Functional Magnetic Resonance Imaging Lab

Presurgical fMRI

For a standard presurgical fMRI, the following guide may be useful:

A. On a Linux workstation

• Go to DICOM repository (typically /md2/dicom/), start DICOMreceive client: rcvdicom

B. In the scanner room

• Morphological and BOLD ("functional") MR imaging data transfer to FMRI1 or FMRI2 (performed by a technician)
• Burning data to a CD-ROM, study label has 8 characters – leave dashes "-" out (performed by a technician)

C. On a Linux workstation

• 1) Assess the study code from the protocol (e.g. TM-PMP-030).
• 2) Assess the task order from the protocol, check for any incomplete runs. In non-standard cases some changes to the standard procedure may be necessary.
  
• 3) Run fmriStats.sh -i from the command line and choose the proper letters for the tasks performed by the subject [h - hand, f - foot, t - tongue, g - story, j - speech, u - verbal fluency test, m - any 15s motor design, r - rest (ignored), x - ignored (e.g. for incomplete runs)]. Capital letters mean that the task was right-sided (if applicable).
  
• 4) Assess whether an external MPRAGE is needed. Since only transversal MPRAGE can be reversely converted to DICOM, you need native or re-sliced transversal MPRAGE.
  
  YES: If that an external MPRAGE is needed used (e.g. from previous MRI examination), it has to be sent from the scanner room separately. Back in the Lab, run dicomRename.sh <study code>A (keep th 'A' at the end to provent the conflict with the functional data) from the folder, where the raw DICOM MPRAGE from scanner has been saved (e.g. dicomRename.sh TM-PMP-030A). Proceed to point 7.b.
• 5) Assess whether you want to merge some of the runs into one output (so the surgeon can see all the critical areas in one volume).
  
  YES: Make note of the numbers of the runs (include incomplete runs as well). Numbers can be presented as a list (e.g. 1,2,3), a range (e.g. 1-3), or a combination of both (e.g. 1,3-5). Proceed to point 7.c.
• 6) Move to the directory where the data from scanner is stored (usually /md2/dicom/dir_20140101_000000001/) and if not sure, whose data are stored in the folder, run patname.sh ./
• 7) Run one of the following commands:
  
  7.a) fmriStats.sh -n <study_code> -o <task_order> -d -f (e.g. fmriStats.sh -n TM-PMP-030 -o hfr-d -f)
  
  7.b) fmriStats.sh -n <study_code> -o <task_order> -d -f --mprage <full_path_to_MPRAGE> (e.g. fmriStats.sh -n TM-PMP-030 -o hfr-d -f --mprage /md2/TM-PMP-030A/tmp)
  
  7.c) fmriStats.sh -n <study_code> -o <task_order> -d -f --merge <list_of_runs>(e.g. fmriStats.sh -n TM-PMP-030 -o hfr-d -f --merge 1,2)
  
  NOTE: You can combine commands from steps 6.b and 6.c into one (e.g. fmriStats.sh -n TM-PMP-030 -o hfr -d -f --merge 1,2 --mprage /md2/TM-PMP-030A/tmp). The arguments can be used in any order. Remember to keep spaces between each argument and the following value.
• 8. Check the script standard output for any errors. Do not quit the terminal, log off or turn off the computer unless you have started the analysis with nohup command! After the script is completed, the log is saved in the study directory (e.g. /md2/TM-PMP/TM-PMP-030). If the script crashes, the log is stored in the /usr/local/etc/fmriStats/log/.
• 9. Check the results in the Results directory. You can directly open the links from the on-screen log or open the report.html in the each feat folder (e.g. /md2/TM-PMP/TM-PMP-030/Results/LHand1_1.feat/report.html).
• 10. Check whether there is too much activation.
  
  YES: Re-run optionally the post-stats with different Z-threshold if needed by typing: fmriStats.sh -r -z <Z-threshold> -d. The Z-threshold needs to be a floating-point number with at least one digit after decimal point (not comma!). Remember to add --mprage <full_path_to_Mprage.nii.gz> if an external Mprage was previously used. This external extracted MPRAGE is usually saved in the Mprage/Mprage.nii.gz in the study folder (e.g. fmriStats.sh -r -z 5.0 -d --mprage /md2/TM-PMP/TM-PMP-030/Mprage/Mprage.nii.gz). Add --merge <list_of_runs> if you want to re-create the merged file as well.
• 11. You can check the exported DICOM files in <task_name>-conv in the study folder (e.g. /md2/TM-PMP/TM-PMP-030/LHand1_1-conv). You can open the DICOM files in aeskulap viewer by simply typing aeskulap ./* in the folder where the data is. Alternatively, you can convert the files back to the NIFTI by dcm2nii * from within the folder.
• 12. Burn the DICOM files using Brasero software:
  
  12.a) Insert an empty CD.
  12.b) Run brasero from the command line.
  12.c) Create a new data project.
  12.d) Add ALL the DICOM files from ONE folder (the navigation device accepts only one volume per CD). The files have to be in the CD's root directory!
  11.e) Start burning (with default settings).
  
  NOTE: Step 11 has to be repeated for each volume separately (i.e. on separate CD's)
• 13. Take the burnt CD to the operating theatre and upload the DICOM data.
• 14. If you made it this far, you did a perfect job. Just hope, that surgeons will do the same ;-)

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