNI) template, but
that the aparc+aseg parcellation was not resliced to match the 4D
functional data?

Is there another aparc+aseg that's of dimensions matching the volumetric 4D
data (in MNINonLinear) that can be directly overlaid?

Thanks,
Joelle



On Tue, Dec 15, 2015 at 1:02 PM, Harms, Michael  wrote:

>
> Also, we encourage you to work in CIFTI-land so as to have a surface-based
> analysis of the cortical data.  But to answer your question, volumetric
> versions of both those FS parcellations are available in each subject's
> MNINonLinear folder; e.g.,
> 100307/MNINonLinear/aparc+aseg.nii.gz
> 100307/MNINonLinear/aparc.a2009s+aseg.nii.gz
>
> Those particular files should be part of the standard Structural package.
>
> cheers,
> -MH
>
>
> --
> Michael Harms, Ph.D.
>
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO  63110 Email: mha...@wustl.edu
>
>
>
> On 12/15/15 11:51 AM, "Greg Burgess"  wrote:
>
> Hi Joelle,
>
> You should be aware of potential issues with using anatomically-defined
> ROIs for rfMRI network analysis.
>
> Smith, S. M., Miller, K. L., Salimi-Khorshidi, G., Webster, M., Beckmann,
> C. F., Nichols, T. E., et al. (2011). Network modelling methods for FMRI.
> NeuroImage, 54(2), 875–891.
> http://doi.org/10.1016/j.neuroimage.2010.08.063
>
> Gordon, E. M., Laumann, T. O., Adeyemo, B., Huckins, J. F., Kelley, W. M.,
> & Petersen, S. E. (2014). Generation and Evaluation of a Cortical Area
> Parcellation from Resting-State Correlations. Cerebral Cortex.
> http://doi.org/10.1093/cercor/bhu239
>
> --Greg
>
> 
> Greg Burgess, Ph.D.
> Staff Scientist, Human Connectome Project
> Washington University School of Medicine
> Department of Neuroscience
> Phone: 314-362-7864
> Email: gburg...@wustl.edu
>
> On Dec 15, 2015, at 11:24 AM, Joelle Zimmermann <
> joelle.t.zimmerm...@gmail.com> wrote:
> Hi Michael,
> Thanks! So currently, the 2 available parcellation schemes are the
> Freesurfer Desikan-Killiany (aparc+aseg.mgz) and Destrieux
> (aparc.a2009s+aseg.mgz) in the structural extended preprocessed/T1w/mri
> folder? Im presuming these are in the subject's T1 individual subject
> space.
> Are you aware whether these parcellation schemes are already available in
> the MNI standard space? The goal is to parcellate the functional BOLD data
> (which are currently in MNI standard space; Ie in the FIX extended package,
> the MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean.nii).
> Or alternatively, if you could point me to where the volumetric functional
> BOLD data in T1 space is (I cannot locate it in the FIX extended package -
> this only seems to have func already normalized to MNI), I could directly
> apply the aparc+aseg parcellation (that's in T1 space) to this.
> Thanks,
> Joelle
> On Tue, Dec 15, 2015 at 10:46 AM, Harms, Michael  wrote:
> Hi,
> The only purely anatomical parcellation that is available currently are
> those provided by FreeSurfer, which you seem to be familiar with.
> If you are interested in a functional parcellation, there is the Gordon et
> al. parcellation derived from non-HCP rfMRI data.  A parcellation that
> incorporates the myelin maps and rfMRI data and which is specifically
> derived from a subset of HCP participants is in the works (from Matt G.)
> cheers,
> -MH
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.  Tel: 314-747-6173
> St. Louis, MO  63110  Email: mha...@wustl.edu
> From: Joelle Zimmermann 
> Date: Tuesday, December 15, 2015 9:35 AM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] ROI parcellation
> Hi everyone,
> Does HCP have a specific ROI parcellation that is commonly
> used/recommended? I  would prefer to begin with anatomically (rather than
> functionally defined) ROIs.
> My goal is to parcellate the voxel-wise time series into larger ROIs. I've
> previously used the Desikan-Killiany atlas, but ideally would be interested
> in using something with a finer parcellation.
> The only HCP parcellation I

Re: [HCP-Users] ROI parcellation

2015-12-17 Thread Harms, Michael 







Hi,
Yes to your 1st question; No to your 2nd.  If you want to go that direction (which again we don't recommend), you'll have to do the resampling yourself and make decisions about how you want to resample the high resolution 0.7 mm aparc+aseg.nii.gz into
 the lower 2 mm resolution functional volumes.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: Joelle Zimmermann <joelle.t.zimmerm...@gmail.com>
Date: Thursday, December 17, 2015 9:10 AM
To: "Harms, Michael" <mha...@wustl.edu>
Cc: Greg Burgess <gcburg...@gmail.com>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] ROI parcellation





Hi Michael and all,


My goal is to use the aparc+aseg (in MNI from the standard Structural package 100307/MNINonLinear/aparc+aseg.nii.gz)as a parcellation for the volumetric 4D FIX extended
 clean data that's in MNI (100307/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000_clean.nii.gz). However, the aparc+aseg and the fMRI volumetric 4D data are of different dimensions and resolution.

