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'''Index'''
<<TableOfContents>>


= Name =
qdec_glmfit - wrapper for mri_glmfit that outputs a .qdec file

= Synopsis =
qdec_glmfit --data-table FILE --average-subject SUBJECT --analysis-name NAME [--discrete-factor FACTOR [--discrete-factor FACTOR]] [--continuous-factor FACTOR [--continuous-factor FACTOR]] --measurement MEASUREMENT --hemipshere lh|rh --smootheness SMOOTHNESS --output FILE [--working-dir DIR] [--subjects-dir DIR]

= Arguments =

== Required Flagged Arguments ==

|| --data-table, -d FILENAME || Input qdec.table.dat file ||
|| --average-subject, -a SUBJECT || Average subject name ||
|| --analysis-name, -n STRING ||  Name for analysis ||
|| --measurement, -m SRING || Measurement name ||
|| --hemisphere, -h lh|rh || Hemipshere to use ||
|| --smoothness, -t INTEGER || Smoothness to use ||
|| --output, -o FILENAME || Output .qdec filename ||

== Optional Flagged Arguments ==

|| --working-dir, -w DIR || Directory in which to generate temporary data (default /tmp) ||
|| --subjects-dir, -s DIR || Directory in which to find the average subject (default SUBJECTS_DIR env var) ||
|| --discrete-factor, -f STRING || Discrete factor (up to 2) ||
|| --continuous-factor, -c STRING || Continuous factor (up to 2) ||
 
= Description =

This program internally calls mri_glmfit but provides an interface that is similar to Qdec's (the visualzation program) and has fewer, simpler options. Instead of generating a directory of results, it generates a Qdec Project File, or a .qdec file, which can be loaded in Qdec.

= Examples =
== Example 1 ==

{{{
./qdec_glmfit \
  --data-table ~/subjects/qdec/qdec_data_table.dat \
  --working-dir /tmp \
  --subjects-dir ~/subjects \
  --average-subject fsaverage \
  --analysis-name thickness-diagnosis_and_iq-lh10 \
  --discrete-factor diagnosis \
  --continuous-factor IQ --continuous-factor age \
  --measurement thickness \
  --hemisphere lh \
  --smoothness 10 \
  --output Test.qdec
}}}

= Bugs =
None

= See Also =
[[mri_glmfit]], [[Qdec]]

= Links =
FreeSurfer

= Reporting Bugs =
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

= Author/s =
KevinTeich, NickSchmansky