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_______________________________________________I’m assuming you have sourced Freesurfer environment. Since you have identified the DICOM series to convert and have the list of DICOM files available, you can use ‘mri_convert’ directly:
mri_convert /Users/bram.dejong/Downloads/mri/./DICOM/000009 myscan.mgz --dcm2niix-dicom-flist log/5-dicomflst.txt
Yujing
From: Bram de Jong <bram.dejong@gmail.com>
Sent: Friday, September 12, 2025 7:55 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Newbie: loading DICOM...
External Email - Use Caution
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
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