I'm assuming that the warp was really done in the same (MNI) template, but that the aparc+aseg parcellation was not resliced to match the 4D functional data?


Is there another aparc+aseg that's of dimensions matching the volumetric 4D data (in MNINonLinear) that can be directly overlaid?



Thanks,
Joelle









On Tue, Dec 15, 2015 at 1:02 PM, Harms, Michael 
<mha...@wustl.edu> wrote:





Also, we encourage you to work in CIFTI-land so as to have a surface-based analysis of the cortical data.  But to answer your question, volumetric versions of both those FS parcellations
 are available in each subject's MNINonLinear folder; e.g., 
100307/MNINonLinear/aparc+aseg.nii.gz

100307/MNINonLinear/aparc.a2009s+aseg.nii.gz


Those particular files should be part of the standard Structural package.


cheers,
-MH






-- 
Michael Harms, Ph.D.


---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel:
314-747-6173
St. Louis, MO  63110Email:
mha...@wustl.edu









On 12/15/15 11:51 AM, "Greg Burgess" <gcburg...@gmail.com> wrote:


Hi Joelle,


You should be aware of potential issues with using anatomically-defined ROIs for rfMRI network analysis.


Smith, S. M., Miller, K. L., Salimi-Khorshidi, G., Webster, M., Beckmann, C. F., Nichols, T. E., et al. (2011). Network modelling methods for FMRI. NeuroImage, 54(2), 875–891.
http://doi.org/10.1016/j.neuroimage.2010.08.063


Gordon, E. M., Laumann, T. O., Adeyemo, B., Huckins, J. F., Kelley, W. M., & Petersen, S. E. (2014). Generation and Evaluation of a Cortical Area Parcellation from Resting-State Correlations. Cerebral
 Cortex. http://doi.org/10.1093/cercor/bhu239


--Greg



Greg Burgess, Ph.D.
Staff Scientist, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience
Phone: 
314-362-7864
Email: 
gburg...@wustl.edu



On Dec 15, 2015, at 11:24 AM, Joelle Zimmermann <joelle.t.zimmerm...@gmail.com> wrote:

Hi Michael,

Thanks! So currently, the 2 available parcellation schemes are the Freesurfer Desikan-Killiany (aparc+aseg.mgz) and Destrieux (aparc.a2009s+aseg.mgz) in the structural extended preprocessed/T1w/mri folder? Im presuming these are in the subject's T1 individual
 subject space. 

Are you aware whether these parcellation schemes are already available in the MNI standard space? The goal is to parcellate the functional BOLD data (which are currently in MNI standard space; Ie in the FIX extended package, the MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean.nii).
 Or alternatively, if you could point me to where the volumetric functional BOLD data in T1 space is (I cannot locate it in the FIX extended package - this only seems to have func already normalized to MNI), I could directly apply the aparc+aseg parcellation
 (that's in T1 space) to this. 

Thanks,
Joelle



On Tue, Dec 15, 2015 at 10:46 AM, Harms, Michael <mha...@wustl.edu> wrote:

Hi,
The only purely anatomical parcellation that is available currently are those provided by FreeSurfer, which you seem to be familiar with.

If you are interested in a functional parcellation, there is the Gordon et al. parcellation derived from non-HCP rfMRI data.  A parcellation that incorporates the myelin maps and rfMRI data and which is specifically derived from a subset of HCP participants
 is in the works (from Matt G.)

cheers,
-MH

-- 
Michael Har

Re: [HCP-Users] ROI parcellation

2015-12-15 Thread Harms, Michael 







Hi,
The only purely anatomical parcellation that is available currently are those provided by FreeSurfer, which you seem to be familiar with.


If you are interested in a functional parcellation, there is the Gordon et al. parcellation derived from non-HCP rfMRI data.  A parcellation that incorporates the myelin maps and rfMRI data and which is specifically derived from a subset of HCP participants
 is in the works (from Matt G.)


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: Joelle Zimmermann 
Date: Tuesday, December 15, 2015 9:35 AM
To: "hcp-users@humanconnectome.org" 
Subject: [HCP-Users] ROI parcellation





Hi everyone,


Does HCP have a specific ROI parcellation that is commonly used/recommended? I  would prefer to begin with anatomically (rather than functionally defined) ROIs.


My goal is to parcellate the voxel-wise time series into larger ROIs. I've previously used the Desikan-Killiany atlas, but ideally would be interested in using something with a finer parcellation. 


The only HCP parcellation I was able to find was the parcellation from the ICA decomposition (resulting in one timeseries per ICA component), with 25, 50, 100, 200, 300 components. However, I don't think this is something I am interested in, as a single
 node (ie component) may comprise voxels that are scattered across the brain.


Is there anything like an anatomical ROI parcellation that's typically used by HCP people?


Thanks,
Joelle





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