Examples of sub-millimeter, 7T, T1-weighted EPI datasets acquired with the T123DEPI sequence

These imaging data are examples of sub-millimeter resolution T1-weighted EPI (Echo Planar Imaging) acquired using the T123DEPI (T1-imaging with 2 3D-EPIs) sequence [1]; functional MRI data with matching resolution and distortion, and MP2RAGE (Magnetization Prepared 2 Rapid Acquisition Gradient Echoes) anatomical images [2], from the same subjects. Data from two protocols and subjects presented in the paper describing the sequence [1] are made available here: 1) 0.8 mm protocol: whole brain, axial T123DEPI T1-weighted images; a 5-minute fMRI run with the same orientation and 27 mm coverage in the slice selection direction, covering the primary visual cortex. fMRI data were acquired while the volunteer viewed a flashing checkerboard stimulus; the unsmoothed GLM results of the fMRI and a 0.64 mm resolution MP2RAGE from the same subject. These data are from Experiment 3 in [1] 2) 0.7 mm protocol: partial brain T123DEPI T1-weighted images with longer or shorter readouts; matching coronal echo planar images again acquired while viewing a flashing checkerboard stimulus and a 0.64 mm whole brain MP2RAGE from the same subject. These data are from Experiment 1 in [1]


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These imaging data are examples of sub-millimeter resolution T 1 -weighted EPI (Echo Planar Imaging) acquired using the T 1 23DEPI (T 1 -imaging with 2 3D-EPIs) sequence [1]; functional MRI data with matching resolution and distortion, and MP2RAGE (Magnetization Prepared 2 Rapid Acquisition Gradient Echoes) anatomical images [2], from the same subjects. Data from two protocols and subjects presented in the paper describing the sequence [1] are made available here: 1) 0.8 mm protocol: whole brain, axial T 1 23DEPI T 1 -weighted images; a 5-minute fMRI run with the same orientation and 27 mm coverage in the slice selection direction, covering the primary visual cortex. fMRI data were acquired while the volunteer viewed a flashing checkerboard stimulus; the unsmoothed GLM results of the fMRI and a 0.64 mm resolution MP2RAGE from the same subject. These data are from Experiment 3 in [1] 2) 0.7 mm protocol: partial brain T 1 23DEPI T 1 -weighted images with longer or shorter readouts; matching coronal echo planar images again acquired while viewing a flashing  [2]. Functional data were motion corrected in SPM and a GLM (General Linear Model) analysis was run with the task described by a boxcar convolved with the canonical hrf. The 0.7 mm data were smoothed with a Gaussian of FWHM 0.7 mm prior to the GLM analysis to improve visualization of the results.

Experimental features
The T 1 23DEPI sequence is a version of the MP2RAGE where the GRE (Gradient Recalled Echo) readout has been replaced by a 3D-EPI readout. The possibility to acquire the 3D-EPI in blocks of several readouts (TFEPI or Turbo FLASH EPI in Philips language) allows optimizing the inversion times similarly as suggested for the MP2RAGE. Both the MP2RAGE and T 1 23DEPI data were acquired using the MISS (Multiple Instantaneously Switchable Scans) functionality provided by the scanner vendor. Data source location Data were acquired at the Spinoza Centre in Amsterdam Data accessibility Data are included in this article Value of the data These data are an example of sub-millimeter fMRI data acquired with a 7 T MRI scanner. Researchers can use these to test their own co-registration or full laminar analysis pipelines. The whole brain MP2RAGE and T 1 23DEPI data have already been successfully run through the Freesurfer (https://surfer. nmr.mgh.harvard.edu/) pipeline, but many other pipelines remain to be tested.
These data can also be used as an instruction/training dataset for researchers commencing work in the field of laminar imaging.
The T 1 23DEPI data could be compared to VASO (Vascular Space Occupancy [3]) data acquired on the Siemens or Philips systems in terms of image quality; the imaging sequences are very similar although the optimal inversion times for blood nulling (in VASO) and T 1 -contrast (in T 1 23DEPI) differ.

Data
These fMRI data are examples of sub-millimeter fMRI data. The 0.7 and 0.8 mm data were both acquired on a 7T Philips system, along with echo planar images with T 1 contrast (T 1 23DEPI) and MP2RAGE data as anatomical reference.

