Add ROIs to BrainSuiteAtlas1

Forums Forums Surface and Volume Registration (SVReg) Add ROIs to BrainSuiteAtlas1

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    • #707
      carnico
      Participant

      Dear brainsuite users,

      I’ve 14 rois (binary nii.gz files) in the same space of BrainSuiteAtlas1. I would add them to this atlas.

      However, I’m not sure how to add them.

      I’ve read the step to create the custom atlas, but I don’t understand how to proceed.

      Do I have to load my ROIs in the subbasename.label.nii.gz (subbasename.svreg.label.nii.gz does not exist in the BrainSuiteAtlas1 folder) and then load the *.nii.gz file of each custom rois to assign the a description? In this way, if I save the new label file I found only one label.

      Thanks a lot for the help.

      Best regards.

      Nicolò

    • #713
      sychoi
      Participant

      You might not need to create a custom atlas in your case because a lot of the necessary components is already provided.

      Quick question first, are any of these labels cortical? Or are all subcortical and/or outside the cerebrum?

    • #715
      carnico
      Participant

      Dear sychoi,

      thanks for the answer. The ROIs I would include are from the Juelich Atlas, in particular the visual pathways, listed below.

      Lateral_geniculate_body_L
      Lateral_geniculate_body_R
      Optic_radiation_L
      Optic_radiation_R
      Visual_cortex_V1_BA17_L
      Visual_cortex_V1_BA17_R
      Visual_cortex_V2_BA18_L
      Visual_cortex_V2_BA18_R
      Visual_cortex_V3V_L
      Visual_cortex_V3V_R
      Visual_cortex_V4_L
      Visual_cortex_V4_R
      Visual_cortex_V5_L
      Visual_cortex_V5_R

      The lateral geniculate nucleus are already in the BrainSuiteAtlas1, but I would include the Juelich atlas ones because they’re a little bigger and positioned slightly different.
      Some ROIs are pure white matter (optic radiation), others grey matter or, at least, they should be, since V1 ROI, for example, included also some white matter portion.

      By the way, I’ve managed to draw these ROIs in the BrainSuiteAtlas1 (briefly: Juelich 1 mm Atlas previously registered to the BrainSuiteAtlas1 > extraction of the ROIs of interest > binary transformation > loading in BS > mask transformation > draw the ROIs inside the masks > save the new atlas with the descriptions > copy the atlas in BS svreg directory > modify the svregmanifest xml file) but the process halted during svreg.

      I think there is a problem with these ROIs.

      Another strange thing that happens is the following. If I load my custom atlas (which is BSatlas1 with added ROIs) an then load the mri label file, when I go to label tool in label description tab, I found the description of the original labels, not the modified description whit added labels, despite in my custom atlas folder there is the modified description file. To see them, i’ve to load the labeldescription file manually.

      Thanks a lot for the support.

      Best Regards

    • #724
      Anand Joshi
      Moderator

      Please edit the brainsuite_labeldescription.xml file according to the edits that you have made.
      This file is located in the BrainSuiteAtlas1 directory that you are editing. It contains ROI ID, ROI name and colors for the ROIs.
      BrainSuite associates ROI IDs and label names using this file.

    • #740
      carnico
      Participant

      Dear Anand,

      i’ve already done, actually.

      screen

      And if i load my modified mri label file, BS load the default brainsuite_labeldescription.xml, despite the fact it is in my custom atlas folder. In this folder, that contains modified label file previously mentioned, there is only the modified brainsuite_labeldescription.xml.

      Best Regards

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