Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Looks like it does what you wanted. Side note, if you have multiple
non-overlapping ROIs to do this with, you could also make them into a
dlabel file, then use -cifti-parcellate on the timeseries, and do a
-cifti-cross-correlation using it and the smoothed dtseries. However,
you'll need to figure out the correct order of files in the cross
correlation to avoid needing -cifti-transpose to display it the way you
want.
Tim
On Thu, May 4, 2017 at 4:28 PM, Ely, Benjamin <benjamin@mssm.edu> wrote:
> Good to know, thanks - that's consistent with what I'm seeing. Will keep
> the transformation for now. For future ref to anyone trying this, the
> corrected sequence is:
>
> 1) Extract mean unsmoothed ROI data to text:
> wb_command -cifti-roi-average ${sub}_${run}.dtseries.nii
> roi_data_${sub}_${run}_unsmoothed.txt -vol-roi ${sub}_roi_mask.nii
> 2) Convert extracted ROI data to cifti:
> wb_command -cifti-create-scalar-series roi_data_${sub}_${run}_unsmoothed.txt
> roi_data_${sub}_${run}_unsmoothed.dscalar.nii -transpose -series SECOND 0 1
> 3) Cross-correlate this new ROI timeseries cifti with the smoothed
> whole-brain cifti data and (optionally) z transform:
> wb_command -cifti-cross-correlation ${subject}_${run}_smoothed.dtseries.nii
> roi_data_${sub}_${run}_unsmoothed.dscalar.nii
> z_correlation_${sub}_${run}.dscalar.nii -fisher-z
> 4) Repeat for all runs and average:
> wb_command -cifti-average z_correlation_${sub}_average.dscalar.nii \
>
> -cifti z_correlation_${sub}_run1.dscalar.nii \
>
> -cifti z_correlation_${sub}_run2.dscalar.nii \
>
> -cifti z_correlation_${sub}_run3.dscalar.nii \
>
> -cifti z_correlation_${sub}_run4.dscalar.nii
>
> --
> *From:* Benjamin Risk [bb...@cornell.edu]
> *Sent:* Thursday, May 04, 2017 2:34 PM
> *To:* Harms, Michael
> *Cc:* Ely, Benjamin
> *Subject:* Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
>
> That's true, but the sample correlation coefficient is asymptotically
> normal. I agree with Benjamin based on some correlations I looked at from
> HCP data. They do tend to be pretty Gaussian because the number of time
> points is large and the correlations I looked at were not close to 1 or
> -1.
>
> Even when the correlations are close to Gaussian, the Fisher-transform is
> variance stabilizing and results in a standard Gaussian, which is nice for
> hypothesis testing. But there are cases where you might not want to
> transform, e.g., interpretability.
>
> On Thu, May 4, 2017 at 1:49 PM, Harms, Michael <mha...@wustl.edu> wrote:
>
>>
>> To be clear, depending on the r-value, the Fisher’s z-transform may not
>> change the value much, but that doesn’t mean that the correlation
>> (Pearson’s r) has a *distribution* that is close to Gaussian.
>>
>> 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 <(314)%20747-6173>
>> St. Louis, MO 63110 Email: mha...@wustl.edu
>>
>> From: "Ely, Benjamin" <benjamin@mssm.edu>
>> Date: Thursday, May 4, 2017 at 12:43 PM
>> To: Michael Harms <mha...@wustl.edu>, "Glasser, Matthew" <
>> glass...@wustl.edu>, "HCP-Users@humanconnectome.org" <
>> HCP-Users@humanconnectome.org>
>> Subject: RE: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
>>
>> Ah that makes sense, thanks! The effect of the z transformation is quite
>> subtle (as expected since the correlation distributions are close to
>> gaussian before transformation).
>> --
>> *From:* Harms, Michael [mha...@wustl.edu]
>> *Sent:* Thursday, May 04, 2017 10:21 AM
>> *To:* Ely, Benjamin; Glasser, Matthew; HCP-Users@humanconnectome.org
>> *Subject:* Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
>>
>>
>> I would probably z transform before averaging across runs, so that you
>> are averaging something with at least an approximately gaussian
>> distribution.
