[RESOLVED] Adding nocheck argument to PreFreesurfer

Use Questions
1

Hi Qunex devs,

I am running prefreesurfer on 7T Siemens data that has large echodiff of 10.26 ms. This raises a warning during the prefreesurfer pipeline

FieldMapPreprocessingAll.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
FieldMapPreprocessingAll.sh: FSLDIR: /opt/fsl/fsl
FieldMapPreprocessingAll.sh: HCPPIPEDIR_Global: /opt/HCP/HCPpipelines/global/scripts
Mon Jan 8 14:16:43 EST 2024:FieldMapPreprocessingAll.sh: Field Map Preprocessing and Gradient Unwarping
Mon Jan 8 14:16:43 EST 2024:FieldMapPreprocessingAll.sh: START
Unlikely difference in TE found: dTE = 10.26 milliseconds
Expecting values between 0.1 and 10.0 milliseconds
To force the script to use this value use the --nocheck argument

Is there a way to force the script to use this value within Qunex? I tried running with --nocheck=yes, but that didn’t do anything. If I run the script with --hcp_echodiff=9.99 it runs smoothly, so large echodiff is definitely what throws the script off.

here is my command:

qunex_container hcp_pre_freesurfer \
    --container="gitlab.qunex.yale.edu:5002/qunex/qunexcontainer:0.98.6" \
    --sessionsfolder="/Users/kolobarica/Desktop/pals/sessions" \
    --sessions="PALS_04" \
    --batchfile="/Users/kolobarica/Desktop/pals/processing/batch.txt" \
    --overwrite=yes \
    --parsessions=1 \
    --hcp_avgrdcmethod='SiemensFieldMap' \
    --hcp_brainsize=170 \
    --hcp_t1samplespacing=0.000004 \
    --hcp_t2samplespacing=0.0000037 \
    --hcp_unwarpdir=y \
    --nocheck=yes \
    --hcp_echodiff=10.26 \
    --hcp_seunwarpdir=y \
    --hcp_seechospacing=0.0000041
2

Hi,

this is a bit tricky. QuNex runs HCP PreFreeSurfer, which as a part of its steps runs FSL’s fsl_prepare_fieldmap. fsl_prepare_fieldmap is the one that should be executed with the --nocheck option. So, to get this option available through QuNex, it would first need to be available through HCP Pipelines. I will talk with HCP folks if this is something they would be interested in and I can then code it as this seems like something useful and easy to do.

Before that happens you have a workaround, what you can do is:

Step 1: Create a local copy of HCP pipelines (let’s say in /Users/kolobarica/Desktop/HCPpipelines, adapt this path as suits your system). Execute the following in terminal:

cd /Users/kolobarica/Desktop
git clone git@github.com:Washington-University/HCPpipelines.git

Step 2: Now we have HCPpipelines located on our disk at /Users/kolobarica/Desktop/HCPpipelines. Next, we need to add the --nocheck flag to the appropriate location. To do this, edit this file:
/Users/kolobarica/Desktop/HCPpipelines/global/scripts/FieldMapPreprocessingAll.sh and add the --nocheck to line 138 in it. So that line becomes:

${FSLDIR}/bin/fsl_prepare_fieldmap SIEMENS ${WD}/Phase ${WD}/Magnitude_brain ${WD}/FieldMap ${DeltaTE} --nocheck

Step 3: Run QuNex by overwriting the HCPpipelines in the container with the modified version you have sitting outside.

qunex_container hcp_pre_freesurfer \
    --container="gitlab.qunex.yale.edu:5002/qunex/qunexcontainer:0.98.6" \
    --sessionsfolder="/Users/kolobarica/Desktop/pals/sessions" \
    --sessions="PALS_04" \
    --batchfile="/Users/kolobarica/Desktop/pals/processing/batch.txt" \
    --overwrite=yes \
    --parsessions=1 \
    --hcp_avgrdcmethod='SiemensFieldMap' \
    --hcp_brainsize=170 \
    --hcp_t1samplespacing=0.000004 \
    --hcp_t2samplespacing=0.0000037 \
    --hcp_unwarpdir=y \
    --nocheck=yes \
    --hcp_echodiff=10.26 \
    --hcp_seunwarpdir=y \
    --hcp_seechospacing=0.0000041 \
    --dockeropt="-v /Users/kolobarica/Desktop/HCPpipelines:/opt/HCP/HCPpipelines"

The important thing is the --dockeropt parameter at the end. What this does is it binds a folder on the system’s volume (-v) over a folder inside the container’s volume. In our case it binds the HCPpipelines sitting in your desktop folder over the ones in the container and this should attach the --nocheck parameter to the relevant script.

Let me know how it goes.

Best, Jure

3

Another possibility might be that you have your units wrong. Apparently, the default TE value for the Siemens 7T scanner is 1.026 ms.

Best, Jure

4

Thanks Jure, I’ll give this workaround a try!

One last question for you, do you know if qunex has the ability to prep data for Freesurfer with extra bias correction + do submillimiter recon? E.g. see here: HighFieldRecon - Free Surfer Wiki

5

Hi,

Per my understanding of HighFieldRecon - Free Surfer Wiki, you need to do the firrst step manually on apropriate FS input files. Next you just need to run FS, for any extra args hcp_freesurfer uses:

        --hcp_fs_extra_reconall (str, default ''):
            A string with extra parameters to pass to FreeSurfer recon-all.
            The extra parameters are to be listed in a pipe ('|') separated
            string. Parameters and their values need to be listed
            separately. E.g. to pass `-norm3diters 3` to reconall, the
            string has to be: "-norm3diters|3".
            (Please note that it will only be used when HCP Pipelines are
            used. It is not implemented in hcpmodified!)

Best, Jure