Hello again, Don'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'm at quite a loss and would appreciate a look.
Thanks and best, Daniel On Fri, May 11, 2012 at 11:49 AM, Daniel Cole <dcol...@u.rochester.edu>wrote: > 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. > > --- > > 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 > * > * > > -- > Daniel Cole > University of Rochester > Brain and Cognitive Sciences > dcol...@u.rochester.edu > > -- Daniel Cole University of Rochester Brain and Cognitive Sciences dcol...@u.rochester.edu
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