Hello, 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
1. I set up my subject's directories according to the freesurfer tutorial powerpoint and declare my environmental variables using- <*export FREESURFER_HOME=/Volumes/RCBI/freesurfer* *export SUBJECTS_DIR=/Volumes/rcbiUsers/dcole/Retinotopy* *source $FREESURFER_HOME/SetUpFreeSurfer.sh*>
Bold data renamed to f.nii.gz and placed into run folders (001, 002, etc)
rtopy.par=" stimtype polar direction neg"
2. I then reconstruct the strucutural data using- <*recon-all -i /Volumes/rcbiUsers/dcole/Retinotopy/VG01/raw/VGP01_001.dcm -subjid VG01*>
3. I create the subjectname file, run preprocessing, and make the analysis files. <*preproc-sess -surface self lhrh -fwhm 5 -sf sessid -fsd bold* *mkanalysis-sess -analysis rtopy.self.lh -surface self lh -TR 1.2 -abblocked 38.4 -fsd bold -fwhm 5* *mkanalysis-sess -analysis rtopy.self.rh -surface self rh -TR 1.2 -abblocked 38.4 -fsd bold -fwhm 5*>
4. Then I run the analysis using- <*selxavg3-sess -analysis rtopy.self.lh -sf sessid* *selxavg3-sess -analysis rtopy.self.lh -sf sessid*> ~This step was giving me an error until I added "faux" 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.
5. Create occipital patch with (http://www.alivelearn.net/?p=65) as guideline. Flatten patch using- <*mris_flatten -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat* *mris_flatten -w 0 -distances 20 7 rh.occip.patch.3d rh.occip.patch.flat*>
And create fieldsign map using- <*fieldsign-sess -a rtopy.self.lh -occip -sf sessid* *fieldsign-sess -a rtopy.self.rh -occip -sf sessid*> ~Error that analysis isn't retinotopy (because I used -abblocked), retrying step 3 with -retinotopy allowed me to create the fieldsign map.
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For the -abblocked and -retinotopy analysis I am able to look at the results using <*tksurfer-sess -a rtopy.self.lh -sf sessid*>*.* My questions are: - Should I be using -abblocked or -retinotopy for a polar only design? - Is it ok to create "faux" eccentricity folders and then only look at the polar data? - Why is it for either of these analyses I can't view the angle map using <*tksurfer-sess -a rtopy.self.?h -s sessid -map angle*>? In fact the angle file is not created.
Thanks so much for your time and help.
Daniel * *