Hello,<div><br></div><div>I am attempting to use the Qdec Analysis for longitudinal data. Specifically, each subject has two timepoints, and belongs to one of two groups. Each subject has an accompanying age and painUnpleasantness rating. I do not have a &#39;time in years&#39; variable, and instead listed the timepoint as baseline = 0, and post=1.</div>


<div><br></div><div>Thus far, what is done is the PREPROCESSING (listed below as step #3). Thus, every subject has a directory <span style="border-collapse:collapse;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px">labeled &quot;WB101_1.long.WB101_template&quot;, and another labeled &quot;WB101_template&quot;.</span></div>

<div><font color="#222222" face="arial, sans-serif"><span style="border-collapse:collapse"><br></span></font></div><div><font color="#222222" face="arial, sans-serif"><span style="border-collapse:collapse">I am on the POSTPROCESSING (listed as step #4). I would like to confirm that this is the correct sequence of events to use the Qdec Analysis tool to do a mixed linear effects models analysis or mixed ANOVA analysis. <br>

</span></font><div><br></div><div><br></div><div><div>#1. INITIALIZATION</div><div><br></div><div>freesurfer</div><div>tksurfer 005 brainmask.mgz</div>
<div><br></div><div><br></div><div>#2. SET SUBJECT DIRECTORY</div><div><br></div><div>export SUBJECTS_DIR=/study/NCCAM/Data/MRI/processed/structural/freesurfer</div><div>cd /study/NCCAM/Data/MRI/processed/structural/freesurfer/</div>


<div><br></div><div><br></div><div>#3. PREPROCESSING LONGITUDINAL</div><div><br></div><div>recon-all -base ${subject}_template -tp ${subject}_1 -tp ${subject}_2 -all</div><div>recon-all -long ${subject}_1 ${subject}_template -all </div>


<div>recon-all -long ${subject}_2 ${subject}_template -all </div><div>   </div><div>   </div><div>#4. POSTPROCESSING LONGITUDINAL BY CREATING QDEC TABLE</div><div>#Example file named: long.qdec.table.dat</div><div><br></div>


<div>fsid<span style="white-space:pre-wrap">		</span>fsid-base<span style="white-space:pre-wrap">		</span>group<span style="white-space:pre-wrap">	</span>age<span style="white-space:pre-wrap">		</span>painUnp<span style="white-space:pre-wrap">		</span>tp</div>


<div>WB101_1<span style="white-space:pre-wrap">		</span>WB101_template<span style="white-space:pre-wrap">	</span>MNP<span style="white-space:pre-wrap">		</span>65.72<span style="white-space:pre-wrap">	</span>11.7  0</div>


<div>WB401_1<span style="white-space:pre-wrap">		</span>WB401_template<span style="white-space:pre-wrap">	</span>LTM<span style="white-space:pre-wrap">		</span>59<span style="white-space:pre-wrap">		</span>11.6  0</div>
<div>WB101_2<span style="white-space:pre-wrap">		</span>WB101_template<span style="white-space:pre-wrap">	</span>MNP<span style="white-space:pre-wrap">		</span>65.72<span style="white-space:pre-wrap">	</span>8.6   1</div>


<div>WB401_2<span style="white-space:pre-wrap">		</span>WB401_template<span style="white-space:pre-wrap">	</span>LTM<span style="white-space:pre-wrap">		</span>59<span style="white-space:pre-wrap">		</span>        1</div>


<div><br></div><div><br></div><div>#5. OPEN QDEC TABLE</div><div><br></div><div>gedit qdec/long.qdec.table.dat</div><div><br></div><div><br></div><div>#6. CREATE a qdec/measures.Qdecrc file in the qdec directory that contains the following line, so that the QDEC analysi know about new files. </div>


<div>#Example file named: measures.Qdecrc</div><div><br></div><div>MEASURE1 = long.thickness-avg</div><div>MEASURE2 = long.thickness-rate</div><div>MEASURE3 = long.thickness-pc1</div><div>MEASURE4 = long.thickness-spc</div>


<div><br></div><div><br></div><div>#7. CREATE file for each discrete (categorical) factor</div><div>#Example file named: group.levels</div><div><br></div><div>MNP</div><div>LTM</div><div><br></div><div><br></div><div>#8. Pre-smooth fsaverage surfaces </div>


<div>#Qdec needs each subject to have pre-computed smoothed data for the target surface (fsaverage is the default) for each measure (thickness, sulc, area, curv, etc.). Your SUBJECTS_DIR should contain either a link or a copy of the &#39;fsaverage&#39; subject found in your $FREESURFER_HOME/subjects directory. Presmoothing the data onto the target surface is not part of the normal recon processing stream, but you can easily create this data with recon-all, using the command:</div>


<div><br></div><div>recon-all -s &lt;subject&gt; -qcache</div><div><br></div><div><br></div><div>#9. Shrink qdec table from a longitudinal form to a cross sectional form, in order to run the QDEC group analysis.</div><div>


<br></div><div>long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out ./qdec/cross.qdec.table.dat</div><div><br></div><div><br></div><div>#10. PREPARE DATA QCACHE</div><div><br></div><div>long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time tp --qcache fsaverage</div>


<div><br></div><div><br></div><div>#11. Open pial surface of left hemi on average subject. Open symmetrized percent change. </div><div>#--qcache flag of long_mris_slopes has been registered and mapped all results to the average subject  </div>


<div><br></div><div>tksurfer fsaverage lh pial -overlay $SUBJECTS_DIR/OAS2_0001/surf/lh.long.thickness-spc.fwhm15.fsaverage.mgh -aparc</div><div><br></div><div><br></div><div>#12. Run the QDEC analysis on the qdec table: </div>


<div><br></div><div>qdec --table ./qdec/cross.qdec.table.dat</div><div><br></div><div><br></div><div>#13. Use GUI as indicated by <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis" target="_blank">http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis</a></div>


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