>>
>> 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 <(314)%20747-6173>
>> St. Louis, MO 63110 Email: mha...@wustl.edu
>>
>&g
Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Good to know, thanks - that's consistent with what I'm seeing. Will keep the
transformation for now. For future ref to anyone trying this, the corrected
sequence is:
1) Extract mean unsmoothed ROI data to text:
wb_command -cifti-roi-average ${sub}_${run}.dtseries.nii
roi_data_${sub}_${run}_unsmoothed.txt -vol-roi ${sub}_roi_mask.nii
2) Convert extracted ROI data to cifti:
wb_command -cifti-create-scalar-series roi_data_${sub}_${run}_unsmoothed.txt
roi_data_${sub}_${run}_unsmoothed.dscalar.nii -transpose -series SECOND 0 1
3) Cross-correlate this new ROI timeseries cifti with the smoothed whole-brain
cifti data and (optionally) z transform:
wb_command -cifti-cross-correlation ${subject}_${run}_smoothed.dtseries.nii
roi_data_${sub}_${run}_unsmoothed.dscalar.nii
z_correlation_${sub}_${run}.dscalar.nii -fisher-z
4) Repeat for all runs and average:
wb_command -cifti-average z_correlation_${sub}_average.dscalar.nii \
-cifti z_correlation_${sub}_run1.dscalar.nii \
-cifti z_correlation_${sub}_run2.dscalar.nii \
-cifti z_correlation_${sub}_run3.dscalar.nii \
-cifti z_correlation_${sub}_run4.dscalar.nii
From: Benjamin Risk [bb...@cornell.edu]
Sent: Thursday, May 04, 2017 2:34 PM
To: Harms, Michael
Cc: Ely, Benjamin
Subject: Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
That's true, but the sample correlation coefficient is asymptotically normal. I
agree with Benjamin based on some correlations I looked at from HCP data. They
do tend to be pretty Gaussian because the number of time points is large and
the correlations I looked at were not close to 1 or -1.
Even when the correlations are close to Gaussian, the Fisher-transform is
variance stabilizing and results in a standard Gaussian, which is nice for
hypothesis testing. But there are cases where you might not want to transform,
e.g., interpretability.
On Thu, May 4, 2017 at 1:49 PM, Harms, Michael
<mha...@wustl.edu<mailto:mha...@wustl.edu>> wrote:
To be clear, depending on the r-value, the Fisher’s z-transform may not change
the value much, but that doesn’t mean that the correlation (Pearson’s r) has a
*distribution* that is close to Gaussian.
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<tel:(314)%20747-6173>
St. Louis, MO 63110 Email: mha...@wustl.edu<mailto:mha...@wustl.edu>
From: "Ely, Benjamin" <benjamin@mssm.edu<mailto:benjamin@mssm.edu>>
Date: Thursday, May 4, 2017 at 12:43 PM
To: Michael Harms <mha...@wustl.edu<mailto:mha...@wustl.edu>>, "Glasser,
Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>,
"HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>"
<HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>>
Subject: RE: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Ah that makes sense, thanks! The effect of the z transformation is quite subtle
(as expected since the correlation distributions are close to gaussian before
transformation).
From: Harms, Michael [mha...@wustl.edu<mailto:mha...@wustl.edu>]
Sent: Thursday, May 04, 2017 10:21 AM
To: Ely, Benjamin; Glasser, Matthew;
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
Subject: Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
I would probably z transform before averaging across runs, so that you are
averaging something with at least an approximately gaussian distribution.
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<tel:(314)%20747-6173>
St. Louis, MO 63110 Email: mha...@wustl.edu<mailto:mha...@wustl.edu>
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Ely, Benjamin"
<benjamin@mssm.edu<mailto:benjamin@mssm.edu>>
Date: Wednesday, May 3, 2017 at 11:46 PM
To: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>,
"HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>"
<HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Hi Matt,
Thanks for getting back to me - after some further tinkering, I think this
command sequence yields the desired output:
1) Extract mean unsmoothed ROI data to text:
wb_command -cifti-roi-average ${subject}_${run}
Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
To be clear, depending on the r-value, the Fisher’s z-transform may not change
the value much, but that doesn’t mean that the correlation (Pearson’s r) has a
*distribution* that is close to Gaussian.
