R08.09.01.03 · 任务小类

神经影像质控与掩膜编辑

Neuroimaging QC & mask editing

Inspect scans, pick failures and edit masks.

20 条本项目编写的提案 · 分类 v1.1 · 新增基准运行 0 次。下方验证方式与部分得分规则是设计，不是执行结果。

典型应用: FSLeyes · FreeView · MRIcroGL
小类 GUI 需求标签: G3 · 仅 GUI

任务提案 · 20

展开查看完整原文与建议检查方式；两种界面均保留提案英文原文。

R08.09.01.03-T01 Choose the best skull-strip among three candidates in FSLeyes

原始指令

In FSLeyes load input/T1.nii.gz with the three candidate masks in input/masks/ as overlays. Inspect axial, coronal and sagittal views for over- and under-stripping, then write output/qc_result.json with chosen_mask, verdict (pass or fail) and a one-sentence rationale.

平台: mac · macOS lin · Linux
应用: FSLeyes
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 nav · 平移 / 缩放 / 滚动 vis · 视觉判断
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 3 / 5

建议验证方式

chosen_mask and verdict must equal gold exactly; rationale keyword-checked for the deciding defect (temporal-lobe loss or neck inclusion). Mask Dice values are withheld and the masks' file names carry no hint. FSL command-line tools and nibabel are absent from the image, and FSLeyes' Python shell and --runscript are disabled.

建议部分得分

60% chosen mask; 25% verdict; 15% rationale names the defect.

R08.09.01.03-T02 Label eight fMRI runs pass or fail from mean and standard-deviation images

原始指令

In FSLeyes open the 8 runs in input/func/ with their mean and tSD images. Judge each for signal dropout, ghosting, spiking and gross motion, and write output/qc.csv with run, verdict and the artifact type for failures.

平台: mac · macOS lin · Linux
应用: FSLeyes
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: nav · 平移 / 缩放 / 滚动 vis · 视觉判断 click · 指向与点击
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 3 / 5

建议验证方式

Verdicts must match the expert labels for all 8 runs; artifact types must match the seeded defect per failing run (3 fail). No motion-parameter files are provided. FSL command-line tools and nibabel are absent from the image, and FSLeyes' Python shell and --runscript are disabled.

建议部分得分

70% verdicts (8.75 pts each); 30% artifact types.

R08.09.01.03-T03 Report the atlas label at a cluster peak in FSLeyes

原始指令

In FSLeyes load input/MNI152_T1_2mm.nii.gz, overlay input/zstat1.nii.gz thresholded at 3.1, add the Harvard-Oxford cortical atlas, navigate to the peak voxel of the largest cluster, and write its MNI coordinates and the atlas label to output/answer.json.

平台: mac · macOS lin · Linux
应用: FSLeyes
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: click · 指向与点击 nav · 平移 / 缩放 / 滚动 vis · 视觉判断
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 2 / 5

建议验证方式

Coordinates within 4 mm of the gold peak and the label string equal to the Harvard-Oxford label at that location.

建议部分得分

50% peak location; 50% atlas label.

R08.09.01.03-T04 Edit a brain mask in FSLeyes to remove an included eye globe

原始指令

Load input/T1.nii.gz and input/brain_mask.nii.gz in FSLeyes. The mask wrongly includes the right eye globe and part of the optic nerve. Use the edit tools (brush, fill, erase with a selected 3D region) to remove them without eroding cortex, and save output/brain_mask_fixed.nii.gz.

平台: mac · macOS lin · Linux
应用: FSLeyes
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: path · 连续路径 click · 指向与点击 vis · 视觉判断 nav · 平移 / 缩放 / 滚动
工作产物: WP10 · 标注
条件: 未声明
提案难度: 3 / 5

建议验证方式

Dice ≥0.95 with the gold corrected mask; zero voxels remaining inside the gold eye-globe ROI; ≥99% of gold cortical mask voxels retained. FSL command-line tools and nibabel are absent from the image, and FSLeyes' Python shell and --runscript are disabled.

