Problem of find images when use "papaya-builder.sh -atlas myAtlas.xml"

[cirongliu]

I was trying to use the "papaya-builder.sh -atlas myAtlas.xml" to build with a custom atlas.

However, during the building, the program will always automatically add "null/" to the file location declared in the XML file. For example, I put "Talairach.xml" and "Talairach_labels_1mm.nii.gz" in the same folder of "papaya-builder.sh" and ran "papaya-builder.sh -atlas Talairach.xml", here was the outcome:
"
Cleaning output directory...
Including atlas Talairach.xml
Using atlas image file null/Talairach_labels_1mm.nii.gz
Problem finding atlas file. Reason: Source 'null/Talairach_labels_1mm.nii.gz' does not exist
Compressing JavaScript...
Further compressing...
Done! See build folder for output...

"

How to remove the "null"?

Thanks!

[cirongliu]

Thanks. I found the solution after several testing. I need add path to the myAtlas.xml as well. It should be

"papaya-builder.sh -atlas /path/myAtlas.xml"

[juan-d]

Hello,

When trying to use papaya-builder.sh -atlas myAtlas.xml (in macOS Catalina), I am getting the following error:

Exception in thread "main" org.json.JSONException: JSONObject["images"] not found.
at org.json.JSONObject.get(JSONObject.java:473)
at org.json.JSONObject.getJSONObject(JSONObject.java:573)
at edu.uthscsa.ric.papaya.builder.Atlas.findImageFile(Atlas.java:76)
at edu.uthscsa.ric.papaya.builder.Atlas.createAtlas(Atlas.java:37)
at edu.uthscsa.ric.papaya.builder.Builder.main(Builder.java:257)

I have tried numerous things so that 'images' (which I assume are the 'imagefile' and the 'summaryimagefile' in the FSL Atlas Specification) can be found by the builder script.

This is my directory structure:

Papaya
├── LICENSE
├── README.md
├── atlas
 | ├── myImage.nii
 | └── mySummaryimage.nii
├── build
├── build.properties
├── docs
├── lib
├── myAtlas.xml
├── myImage.nii
├── mySummaryimage.nii
├── package-lock.json
├── package.json
├── papaya-builder.sh
├── release
├── src
└── tests

I am running papaya-builder.sh form inside this folder.

This is the header in my xml file (myAtlas.xml):

<?xml version="1.0" encoding="ISO-8859-1"?>
<atlas version="1.0">
  <header>
    <name>My Atlas</name>
    <type>Label</type>
    <imagefile>/atlas/myImage/</imagefile>
    <summaryimagefile>/atlas/mySummaryimage/</summaryimagefile>
  </header>
  <data>

I have tried placing myImage.nii (4D image with a region in each volume) and mySummaryimage.nii (3D image with all labelled regions I a single volume) in an atlas folder inside the Papaya folder (/Papaya/atlas/), with the xml header as above, and in the same directory as myAtlas.xml (within the /Papaya/ folder). In the latter case, I have amended the xml header this way:

<imagefile>/myImage/</imagefile>
<summaryimagefile>/mySummaryimage/</summaryimagefile>

As per the previous comment in this thread, I have also tried to provide the path to myAtlas.xml when running papaya-builder.sh. None of this has worked.

I would greatly appreciate any help with this issue.