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: "Ely, Benjamin" <benjamin@mssm.edu<mailto:benjamin@mssm.edu>>
Date: Thursday, May 4, 2017 at 12:43 PM
To: Michael Harms <mha...@wustl.edu<mailto:mha...@wustl.edu>>, "Glasser,
Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>,
"HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>"
<HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>>
Subject: RE: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Ah that makes sense, thanks! The effect of the z transformation is quite subtle
(as expected since the correlation distributions are close to gaussian before
transformation).
From: Harms, Michael [mha...@wustl.edu<mailto:mha...@wustl.edu>]
Sent: Thursday, May 04, 2017 10:21 AM
To: Ely, Benjamin; Glasser, Matthew;
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
Subject: Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
I would probably z transform before averaging across runs, so that you are
averaging something with at least an approximately gaussian distribution.
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<mailto:mha...@wustl.edu>
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Ely, Benjamin"
<benjamin@mssm.edu<mailto:benjamin@mssm.edu>>
Date: Wednesday, May 3, 2017 at 11:46 PM
To: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>,
"HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>"
<HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Hi Matt,
Thanks for getting back to me - after some further tinkering, I think this
command sequence yields the desired output:
1) Extract mean unsmoothed ROI data to text:
wb_command -cifti-roi-average ${subject}_${run}.dtseries.nii
roi_data_${sub}_${run}_unsmoothed.txt -vol-roi ${sub}_roi_mask.nii # probably
works for surface-based ROIs as well but I haven't tested
2) Convert extracted ROI data to cifti:
wb_command -cifti-create-scalar-series roi_data_${sub}_${run}_unsmoothed.txt
roi_data_${sub}_${run}_unsmoothed.dscalar.nii -transpose -series SECOND 0 1
3) Cross-correlate this new ROI timeseries cifti with the smoothed whole-brain
cifti data:
wb_command -cifti-cross-correlation ${subject}_${run}_smoothed.dtseries.nii
roi_data_${sub}_${run}_unsmoothed.dscalar.nii
correlation_${sub}_${run}.dscalar.nii
4) Repeat for all runs and average:
wb_command -cifti-average correlation_${sub}_average.dscalar.nii -cifti
correlation_${sub}_run1.dscalar.nii -cifti correlation_${sub}_run2.dscalar.nii
-cifti correlation_${sub}_run3.dscalar.nii -cifti
correlation_${sub}_run4.dscalar.nii
5) Fisher z transform results:
wb_command -cifti-math "atanh(x)" z_correlation_${sub}_average.dscalar.nii -var
x correlation_${sub}_average.dscalar.nii
The resulting files appear as expected (similar to the
smoothed-ROI-to-smoothed-cifti results but with more variation/less smooth
appearance). Please let me know if you see any errors.
Thanks again!
-Ely
From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>]
Sent: Wednesday, May 03, 2017 11:32 PM
To: Ely, Benjamin;
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
Subject: Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Hi Ely,
We don’t have a function like this yet, but have been discussing making one. I
think matlab is your best bet at this time.
Peace,
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Ely, Benjamin"
<benjamin@mssm.edu<mailto:benjamin....@mssm.edu>>
Date: Wednesday, May 3, 2017 at 10:06 PM
To: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>"
<HCP-Users@humanconnectome.org<mailto:HCP-Users@humanc
Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Ah that makes sense, thanks! The effect of the z transformation is quite subtle
(as expected since the correlation distributions are close to gaussian before
transformation).
From: Harms, Michael [mha...@wustl.edu]
Sent: Thursday, May 04, 2017 10:21 AM
To: Ely, Benjamin; Glasser, Matthew; HCP-Users@humanconnectome.org
Subject: Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
I would probably z transform before averaging across runs, so that you are
averaging something with at least an approximately gaussian distribution.
