Difference between revisions of "Data:DBP2:Harvard"
From NAMIC Wiki
| (16 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
| − | Back to [[DBP2:Harvard|Harvard DBP 2]], [[Data:DBP2|DBP 2 Data]] | + | Back to [[DBP2:Harvard|Harvard DBP 2]], [[Data:DBP2|DBP 2 Data]] |
__NOTOC__ | __NOTOC__ | ||
== Harvard Data == | == Harvard Data == | ||
| Line 5: | Line 5: | ||
=== Data Access === | === Data Access === | ||
| − | + | To download this data, click on the following links: >> DATA AVAILABLE ON BIRN as of 9/17/08. | |
| − | === | + | * Ensure you are logged into the [https://portal.nbirn.net portal] |
| − | + | * Download all data [https://portal.nbirn.net/gridsphere/gridsphere?cid=srbfilebrowser&gs_action=moveUpDir&gv7_dirpath=%2Fhome%2FProjects%2FNAMIC__0003%2FFiles%2FPNL%2F3T_strct_dti_fmri%2Fcase01017&up=gv7&JavaScript=enabled|PNL 3T Data] | |
| − | + | ** Here is the pathway in BIRN once you're logged in: /home/Projects/NAMIC__0003/Files/PNL/3T_strct_dti_fmri | |
| − | + | ** There are 20 cases; ten are Normal Controls and ten are Schizophrenic. In each case folder, there are 10 files, described here: | |
| − | + | *** 01###-t1w.nrrd is the weighted T1 scan. | |
| − | + | *** 01###-t2w.nrrd is the weighted T2 scan. | |
| − | + | *** 01###-t2w_mask.nrrd is a labelmap of the ICC based on the T2. | |
| − | + | *** 000008.SER-anon.tgz is the fMRI scan (zipped tar ball) - - Note: there in no fMRI scan for case01073 | |
| − | + | *** 01###-dwi.nhdr (references 01###-dwi.raw.gz) is the raw DTI scan. | |
| − | + | *** 01###-dwi-filt-Ed.nhdr (references 01###-dwi-filt-Ed.raw.gz) is the dwi scan after noise filtering and eddy current and head motion correction. | |
| − | + | *** brainmask.mgz is a T1 grayscale image that has the skull & dura-matter stripped. | |
| − | + | *** aparc+aseg.mgz is a freesurfer segmentation of the t1w image. | |
| − | + | *[https://portal.nbirn.net/gridsphere/gridsphere?cid=srbfilebrowser&gs_action=gotoDirectory&rcS_dirpath=%2Fhome%2FProjects%2FNAMIC__0003%2FFiles%2FPNL%2F3T_strct_dti_fmri&up=rcS&JavaScript=enabled Spreadsheets giving diagnosis, gender, age of subjects, and some neuropsych info] | |
| − | === | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
=== Data Description === | === Data Description === | ||
| − | * '''Structural | + | * '''Structural MRI (sMRI)''' For the Structural MRI volume measurements, images will be acquired using a 3T GE) at BWH in Boston, MA. We will use an 8 Channel coil in order to perform parallel imaging using ASSET (Array Spatial Sensitivity Encoding techniques, GE) with a SENSE-factor (speed-up) of 2. The structural MRI acquisition protocol will include two MRI pulse sequences. The first results in contiguous spoiled gradient-recalled acquisition (fastSPGR) with the following parameters; TR=7.4ms, TE=3ms, TI=600, 10 degree flip angle, 25.6cm^2 field of view, matrix=256x256. The voxel dimensions are 1x1x1 mm. The second- XETA (eXtended Echo Train Acquisition) produces a series of contiguous T2-weighted images (TR=2500ms, TE=80ms, 25.6 cm^2 field of view, 1 mm slice thickness). Voxel dimensions are 1x1x1 mm. |
| − | + | * '''Diffusion Tensor Imaging (DTI)''' DTI scans will be acquired on a 3 Tesla GE system using an echo planar imaging (EPI) DTI Tensor sequence. We will use a double echo option to reduce eddy-current related distortions (Heid 2000; Alexander 1997). To reduce impact of EPI spatial distortion, we will use an 8 Channel coil that will allow us to perform parallel imaging using ASSET (Array Spatial Sensitivity Encoding Techniques, GE) with a SENSE-factor (speed-up) of 2. We will acquire 51 directions with b=*9*00, 8 baseline scans with b=0. The following scan parameters will be used: TR 17000 ms, TE 78 ms, FOV 24 cm, 144x144 encoding steps, 1.7 mm slice thickness. We will acquire 85 axial slices parallel to the AC-PC line covering the whole brain. In addition, Bo field inhomogeneity maps will be collected. | |
| − | + | * '''Resting State fMRI''' This sequence is an additional EPI BOLD sequence that requires Brain Wave software, available only with 8 Channel coil. It's a resting state fMRI that was 10 minutes long, and contains 200 repetitions of a high resolution EPI scan (96x96 in plane, 3mm thickness, TR-3000 ms, TE=30, 39 slices, ASSETT). Subjects closed their eyes and rested while the magnet is running. | |
| − | * '''DTI | ||
| − | |||
| − | ** | ||
| − | * | ||
=== Data Contact === | === Data Contact === | ||
If you have any questions about the data, please contact Sylvain Bouix (sylvain@bwh.harvard.edu) or Doug Terry (dougt@bwh.harvard.edu) at Harvard. | If you have any questions about the data, please contact Sylvain Bouix (sylvain@bwh.harvard.edu) or Doug Terry (dougt@bwh.harvard.edu) at Harvard. | ||
Latest revision as of 17:15, 17 September 2008
Home < Data:DBP2:HarvardBack to Harvard DBP 2, DBP 2 Data
Harvard Data
Data Access
To download this data, click on the following links: >> DATA AVAILABLE ON BIRN as of 9/17/08.
