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Hi all,
Absolute newbie alert... End goal: 3D printing the brain of my son! After reading through the tutorial, I got stuck. I have a DICOM file, which I looked at with dcmunpack:
❯ dcmunpack -src . -scanonly scan.log if: Empty if. then: Command not found.
cd /Users/bram.dejong/Downloads/flux-mri /Applications/freesurfer/8.1.0/bin/dcmunpack -src . -scanonly scan.log
-rwxr-xr-x 1 root wheel 50442 Jul 19 01:21 /Applications/freesurfer/8.1.0/bin/dcmunpack --------------------------------------- --------------------------------------- Searching for matching files Thu Sep 11 17:23:02 CEST 2025 Found 1511 total files. Interrogating each and every one of them. Be patient. mri_probedicom --dcm2niix-dicom-dump /Users/bram.dejong/Downloads/flux-mri/. ./log/scan.log Found 1505 DICOM file(s) Found 20 unique series: 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
DICOM Pre-process Summary: 5 t1_vibe_fl3d_sag_0.9mm 0 000009 6 t1_vibe_fl3d_sag_0.9mm_MPR_Tra 0 000171 7 t1_vibe_fl3d_sag_0.9mm_MPR_Cor 0 000331 8 t2_tse_tra_3mm_fss_DRBS 0 001467 9 t2-flair_tir_tra_3mm_DRBS 0 000511 10 dwi-resolve_3scan_trace_tra_p2_160_TRACEW 0 000587 11 dwi-resolve_3scan_trace_tra_p2_160_ADC 0 000549 12 tof_fl3d_tra_CS4 0 000625 13 tof_fl3d_tra_CS4_MIP_SAG 0 001466 14 tof_fl3d_tra_CS4_MIP_COR 0 001426 15 tof_fl3d_tra_CS4_MIP_TRA 0 001427 16 tof_fl3d_tra_CS4_MIP_Radials 0 000761 17 tof_fl3d_tra_CS4 0 000773 18 tof_fl3d_tra_CS4_MIP_SAG 0 001425 19 tof_fl3d_tra_CS4_MIP_COR 0 001069 20 tof_fl3d_tra_CS4_MIP_TRA 0 001424 21 tof_fl3d_tra_CS4_MIP_Radials 0 001412 22 t1_vibe_fl3d_sag_0.9mm+gd 0 001070 23 t1_vibe_fl3d_sag_0.9mm_MPR_Tra 0 000909 24 t1_vibe_fl3d_sag_0.9mm_MPR_Cor 0 001232
Started at Thu Sep 11 17:23:02 CEST 2025 Thu Sep 11 17:23:06 CEST 2025 dcmunpack done
I figured out I need to use load series 5, t1_vibe_fl3d_sag_0.9mm into Freesurfer.
Looking at the log:
❯ cat log/5-dicomflst.txt /Users/bram.dejong/Downloads/mri/./DICOM/000009 /Users/bram.dejong/Downloads/mri/./DICOM/000010 /Users/bram.dejong/Downloads/mri/./DICOM/000011 /Users/bram.dejong/Downloads/mri/./DICOM/000012 [SNIP] /Users/bram.dejong/Downloads/mri/./DICOM/000170
How do I now direct Freesurf to only pick only series 5 rather than all files in the DICOM?
Greetings,
Bram