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:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Ely, Benjamin"
<benjamin@mssm.edu<mailto:benjamin@mssm.edu>>
Date: Wednesday, May 3, 2017 at 11:46 PM
To: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>,
"HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>"
<HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Hi Matt,
Thanks for getting back to me - after some further tinkering, I think this
command sequence yields the desired output:
1) Extract mean unsmoothed ROI data to text:
wb_command -cifti-roi-average ${subject}_${run}.dtseries.nii
roi_data_${sub}_${run}_unsmoothed.txt -vol-roi ${sub}_roi_mask.nii # probably
works for surface-based ROIs as well but I haven't tested
2) Convert extracted ROI data to cifti:
wb_command -cifti-create-scalar-series roi_data_${sub}_${run}_unsmoothed.txt
roi_data_${sub}_${run}_unsmoothed.dscalar.nii -transpose -series SECOND 0 1
3) Cross-correlate this new ROI timeseries cifti with the smoothed whole-brain
cifti data:
wb_command -cifti-cross-correlation ${subject}_${run}_smoothed.dtseries.nii
roi_data_${sub}_${run}_unsmoothed.dscalar.nii
correlation_${sub}_${run}.dscalar.nii
4) Repeat for all runs and average:
wb_command -cifti-average correlation_${sub}_average.dscalar.nii -cifti
correlation_${sub}_run1.dscalar.nii -cifti correlation_${sub}_run2.dscalar.nii
-cifti correlation_${sub}_run3.dscalar.nii -cifti
correlation_${sub}_run4.dscalar.nii
5) Fisher z transform results:
wb_command -cifti-math "atanh(x)" z_correlation_${sub}_average.dscalar.nii -var
x correlation_${sub}_average.dscalar.nii
The resulting files appear as expected (similar to the
smoothed-ROI-to-smoothed-cifti results but with more variation/less smooth
appearance). Please let me know if you see any errors.
Thanks again!
-Ely
From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>]
Sent: Wednesday, May 03, 2017 11:32 PM
To: Ely, Benjamin;
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
Subject: Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Hi Ely,
We don’t have a function like this yet, but have been discussing making one. I
think matlab is your best bet at this time.
Peace,
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Ely, Benjamin"
<benjamin@mssm.edu<mailto:benjamin@mssm.edu>>
Date: Wednesday, May 3, 2017 at 10:06 PM
To: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>"
<HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>>
Subject: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Hi everyone,
I'm running some connectivity analyses following the procedure outlined in this
thread
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg04403.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_hcp-2Dusers-40humanconnectome.org_msg04403.html=DwMF-g=shNJtf5dKgNcPZ6Yh64b-A=wkbWuLo29rcKlS_jqY-IWyhtdbOPOJ4YiqipZSzm0r4=yPHnchyPW8zwQAjrQNcCAh2TbX5ft58rzU3tH0B6K54=XOJJuzw82VOhaCYWwXk5uBoLsl8E7AyfiW_3Uz35EJo=>.
Since my ROIs are fairly small, I'd like to calculate the correlation between
the mean unsmoothed timeseries of each ROI (i.e. "smoothed" only by averaging
within the ROI) and the subject's smoothed cifti data. However, the wb_command
-cifti-average-roi-correlation function only generates correlations from an ROI
within the same cifti file, and none of the other functions seem appropriate
(possibly -cifti-cross-correlation where one input is a cifti containing a
single row with the mean unsmoothed timeseries, but I couldn't get this to
work). Is there a stra
Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
I would probably z transform before averaging across runs, so that you are
averaging something with at least an approximately gaussian distribution.
