Data Transfer

Data transfer

Data acquired on the scanner are automatically sent to the neighboring workstation. To transfer your data to your local lab server, go to the neighboring workstation and run cfmricp. This will gather all of your scan series, any physio files collected during your session, and also include a cfmricp_log.txt file. Scan series will be organized in order of acquisition. Physio files can be found under the physio/ subdirectory. Please contact Conan Chen or Aaron Jacobson for any questions about data transfer.

cfmricp example

The script cfmricp will list out datasets, prompt for your choices of dataset to transfer, server, username, and folder name on your destination server. Below, we entered blank (defaults to the last listed dataset), servername, user, and 20220301_Subject00A_Session1. The dataset is transferred to user@servername:~/data/20220301_Subject00A_Session1.

user@workstation: cfmricp

...

20220228__birnMon_20220228_adj__30000022022517415364600000037/
20220301__birnTues_20220301_adj__30000022022517415364600000040/
20220301__Subject00A_MRI1__30000022022517415364600000043/

Enter the dataset you want to transfer (enter blank for last listed dataset):
Enter the server you want to transfer to: servername
Enter your username on the server: user
Enter the folder under ~/data you want to transfer into (if folder does not exist, it will be created): 20220301_NeuromelaninScan

Transferring dataset: 20220301__Subject00A_MRI1__30000022022517415364600000043/
Transferring into: user@servername:~/data/20220301_Subject00A_Session1

Starting transfer...

No physio files detected.

If you expected physio files, please contact Conan Chen or Aaron Jacobson for assistance.

user@servername's password:
sending incremental file list
./
cfmricp_log.txt
          1,435 100%    0.00kB/s    0:00:00 (xfr#1, to-chk=962/964)
0001_Localizer/
0001_Localizer/MR.1.3.12.2.1107.5.2.43.166239.2022030115222828073679945
        260,354 100%    5.64MB/s    0:00:00 (xfr#2, to-chk=950/964)

...

0101_1/MR.1.3.12.2.1107.5.2.43.166239.30000022022701404093400001904
     145,032 100%  222.00kB/s    0:00:00 (xfr#952, to-chk=0/964)

sent 317,393,852 bytes  received 18,199 bytes  27,601,047.91 bytes/sec
total size is 317,253,969  speedup is 1.00

Transfer via cfmricp complete.

In the destination location user@servername:~/data/20220301_Subject00A_Session1, the files are organized into folders corresponding to each scan. Each folder contains the DICOM files from that scan. The folder 0099_PhoenixZIPReport can typically be ignored - these are special DICOMs used to recreate protocols on scanners, but do not containing imaging data. The physio subfolder contains any physio files that were acquired during the session.

user@servername: ls -1
0001_Localizer
0002_t1_mprage_sag_p2_iso
0003_t2_axial_flair
0004_ABCD_fMRI_rest
0005_ABCD_fMRI_rest_PMU
0006_ABCD_fMRI_DistortionMap_PA
0007_ABCD_fMRI_DistortionMap_AP
0008_ABCD_fMRI_rest
0009_ABCD_fMRI_rest_PMU
0010_ABCD_dMRI_DistortionMap_PA
0011_ABCD_dMRI_DistortionMap_AP
0012_ABCD_dMRI
0013_PhoenixZIPReport
cfmricp_log.txt
physio
user@servername:
user@servername: ls -1 physio/
Pilot1_03012022.puls
Pilot1_03012022.resp

An example log is shown below.

*****************************************************
 Data Transfer (cfmricp) Log
*****************************************************
 Notes:
 If you request transfer (can say no), you need:
  1. server name (cfmri, fmriserver, fmrimems, etc)
  2. user id on the server
  3. destination folder name under ~/data/
     If the folder already exists under ~/data/
     the new files will be appended to the folder.
     Otherwise, the new directory will be created.

*****************************************************
 Session
*****************************************************
 Initiation Date: 20220301

 Protocol:   R21_BOLD_DTI
 Start time: 15:12:23
 End time:   15:51:19

*****************************************************
 Scan Directories
*****************************************************

 0001_Localizer
 0002_t1_mprage_sag_p2_iso
 0003_t2_axial_flair
 0004_ABCD_fMRI_rest
 0005_ABCD_fMRI_rest_PMU
 0006_ABCD_fMRI_DistortionMap_PA
 0007_ABCD_fMRI_DistortionMap_AP
 0008_ABCD_fMRI_rest
 0009_ABCD_fMRI_rest_PMU
 0010_ABCD_dMRI_DistortionMap_PA
 0011_ABCD_dMRI_DistortionMap_AP
 0012_ABCD_dMRI
 0013_PhoenixZIPReport

*****************************************************
 Physios
*****************************************************

 Pilot1_03012022.puls
 Pilot1_03012022.resp