JFRC2010_3D_Mask.nrrd is not a valid choice for "mask" in line 1612

[mollykirk16]

Hello,

I am running this through FIJI and my input data is eGFP labeled IHC data which has been registered to JFRC2 using the Cachero settings in CMTK. The data is located in my documents and the masks are located in the plugins folder on my hard drive. I am consistently getting this error <"JFRC2010_3D_Mask.nrrd" is not a valid choice for "mask" in line 1612>.

1612 run("Mask Median Subtraction", "mask=JFRC2010_3D_Mask.nrrd data="+stackSt+" %="+MedianSub+" subtract histogram="+histave+"");
1613 selectWindow("JFRC2010_3D_Mask.nrrd");

I would greatly appreciate your help with this if you can.

Best,

Molly Jane Kirk

[HideoOtsuna]

Hi, Please open a mask color depth MIP (CDM) and the searching CDM stack in Fiji. Then run the CDM search plugin. Thank you, Hideo

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On Nov 23, 2020, at 8:32 PM, mollykirk16 ***@***.***> wrote: Hello, I am running this through FIJI and my input data is eGFP labeled IHC data which has been registered to JFRC2 using the Cachero settings in CMTK. The data is located in my documents and the masks are located in the plugins folder on my hard drive. I am consistently getting this error <"JFRC2010_3D_Mask.nrrd" is not a valid choice for "mask" in line 1612>. 1612 run("Mask Median Subtraction", "mask=JFRC2010_3D_Mask.nrrd data="+stackSt+" %="+MedianSub+" subtract histogram="+histave+""); 1613 selectWindow("JFRC2010_3D_Mask.nrrd"); I would greatly appreciate your help with this if you can. Best, Molly Jane Kirk — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#7>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADBJIL6QEHUYPYXDKLR6XKDSRMELFANCNFSM4UAHL5JA>.