Hi Daniel, did you miss my responses from last week? doug

-------- Original Message -------- Subject: Re: [Freesurfer] FsFastIndividual Retinotopy - Polar Only Date: Fri, 11 May 2012 12:49:32 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu

Hi Daniel, answers below doug

On 05/11/2012 11:49 AM, Daniel Cole 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.

Field sign is meaningless because you need polar and eccen

---

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?

retinotopy is fine as long as you have the faux eccen

• Is it ok to create "faux" eccentricity folders and then only look at

the polar data?

yes

• 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.

It won't be created for the abblocked, but it should be for the retinotopy. Can you double check? Note that the fieldsign is meaningless. doug

Thanks so much for your time and help.

Daniel / /

-- Daniel Cole University of Rochester Brain and Cognitive Sciences dcole10@u.rochester.edumailto:dcole10@u.rochester.edu

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hey Doug, Sorry I did miss your response last time, thank you for the advice.

I tried running the analysis again and this time it did create the angle file. However, now I'm running into a different problem.

I can get the angle map to show up on the surface of my subject's brain but I can'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?

Thanks so much, Daniel

On Wed, May 16, 2012 at 9:21 AM, Daniel Cole dcole10@u.rochester.eduwrote:

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

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 dcole10@u.rochester.edu

-- Daniel Cole University of Rochester Brain and Cognitive Sciences dcole10@u.rochester.edu