Hi Jessica, use yhat = X(:,[1 2 3]*beta([1 2 3])
using only 1, 2, 3 will remove the effects of all the other variable
doug
On 5/19/2020 11:45 AM, Hua, Jessica wrote:
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After running the permutation and finding significant clusters, I am trying to calculate the value for each participant for these significant clusters.
The perm.th30.abs.y.ocn.dat contain the raw values, and I am trying to get the adjusted values accounting for age, sex, and ICV (this is a three group design).
The X matrix was 240x12 (see attached file)
- Column 1: 1s for Group 1 and 0s for Group 2 and 0s for Group 3
- Column 2: 0s for Group 1 and 1s for Group 2 and 0s for Group 3
- Column 3: 0s for Group 1 and 0s for Group 2 and 1s for Group 3
- Column 4: Age for Group 1 and 0s for Group 2 and 0s for Group 3
- Column 5: 0s for Group 1 and Age for Group 2 and 0s for Group 3
- Column 6: 0s for Group 1 and 0s for Group 2 and Age for Group 3
- Column 7: Sex for Group 1 and 0s for Group 2 and 0s for Group 3
- Column 8: 0s for Group 1 and Sex for Group 2 and 0s for Group 3
- Column 9: 0s for Group 1 and 0s for Group 2 and Sex for Group 3
- Column 10: zICV for Group 1 and 0s for Group 2 and 0s for Group 3
- Column 11: 0s for Group 1 and zICV for Group 2 and 0s for Group 3
- Column 12: 0s for Group 1 and 0s for Group 2 and zICV for Group 3
I was not sure how to modify the last line in your code in order to calculate adjusted values accounting for age, sex, and ICV for each participant.
Your code:
There is not an easy way to do it, but you can do it in matlab cd glmdir X = load('Xg.dat'); y = load('perm.th30.abs.y.ocn.dat'); beta = inv(X'*X)*X'*y; yhat = X(:,[i j k ...]*beta([i j k ...])
where i j k ... indicate the factors you want keep in your data. Each factor gets a column in the design matrix (and a beta). If you need help figuring this out, send the fsgd file.
Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri
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Today's Topics:
1. Re: vol2subfield single time course from multiple regions (stdp82@virgilio.it) 2. Re: Longitudinal edits on norm.mgz instead of brainmask (Douglas N. Greve) 3. Re: Volume timeseries to native and fsaverage (Douglas N. Greve) 4. Re: Group Analysis Covariates (Hua, Jessica) 5. Re: Group Analysis Covariates (Hua, Jessica) 6. Re: qdec and mris_anatomical_stats help (Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience) 7. Re: Robust Regression with Univariate LME (Hua, Jessica) 8. Re: Longitudinal edits on norm.mgz instead of brainmask (Elena Pozzi) 9. Freesurfer hippocampal segmentation in patient with temporal lesion (Linda Zhang) 10. Unable to visualize last Topics (Ferraro, Pilar) 11. freesurfer subcortical segmentation (ZhangBo) 12. FREESURFER-7.1: recon-all exited with error "ERROR: cannot find or read transforms/talairach.m3z" (Safi Ullah .)
Message: 1 Date: Mon, 18 May 2020 18:46:35 +0200 (CEST) From: stdp82@virgilio.it Subject: Re: [Freesurfer] vol2subfield single time course from multiple regions To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu, Bruce Fischl fischl@nmr.mgh.harvard.edu Cc: "Douglas N. Greve" dgreve@mgh.harvard.edu Message-ID: 163566753.837213.1589820395908@mail1.virgilio.it Content-Type: text/plain; charset="utf-8"
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thanks!
Il 18 maggio 2020 alle 16.23 Bruce Fischl <
fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > ha scritto:
--replaceonly <label 1 to remove> <label 1 to replace with> \ --replaceonly <label 2 to remove> <label 2 to replace with> \ . . .
On Mon, 18 May 2020, stdp82@virgilio.it
mailto:stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:
> > External Email - Use Caution
As reported in previous mails I have do it but with some
problems.
Moreover, how can I do with multiple arguments (more than 2)?
