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A: SEEG data archive
All data are currently stored at /space/maki7/1/nissen_eegmri
. This will be taken as the ROOT
.
NOTE: The log file for SEEG projects is here.
Inside ROOT
, tasked_seeg
is the folder to store SEEG data, including raw data and processed data. There are four folders within ROOT/tasked_seeg
:
anaeeg anaimg rawdata raweeg
This folder includes sub-folders named after projects, such as AV
, MOTOR
, and Tone
. These are the EEG analysis results, including both preprocessing (such as ROOT/anaeeg/Tone/preprocessing
) and analyses after processing (such as ERP at ROOT/anaeeg/Tone/erp
and source modeling at ROOT/anaeeg/Tone/source_modeling_wb
).
There are different folders named after projects, such as AV
, CCEP
, and Tone
.
fhlin@rolle9:/space/maki7/1/nissen_eegmri/tasked_seeg/anaeeg$ ls
AV CCEP Motor Tone ToneAEP
For example, in project Tone
, there were analysis results saved in sub-folders
fhlin@rolle9:/space/maki7/1/nissen_eegmri/tasked_seeg/anaeeg/Tone$ ls
data_re_ref_SeegCh erp preprocessing source_modeling_wb
-
erp
: event-related potentials -
preprocessing
: Results after EEG/SEEG preprocessing -
source_modeling_wb
: Results for whole-brain source modeling
NOTE: Different projects have different analysis procedures and thus different results. The sub-folder names vary among projects.
Analysis results from different patients were stored inside in separate folders named after each patient inside each analysis result sub-folder.
fhlin@rolle9:/space/maki7/1/nissen_eegmri/tasked_seeg/anaeeg/Tone/preprocessing$ ls
anaeeg s012 s019 s031 s033 s036 s041 s046 s050 s052 s054
This folder includes sub-folders named after projects, such as AV
, MOTOR
, and Tone
. These are the image analysis results. Image analysis results in different projects were saved in separate sub-folders.
fhlin@rolle9:/space/maki7/1/nissen_eegmri/tasked_seeg/anaimg$ ls
3dslicer AV ChineseTalk DTI freesurfer Motor nii PicNaming_V2 Tone ToneAEP
-
This is the folder to store the FreeSurfer reconstructions using MRI obtained before and after electrode implantation. For patient, for example, s041, these are folder
s041
ands041_post
, respectively. -
There is also
s041_contact_loc
folder, which stores the electrode contact locations in native pre-surgery MRI space. This procedures are described here and here. -
The registration file (register.dat) from the post-surgery to pre-surgery MRI in the native space is stored at
tmp
folder inside the FreeSurfer reconstruction of post-surgery MRI. This file is required in SEEG source modeling. See this page (step #3) for further details.
fhlin@rolle9:/space/maki7/1/nissen_eegmri/tasked_seeg/anaimg/freesurfer/s041_post/tmp$ ls
register2_rr.dat.log register2_rr.dat.param register.dat register.dat.log.old register.dat.param
register2_rr.dat.mincost register2_rr.dat.sum register.dat.log register.dat.mincost register.dat.sum
There are different folders named after projects, such as AV
, Motor
, and Tone
. These are analysis results and they were saved in sub-folders named after patients. For example, inside Tone
, there are different patients (s0??).
batch_contrast_manager_tone_1.m processing_fmri_spm.m s013 s019_missing_a_lot s023 s026 s032 s039 s043_no_seeg s048 s053
generate_SOA_Tone.m read_EPI_Tone_v3.m s014 s020_missing_a_lot s024 s028 s034 s041 s044 s050 s054
preprocessing_fmri_spm.m s012 s015 s021 s025 s031 s037 s042_no_seeg s047 s052
Inside s044
, for example, there are different analysis results:
fhlin@rolle9:/space/maki7/1/nissen_eegmri/tasked_seeg/anaimg/Tone/s044$ ls
preprocessing SOA spm_TONE_wo_normalize
-
SOA
: Stimulus onset asynchrony (SOA) of the interested events -
preprocessing
: SPM preprocessing results -
spm_TONE_wo_normalize
: SPM GLM results
NOTE: Different projects have different analysis procedures and thus different results. The file names and sub-folders vary among projects.
This folder includes sub-folders named after patients, such as s041
, s045
, and s047
. These are raw NII files from the hospital. All files from the same patients are stored in one sub-folder. NII files include pre-surgery MRI (0_Pre-SEEG data
folder), post-surgery MRI (4_Post-SEEG images
), post-surgery CT (4_Post-SEEG images
), and other clinically relevant texts, images, data.
Rawdata from each patient were saved in separate sub-folders.
fhlin@rolle9:/space/maki7/1/nissen_eegmri/tasked_seeg/rawdata$ ls
filemaker s025 s034 s039 s041 s042 s043 s044 s045 s046 s047 s048 s049 s050 s051 s052 s053 s054 s055 s056 s057 s058
Within each patient, there were different categories. For example, patient s041 contains the following folders.
fhlin@rolle9:/space/maki7/1/nissen_eegmri/tasked_seeg/rawdata/s041$ ls
0_Pre-SEEG data 2_Treatment eeg_AV eeg_blink eeg_PicNaming fMRI_AV fMRI_T1 s041_xxx_45248893_bitemporal epilepsy_Lt dominant .txt
1_Pre-Plan 4_Post-SEEG images eeg_BE eeg_CCEP eeg_Tone fMRI_PicNaming fMRI_Tone
- 0_Pre-SEEG data: patient's medical history and demographic info. Pre-surgery MRI.
- 1_Pre-Plan: electrode planning info.
- 2_Treatment
- 3_Monitoring and mapping
- 4_Post-SEEG images: Post-surgery CT (
post-CT
folder) and MRI (post-MR
folder).
There are also recordings and images for various projects. These were saved in sub-folders named after each project. For example, patient s041 had SEEG recordings (.edf files) for AV, CCEP, PicNaming, and Tone projects in eeg_AV
, eeg_CCEP
, eeg_PicNaming
, and eeg_Tone
folders, respectively. Analogously, the fMRI_ folders saved fMRI data, including DICOM and SOA files, for different projects.
This folder includes sub-folders named after patients, such as s041
, s045
, and s047
. These are raw SEEG files from the hospital. All files from the same patients are stored in one sub-folder.