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--- other:dsx:xmanager:tutorials:using_the_subject_populator [2024/07/17 15:09] – sgranger
+++ other:dsx:xmanager:tutorials:using_the_subject_populator [2025/02/15 06:49] (current) – Cleaned up page and added headers. wikisysop
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-====== Using_the_Subject_Populator ======
+====== Using the Subject Populator ======
-||
 The Subject Populator is a utility in xManager that fills out the items in a subject file, based on data files that it finds in a folder that you specify. It can be helpful when you are starting a new study and need to create a subject file with all the appropriate sessions, trackable objects, configurations, and trials. If all of the subjects in your study have the same trials, then you can use a subject template for creating subsequent subject files. However, if the trials differ from subject to subject, you can use the Subject Populator to fill out the subject file for each one.
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 {{:xMan_SubjectPopulator.png}}
+===== Usage =====
 To use this utility, follow these steps:
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   - Press OK to populate the subject file.
-This utility is designed to work with a top-level folder (e.g., Subject01) that contains subfolders for the trial data (e.g., Subject01/Trials) and trackable objects (e.g., Subject01/Bones). If the subject contains multiple sessions, then each session’s data must be in a subfolder with the name of the session (e.g., Subject01/Session1/Trials, Subject01/Session2/Bones). Exception: If there are multiple sessions and there is trackable object data in a folder such as Subject01/Bones, it will be added to //every// session in the subject. If you have trackable object data for individual sessions, then put it in the session folders (e.g., Subject01/Session2/Bones).
+===== Considerations =====
+This utility is designed to work with a top-level folder (e.g., Subject01) that contains subfolders for the trial data (e.g., Subject01/Trials) and trackable objects (e.g., Subject01/Bones). If the subject contains multiple sessions, then each session’s data must be in a subfolder with the name of the session (e.g., Subject01/Session1/Trials, Subject01/Session2/Bones).
+**Exception**: If there are multiple sessions and there is trackable object data in a folder such as Subject01/Bones, it will be added to //every// session in the subject. If you have trackable object data for individual sessions, then put it in the session folders (e.g., Subject01/Session2/Bones).
 Scan data works similarly to trackable object data, in that it can be put in session folders or in the top-level subject folder. The difference is that you can have separate folders for CT and MRI (e.g., Subject01/CT, Subject01/MRI, Subject01/Session1/CT, Subject02/Session2/MRI). However, both CT and MRI data end up in the same place (in the Scan Data section for the session). Each folder of scan data should contain DICOM images that have the same size, spacing, and orientation. For example, if in a knee study you have slices at the hip and ankle for determining joint centers, then the files should be divided into three folders (e.g., Subject01/CT/hip, Subject01/CT/knee, Subject01/CT/ankle). None of these folders should contain scout scans or other extraneous files.
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 If your X-ray files use the standard Phantom naming convention (<trial>_Cam_<camera>_Cine1.cine), xManager will be able to extract the trial names and view (camera) names from them. If they do not use this format, they must use the following format: <trial>_<view>.cine (or .tif).
-If you will be using Surface3D to segment the scan data and create image and surface files for the trackable objects, then when you are populating the subject file there will probably not yet be any object files to process. If there are, whether you created them earlier in Surface3D or in a third-party program, they must be in a folder with the name of the object (e.g., Subject01/Bones/Femur_R, Subject01/Bones/Tibia_R) and every object file must contain the name of the object (case-sensitive). xManager will process segmented image files, surface files, ROI surface files, and inner surface files, if you specify the appropriate key phrases in the dialog. For segmented image files in the raw format, xManager will extract the dimensions and voxel size from the file name, assuming that the dimensions are immediately followed by the voxel size, with all six values separated by underscores. You can also put items like "16bit" and "LE" (little-endian) in the file name and xManager will extract them. Bit-depth is not necessary, though, because xManager will calculate it from the dimensions and the file size. For example, with this file name: Femur_R_283_221_180_3125_3125_5_LE.raw the extracted image dimensions will be 283x221x180 voxels, with a voxel size of 0.3125x0.3125x0.5 mm and using the little-endian format.
+===== Surface3D =====
+If you will be using [[other:dsx:surface3d:surface3d_overview|Surface3D]] to segment the scan data and create image and surface files for the trackable objects, then when you are populating the subject file there will probably not yet be any object files to process. If there are, whether you created them earlier in Surface3D or in a third-party program, they must be in a folder with the name of the object (e.g., Subject01/Bones/Femur_R, Subject01/Bones/Tibia_R) and every object file must contain the name of the object (case-sensitive).
+xManager will process segmented image files, surface files, ROI surface files, and inner surface files, if you specify the appropriate key phrases in the dialog. For segmented image files in the raw format, xManager will extract the dimensions and voxel size from the file name, assuming that the dimensions are immediately followed by the voxel size, with all six values separated by underscores. You can also put items like "16bit" and "LE" (little-endian) in the file name and xManager will extract them. Bit-depth is not necessary, though, because xManager will calculate it from the dimensions and the file size.
+For example, with this file name: Femur_R_283_221_180_3125_3125_5_LE.raw the extracted image dimensions will be 283x221x180 voxels, with a voxel size of 0.3125x0.3125x0.5 mm and using the little-endian format.
+===== Options =====
 It is recommended that you select the //Use Relative Path Shortcuts// option. If selected, when xManager adds a path shortcut to the subject file (e.g., shortcut to the X-ray folder, to the objects folder), the path will be relative to the folder containing the subject file. Making all path shortcuts relative to the subject file makes it easier to move the data folder to another location on your computer or to another computer. However, this is not practical if some of the data must be kept on a shared network drive.