建议部分得分

40% eye removed; 35% Dice overall; 25% cortex preserved.

R08.09.01.03-T05 Fix a FreeSurfer white-matter surface error with control points in FreeView

原始指令

In FreeView load subject input/sub-01 (T1, wm.mgz, surfaces). The white surface under-includes white matter in the left superior frontal region (shown in input/hint.png). Add control points there, save them as control.dat, rerun the pial/white regeneration step, and save output/lh.white plus output/control.dat.

平台: lin · Linux mac · macOS
应用: FreeView · FreeSurfer
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 vis · 视觉判断 nav · 平移 / 缩放 / 滚动
工作产物: WP10 · 标注
条件: long · 长流程
提案难度: 5 / 5

建议验证方式

Control points lie inside the gold defect region (≥80% within it, ≤5 outside); after rerun, surface-to-gold distance in the region drops below 0.7 mm mean and surfaces elsewhere change by <0.2 mm mean. recon-all is the only command-line step allowed; control.dat must be saved from FreeView's point-set tool.

建议部分得分

35% control points placed correctly; 40% surface corrected in region; 25% no change elsewhere.

R08.09.01.03-T06 Edit a wm.mgz to erase a misclassified voxel cluster in FreeView

原始指令

In FreeView open input/sub-02/mri/T1.mgz and wm.mgz. A cluster of non-white-matter voxels near the left temporal pole is labelled 255. Erase exactly that cluster with the voxel-edit tool (leaving other 255 voxels untouched) and save output/wm_edited.mgz.

平台: lin · Linux mac · macOS
应用: FreeView
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: path · 连续路径 click · 指向与点击 vis · 视觉判断 nav · 平移 / 缩放 / 滚动
工作产物: WP10 · 标注
条件: 未声明
提案难度: 3 / 5

建议验证方式

All gold erroneous voxels set below 110; ≥99.5% of other 255 voxels unchanged; no new 255 voxels added. The cluster is not separable by intensity threshold alone. FreeView's command console and -cmd files are disabled, and FSL, nibabel and FreeSurfer mri_* editors are absent from the image.

建议部分得分

50% cluster removed; 35% other voxels preserved; 15% no additions.

R08.09.01.03-T07 Judge EPI-to-T1 registration quality for four subjects in FSLeyes

原始指令

In FSLeyes load the four registered EPI images in input/reg/ over their T1s and inspect edge alignment at the ventricles and cortical boundary. Write output/reg_qc.csv with subject, verdict and the direction of misregistration for failures (e.g., 'EPI shifted posteriorly').

平台: mac · macOS lin · Linux
应用: FSLeyes
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: nav · 平移 / 缩放 / 滚动 vis · 视觉判断 click · 指向与点击
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 3 / 5

建议验证方式

Verdicts match gold for all four; for the two failures the stated direction must match the sign of the applied shift in the seeded transforms. Transform files are not provided. FSL command-line tools and nibabel are absent from the image, and FSLeyes' Python shell and --runscript are disabled.

建议部分得分

60% verdicts; 40% directions for failures.

R08.09.01.03-T08 Create a lesion mask by hand on a FLAIR image in FSLeyes

原始指令

Load input/FLAIR.nii.gz in FSLeyes and create a new mask overlay. Draw the periventricular white-matter hyperintensity lesions visible across slices 40–70 with the brush, excluding normal septal and ependymal signal, and save output/lesion_mask.nii.gz plus the total lesion volume (mL) in output/answer.json.

平台: mac · macOS lin · Linux
应用: FSLeyes
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: path · 连续路径 click · 指向与点击 vis · 视觉判断 nav · 平移 / 缩放 / 滚动
工作产物: WP10 · 标注
条件: long · 长流程
提案难度: 4 / 5

建议验证方式

Dice ≥0.70 with the expert lesion mask, false-positive volume ≤25% of lesion volume, and volume within 20% of expert value. Intensity thresholding alone yields Dice ~0.5 on this scan (reference attempt). FSL command-line tools and nibabel are absent from the image, and FSLeyes' Python shell and --runscript are disabled.