Experimental design, materials and methods
Both participants were healthy volunteers, scanned at 7T (Philips, Netherlands) with a 32-channel receive and 2-channel transmit volume coil (Nova Medical, USA) using the acquisition protocols specified below. Volunteers provided written informed consent prior to participating in the session. The protocol was approved by the ethics committee (METC) of the Amsterdam Medical Centre. All acquisition protocols for MP2RAGE and T 1 23DEPI were generated using the MISS (Multiple Instantaneously Switchable Scans) functionality on the Philips platform.
Both the MP2RAGE and T 1 23DEPI first and second inversion images were exported and subsequently combined in MATLAB (https://github.com/JosePMarques/MP2RAGE-related-scripts/). Because of the transmit-coil sensitivity map used in the SENSE (SENSitivity Encoding) reconstruction online, the combined phase images do not contain phase singularities and the combination can be done post-coil combination. In the MP2RAGE combination, an inversion efficiency of 0.96 was assumed.
The 0.8 mm data are from Experiment 3 in [1]. For the 0.8 mm datasets, the 3D-EPI parameters were: TE (echo time) ¼ 25.5 ms, TR (repetition time) ¼ 53 ms, EPI factor ¼ 27, SENSE undersampling factor 4 (LR, Left-Right direction), slice oversampling factor 1.1, volume acquisition time 3.9 s. The FOV (Field of View) for this acquisition was not matched to that of the T 1 23DEPI, being only 27 mm in the HF direction (34 slices) while the T 1 23DEPI covered the entire brain. As the EPI factor, in-plane FOV, bandwidth and slice orientation remained the same, all distortions are equal between fMRI and T 1 23DEPI. For the functional run, the volunteer viewed a black and white checkerboard on a gray background alternating at 8 Hz, 10 s on, 20 s off, for 10 cycles [4]. The echo planar images (FUNC08.nii) and SPM t-score results (FUNC08SPM.nii) are provided.
The 0.7 mm data are from Experiment 1 in 0.7 [1]. In the 0.7 dataset two T 1 23DEPI's were acquired with different block lengths. T 1 23DEPI protocols with 3D-EPI readouts split into either 2 or 4 k-space sections (blocks) were acquired. A high-resolution (0.7 mm isotropic) 3D-EPI protocol previously used for sub-millimeter fMRI acquisitions [5] was used to acquire functional data and the T 1 23DEPI acquisition parameters were matched to its sequence parameters. The 3D-EPI protocol parameters were: FOV 120 * 131 * 24 mm 3 , matrix size 172 * 188 * 34, TR/TE ¼ 57 ms/28 ms, EPI factor ¼ 27, SENSE undersampling factor 3.5 (LR) * 1.3 (AP), slice oversampling factor 1.28, 68 EPI readouts (segments) per volume, volume acquisition time 3.9 s. No fat saturation was used. The stimulus was the same black and white checkerboard on a gray background, again alternating at 8 Hz, 10 s on, 20 s off, for 10 cycles [4]. The echo planar images (FUNC07.nii) and SPM t-score results (FUNC07SPM.nii) are provided.
The minimum inversion time of the first readout (TI 1 ) in the 2-block protocol was limited by the length of the readout block. For the 2-block protocol this readout block length was 1.94 s, for the 4block protocol it was 1.03 s. Parameters for the 2-block T 1 23DEPI were: TR T123DEPI 10 s, TI 1 /TI 2 ¼ 1200/ 3800 ms, α 1 /α 2 ¼ 14/10 degrees, TR ¼ 57 ms, 34 readouts per block, total 2 blocks per volume. FOV ¼ 120 * 131 * 24, voxel size 0.7 * 0.7 * 0.7 mm, 4 averages, total acquisition time 80 s. The first and second inversion images are provided (T123DEPI07_bl2_INV1.nii; T123DEPI07_bl2_INV1ph.nii; T123DEPI07_bl2_INV2.nii; T123DEPI07_bl2_INV2ph.nii;) and the resulting T 1 -weighted image (T123DEPI07_bl2M.nii) and T 1 -map (T123DEPI07_bl2_T1M.nii). An intensity based mask of the second inversion image was used to suppress the noise in the background of the T 1 -weighted image and the T 1 -map.