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:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Ely, Benjamin"
<benjamin@mssm.edu<mailto:benjamin@mssm.edu>>
Date: Wednesday, May 3, 2017 at 11:46 PM
To: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>,
"HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>"
<HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Hi Matt,
Thanks for getting back to me - after some further tinkering, I think this
command sequence yields the desired output:
1) Extract mean unsmoothed ROI data to text:
wb_command -cifti-roi-average ${subject}_${run}.dtseries.nii
roi_data_${sub}_${run}_unsmoothed.txt -vol-roi ${sub}_roi_mask.nii # probably
works for surface-based ROIs as well but I haven't tested
2) Convert extracted ROI data to cifti:
wb_command -cifti-create-scalar-series roi_data_${sub}_${run}_unsmoothed.txt
roi_data_${sub}_${run}_unsmoothed.dscalar.nii -transpose -series SECOND 0 1
3) Cross-correlate this new ROI timeseries cifti with the smoothed whole-brain
cifti data:
wb_command -cifti-cross-correlation ${subject}_${run}_smoothed.dtseries.nii
roi_data_${sub}_${run}_unsmoothed.dscalar.nii
correlation_${sub}_${run}.dscalar.nii
4) Repeat for all runs and average:
wb_command -cifti-average correlation_${sub}_average.dscalar.nii -cifti
correlation_${sub}_run1.dscalar.nii -cifti correlation_${sub}_run2.dscalar.nii
-cifti correlation_${sub}_run3.dscalar.nii -cifti
correlation_${sub}_run4.dscalar.nii
5) Fisher z transform results:
wb_command -cifti-math "atanh(x)" z_correlation_${sub}_average.dscalar.nii -var
x correlation_${sub}_average.dscalar.nii
The resulting files appear as expected (similar to the
smoothed-ROI-to-smoothed-cifti results but with more variation/less smooth
appearance). Please let me know if you see any errors.
Thanks again!
-Ely
From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>]
Sent: Wednesday, May 03, 2017 11:32 PM
To: Ely, Benjamin;
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
Subject: Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Hi Ely,
We don’t have a function like this yet, but have been discussing making one. I
think matlab is your best bet at this time.
Peace,
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Ely, Benjamin"
<benjamin@mssm.edu<mailto:benjamin@mssm.edu>>
Date: Wednesday, May 3, 2017 at 10:06 PM
To: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>"
<HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>>
Subject: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Hi everyone,
I'm running some connectivity analyses following the procedure outlined in this
thread
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg04403.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_hcp-2Dusers-40humanconnectome.org_msg04403.html=DwMF-g=shNJtf5dKgNcPZ6Yh64b-A=wkbWuLo29rcKlS_jqY-IWyhtdbOPOJ4YiqipZSzm0r4=yPHnchyPW8zwQAjrQNcCAh2TbX5ft58rzU3tH0B6K54=XOJJuzw82VOhaCYWwXk5uBoLsl8E7AyfiW_3Uz35EJo=>.
Since my ROIs are fairly small, I'd like to calculate the correlation between
the mean unsmoothed timeseries of each ROI (i.e. "smoothed" only by averaging
within the ROI) and the subject's smoothed cifti data. However, the wb_command
-cifti-average-roi-correlation function only generates correlations from an ROI
within the same cifti file, and none of the other functions seem appropriate
(possibly -cifti-cross-correlation where one input is a cifti containing a
single row with the mean unsmoothed timeseries, but I couldn't get this to
work). Is there a straightforward way to generate these correlations using
workbench, or will I need to e.g. write a matlab script? My ROIs are
subcortical (voxel-based), if that matters.
Thank you!
-Ely
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Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Hi Ely,
That looks okay to me on a quick pass, but perhaps Tim will see something I
don’t.
Peace,
Matt.
From: "Ely, Benjamin" <benjamin@mssm.edu<mailto:benjamin@mssm.edu>>
Date: Wednesday, May 3, 2017 at 11:46 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>,
"HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>"
<HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>>
Subject: RE: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Hi Matt,
Thanks for getting back to me - after some further tinkering, I think this
command sequence yields the desired output:
1) Extract mean unsmoothed ROI data to text:
wb_command -cifti-roi-average ${subject}_${run}.dtseries.nii
roi_data_${sub}_${run}_unsmoothed.txt -vol-roi ${sub}_roi_mask.nii # probably
works for surface-based ROIs as well but I haven't tested
2) Convert extracted ROI data to cifti:
wb_command -cifti-create-scalar-series roi_data_${sub}_${run}_unsmoothed.txt
roi_data_${sub}_${run}_unsmoothed.dscalar.nii -transpose -series SECOND 0 1
3) Cross-correlate this new ROI timeseries cifti with the smoothed whole-brain
cifti data:
wb_command -cifti-cross-correlation ${subject}_${run}_smoothed.dtseries.nii
roi_data_${sub}_${run}_unsmoothed.dscalar.nii
correlation_${sub}_${run}.dscalar.nii
4) Repeat for all runs and average:
wb_command -cifti-average correlation_${sub}_average.dscalar.nii -cifti
correlation_${sub}_run1.dscalar.nii -cifti correlation_${sub}_run2.dscalar.nii
-cifti correlation_${sub}_run3.dscalar.nii -cifti
correlation_${sub}_run4.dscalar.nii
5) Fisher z transform results:
wb_command -cifti-math "atanh(x)" z_correlation_${sub}_average.dscalar.nii -var
x correlation_${sub}_average.dscalar.nii
The resulting files appear as expected (similar to the
smoothed-ROI-to-smoothed-cifti results but with more variation/less smooth
appearance). Please let me know if you see any errors.
