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