Skip to content

GE 3T EPI Pfile Conversion (mux2nii)

Jump to bottom
Carl Helmick edited this page Jun 16, 2021 · 1 revision

RS Pfile to NIFTI Conversion Details:

(typically 1-3 hours per subject) The resting state sequence from the scanner is custom built for us, and as such requires a number of extra steps. Manually downloading the Pfiles from the BIOTIC server "Lauterbur" one of the extra steps. Once the data is fully transferred, a second step is requied to 'recon' the raw Pfiles (conversion from frequency "K-space" with 32-channels and 3x multi-banding into image-space), and then saved into neurimaging data format NIFTI (.nii/.nii.gz).

There should be 3 sets of Pfiles, this is how they correspond to the scanner sequences:

Scanner Time Pfile Description
EPI NoMUX Cal 00:28 ~700 mb, lowest numeric title This is a scan with no multiband factor and minimal distortion, will later be used as an SBRef in the minimal preprocessing pipelines.
EPI Bomap - Rev 00:15 ~300mb, higher numeric title This is a few volumes of the RS sequence acquired in a reversed phase encode direction. Will be used to estimate and correct the distortion.
EPI MUX 3MM RS 08:06 ~15gb, highest numeric title This is the main resting state scan where we acquire 500 volumes in a sub-second TR. As you can see it is by far the largest, and if it is smaller than 15gb then something went wrong with the scan. 
$ ls -l /shared/uher/FORBOW/rawdata/100_C_20190320/RS/
-rwxrwxrwx 1 uher  217820581 Mar 20  2019 20190320-0630_E12985_P13824.7.bz2
-rw-r--r-- 1 uher      68132 Mar 20  2019 20190320-0630_E12985_P13824.7_hdr.txt
-rw-rw-rw- 1 uher        861 Mar 20  2019 20190320-0630_E12985_P13824.7_param.dat
-rw-r--r-- 1 uher    3703044 Mar 20  2019 20190320-0630_E12985_P13824.7_ref.h5
-rwxrwxrwx 1 uher      55872 Mar 20  2019 20190320-0630_E12985_P13824.7_vrgf.dat
-rwxrwxrwx 1 uher  122288141 Mar 20  2019 20190320-0630_E12985_P14336.7.bz2
-rw-r--r-- 1 uher      55172 Mar 20  2019 20190320-0630_E12985_P14336.7_hdr.txt
-rw-rw-rw- 1 uher        863 Mar 20  2019 20190320-0630_E12985_P14336.7_param.dat
-rw-r--r-- 1 uher    1236076 Mar 20  2019 20190320-0630_E12985_P14336.7_ref.h5
-rwxrwxrwx 1 uher      55872 Mar 20  2019 20190320-0630_E12985_P14336.7_vrgf.dat
-rwxrwxrwx 1 uher 3930176862 Mar 20  2019 20190320-0630_E12985_P14848.7.bz2
-rw-r--r-- 1 uher      55160 Mar 20  2019 20190320-0630_E12985_P14848.7_hdr.txt
-rw-rw-rw- 1 uher        861 Mar 20  2019 20190320-0630_E12985_P14848.7_param.dat
-rw-r--r-- 1 uher    1236076 Mar 20  2019 20190320-0630_E12985_P14848.7_ref.h5
-rwxrwxrwx 1 uher      55872 Mar 20  2019 20190320-0630_E12985_P14848.7_vrgf.dat

Note, each Pfile is compressed with bzip2 (showing .bz2 extension(), and is accompanied by _hdr.txt, _vrgf.dat _param.dat and _ref.h5 files. Occasionally there may be extra sets of Pfiles, most likely from re-running the main sequence if excessive head motion was suspected. If there is a lone Pfile, lowest in numeric title and a small size, unaccompanied by the above dat files, this is likely a shim, and while unnecessary for analysis it may cause the mux2nii script to fail, so create a new folder in the subject RS directory called shim and move that file there.

  • Update: now this is automatically taken care of in the conversion script. The Pfile could also be EPI or spectroscopy (MRS) data from another study.

Once the rawdata subject RS folder is organized, we will convert the RAW Pfiles into NIFTI, and compress the original raw Pfiles with bzip2 compression.

