Diff for "Qdec" - Free Surfer Wiki

⇤ ← Revision 2 as of 2007-03-30 14:08:18 →

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Editor: NickSchmansky

Comment:

← Revision 23 as of 2015-05-15 15:08:23 → ⇥

Size: 350

Editor: NickSchmansky

Comment:

Deletions are marked like this.

Additions are marked like this.

== Introduction ==
QDEC is a single-binary application, named 'qdec', included in the Freesurfer distribution. QDEC is an acronym for Query, Design, Estimate, Contrast. It is intended to aid researchers performing inter-subject / group averaging and inference on the morphometry data (cortical surface and volume) produced by the Freesurfer processing stream. Prior to usage of qdec, all subcortical segmentation and surface reconstructions for all subjects in a study must be complete. The 'recon-all' script performs that work, and is not the subject of this document.

= QDEC Links Page =

The qdec binary is a GUI front-end to a 'statistics engine' (the mri_glmfit binary, included in Freesurfer, currently fills this role) intended to:

1. select the subjects meeting the criteria under study
1. generate the necessary input to the stats engine, which, for mris_glm, includes:
  1. a '''Design''' matrix (called '''X''' in the GLM equation) containing the explanatory variables,
  1. a parameter '''Estimate''' matrix (called '''A''' in the GLM equation), and
  1. the '''Contrast''' vector(s)
1. generate and optionally display the output data and/or images

Without the aid of the qdec tool, a researcher has to manually perform the stats analysis, which, when using the mri_glmfit utility, requires an 'FSDG' file which specifies the X and A matrices for the group of subjects under study, and manually specify the contrast vector(s) for the hypothesis to test. This can be quite tedious, and greatly slows down the "Test for an effect of factor X" research process. This is, in fact, the procedure described in the [wiki:Self:FsTutorial/GroupAnalysis 'Group Analysis' tutorial].

== Setup ==

=== recon-all ===
Prior to using the qdec application, your group subject data must be processed by the standard Freesurfer processing stream, via the recon-all script. [http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial A freesurfer tutorial is available.] This processing stream supplies the surfaces and morphometry data on each subject.

=== qdec.table.dat ===
The primary input to qdec is a text file containing the subject IDs, and discrete and continuous factors, in table format. Here is an example file:
{{{
fsid gender age diagnosis Left-Cerebral-White-Matter
011121_vc8048 Female 70 Demented 202291
021121_62313-2 Female 71 Demented 210188
010607_vc7017 Female 73 Nondemented 170653
021121_vc10557 Male 75 Demented 142029
020718_62545 Male 76 Demented 186087
020322_vc8817 Male 77 Nondemented 149810
}}}

== Usage ==

First, set your SUBJECTS_DIR environment variable to point at your group subjects directory:
{{{
setenv SUBJECTS_DIR /space/boing/users/me/subjects/my_big_study
}}}

Or, there is a sample data set you can use to learn:
{{{
setenv SUBJECTS_DIR /autofs/space/sake_025/users/nicks/subjects/qdec3
}}}

Then, setup the 'dev' Freesurfer environment, which contains qdec:
{{{
source /usr/local/freesurfer/nmr-dev-env
}}}

For display purposes, you will need to have an average subject included in this subject group. Freesurfer's fsaverage will do fine:
{{{
cd $SUBJECTS_DIR
ln -s $FREESURFER_HOME/subjects/fsaverage
}}}

Now start qdec:
{{{
qdec &
}}}

* [[FsTutorial/QdecGroupAnalysis_freeview|Tutorial]]
* [[http://xwiki.nbirn.net/xwiki/bin/view/Morphometry%2DBIRN/mBIRN_Slicer_3|Slicer and QDEC]]
* [[QdecProject|Project development]]
* [[QdecProjectFileFormat|.qdec project file format]]
* [[http://www.na-mic.org/Slicer/Download/Data/TEST4.qdec|Sample .qdec file]]