- Ensure you are logged into the portal
- Download all data 3T Data
- Here is the pathway in BIRN once you're logged in: /home/Projects/NAMIC__0003/Files/PNL/3T_strct_dti_fmri
- There are 20 cases; ten are Normal Controls and ten are Schizophrenic. In each case folder, there are 10 files, described here:
- 01###-t1w.nrrd is the weighted T1 scan.
- 01###-t2w.nrrd is the weighted T2 scan.
- 01###-t2w_mask.nrrd is a labelmap of the ICC based on the T2.
- 000008.SER-anon.tgz is the fMRI scan (zipped tar ball) - - Note: there in no fMRI scan for case01073
- 01###-dwi.nhdr (references 01###-dwi.raw.gz) is the raw DTI scan.
- 01###-dwi-filt-Ed.nhdr (references 01###-dwi-filt-Ed.raw.gz) is the dwi scan after noise filtering and eddy current and head motion correction.
- brainmask.mgz is a T1 grayscale image that has the skull & dura-matter stripped.
- aparc+aseg.mgz is a freesurfer segmentation of the t1w image.
- Spreadsheets giving diagnosis, gender, age of subjects, and some neuropsych info
Data Description
- Structural MRI (sMRI) For the Structural MRI volume measurements, images will be acquired using a 3T GE) at BWH in Boston, MA. We will use an 8 Channel coil in order to perform parallel imaging using ASSET (Array Spatial Sensitivity Encoding techniques, GE) with a SENSE-factor (speed-up) of 2. The structural MRI acquisition protocol will include two MRI pulse sequences. The first results in contiguous spoiled gradient-recalled acquisition (fastSPGR) with the following parameters; TR=7.4ms, TE=3ms, TI=600, 10 degree flip angle, 25.6cm^2 field of view, matrix=256x256. The voxel dimensions are 1x1x1 mm. The second- XETA (eXtended Echo Train Acquisition) produces a series of contiguous T2-weighted images (TR=2500ms, TE=80ms, 25.6 cm^2 field of view, 1 mm slice thickness). Voxel dimensions are 1x1x1 mm.
- Diffusion Tensor Imaging (DTI) DTI scans will be acquired on a 3 Tesla GE system using an echo planar imaging (EPI) DTI Tensor sequence. We will use a double echo option to reduce eddy-current related distortions (Heid 2000; Alexander 1997). To reduce impact of EPI spatial distortion, we will use an 8 Channel coil that will allow us to perform parallel imaging using ASSET (Array Spatial Sensitivity Encoding Techniques, GE) with a SENSE-factor (speed-up) of 2. We will acquire 51 directions with b=*9*00, 8 baseline scans with b=0. The following scan parameters will be used: TR 17000 ms, TE 78 ms, FOV 24 cm, 144x144 encoding steps, 1.7 mm slice thickness. We will acquire 85 axial slices parallel to the AC-PC line covering the whole brain. In addition, Bo field inhomogeneity maps will be collected.
- Resting State fMRI This sequence is an additional EPI BOLD sequence that requires Brain Wave software, available only with 8 Channel coil. It's a resting state fMRI that was 10 minutes long, and contains 200 repetitions of a high resolution EPI scan (96x96 in plane, 3mm thickness, TR-3000 ms, TE=30, 39 slices, ASSETT). Subjects closed their eyes and rested while the magnet is running.
Data Contact
If you have any questions about the data, please contact Sylvain Bouix (sylvain@bwh.harvard.edu) or Doug Terry (dougt@bwh.harvard.edu) at Harvard.
