Hey Doug,<div>Sorry I did miss your response last time, thank you for the advice.</div><div><br></div><div>I tried running the analysis again and this time it did create the angle file.  However, now I&#39;m running into a different problem.</div>
<div><br></div><div>I can get the angle map to show up on the surface of my subject&#39;s brain but I can&#39;t get the color wheel overlay to work.  When I select it the surface of the brain goes black and the segmentation lines are the only things remaining.  Is the color wheel display not working a known issue by any chance?</div>
<div><br></div><div>Thanks so much,</div><div>Daniel<br><br><div class="gmail_quote">On Wed, May 16, 2012 at 9:21 AM, Daniel Cole <span dir="ltr">&lt;<a href="mailto:dcole10@u.rochester.edu" target="_blank">dcole10@u.rochester.edu</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello again,<div>Don&#39;t mean to be a bother.  I was wondering if anyone had any thoughts on what possibly be going wrong during my retinotopic analysis that I posted.  I&#39;m at quite a loss and would appreciate a look.</div>

<div><br></div><div>Thanks and best,</div><div>Daniel<div><div class="h5"><br><br><div class="gmail_quote">On Fri, May 11, 2012 at 11:49 AM, Daniel Cole <span dir="ltr">&lt;<a href="mailto:dcole10@u.rochester.edu" target="_blank">dcole10@u.rochester.edu</a>&gt;</span> wrote:<br>

<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello,<div>I have some questions regarding the FsFastIndividual pipeline.  I hope you can take a look at the commands I have run and give me some insight into what the problem might potentially be.  I have 5 rotating wedge stimuli runs</div>


<div><br></div><div>1. I set up my subject&#39;s directories according to the freesurfer tutorial powerpoint and declare my environmental variables using-</div><div>&lt;<i><font face="georgia, serif">export FREESURFER_HOME=/Volumes/RCBI/freesurfer</font></i></div>


<div><i><font face="georgia, serif">export SUBJECTS_DIR=/Volumes/rcbiUsers/dcole/Retinotopy</font></i></div><div><i><font face="georgia, serif">source $FREESURFER_HOME/SetUpFreeSurfer.sh</font></i>&gt;</div>
<div><br></div><div>Bold data renamed to f.nii.gz and placed into run folders (001, 002, etc)</div><div><br></div><div>rtopy.par=&quot;</div><div>stimtype polar</div><div>direction neg&quot;</div><div><br></div><div>2. I then reconstruct the strucutural data using-</div>


<div>&lt;<i><font face="georgia, serif">recon-all -i /Volumes/rcbiUsers/dcole/Retinotopy/VG01/raw/VGP01_001.dcm -subjid VG01</font></i>&gt;</div><div><br></div><div>3. I create the subjectname file, run preprocessing, and make the analysis files.</div>


<div>&lt;<i><font face="georgia, serif">preproc-sess -surface self lhrh -fwhm 5 -sf sessid -fsd bold</font></i></div><div><i><font face="georgia, serif">mkanalysis-sess -analysis rtopy.self.lh -surface self lh -TR 1.2 -abblocked 38.4 -fsd bold -fwhm 5</font></i></div>


<div><i><font face="georgia, serif">mkanalysis-sess -analysis rtopy.self.rh -surface self rh -TR 1.2 -abblocked 38.4 -fsd bold -fwhm 5</font></i>&gt;</div><div><div><br></div><div>4. Then I run the analysis using-</div>
<div>&lt;<i><font face="georgia, serif">selxavg3-sess -analysis rtopy.self.lh -sf sessid</font></i></div><div><i><font face="georgia, serif">selxavg3-sess -analysis rtopy.self.lh -sf sessid</font></i>&gt;</div>
<div>~This step was giving me an error until I added &quot;faux&quot; eccentricity run folders with runs 1-5 functional data copied and rtopy.par files with stimtype eccen.  Rerunning these 2 steps with the faux eccentricity data fixed the error message.</div>


<div><br></div><div>5. Create occipital patch with (<a href="http://www.alivelearn.net/?p=65" target="_blank">http://www.alivelearn.net/?p=65</a>) as guideline.  Flatten patch using- </div><div>&lt;<i><font face="georgia, serif">mris_flatten -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat</font></i></div>


<div><i><font face="georgia, serif">mris_flatten -w 0 -distances 20 7 rh.occip.patch.3d rh.occip.patch.flat</font></i>&gt;</div><div><br></div><div>And create fieldsign map using-</div><div>&lt;<i><font face="georgia, serif">fieldsign-sess -a rtopy.self.lh -occip -sf sessid</font></i></div>


<div><i><font face="georgia, serif">fieldsign-sess -a rtopy.self.rh -occip -sf sessid</font></i>&gt;</div><div>~Error that analysis isn&#39;t retinotopy (because I used -abblocked), retrying step 3 with -retinotopy allowed me to create the fieldsign map.</div>


<div><br></div><div>---</div><div><br></div><div>For the -abblocked and -retinotopy analysis I am able to look at the results using &lt;<i><font face="georgia, serif">tksurfer-sess -a rtopy.self.lh -sf sessid</font></i>&gt;<i>.</i></div>


<div>My questions are:</div><div>- Should I be using -abblocked or -retinotopy for a polar only design?</div><div>- Is it ok to create &quot;faux&quot; eccentricity folders and then only look at the polar data?</div><div>


- Why is it for either of these analyses I can&#39;t view the angle map using &lt;<span style="border-collapse:collapse"><i><font face="georgia, serif">tksurfer-sess -a rtopy.self.?h -s sessid -map angle</font></i><font face="Arial, &#39;Lucida Grande&#39;, sans-serif">&gt;? In fact the angle file is not created.</font></span></div>


<div><span style="border-collapse:collapse"><font face="Arial, &#39;Lucida Grande&#39;, sans-serif"><br></font></span></div><div><span style="border-collapse:collapse"><font face="Arial, &#39;Lucida Grande&#39;, sans-serif">Thanks so much for your time and help.</font></span></div>

<span><font color="#888888">
<div><span style="border-collapse:collapse"><font face="Arial, &#39;Lucida Grande&#39;, sans-serif"><br></font></span></div><div><span style="border-collapse:collapse"><font face="Arial, &#39;Lucida Grande&#39;, sans-serif">Daniel</font></span></div>


<div><i><br></i></div><div><br></div>-- <br><div>Daniel Cole</div><div>University of Rochester</div><div>Brain and Cognitive Sciences</div><div><a href="mailto:dcole10@u.rochester.edu" target="_blank">dcole10@u.rochester.edu</a></div>


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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div>Daniel Cole</div><div>University of Rochester</div><div>Brain and Cognitive Sciences</div><div><a href="mailto:dcole10@u.rochester.edu" target="_blank">dcole10@u.rochester.edu</a></div>

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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div>Daniel Cole</div><div>University of Rochester</div><div>Brain and Cognitive Sciences</div><div><a href="mailto:dcole10@u.rochester.edu" target="_blank">dcole10@u.rochester.edu</a></div>
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