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dorianps / LINDA

Lesion Identification with Neighborhood Data Analysis
Apache License 2.0
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Failing on ITK #34

Closed ramBrain closed 1 year ago

ramBrain commented 1 year ago

Dear developers,

I am attempting to run LINDA, but I get this:

16:49 Starting LINDA v0.5.1
16:49 Creating folder: /mnt/d/<pathtosub>/sub-005/linda
16:49 Loading file: sub-005_ses-01_T1w_3D.nii ...
16:49 Loading template...
16:49 Skull stripping... (long process)/home/ramtin/ITKR/src/itks/Modules/IO/TransformBase/src/itkTransformFileWriterSpecializations.cxx:159:
ITK ERROR: TransformFileWriterTemplate(0x5590f9de3740): Could not create Transform IO object for writing file /tmp/RtmptlQNam/antsr24725103c3cf_InitialAff.mat
  There are no registered Transform IO factories.
  Please visit https://www.itk.org/Wiki/ITK/FAQ#NoFactoryException to diagnose the problem.

Transform file does not exist: /tmp/RtmptlQNam/antsr24725103c3cf_InitialAff.mat
Error in antsRegistration(tem, img, typeofTransform = regtype, initialTransform = initafffn,  : 
  Registration failed. Use verbose mode to diagnose.
Calls: linda_predict ... n4_skull_strip -> do.call -> <Anonymous> -> antsRegistration
Execution halted

I went on the suggested website there, but it was not helpful at all. Any clue for a workaround?

Thank you, Ramtin

dorianps commented 1 year ago

Linda has not changed for long time, so this is either related to ITK/Anëtar or to some system issue. Please open an issue on ANTsR GitHub page with the same information. Also try to get versions for all packages like ITK and ANTsR, etc and state the system OS version you are in.

Dorian

On Tue, Mar 14, 2023, 11:55 AM ramBrain @.***> wrote:

Dear developers,

I am attempting to run LINDA, but I get this:

16:49 Starting LINDA v0.5.1 16:49 Creating folder: /mnt/d//sub-005/linda 16:49 Loading file: sub-005_ses-01_T1w_3D.nii ... 16:49 Loading template... 16:49 Skull stripping... (long process)/home/ramtin/ITKR/src/itks/Modules/IO/TransformBase/src/itkTransformFileWriterSpecializations.cxx:159: ITK ERROR: TransformFileWriterTemplate(0x5590f9de3740): Could not create Transform IO object for writing file /tmp/RtmptlQNam/antsr24725103c3cf_InitialAff.mat There are no registered Transform IO factories. Please visit https://www.itk.org/Wiki/ITK/FAQ#NoFactoryException to diagnose the problem.

Transform file does not exist: /tmp/RtmptlQNam/antsr24725103c3cf_InitialAff.mat Error in antsRegistration(tem, img, typeofTransform = regtype, initialTransform = initafffn, : Registration failed. Use verbose mode to diagnose. Calls: linda_predict ... n4_skull_strip -> do.call -> -> antsRegistration Execution halted

I went on the suggested website there, but it was not helpful at all. Any clue for a workaround?

Thank you, Ramtin

— Reply to this email directly, view it on GitHub https://github.com/dorianps/LINDA/issues/34, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACFJU7PIZBSW4TOAK54RJEDW4CIFJANCNFSM6AAAAAAV2UKNQY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

ramBrain commented 1 year ago

I will do as suggested, many thanks.

Kind regards, Ramtin