Dear Chris

I have an occasional problem where dcm2niix does not convert all the DICOM files in a directory. If I point it to the directory for that study, it converts everything. If I point it to the root DICOM directory, or the patient directory, it detects the right number of files, but does not convert them all. In looking into this I found it also converts different numbers of images for some series depending upon the source directory.

I'm attaching output from dcm2niix and will share anonymised images on Dropbox.

Here's a summary of the logs:

Source directory 'DICOM'
Found 2184 DICOM image(s)
Convert 549 DICOM as tmp2/GP_012_20170614125337_s8_Carotids_0.625mm (512x512x549x1)
Convert 115 DICOM as tmp2/GP_012_20170614125337_s607_Carotid_MIP_3mm_Axial (512x512x115x1)
Convert 53 DICOM as tmp2/GP_012_20170614125337_s606_Carotid_MIP_3mm_Sag (512x512x53x1)
Convert 352 DICOM as tmp2/GP_012_20170614125337_s5_Perfusion_Axial_5mm (512x512x16x22)
Convert 58 DICOM as tmp2/GP_012_20170614125337_s605_Carotid_MIP_3mm_Cor (512x512x58x1)
Convert 256 DICOM as tmp2/GP_012_20170614125337_s3_0.625mm_Standard (512x512x256x1)
Convert 14 DICOM as tmp2/GP_012_20170614125337_s7_Test_Bolus (512x512x1x14)
Convert 96 DICOM as tmp2/GP_012_20170614125337_s4_Perfusion_Axial_5mm (512x512x16x6)
Convert 49 DICOM as tmp2/GP_012_20170614125337_s603_Axial_3mm (512x512x49x1)
Convert 8 DICOM as tmp2/GP_012_20170614125337_s6_Test_Bolus (512x512x1x8)
Convert 1 DICOM as tmp2/GP_012_20170614125337_s999_Dose_Report (512x512x1x1)
Convert 64 DICOM as tmp2/GP_012_20170614125337_s2_2.5mm_Axials (512x512x64x1)
Convert 64 DICOM as tmp2/GP_012_20170614125337_s601_Cor_3mm (512x512x64x1)
Convert 56 DICOM as tmp2/GP_012_20170614125337_s602_Sag_3mm (512x512x56x1)
Convert 2 DICOM as tmp2/GP_012_20170614125337_s1_Scout (888x826x2x1)
Convert 2 DICOM as tmp2/GP_012_20170615154507_s1_Scout (888x367x2x1)

Source directory for study 1
Found 1698 DICOM image(s)
Convert 549 DICOM as tmp3/GP_012_20170614125337_s8_Carotids_0.625mm (512x512x549x1)
Convert 115 DICOM as tmp3/GP_012_20170614125337_s607_Carotid_MIP_3mm_Axial (512x512x115x1)
Convert 53 DICOM as tmp3/GP_012_20170614125337_s606_Carotid_MIP_3mm_Sag (512x512x53x1)
Convert 352 DICOM as tmp3/GP_012_20170614125337_s5_Perfusion_Axial_5mm (512x512x16x22)
Convert 58 DICOM as tmp3/GP_012_20170614125337_s605_Carotid_MIP_3mm_Cor (512x512x58x1)
Convert 224 DICOM as tmp3/GP_012_20170614125337_s3_0.625mm_Standard (512x512x224x1)
Convert 14 DICOM as tmp3/GP_012_20170614125337_s7_Test_Bolus (512x512x1x14)
Convert 96 DICOM as tmp3/GP_012_20170614125337_s4_Perfusion_Axial_5mm (512x512x16x6)
Convert 49 DICOM as tmp3/GP_012_20170614125337_s603_Axial_3mm (512x512x49x1)
Convert 8 DICOM as tmp3/GP_012_20170614125337_s6_Test_Bolus (512x512x1x8)
Convert 1 DICOM as tmp3/GP_012_20170614125337_s999_Dose_Report (512x512x1x1)
Convert 56 DICOM as tmp3/GP_012_20170614125337_s2_2.5mm_Axials (512x512x56x1)
Convert 64 DICOM as tmp3/GP_012_20170614125337_s601_Cor_3mm (512x512x64x1)
Convert 56 DICOM as tmp3/GP_012_20170614125337_s602_Sag_3mm (512x512x56x1)
Convert 2 DICOM as tmp3/GP_012_20170614125337_s1_Scout (888x826x2x1)

Source directory for study 2
Found 486 DICOM image(s)
Convert 1 DICOM as tmp2/GP_012_20170615154507_s999_Dose_Report (512x512x1x1)
Convert 49 DICOM as tmp2/GP_012_20170615154507_s602_Sag_3mm (512x512x49x1)
Convert 256 DICOM as tmp2/GP_012_20170615154507_s3_0.625mm_Standard (512x512x256x1)
Convert 2 DICOM as tmp2/GP_012_20170615154507_s1_Scout (888x367x2x1)
Convert 64 DICOM as tmp2/GP_012_20170615154507_s601_Cor_3mm (512x512x64x1)
Convert 64 DICOM as tmp2/GP_012_20170615154507_s2_2.5mm_Axials (512x512x64x1)
Convert 49 DICOM as tmp2/GP_012_20170615154507_s603_Axial_3mm (512x512x49x1)

[EDIT: attached log before saving]