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 dcole10@u.rochester.eduwrote:
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
- 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"
- I then reconstruct the strucutural data using-
<*recon-all -i /Volumes/rcbiUsers/dcole/Retinotopy/VG01/raw/VGP01_001.dcm -subjid VG01*>
- 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*>
- 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.
- 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 dcole10@u.rochester.edu