Thanks again!
-Ely
From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>]
Sent: Wednesday, May 03, 2017 11:32 PM
To: Ely, Benjamin;
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
Subject: Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Hi Ely,
We don’t have a function like this yet, but have been discussing making one. I
think matlab is your best bet at this time.
Peace,
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Ely, Benjamin"
<benjamin@mssm.edu<mailto:benjamin@mssm.edu>>
Date: Wednesday, May 3, 2017 at 10:06 PM
To: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>"
<HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>>
Subject: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Hi everyone,
I'm running some connectivity analyses following the procedure outlined in this
thread
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg04403.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_hcp-2Dusers-40humanconnectome.org_msg04403.html=DwMF-g=shNJtf5dKgNcPZ6Yh64b-A=wkbWuLo29rcKlS_jqY-IWyhtdbOPOJ4YiqipZSzm0r4=yPHnchyPW8zwQAjrQNcCAh2TbX5ft58rzU3tH0B6K54=XOJJuzw82VOhaCYWwXk5uBoLsl8E7AyfiW_3Uz35EJo=>.
Since my ROIs are fairly small, I'd like to calculate the correlation between
the mean unsmoothed timeseries of each ROI (i.e. "smoothed" only by averaging
within the ROI) and the subject's smoothed cifti data. However, the wb_command
-cifti-average-roi-correlation function only generates correlations from an ROI
within the same cifti file, and none of the other functions seem appropriate
(possibly -cifti-cross-correlation where one input is a cifti containing a
single row with the mean unsmoothed timeseries, but I couldn't get this to
work). Is there a straightforward way to generate these correlations using
workbench, or will I need to e.g. write a matlab script? My ROIs are
subcortical (voxel-based), if that matters.
Thank you!
-Ely
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The materials in this message are private and may contain Protected Healthcare
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intended recipient, be advised that any unauthorized use, disclosure, copying
or the tak
Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Hi Matt,
Thanks for getting back to me - after some further tinkering, I think this
command sequence yields the desired output:
1) Extract mean unsmoothed ROI data to text:
wb_command -cifti-roi-average ${subject}_${run}.dtseries.nii
roi_data_${sub}_${run}_unsmoothed.txt -vol-roi ${sub}_roi_mask.nii # probably
works for surface-based ROIs as well but I haven't tested
2) Convert extracted ROI data to cifti:
wb_command -cifti-create-scalar-series roi_data_${sub}_${run}_unsmoothed.txt
roi_data_${sub}_${run}_unsmoothed.dscalar.nii -transpose -series SECOND 0 1
3) Cross-correlate this new ROI timeseries cifti with the smoothed whole-brain
cifti data:
wb_command -cifti-cross-correlation ${subject}_${run}_smoothed.dtseries.nii
roi_data_${sub}_${run}_unsmoothed.dscalar.nii
correlation_${sub}_${run}.dscalar.nii
4) Repeat for all runs and average:
wb_command -cifti-average correlation_${sub}_average.dscalar.nii -cifti
correlation_${sub}_run1.dscalar.nii -cifti correlation_${sub}_run2.dscalar.nii
-cifti correlation_${sub}_run3.dscalar.nii -cifti
correlation_${sub}_run4.dscalar.nii
5) Fisher z transform results:
wb_command -cifti-math "atanh(x)" z_correlation_${sub}_average.dscalar.nii -var
x correlation_${sub}_average.dscalar.nii
The resulting files appear as expected (similar to the
smoothed-ROI-to-smoothed-cifti results but with more variation/less smooth
appearance). Please let me know if you see any errors.
