Beauchamp:ALICE: Difference between revisions
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(New page: This page shows the steps used by the ALICE package to localize electrodes. These steps are called from within a Matlab GUI) |
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This page shows the steps used by the ALICE package to localize electrodes. These steps are called from within a Matlab GUI | This page shows the steps used by the ALICE package to localize electrodes. These steps are called from within a Matlab GUI. | ||
The GUI has three steps. | |||
Here is the log file from the first step (an edited version of /Volumes/data/UT/YBK/ALICE/log_info/Step1_log.txt with comments added ) | |||
MRI scan selected: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/data/MRI/YBK_T1.nii | |||
FS segmentation selected: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/data/FreeSurfer/t1_class.nii | |||
This file was originally called YBK_fs_ribbon_rh_class.nii **not sure where it came from | |||
CT scan selected: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/data/CT/CT_highresRAI.nii | |||
This file was originally called YBK_CT.nii | |||
Aligning CT to MRI... This might take several minutes. Please wait... | |||
tcsh -x alignCTtoT1_shft_res.csh -CT_path CT_highresRAI.nii -T1_path../MRI/YBK_T1.nii | |||
CT and MRI have been co-registered. Please check the results before proceeding. | |||
ALICE directory located: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/ | |||
Please proceed to Step 1. | |||
MRI scan selected: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/data/MRI/YBK_T1.nii | |||
FS segmentation selected: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/data/FreeSurfer/t1_class.nii | |||
CT scan selected: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/data/CT/CT_highresRAI.nii | |||
Saved subject name, cluster settings and grid settings loaded. | |||
ALICE directory located: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/ | |||
Please proceed to Step 1. | |||
MRI scan selected: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/data/MRI/YBK_T1.nii | |||
FS segmentation selected: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/data/FreeSurfer/t1_class.nii | |||
CT scan selected: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/data/CT/CT_highresRAI.nii | |||
Saved subject name, cluster settings and grid settings loaded. | |||
Aligning CT to MRI... This might take several minutes. Please wait... | |||
tcsh -x alignCTtoT1_shft_res.csh -CT_path CT_highresRAI.nii -T1_path../MRI/YBK_T1.nii | |||
CT and MRI have been co-registered. Please check the results before proceeding. | |||
Revision as of 10:37, 21 July 2017
This page shows the steps used by the ALICE package to localize electrodes. These steps are called from within a Matlab GUI.
The GUI has three steps.
Here is the log file from the first step (an edited version of /Volumes/data/UT/YBK/ALICE/log_info/Step1_log.txt with comments added )
MRI scan selected: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/data/MRI/YBK_T1.nii
FS segmentation selected: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/data/FreeSurfer/t1_class.nii
This file was originally called YBK_fs_ribbon_rh_class.nii **not sure where it came from
CT scan selected: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/data/CT/CT_highresRAI.nii
This file was originally called YBK_CT.nii
Aligning CT to MRI... This might take several minutes. Please wait... tcsh -x alignCTtoT1_shft_res.csh -CT_path CT_highresRAI.nii -T1_path../MRI/YBK_T1.nii CT and MRI have been co-registered. Please check the results before proceeding. ALICE directory located: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/ Please proceed to Step 1. MRI scan selected: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/data/MRI/YBK_T1.nii FS segmentation selected: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/data/FreeSurfer/t1_class.nii CT scan selected: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/data/CT/CT_highresRAI.nii Saved subject name, cluster settings and grid settings loaded. ALICE directory located: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/ Please proceed to Step 1. MRI scan selected: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/data/MRI/YBK_T1.nii FS segmentation selected: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/data/FreeSurfer/t1_class.nii CT scan selected: /Users/fosterlab/Documents/MATLAB/CTMR/DATA/YBK/ALICE/data/CT/CT_highresRAI.nii Saved subject name, cluster settings and grid settings loaded. Aligning CT to MRI... This might take several minutes. Please wait... tcsh -x alignCTtoT1_shft_res.csh -CT_path CT_highresRAI.nii -T1_path../MRI/YBK_T1.nii CT and MRI have been co-registered. Please check the results before proceeding.
