Ex vivo 9.4T MRI of rectal cancer specimens after neoadjuvant therapy: structural and microstructural imaging dataset

Ex vivo 9.4T MRI of rectal cancer specimens after neoadjuvant therapy: structural and microstructural imaging dataset This dataset includes high-resolution (9.4 T) MRI of ex vivo total mesorectal excision (TME) surgical specimens from rectal cancer patients scanned after neoadjuvant therapy (NAT). The data were acquired to investigate whether high-resolution ex vivo diffusion MRI (dMRI) can characterize the properties of rectal wall tissue components - distinguishing residual tumour from treatment-induced fibrosis - more effectively than conventional T2-weighted imaging. Associated publication The acquisition and processing methods are described in: Fouto, A. R., Calá, H., Moreira, S., Shemesh, N., Fernandez, L., Couto, N., Herrando, I., Nougaret, S., Popita, R., Brito, J., Ouro, S., Chambel, M., Papanikolaou, N., Parvaiz, A., Heald, R. J., Castillo-Martin, M., Santiago, I., & Ianus, A. (2026). High-resolution advanced diffusion MRI of rectal cancer surgical specimens: correlating microstructural characteristics with histology. medRxiv. https://doi.org/10.64898/2026.04.02.26350055 Data description This dataset contains MRI data from five ex vivo rectal cancer specimens. For each specimen, the corresponding data are stored in a separate folder (sub-specimen001, sub-specimen002, ... sub-specimen005). Unzip the compressed restage-ex_vivo_v1.zip. This will extract the folder restage-ex_vivo_v1 containing version 1 of the ex vivo MRI data. Inside, you will find sub-folders sub-specimen001, sub-specimen002, ... sub-specimen005. Each specimen folder is organized into two sub-folders, anat and dwi: anat/ - structural MRI · *_T2_multi-echo.nii.gz: multi-slice multi-echo (MSME) structural MRI volume (8 echoes) · *_T2_multi-echo.json: file with the corresponding acquisition parameters dwi/ - diffusion MRI · *_dwi.nii.gz: diffusion-weighted MRI volume (4D) · *_dwi.bval: b-values used in the diffusion acquisition (one per volume; b = 1500 and 3000 s/mm²) · *_dwi.bvec: gradient directions corresponding to each diffusion volume (15 directions) · *_dwi.json: file with the corresponding acquisition parameters The "derivatives" folder contains manually-drawn tissue masks (regions of interest) defined on selected MRI slices, used for the radiology-histology correlation analysis described in the associated publication. Masks are provided per slice, since each mask corresponds to an MRI slice that was matched to a histological section. Each mask is a binary NIfTI file (.nii.gz) co-registered with the corresponding specimen's diffusion MRI volume. derivatives/ | |-- sub-specimen001/ | |-- sub-specimen001_mask_fibrosis_sliceNN.nii.gz Binary mask of fibrosis on slice NN. | |-- sub-specimen001_mask_<tissue>_sliceNN.nii.gz [Other tissue masks on slice NN] | |-- sub-specimen003/ | |-- ... | (and so on for the remaining specimens) Mask naming convention: sub-specimen<ID>_mask_<tissue>_slice<NN>.nii.gz Where <tissue> identifies the tissue type [e.g. fibrosis, tumour, mucosa, submucosa, muscle] and <NN> is the slice number in the corresponding diffusion MRI volume. Acquisition All data were acquired on a 9.4 T Bruker BioSpec preclinical MRI system (86 mm Tx/Rx coil) at 22 °C. Specimens were fixed in formalin (36 h) followed by PBS (4 h) and mounted in Fomblin for scanning. Fat suppression was applied to both sequences. Diffusion MRI (2D): TR/TE = 11,000/24 ms; 130 slices; matrix 140 × 130; isotropic resolution 0.5 mm³; 2 b0 images; b = 1500 and 3000 s/mm²; 15 diffusion directions. Structural MRI (MSME): TR = 25,000 ms; 8 echoes (TE = 10–80 ms); same geometric parameters as the diffusion acquisition. One specimen (specimen001) was acquired with a different MSME