SHARD pipeline--command file not found error

1

Hii Daan,

Great greetings to you from your previous student Jiaxin! I am currently working on reconstruction using SHARD pipeline, but encountering with some strange errors.

I firstly tried to install the external module on a local machine by the script you provided in github specifically for installment. However, it seems it’s not capable to link to the right address locally by those script lines.

Thus I put the files into the corresponding file folds manually. The consequence was that when running the dwimotioncorrect command with given dhcp data, it came out to be hindered by ‘file not found error’.

the details should be as following:

dwimotioncorrect: [DEBUG] run.exe_name() (from run.py:339): mrfieldunwarp -> mrfieldunwarp
dwimotioncorrect: [DEBUG] run.version_match() (from run.py:566): Command mrfieldunwarp not found in MRtrix3 bin/ directory
dwimotioncorrect: [DEBUG] run.exe_name() (from run.py:568): mrfieldunwarp -> mrfieldunwarp
dwimotioncorrect: [DEBUG] run._shebang() (from run.py:340): File "mrfieldunwarp": Could not find file to query
dwimotioncorrect: [DEBUG] run.command() (from dwimotioncorrect:288): To execute: [['mrfieldunwarp', 'in.mif', 'field.mif', 'unwarped.mif']]
Command:  mrfieldunwarp in.mif field.mif unwarped.mif

dwimotioncorrect: [ERROR] mrfieldunwarp in.mif field.mif unwarped.mif (dwimotioncorrect:288)
dwimotioncorrect: [ERROR] Information from failed command:
dwimotioncorrect:
                  [WinError 2] ϵͳ▒Ҳ▒▒▒ָ▒▒▒▒▒ļ▒▒▒

I checked and found that the files reported to be perhaps missing including ‘in.mif’ and ‘field.mif’ had been created correctly and deposited in the scratch working directory. Therefore the error might be erroneous command implementation of ‘mrfieldunwarp’.

I am wondering if you could have a look at this and give me some suggestions.Thank you.

Yours,
Jiaxin

1 Like
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Hi Jiaxin,

Nice to hear from you. It’s difficult to know what’s going on if the error message of the command is not displayed. Do you get this issue at the start or after one or several iterations? All I can recommend at this stage is to check that the field map has the same image transform, resolution and image dimensions as the dMRI data, although I think there’s a check in the code that should flag such problems.

I’m on leave for the next two weeks, but email me the dataset if you want me to have look afterwards.

Cheers
Daan