-  ⇤ ← Revision 2 as of 2007-03-30 14:08:18 → 
  Size: 3283
  Editor: NickSchmansky
  Comment:
+   ← Revision 23 as of 2015-05-15 15:08:23 → ⇥
  Size: 350
  Editor: NickSchmansky
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-== Introduction ==
QDEC is a single-binary application, named 'qdec', included in the Freesurfer distribution.  QDEC is an acronym for Query, Design, Estimate, Contrast.  It is intended to aid researchers performing inter-subject / group averaging and inference on the morphometry data (cortical surface and volume) produced by the Freesurfer processing stream.  Prior to usage of qdec, all subcortical segmentation and surface reconstructions for all subjects in a study must be complete.  The 'recon-all' script performs that work, and is not the subject of this document.
+= QDEC Links Page =
-Line 4:
+Line 3:
-The qdec binary is a GUI front-end to a 'statistics engine' (the mri_glmfit binary, included in Freesurfer, currently fills this role) intended to:

 1. select the subjects meeting the criteria under study
 1. generate the necessary input to the stats engine, which, for mris_glm, includes:
  1. a '''Design''' matrix (called '''X''' in the GLM equation) containing the explanatory variables,
  1. a parameter '''Estimate''' matrix (called '''A''' in the GLM equation), and
  1. the '''Contrast''' vector(s)
 1. generate and optionally display the output data and/or images

Without the aid of the qdec tool, a researcher has to manually perform the stats analysis, which, when using the mri_glmfit utility, requires an 'FSDG' file which specifies the X and A matrices for the group of subjects under study, and manually specify the contrast vector(s) for the hypothesis to test.  This can be quite tedious, and greatly slows down the "Test for an effect of factor X" research process.  This is, in fact, the procedure described in the [wiki:Self:FsTutorial/GroupAnalysis 'Group Analysis' tutorial].

== Setup ==

=== recon-all ===
Prior to using the qdec application, your group subject data must be processed by the standard Freesurfer processing stream, via the recon-all script.  [http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial A freesurfer tutorial is available.]  This processing stream supplies the surfaces and morphometry data on each subject.

=== qdec.table.dat ===
The primary input to qdec is a text file containing the subject IDs, and discrete and continuous factors, in table format.  Here is an example file:
{{{
fsid            gender  age diagnosis   Left-Cerebral-White-Matter
011121_vc8048   Female  70  Demented    202291
021121_62313-2  Female  71  Demented    210188
010607_vc7017   Female  73  Nondemented 170653
021121_vc10557  Male    75  Demented    142029
020718_62545    Male    76  Demented    186087
020322_vc8817   Male    77  Nondemented 149810
}}}

== Usage ==

First, set your SUBJECTS_DIR environment variable to point at your group subjects directory:
{{{
setenv SUBJECTS_DIR /space/boing/users/me/subjects/my_big_study
}}}

Or, there is a sample data set you can use to learn:
{{{
setenv SUBJECTS_DIR /autofs/space/sake_025/users/nicks/subjects/qdec3
}}}

Then, setup the 'dev' Freesurfer environment, which contains qdec:
{{{
source /usr/local/freesurfer/nmr-dev-env
}}}

For display purposes, you will need to have an average subject included in this subject group.  Freesurfer's fsaverage will do fine:
{{{
cd $SUBJECTS_DIR
ln -s $FREESURFER_HOME/subjects/fsaverage
}}}

Now start qdec:
{{{
qdec &
}}}
+ * [[FsTutorial/QdecGroupAnalysis_freeview|Tutorial]]
 * [[http://xwiki.nbirn.net/xwiki/bin/view/Morphometry%2DBIRN/mBIRN_Slicer_3|Slicer and QDEC]]
 * [[QdecProject|Project development]]
 * [[QdecProjectFileFormat|.qdec project file format]]
 * [[http://www.na-mic.org/Slicer/Download/Data/TEST4.qdec|Sample .qdec file]]