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dcmunpack -src  <dicomdir>  -targ <sessionid> -fsfast -run <runno> <subdir-under-targ> <format> <fname>

 

1. specify full path to your dicom directory for ‘-src <dicomdir>’

2. specify full path for ‘-targ <seesionid>’, or it will be created under the directory where you ran dcmunpack

3. I think you should see ‘Found 18 unique series: 1 2 …’ in the output. I believe <runno> should be one of these series Nos.

 

Best,

 

Yujing

 

 

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Sara Teso Cuesta
Sent: Friday, June 30, 2023 1:05 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] dcmunpack: Issues with the -run argument

 

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Hello FreeSurfer Developers,

 

I am trying to use dcmunpack to transform dicom images to a nifti format inside a FSFAST formatted directory (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/fsfastrestingstatetutorial), however I am having issues understanding how to use properly the -run argument.

 

This is the command I am trying to use:

 

dcmunpack -src  fMRI_dir  -targ sessionid -fsfast -run 2 rest nii.gz f.nii.gz

 

I assume I am making some mistakes with the command, specially with the run arguments since this is the error that I got in the terminal: ERROR: could not find run 2 in data


My directory contains fMRIs downloaded directly from the ADNI database and grouped in folders following this structure:

/fMRI_dir/subject_id/Axial_rsfMRI/date/image_uid/dicom images

I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to solve this?

1) FreeSurfer version: freesurfer_ubuntu20-7.4.0_amd64.deb
2) Platform: Ubuntu 20.04 in WSL

 

Thanks for your help.