Beauchamp:Lab Notebook
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Beauchamp Lab
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MRI
Electrophysiology Protocols
After analysing fMRI data, upload the entire contents of the AFNI and SUMA directories to Xfiles. This can be simplfied by Apple-K (Connect to Server) in Finder and choosing XFiles;
xfiles.hsc.uth.tmc.edu (129.106.148.217)
then the folders can be dragged from the server to Xfiles, or copied in the command line, easily (without using the Web-based GUI interface).
In the EMU
It is also good to collect 10 minutes of resting data (no stimulation) from as many visual electrodes as possible for later analyses.
After obtaining the CD containing the patient CT data from St. Luke's, use OsiriX to export all images (using the export to DICOM option, and the hierarchical, uncompress options).
CT scans have voxel size 0.488x0.488x1 mm; this may need to be adjusted manually with
3drefit -zdel 1.000 DE_CTSDE+orig
(If the CTs look distorted in AFNI, then the voxel size must be adjusted). Next, the CTs must be registered with the hi-res presurgical MRI anatomy. This may fail because the CT has a coordinate system with a very different origin than the MRI. Registration routines will not work if the input datasets are not in rough alignment. To check this, type
3dinfo DE_CTSDE+orig
returns
R-to-L extent: -124.756 [R] -to- 124.756 [L] -step- 0.488 mm [512 voxels] A-to-P extent: -124.756 [A] -to- 124.756 [P] -step- 0.488 mm [512 voxels] I-to-S extent: -258.000 [I] -to- -86.000 [I] -step- 1.000 mm [173 voxels]
We want the center of the dataset to be roughly at (0,0,0). For this example, this is true for (x,y) but not for z. First, create a copy of the dataset
3dcopy DE_CTSDE+orig DE_CTSDEshift
Then, recenter the z-axis
3drefit -zorigin 80 DE_CTSDEshift+orig
3dinfo returns
R-to-L extent: -124.756 [R] -to- 124.756 [L] -step- 0.488 mm [512 voxels] A-to-P extent: -124.756 [A] -to- 124.756 [P] -step- 0.488 mm [512 voxels] I-to-S extent: -80.000 [I] -to- 92.000 [S] -step- 1.000 mm [173 voxels]
The z-axis is now roughly centered around 0. In AFNI, examine the MR and the shifted CT to make sure they are in rough alignment. Next, use 3dAllineate to align the two datasets.
3dAllineate -base {$ec}anatavg+orig -source DE_CTSDEshift+orig -prefix {$ec}CTSDE_REGtoanatV4 -verb -warp shift_rotate -cost mutualinfo -1Dfile {$ec}CTSDE_REGtoanatXformV4
Check in AFNI to make sure that they alignment is correct. NB: It is also possible to crop the MRI before Allineating since the MR coverage is typically greater than the CT coverage. In a test case, this did not have a big effect.
Things to do
HumanImageDetection
- Can stimuli be vector-based rather than pixel based, so as not to lose resolution with scaling? POSSIBLE if original file is vector-based
- Enable online scrambling LOOKING INTO IT
- Enable online color to black and white conversion LOOKING INTO IT
HumanLetterDetection
- Analyze data from LR to see where the RFs are
Things to Order
staples, stapler
laminator
transfer roller for Dell printer
Installing Matlab
To install Matlab for use in the Beauchamp lab: 1. Download and install matlab here.
Get login name and pw from Mike
Note: you will be prompted to install Java run-time environment 5. This will ease the installation. 2. Place license.dat in the matlab folder when prompted. 3. Find out that Matlab is already onthe computer and cancel installation.