建议部分得分

55% Dice; 25% false-positive control; 20% volume.

R08.09.01.03-T09 Compare Freesurfer aparc segmentation against the T1 and flag mislabelled regions

原始指令

In FreeView load input/sub-03 with aparc+aseg.mgz over T1.mgz. Inspect the segmentation and list in output/errors.csv the three regions with visible label errors (region name, slice range, error type: over-inclusion, under-inclusion or wrong label), judged from anatomy, not statistics.

平台: lin · Linux mac · macOS
应用: FreeView
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: nav · 平移 / 缩放 / 滚动 vis · 视觉判断 hover · 悬停与上下文
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 4 / 5

建议验证方式

Region set must equal the gold three (exact label names); error type must match per region; slice ranges must overlap the gold ranges. The subject's stats files are removed so outlier detection by numbers is unavailable. FreeView's command console is disabled and FreeSurfer stats tools (mri_segstats) are absent from the image.

建议部分得分

60% three regions (20 pts each); 25% error types; 15% slice ranges.

R08.09.01.03-T10 Render a 3D cortical surface with an overlay in MRIcroGL and export a figure

原始指令

In MRIcroGL load input/mni152.nii.gz, add input/zstat.nii.gz as an overlay with threshold 2.3–6 and the 'red-yellow' colour scale, show a left-lateral 3D render (azimuth 270°, elevation 0°), add a colour bar, and save output/surface.png at 1600×1200.

平台: mac · macOS win · Windows lin · Linux
应用: MRIcroGL
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: click · 指向与点击 drag · 拖放 vis · 视觉判断
工作产物: WP03 · 视觉排版
条件: 未声明
提案难度: 3 / 5

建议验证方式

PNG 1600×1200 with SSIM ≥0.85 against the reference render at that view, overlay voxels coloured only where z ≥2.3 (colour-mask check), and a colour bar present. MRIcroGL's Python scripting pane is disabled.

建议部分得分

30% overlay threshold and colours; 35% view; 20% image matches; 15% colour bar.

R08.09.01.03-T11 Pick the correct fieldmap-corrected EPI among three unwarping variants

原始指令

In FSLeyes load input/epi_raw.nii.gz and the three unwarped versions in input/unwarped/ with the T1. Decide which used the correct phase-encoding direction by inspecting frontal and temporal distortion against the T1, and write the choice plus the direction error in the other two to output/answer.json.

平台: mac · macOS lin · Linux
应用: FSLeyes
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: nav · 平移 / 缩放 / 滚动 vis · 视觉判断 click · 指向与点击
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 3 / 5

建议验证方式

Chosen file must equal gold; the stated direction error for each rejected file must match the seeded sign (over-unwarped or inverted). JSON sidecars with PhaseEncodingDirection are withheld. FSL command-line tools and nibabel are absent from the image, and FSLeyes' Python shell and --runscript are disabled.

建议部分得分

50% correct choice; 50% direction diagnosis for the two rejects.

R08.09.01.03-T12 Edit an aseg to correct a hippocampus boundary in FreeView

原始指令

In FreeView load input/sub-04 T1.mgz and aseg.mgz. The left hippocampus label (17) extends into the amygdala across slices given in input/slices.txt. Recut the boundary with the voxel-edit tool so the labels follow the uncal recess, and save output/aseg_edited.mgz.

平台: lin · Linux mac · macOS
应用: FreeView
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: path · 连续路径 click · 指向与点击 vis · 视觉判断 nav · 平移 / 缩放 / 滚动
工作产物: WP10 · 标注
条件: long · 长流程
提案难度: 5 / 5

建议验证方式

Left hippocampus Dice ≥0.90 and amygdala Dice ≥0.88 with the expert edit; voxels of other labels changed <0.5%; total intracranial label volume unchanged within 0.2%. FreeView's command console and -cmd files are disabled, and FSL, nibabel and FreeSurfer mri_* editors are absent from the image.

