HR-pQCT double-stack scan alignment using IPL

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Overview

This package performs batch processing in IPL (Image Processing Language) for Scanco Medical imaging datasets.
It is specifically designed to align double-stack scans with no overlap between the stacks, correcting rotational misalignments around the z-axis and translations in the x-y plane.

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Citation

If you use this code in your work, please cite:

S. Hosseinitabatabaei, S. McCluskey, C. Denton, E. Zimmermann, F. Glorieux, F. Charbonneau, F. Rauch, B.M. Willie.
Bone microstructural and strength changes over one year in children with osteogenesis imperfecta are comparable to age- and sex-matched healthy controls.
Journal of Bone and Mineral Research (JBMR), 2025

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Functionality

This package:

• Aligns stacks of a double-stack scan for:
  • Rotational misalignment (around the z-axis)
  • Translational misalignment (x-y plane)
  • Creates a log file of the analysis in the folder of each scan

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Usage

💡 This package assumes that the standard evaluation has already been completed, such that the trabecular and cortical masks and GOBJs, as well as grayscale and segmented files are available

STEP 1: Download the scripts 0_STACK_ALINGMENT_BATCH.COM, 1_STACK_ALINGMENT_QUE.COM, and 2_STACK_ALINGMENT_IPL_V1.COM on your local computer.

STEP 2: Using a text editor (e.g., notepad), open script 0_STACK_ALINGMENT_BATCH.COM, then list all scans, for which the alignment is needed, as follows:

💡 The input AIM files need to be entered with their full directory. Also, make sure to change the scanner USER to proper name in the examples shown below

@1_STACK_ALINGMENT_QUE.COM   DK0:[USER.DATA.00000001.00000001]C0000001.AIM
@1_STACK_ALINGMENT_QUE.COM   DK0:[USER.DATA.00000002.00000002]C0000002.AIM
...

Where:

• c0000001.aim is your grayscale .AIM file from the double-stack scan.

STEP 3: Transfer the scripts to the login directory of the scanner using an FTP transfer software such as filezilla

💡 Make sure the scripts are transferred in ASCII mode

STEP 4: Open a DECterm window, then run the batch script, as follows:

@0_STACK_ALINGMENT_BATCH.COM

This will submit all the stack alignment jobs to the FAST queue.

💡 To run the stack alignment in interactive mode for a scan at a time, submit the job using this command: @2_STACK_ALINGMENT_IPL_V1.COM DK0:[USER.DATA.00000001.00000001]C0000001.AIM

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Inputs

• Grayscale .AIM file of the potentially misaligned double-stack scan

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Outputs

• Transformation matrix used for alignment
• Pseudo-volumes of adjacent stack slices (see referenced paper for details)
• Aligned grayscale and segmented images
• Aligned trabecular and cortical masks, and corresponding GOBJs
• Log file of the analysis in the folder of each scan

📝 Files created by the analysis

File	Description
*_STACK_ALIGN_TMAT.DAT	Transformation matrix from stack alignment
*_TOP_MERGED.AIM	Pseudo-volume of the top stack
*_BOT_MERGED.AIM	Pseudo-volume of the bottom stack
*_STACK_ALIGNED_SEG.AIM	Segmented aligned stack
*_STACK_ALIGNED.AIM	Grayscale aligned stack
*_ALIGNED_TRAB_MASK.AIM	Aligned trabecular mask (AIM format)
*_ALIGNED_TRAB_MASK.GOBJ	Aligned trabecular mask (GOBJ format)
*_STACK_ALIGNED_MASK.AIM	Aligned periosteal mask (AIM format)
*_STACK_ALIGNED.GOBJ	Aligned periosteal mask (GOBJ format)
*_ALIGNED_CORT_MASK.AIM	Aligned cortical mask (AIM format)
*_ALIGNED_CORT_MASK.GOBJ	Aligned cortical mask (GOBJ format)
*_STACK_ALIGN_EROD.GOBJ	Eroded periosteal contour used for alingment

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Contact

For any questions, contact mahdi.tabatabaei@mail.mcgill.ca