New subject: Freesurfer Digest, Vol 195, Issue 47

19 May 2020

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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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Subject: Freesurfer Digest, Vol 195, Issue 47
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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"
External Email - Use Caution
thanks!
...
Il 18 maggio 2020 alle 16.23 Bruce Fischl < 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 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 > 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 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 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 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 > 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 >
    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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Re: [Freesurfer] Freesurfer Digest, Vol 195, Issue 47