建议部分得分

40% hippocampus Dice; 35% amygdala Dice; 25% no collateral label changes.

R08.09.01.03-T13 Create a sphere ROI at given MNI coordinates in FSLeyes and report its mean value

原始指令

In FSLeyes load input/MNI152_T1_2mm.nii.gz, create a 6 mm radius spherical mask centred at MNI (−42, 18, 24), save it as output/roi.nii.gz, then report the mean of input/cope1.nii.gz inside that ROI in output/answer.json.

平台: mac · macOS lin · Linux
应用: FSLeyes
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: click · 指向与点击 type · 文字与表单 nav · 平移 / 缩放 / 滚动
工作产物: WP10 · 标注
条件: 未声明
提案难度: 2 / 5

建议验证方式

ROI centroid within 2 mm of the target, voxel count equal to the gold sphere ±5%, and the reported mean within 1% of the value computed from the saved ROI.

建议部分得分

40% ROI location; 30% size; 30% mean value.

R08.09.01.03-T14 Build a four-panel QC montage of ten subjects' registrations in FSLeyes

原始指令

For the ten subjects in input/subs/, use FSLeyes to make a QC sheet: for each subject one axial, one coronal and one sagittal snapshot of the registered T1 with MNI edge overlay, assembled into output/qc_montage.png with subject labels, plus output/qc_notes.csv listing the two subjects whose registration fails.

平台: mac · macOS lin · Linux
应用: FSLeyes
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 nav · 平移 / 缩放 / 滚动 vis · 视觉判断
工作产物: WP03 · 视觉排版
条件: long · 长流程
提案难度: 3 / 5

建议验证方式

Montage has 30 panels with readable subject labels (OCR) and edge overlays present; the failing-subject set equals gold exactly. FSL command-line tools and nibabel are absent from the image, and FSLeyes' Python shell and --runscript are disabled.

建议部分得分

40% complete montage; 20% labels and overlays; 40% failing subjects identified.

R08.09.01.03-T15 Identify the dropout-affected region of an EPI and name the likely cause

原始指令

In FSLeyes load input/epi_mean.nii.gz with input/T1.nii.gz. Locate the region of marked signal dropout, report its anatomical label (from the Harvard-Oxford atlas at the dropout centre), its approximate extent in mm³, and the likely physical cause in output/answer.json.

平台: mac · macOS lin · Linux
应用: FSLeyes
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: nav · 平移 / 缩放 / 滚动 vis · 视觉判断 click · 指向与点击
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 3 / 5

建议验证方式

Atlas label must equal gold; extent within a factor of 2 of the gold dropout volume; the stated cause must match the seeded one (air–tissue susceptibility at the sinus) by keyword. FSL command-line tools and nibabel are absent from the image, and FSLeyes' Python shell and --runscript are disabled.

建议部分得分

45% region label; 30% extent; 25% cause.

R08.09.01.03-T16 Control: pick the best skull-strip mask by computed overlap metrics

原始指令

Control pair of T01. From the terminal, compute Dice and Jaccard of each mask in input/masks/ against input/reference_mask.nii.gz (provided here) with FSL or nibabel, and write chosen_mask and verdict to output/qc_result.json.

平台: lin · Linux mac · macOS
应用: FSL · nibabel
交互表面: term · 终端
GUI 需求 · 任务设定: CL · CLI 足够
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: code · 代码与命令
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 2 / 5

建议验证方式

Same chosen_mask and verdict as the T01 gold. Scored as the CLI control of T01; a reference mask is provided here precisely because the GUI task has none.

建议部分得分

60% chosen mask; 25% verdict; 15% metrics reported.

R08.09.01.03-T17 Detect and localize spike artifacts across time in an EPI series

原始指令

In FSLeyes load the 4D series input/func.nii.gz and scrub through time (and use the time-series view at several voxels) to find volumes with spike artifacts. Write output/spikes.csv listing volume indices and the affected slice range, and the total count in output/answer.json.