Thanks again!
-Ely
From: Glasser, Matthew [glass...@wustl.edu]
Sent: Wednesday, May 03, 2017 11:32 PM
To: Ely, Benjamin; HCP-Users@humanconnectome.org
Subject: Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Hi Ely,
We don’t have a function like this yet, but have been discussing making one. I
think matlab is your best bet at this time.
Peace,
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Ely, Benjamin"
<benjamin@mssm.edu<mailto:benjamin@mssm.edu>>
Date: Wednesday, May 3, 2017 at 10:06 PM
To: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>"
<HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>>
Subject: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Hi everyone,
I'm running some connectivity analyses following the procedure outlined in this
thread
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg04403.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_hcp-2Dusers-40humanconnectome.org_msg04403.html=DwMF-g=shNJtf5dKgNcPZ6Yh64b-A=wkbWuLo29rcKlS_jqY-IWyhtdbOPOJ4YiqipZSzm0r4=yPHnchyPW8zwQAjrQNcCAh2TbX5ft58rzU3tH0B6K54=XOJJuzw82VOhaCYWwXk5uBoLsl8E7AyfiW_3Uz35EJo=>.
Since my ROIs are fairly small, I'd like to calculate the correlation between
the mean unsmoothed timeseries of each ROI (i.e. "smoothed" only by averaging
within the ROI) and the subject's smoothed cifti data. However, the wb_command
-cifti-average-roi-correlation function only generates correlations from an ROI
within the same cifti file, and none of the other functions seem appropriate
(possibly -cifti-cross-correlation where one input is a cifti containing a
single row with the mean unsmoothed timeseries, but I couldn't get this to
work). Is there a straightforward way to generate these correlations using
workbench, or will I need to e.g. write a matlab script? My ROIs are
subcortical (voxel-based), if that matters.
Thank you!
-Ely
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The materials in this message are private and may contain Protected Healthcare
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strictly prohibited. If you have received this email in error, please
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Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Hi Ely, We don’t have a function like this yet, but have been discussing making one. I think matlab is your best bet at this time. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Ely, Benjamin" <benjamin@mssm.edu<mailto:benjamin@mssm.edu>> Date: Wednesday, May 3, 2017 at 10:06 PM To: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" <HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>> Subject: [HCP-Users] unsmoothed ROI to smoothed cifti correlation Hi everyone, I'm running some connectivity analyses following the procedure outlined in this thread https://www.mail-archive.com/hcp-users@humanconnectome.org/msg04403.html. Since my ROIs are fairly small, I'd like to calculate the correlation between the mean unsmoothed timeseries of each ROI (i.e. "smoothed" only by averaging within the ROI) and the subject's smoothed cifti data. However, the wb_command -cifti-average-roi-correlation function only generates correlations from an ROI within the same cifti file, and none of the other functions seem appropriate (possibly -cifti-cross-correlation where one input is a cifti containing a single row with the mean unsmoothed timeseries, but I couldn't get this to work). Is there a straightforward way to generate these correlations using workbench, or will I need to e.g. write a matlab script? My ROIs are subcortical (voxel-based), if that matters. Thank you! -Ely ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] unsmoothed ROI to smoothed cifti correlation
Hi everyone, I'm running some connectivity analyses following the procedure outlined in this thread https://www.mail-archive.com/hcp-users@humanconnectome.org/msg04403.html. Since my ROIs are fairly small, I'd like to calculate the correlation between the mean unsmoothed timeseries of each ROI (i.e. "smoothed" only by averaging within the ROI) and the subject's smoothed cifti data. However, the wb_command -cifti-average-roi-correlation function only generates correlations from an ROI within the same cifti file, and none of the other functions seem appropriate (possibly -cifti-cross-correlation where one input is a cifti containing a single row with the mean unsmoothed timeseries, but I couldn't get this to work). Is there a straightforward way to generate these correlations using workbench, or will I need to e.g. write a matlab script? My ROIs are subcortical (voxel-based), if that matters. Thank you! -Ely ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
