Hi, I am trying to do an ACPC transform on Slicer 4.11, and have been unable to determine how to do so. I recently updated from an older version in which I used to be able to complete the transform, but lately it had not been registering the final step (i.e. the actual realignment of the MRI scan) …

In latest Slicer Stable Release (Slicer-4.11), you need to specify both the ACPC line and the Midline curve by placing markups fiducial points. To make the behavior more intuitive, I’ll improve latest Slicer Preview Release (Slicer-4.13) to take a markups line and a markups curve instead. The updat…

Thank you so much for your response! I did have to specify both ACPC and Midline with fiducial points in the last version, but I couldn’t figure out how to do so with the new setup. Is there any way you could upload instructions/screenshots here for how to assign the fiducials to a list and then app…

Hi Andras, Thank you for the new release! I was able to create the two fiducial lists, but I wasn’t sure where to go from there, since I couldn’t find any specific module for an “ACPC Transform.” I’ve attached a few screenshots of what I tried: [1] I would also definitely be willing to write up …

I did a quick recording of how ACPC alignment works in latest Slicer Preview Release: [acpcdemo] It would be great if you could create a nice description/tutorial of how to use it (with a few screenshots). Slicer documentation is now in markdown format, which is the format that this fo…

Thank you so much, this was really helpful. I unfortunately am still coming across an error and haven’t been able to figure out why it’s happening despite trying multiple scans. [Slicer 2-11] It seems like a Read Data error (pasted below). I understand if this is too particular to resolve, and can…

Which Slicer version do you use? Try the following: enable “Preserve CLI module data files” in menu → Edit → Application settings → Developer and restart Slicer, run the module, then check if the referenced json file (such as /var/folders/j1/s687l10s5qxfrs8rwnbv_rpw0000gn/T/Slicer-alexisgiff/BA…

I’m currently using the latest preview release-- 4.13.0-2021-02-04. Unfortunately, I’m still getting the same error across the scans with the json files. Would you advise trying with an earlier version?

I’ve tested the module with the latest Slicer Preview Release (4.13.0-2021-02-11 (revision 29702 / 6942d70)) and it worked well. Please try this version (or the newest Slicer Preview Release). If you still keep having problems then check if your user has write access to “Temporary directory” (in me…

Hi Andras, I tried again with the latest preview release and the same issue is occurring- I’ve attached a photo below of the Modules tab in the menu. The directory that seems to be having issues is the one that is selected, so I’m not sure if there’s anything else I can change. Thank you, Alexis …

Could you attach the complete application logs of a failed execution (in menu: Help / Report a bug)? Preferably upload the log to somewhere (such as pastebin , or to dropbox, onedrive, …) and post just the link here. Thank you!

ACPC Transform for MRI scans- Slicer 4.11

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lassoan (Andras Lasso) February 26, 2021, 10:06pm 17

Thank you! I’ve found it - Slicer ACPC Transformation Instructions

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ACPC Transform for MRI scans- Slicer 4.11

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