平台: mac · macOS lin · Linux
应用: FSLeyes
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: nav · 平移 / 缩放 / 滚动 vis · 视觉判断 av · 音视频时序
工作产物: WP12 · 答案 / 决策
条件: long · 长流程
提案难度: 4 / 5

建议验证方式

Volume index set F1 ≥0.85 against gold (4 spike volumes among 240) and slice ranges overlapping gold; motion-outlier tools (fsl_motion_outliers) are absent from the image. FSLeyes' Python shell and --runscript are disabled.

建议部分得分

60% spike volumes (F1 scaled); 25% slice ranges; 15% count.

R08.09.01.03-T18 Correct a tissue-segmentation leak at the skull in FSLeyes

原始指令

input/gm_mask.nii.gz leaks into dura and skull along the superior convexity. In FSLeyes edit the mask to remove the leak while keeping true grey matter, including in the sulcal depths, and save output/gm_mask_fixed.nii.gz plus the voxel count removed in output/answer.json.

平台: mac · macOS lin · Linux
应用: FSLeyes
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: path · 连续路径 click · 指向与点击 vis · 视觉判断 nav · 平移 / 缩放 / 滚动
工作产物: WP10 · 标注
条件: long · 长流程
提案难度: 4 / 5

建议验证方式

Dice ≥0.93 with the expert mask; ≥90% of gold leak voxels removed; ≤2% of gold grey-matter voxels lost; reported count within 10% of actual change. FSL command-line tools and nibabel are absent from the image, and FSLeyes' Python shell and --runscript are disabled.

建议部分得分

35% leak removal; 35% Dice; 20% GM preservation; 10% count reported.

R08.09.01.03-T19 Draw a tumour segmentation across three modalities in MRIcroGL

原始指令

In MRIcroGL load input/T1c.nii.gz, input/T2.nii.gz and input/FLAIR.nii.gz of the same patient. Draw a mask of the enhancing tumour core using T1c and a second mask of the peritumoural oedema using FLAIR, keeping them non-overlapping, and save output/core.nii.gz and output/edema.nii.gz plus volumes in output/answer.json.

平台: mac · macOS win · Windows lin · Linux
应用: MRIcroGL
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: path · 连续路径 click · 指向与点击 vis · 视觉判断 nav · 平移 / 缩放 / 滚动
工作产物: WP10 · 标注
条件: long · 长流程
提案难度: 5 / 5

建议验证方式

Core Dice ≥0.75 and oedema Dice ≥0.70 against expert masks; overlap between the two submitted masks <2% of core volume; volumes within 20% of expert values. MRIcroGL's Python scripting pane is disabled and FSL/nibabel are removed from the image.

建议部分得分

35% core; 35% oedema; 20% non-overlap; 10% volumes.

R08.09.01.03-T20 Triage a 12-subject structural QC batch and write a reviewer report

原始指令

For the 12 T1s in input/batch/, inspect each in FSLeyes (motion, ringing, coverage, inhomogeneity, incidental findings) and produce output/qc_table.csv with per-subject verdict and artifact tags, plus output/report.md summarizing exclusions and the two subjects needing manual mask editing before reprocessing.

平台: mac · macOS lin · Linux
应用: FSLeyes
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: nav · 平移 / 缩放 / 滚动 vis · 视觉判断 click · 指向与点击
工作产物: WP01 · 文档
条件: long · 长流程
提案难度: 4 / 5

建议验证方式

Verdicts match expert labels for ≥11 of 12; artifact tags match the seeded defects per failing subject; the two edit-needed subjects must be exactly those in gold; report.md must state the exclusion count consistent with the table. FSL command-line tools and nibabel are absent from the image, and FSLeyes' Python shell and --runscript are disabled.

建议部分得分

45% verdicts; 25% artifact tags; 20% edit-needed subjects; 10% consistent report.

已有研究映射

以下沿用研究目录中的基准与小类映射，不是逐题标注、执行记录或产品背书。

Agents' Last Exam (ALE)

神经影像质控与掩膜编辑

任务提案 · 20

原始指令

建议验证方式

建议部分得分

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原始指令

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原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

已有研究映射

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