  • Open Terminal
  • Remote login to Jaylah: ssh uher@jaylah
  • Navigate to rawdata folder: cd /shared/uher/FORBOW/rawdata/
  • Run the script (in background, redirecting output to text file in subject directory): nohup ./_1_scripts/FORBOW_1_run_mux2nii.sh 100_C >100_C_20190320/nohup_mux2nii_20190701-0420.txt 2>&1 &
  • Monitor script with ps command: ps aux | grep '100_C' or htop command ('q' to quit htop)
  • Expect this script to take 1-2 hrs to complete on Jaylah (automatically, using 4-8 CPU Cores).
  • When completed the participant's /RS/ folder will have both a compressed NIFTI .nii.gz and a Matlab .mat output file for each Pfile. There will also be a copy of the Matlab conversion script mux2nii_PBIL.m, the conversion output and error logfiles, respectively: mux2nii-20190701-0422.stdout and mux2nii-20190701-0422.stderr.
$ ls -l /shared/uher/FORBOW/rawdata/100_C_20190320/RS/
-rwxrwxrwx 1 uher  217820581 Mar 20  2019 20190320-0630_E12985_P13824.7.bz2
-rw-r--r-- 1 uher      68132 Mar 20  2019 20190320-0630_E12985_P13824.7_hdr.txt
-rw-r--r-- 1 uher   15951075 Jul  1  2019 20190320-0630_E12985_P13824.7.mat
-rw-r--r-- 1 uher    5645801 Jul  1  2019 20190320-0630_E12985_P13824.7.nii.gz
-rw-rw-rw- 1 uher        861 Mar 20  2019 20190320-0630_E12985_P13824.7_param.dat
-rw-r--r-- 1 uher    3703044 Mar 20  2019 20190320-0630_E12985_P13824.7_ref.h5
-rwxrwxrwx 1 uher      55872 Mar 20  2019 20190320-0630_E12985_P13824.7_vrgf.dat
-rwxrwxrwx 1 uher  122288141 Mar 20  2019 20190320-0630_E12985_P14336.7.bz2
-rw-r--r-- 1 uher      55172 Mar 20  2019 20190320-0630_E12985_P14336.7_hdr.txt
-rw-r--r-- 1 uher   12000878 Jul  1  2019 20190320-0630_E12985_P14336.7.mat
-rw-r--r-- 1 uher    3808284 Jul  1  2019 20190320-0630_E12985_P14336.7.nii.gz
-rw-rw-rw- 1 uher        863 Mar 20  2019 20190320-0630_E12985_P14336.7_param.dat
-rw-r--r-- 1 uher    1236076 Mar 20  2019 20190320-0630_E12985_P14336.7_ref.h5
-rwxrwxrwx 1 uher      55872 Mar 20  2019 20190320-0630_E12985_P14336.7_vrgf.dat
-rwxrwxrwx 1 uher 3930176862 Mar 20  2019 20190320-0630_E12985_P14848.7.bz2
-rw-r--r-- 1 uher      55160 Mar 20  2019 20190320-0630_E12985_P14848.7_hdr.txt
-rw-r--r-- 1 uher 1004385038 Jul  1  2019 20190320-0630_E12985_P14848.7.mat
-rw-r--r-- 1 uher  476552586 Jul  1  2019 20190320-0630_E12985_P14848.7.nii.gz
-rw-rw-rw- 1 uher        861 Mar 20  2019 20190320-0630_E12985_P14848.7_param.dat
-rw-r--r-- 1 uher    1236076 Mar 20  2019 20190320-0630_E12985_P14848.7_ref.h5
-rwxrwxrwx 1 uher      55872 Mar 20  2019 20190320-0630_E12985_P14848.7_vrgf.dat
-rw-r--r-- 1 uher forbow          0 Jul  1  2019 mux2nii-20190701-0422.stderr
-rw-r--r-- 1 uher forbow      34938 Jul  1  2019 mux2nii-20190701-0422.stdout
-rw-r--r-- 1 uher forbow       1721 Jul  1  2019 mux2nii_PBIL.m
Clone this wiki locally