protocol: 6 echoes (TE = 15–90 ms; echo spacing 15 ms). Acknowledgements We would like to thank the Champalimaud Foundation Biobank (CFB) for their work with the pseudonymization of the surgical specimens and FFPE blocks; we would like to thank the grossing technicians of the Service of Anatomic Pathology of the Champalimaud Clinical Centre (CCC), specially João Leonardo Fernandes for generating the sections needed to do the path-rad correlation; we would like to thank the Histology Platform of Champalimaud Research for providing the tissue sections to perform the dual stainings; we would like to thank Raquel Graça-Lopes, MSc, and Marco Pereira of the Service of Anatomic Pathology of the CCC for the digitalization of the histological slides. This work was supported by the Fundação para a Ciência e a Tecnologia (2023.02201.RESTART; THCS/0003/2023) within the framework of the co-funded Transforming Health and Care Systems (THCS) partnership (GA N° 101095654) under the EU Horizon Europe Research and Innovation Programme. AI is also supported by the ERC Horizon Europe Research and Innovation Programme Starting Grant No. 101164674.新辅助治疗后直肠癌离体标本的9.4T磁共振成像：结构与微观结构成像数据集 本数据集包含新辅助治疗（neoadjuvant therapy, NAT）后直肠癌患者的离体全直肠系膜切除术（total mesorectal excision, TME）手术标本的高分辨率（9.4T）磁共振成像数据。本次数据采集旨在探究相较于常规T2加权成像，高分辨率离体弥散磁共振成像（diffusion MRI, dMRI）能否更有效地表征直肠壁组织成分特性，区分残留肿瘤与治疗诱导性纤维化。 关联发表论文 相关采集与处理方法详见： Fouto, A. R., Calá, H., Moreira, S., Shemesh, N., Fernandez, L., Couto, N., Herrando, I., Nougaret, S., Popita, R., Brito, J., Ouro, S., Chambel, M., Papanikolaou, N., Parvaiz, A., Heald, R. J., Castillo-Martin, M., Santiago, I., & Ianus, A. (2026). High-resolution advanced diffusion MRI of rectal cancer surgical specimens: correlating microstructural characteristics with histology. medRxiv. https://doi.org/10.64898/2026.04.02.26350055 数据说明 本数据集包含5份离体直肠癌标本的磁共振成像数据。每份标本的对应数据均存储于独立文件夹（sub-specimen001、sub-specimen002……sub-specimen005）中。 解压压缩包restage-ex_vivo_v1.zip后，将得到包含该离体磁共振成像数据集V1版本的restage-ex_vivo_v1文件夹，其内包含sub-specimen001至sub-specimen005共5个次级文件夹。 每个标本文件夹均分为两个次级文件夹：anat与dwi： anat/ - 结构磁共振成像 · *_T2_multi-echo.nii.gz：多切片多回波（multi-slice multi-echo, MSME）结构磁共振成像体积数据（共8个回波） · *_T2_multi-echo.json：包含对应采集参数的配置文件 dwi/ - 弥散磁共振成像 · *_dwi.nii.gz：弥散加权磁共振成像体积数据（4维） · *_dwi.bval：弥散采集所用的b值文件（每个成像体积对应一个b值，b值为1500和3000 s/mm²） · *_dwi.bvec：对应每个弥散成像体积的梯度方向文件（共15个方向） · *_dwi.json：包含对应采集参数的配置文件 "derivatives"文件夹包含在选定磁共振成像切片上手动绘制的组织掩码（感兴趣区，regions of interest, ROI），用于关联发表论文中提及的放射学-组织病理学相关性分析。由于每个掩码均对应一张与组织病理学切片匹配的磁共振成像切片，因此按切片提供掩码。所有掩码均为与对应标本的弥散磁共振成像体积配准后的二值NIfTI文件（.nii.gz格式）。 derivatives/ ├── sub-specimen001/ │ ├── sub-specimen001_mask_fibrosis_sliceNN.nii.gz：切片NN上的纤维化二值掩码 │ ├── sub-specimen001_mask_<tissue>_sliceNN.nii.gz：切片NN上的其他组织掩码 ├── sub-specimen003/ │ ├── ... └── 其余标本文件夹以此类推 掩码命名规则：sub-specimen<ID>_mask_<tissue>_slice<NN>.nii.gz，其中<ID>为标本编号，<tissue>为组织类型（例如纤维化、肿瘤、黏膜、黏膜下层、肌肉），<NN>为对应弥散磁共振成像体积中的切片编号。 采集参数 所有数据均于22℃下在9.4T Bruker BioSpec临床前磁共振成像系统（配备86mm发射/接收线圈）上采集。标本经福尔马林固定36小时，随后以磷酸盐缓冲液（PBS）浸泡4小时，最后固定于Fomblin中进行扫描。两个成像序列均施加了脂肪抑制。 弥散磁共振成像（2D）：重复时间/回波时间（TR/TE）=11000/24ms；共130层；矩阵尺寸140×130；各向同性分辨率0.5mm³；包含2幅b0图像；b值为1500和3000 s/mm²；共15个弥散方向。 结构磁共振成像（多切片多回波序列，MSME）：重复时间（TR）=25000ms；共8个回波（TE范围10~80ms）；几何参数与弥散磁共振成像采集一致。其中specimen001号标本采用了不同的MSME采集协议：共6个回波（TE范围15~90ms；回波间距15ms）。 致谢 本研究感谢尚帕利莫德基金会生物样本库（Champalimaud Foundation Biobank, CFB）对手术标本与福尔马林固定石蜡包埋（FFPE）块进行的匿名化处理；感谢尚帕利莫德临床中心解剖病理科（Champalimaud Clinical Centre, CCC）的标本制备技师，特别感谢João Leonardo Fernandes为放射学-病理学相关性分析提供组织切片；感谢尚帕利莫德研究中心组织学平台提供组织切片以进行双重染色；感谢尚帕利莫德临床中心解剖病理科的Raquel Graça-Lopes硕士与Marco Pereira完成组织切片的数字化工作。 本研究受欧盟“地平线欧洲”研究与创新计划框架下的联合资助项目“医疗与护理系统转型”（Transforming Health and Care Systems, THCS）（项目编号GA N°101095654），由葡萄牙科学技术基金会（Fundação para a Ciência e a Tecnologia）以编号2023.02201.RESTART、THCS/0003/2023提供资助。本研究同时获得欧洲研究委员会“地平线欧洲”研究与创新计划启动基金（编号101164674）的支持。