>
> > Il 17 maggio 2020 alle 21.30 Bruce Fischl <
fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu
ha scritto:
Hi Stefano
--replaceonly takes two arguments - the label you want to
replace and
the one you want to replace it with
cheers Bruce
On Sun, 17 May 2020, stdp82@virgilio.it
mailto:stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:
>
> > External Email - Use Caution
just a kind reminder
many thanks
>
> > Il 15 maggio 2020 alle 1.05 stdp82@virgilio.it
mailto:stdp82@virgilio.it mailto:stdp82@virgilio.it ha scritto:
>
> > mri_binarize --i
$SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz --replaceonly 8204 --replaceonly 8205 --replaceonly 8206 --replaceonly 8217 --replaceonly 8218 --o $SUBJECTS_DIR/R-Intralaminar.mgz
ERROR: Option 8205 unknown
mri_binarize --i $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz --replaceonly 8204 --replaceonly 8205 --replaceonly 8217 --replaceonly 8218 --o $SUBJECTS_DIR/R-Intralaminar.mgz
ERROR: Option 8217 unknown Il 14 maggio 2020 alle 17.39 "Douglas N. Greve" < dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu >
ha scritto:
>
> > Just add more --replaceonly args
>
> > On 5/14/2020 10:38 AM, stdp82@virgilio.it
mailto:stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:
>
> > External Email - Use Caution
>
> > Moreover, how can I merge, with mri_binarize, more
thalamic regions?
>
> > e.g. 8204 8205 8206 8217 8218
>
> > Il 13 maggio 2020 alle 23.03 "Douglas N.
Greve" < dgreve@mgh.harvard.edu
mailto:dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu > ha
scritto:
>
> > It problably means that seg 8130 does
not exist in the input mgz. Can you confirm that it does?
>
> > On 5/13/2020 12:51 PM,
stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:
>
> > External Email - Use
Caution
>
> > indeed. I would like to merge two
regions and extract the fMRI time serie. if no difference is there, somewhat is wrong. the L-VP file contains the same information of ThalamicNuclei.v10.T1.
>
> > thanks
>
> > Il 13 maggio 2020 alle 17.02
"Douglas N. Greve" < dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu > ha scritto:
>
> > That means there is no
difference
>
> > On 5/13/2020 10:47 AM,
stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:
>
> > External Email - Use
Caution
>
> > is the command line ok?
>
> > by running
>
> > mri_binarize --i
ThalamicNuclei.v10.T1.mgz --replace-only 8130 8133 --o L-VP.mgz
>
> > mri_diff --po
mri/ThalamicNuclei.v10.T1.mgz L-VP.mgz
>
> > I obtain
diffcount 0
>
> > Il 12 maggio 2020 alle
0.53 stdp82@virgilio.it mailto:stdp82@virgilio.it ha scritto:
>
> > by running
mri_diff --po mri/ThalamicNuclei.v10.T1.mgz L-VP.mgz I obtain diffcount 0
>
> > Il 11 maggio
2020 alle 19.18 "Douglas N. Greve" < dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu > ha scritto:
>
> > Try running this
to see if there is a difference mri_diff --po ThalamicNuclei.v10.T1.mgz Left-Ventroposterior.mgz Sometimes it is not easy to see a difference that is just a few voxels
>
> > On 5/11/2020
3:02 AM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:
>
> > External
Email - Use Caution
>
> > By
visualizing the output by freeview, I found that it was the same of ThalamicNuclei.v10.T1.mgz.
>
> > Thanks
>
> > Il
11 maggio 2020 alle 2.19 Bruce Fischl < fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >
ha scritto:
Hi Stefano
can you elaborate? Why do you suspect there is an error?
cheers Bruce On Mon, 11 May 2020, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:
>
> > External
Email - Use Caution
Please, could you check the command line. I suspect that an error is there. Thanks. Stefano
mri_binarize --i ThalamicNuclei.v10.T1.mgz --replace-only 8130
8133 --o Left-Ventroposterior.mgz
>
> > Il
30 aprile 2020 alle 18.51 "Douglas N. Greve" < dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu > ha scritto:
>
> > You
can use mri_binarize --i ThalamicNuclei.v10.T1.mgz --replace-only segid segidreplace ... --o newseg.mgz to create a new segmentation with merged segments, then using vol2subfield with the newseg seg as --sf
>
> > On
4/29/2020 7:57 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:
>
> > External
Email - Use Caution
>
> > Hi
list,
>
> > vol2subfield
--i fmcpr.nii.gz --reg register.dof6.lta --sf ThalamicNuclei.v10.T1.mgz --stats stats.dat --avgwf avgwf.dat --avgwfvol avgwfvol.mgz --o f2subf.nii.gz
>
> > extracts
the time course from each thalamic subregions.
>
> > If
I would like to merge multiple regions (e.g. --id 8115 --id 8116) and extract a single time course from them, which is the way?
>
> > Thanks
>
> > Stefano
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