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Workflows and interfaces for neuroimaging packages
https://nipype.readthedocs.org/en/latest/
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Allow use of glob patterns in in_files for fsl.Merge #3547

Open somso2e opened 1 year ago

somso2e commented 1 year ago

fslmerge command in cmdline already supports glob patterns such as /*/ and /**/ so I don't see a point in them not working in nipype. The reason I'm complaining about this is because of bash's limit when you have a lot of files to merge, each having a really long name.

Running the below command, for example, works perfectly fine: fslmerge -t -tr out.nii.gz /inputs/func/*.nii 3

The equivalent in python would be:

import nipype.interfaces.fsl as fsl
import glob 
files = glob.glob("/inputs/func/*.nii")
merger = fsl.Merge()
merger.inputs.in_files = files
merger.inputs.dimension = 't'
merger.inputs.output_type = 'NIFTI_GZ'
merger.inputs.tr = TR
merger_output = merger.run()

This might lead to a ridiculously long command that could hit bash's limit if the parent directory or the file names are too long.

In my case this is my generated cmdline: 

fslmerge -tr /box/outputs/preprocessed/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516134007484_4962_S150694_I304790_merged.nii.gz /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516134007484_4962_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133638402_4804_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133601450_6660_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133828625_3302_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133907634_1883_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133554223_3315_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133807447_3591_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133921860_1650_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516134102652_5125_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133628624_6462_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133615734_1591_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133509863_2258_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133541787_3163_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133837782_1080_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133751615_6427_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516134122749_5977_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133819679_2513_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133637082_3248_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133825496_1026_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133728242_5386_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133821511_1087_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133623702_4399_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516134056227_3833_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133532188_77_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133507377_4194_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133443642_802_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516134019397_2556_S150694_I304790.nii 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/box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133452993_4480_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133644505_388_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133620061_2749_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133948624_6032_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133937932_2231_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133753417_4721_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133901932_2414_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133752279_599_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133938946_5530_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133512316_1258_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133733295_704_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133548498_4336_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133805062_6138_S150694_I304790.nii /box/test_dataset/002_S_0413/m72/func/ADNI_002_S_0413_MR_Resting_State_fMRI_br_raw_20120516133717008_1834_S150694_I304790.nii 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effigies commented 1 year ago

Bash is expanding the glob in your example, instead of Python. The fix here would be to rewrite run_command() to avoid calling a shell to interpret its command line. I'm not sure what all that would end up breaking, as we almost certainly have depended on this behavior.