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A: SEEG data archive

Fa-Hsuan Lin edited this page Jun 30, 2020 · 4 revisions

Project root

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.

SEEG project folder

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

anaeeg

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).

Project folders

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

anaimg

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

Folder freesurfer

  • 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 and s041_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

Project folders

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.

rawdata

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.

raweeg

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.

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