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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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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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