[RESOLVED] Hcp_pre_freesurfer errors when using Siemens fieldmap

Issues
1

Continuing the discussion from [RESOLVED] Hcp_fmri_volume errors when using Siemens fieldmap:

Description:

Dear Qunex experts, I am getting the same error in hcp_pre_freesurfer pipeline. Both phase and magnitude fieldmaps are present: /unprocessed/FieldMap/1002_FieldMap_Magnitude.nii.gz /unprocessed/FieldMap/1002_FieldMap_Phase.nii.gz and the fieldmaps have fm(1) specified in the batch file (attached). However, I am getting the following error:

Logs:

# Generated by QuNex 0.93.6 on 2022-08-22_20.06.41.541732
#
=================================================================
gmri hcp_pre_freesurfer \
  --sessionsfolder="/storage/brno2/home/pe_so/qunex/ocd/sessions" \
  --sessions="/storage/brno2/home/pe_so/qunex/ocd/processing/batch.txt" \
  --overwrite="no" \
  --logfolder="/storage/brno2/home/pe_so/qunex/ocd/processing/logs" \
  --sessionids="" \
=================================================================

Starting multiprocessing sessions in /storage/brno2/home/pe_so/qunex/ocd/processing/batch.txt with a pool of 1 concurrent processes

---- Running local

Starting processing of sessions 1002 at Monday, 22. August 2022 20:06:41

------------------------------------------------------------
Session id: 1002 
[started on Monday, 22. August 2022 20:06:41]
Running HCP PreFreeSurfer Pipeline [HCPStyleData] ...

---> T1w image file present.
---> T2w image file present.
ERROR: Unknown error occured: 
...................................
Traceback (most recent call last):
  File "/opt/qunex/python/qx_utilities/hcp/process_hcp.py", line 735, in hcp_pre_freesurfer
    fmmag = hcp['fieldmap'][int(fmnum)]['magnitude']
KeyError: 1
...................................

HCP PreFS completed on Monday, 22. August 2022 20:06:41

Thank you for your help,
Petr
batch.txt (3.1 KB)

2

Hi Petr,

can you try setting

--hcp_avgrdcmethod=="SiemensFieldMap"

You can set this in the command call or change line #31 in your batch file. Let me know if this works.

Thanks!

3

Hi Jure,
unfortunately the same error occurs:/
Petr

4

The algorithm looks for the FieldMap Magnitude file with the following pattern:

/storage/brno2/home/pe_so/qunex/ocd/sessions/1002/hcp/1002/unprocessed/FieldMap*/1002*_FieldMap_Magnitude.nii.gz

Can you provide us with contents of

/storage/brno2/home/pe_so/qunex/ocd/sessions/1002/hcp/1002/unprocessed/

And also the contents of any FieldMap subfolders if they exist. Thanks!

5

The files should be at:

/unprocessed/FieldMap1/1002_FieldMap_Magnitude.nii.gz
/unprocessed/FieldMap1/1002_FieldMap_Phase.nii.gz

All of this is created in the import_dicom => create_session_info => setup_hcp pipeline. Did you maybe do any edits to input parameters, files or output folders after you ran this or in the middle of running it?

6

Hi Jure,
this is the content of the /unprocessed folder:

Diffusion FieldMap T1w T2w

./Diffusion:
1002_DWI_dir30_AP.bval 1002_DWI_dir30_AP.bvec 1002_DWI_dir30_AP.nii.gz 1002_DWI_dir30_PA.bval 1002_DWI_dir30_PA.bvec 1002_DWI_dir30_PA.nii.gz

./FieldMap:
1002_FieldMap_Magnitude.nii.gz 1002_FieldMap_Phase.nii.gz

./T1w:
1002_T1w_MPR1.nii.gz

./T2w:
1002_T2w_SPC1.nii.gz

I am not aware to change anything during/after import_dicom => create_session_info => setup_hcp pipeline but I will rerun the steps to be sure.

Thank you, Petr

7

Can you also paste the mapping file here, just so we have all the information, thanks!

So, the problem is that /unprocessed/FieldMap/1002_FieldMap_Magnitude.nii.gz should be stored in /unprocessed/FieldMap1/1002_FieldMap_Magnitude.nii.gz. Let us know if the 1 will be again missing from the FieldMap folder and we will investigate what is going on. We ran some tests but were unable to reproduce the described issue.