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Interestingly enough the process never finished... I ran:

recon-all \
  -subject F \
  -i /Users/bram.dejong/Downloads/mri/DICOM/000009 \
  -hires \
  -parallel -openmp 8 \
  -all

that crashed. With "-hires" removed I let it run for 48 hours (Macbook Air M2) and after a while it got stuck in python (can't remember the command) while using 10% CPU continuously.

Are there any additional flags I could add for debugging?

Bram

On Sat, Sep 13, 2025 at 5:20 PM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:
Passing the DICOM list will avoid the program to scan the whole directory again to retrieve all the DICOMs for the series, which you already have.
From: Bram de Jong <bram.dejong@gmail.com>
Sent: Saturday, September 13, 2025 3:51 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re: Newbie: loading DICOM...
 

        External Email - Use Caution        

Thanks for the help!

It looks like giving the first image of the series was enough to load all the images in the series. Thanks for the help...

My little Mac Air has been crunching numbers for over 16 hours by now...

Bram

On Fri, Sep 12, 2025, 21:55 Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

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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Bram de Jong
Tel: +32 484 15 47 30