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Instruction for SWIFT installation/upgrade

Instruction for SWIFT installation/upgrade Center for Magnetic Resonance Research, University of Minnesota Contact info: Djaudat Idiyatullin idiat001@umn.edu ; Brian Hanna bdhanna@cmrr.umn.edu.

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Instruction for SWIFT installation/upgrade

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  1. Instruction for SWIFT installation/upgrade Center for Magnetic Resonance Research, University of Minnesota Contact info: Djaudat Idiyatullin idiat001@umn.edu; Brian Hanna bdhanna@cmrr.umn.edu

  2. Installation of SWIFT package consist of two main parts: (A) upgrading vnmrsys user directory with necessary macros and files and (B) setting up the remote server computer for offline reconstruction of radial images. (A) • Backup the current vnmrsys directory. • Download the djSWIFTpkg. • Synchronize/create the following folders manually in vnmrsys directory with corresponding folders from the package: cmrr, maclib, psglib, shapelib, template,parlib. • Delete (if exist) vnmrsys/psg directory;

  3. (B) In the root directory of remote computer planned to use for reconstruction of “non-Cartesian” images create a directory: opt/local/recon-wisc. Copy all content located in folder djSWIFTpkg/opt_local_recon-wisc to the newly created directory.

  4. Launch VNMRJ • Start new study, set frequency, do shimming and etc. • In the “Edit” menu, switch the number of viewports from “3” to “1” • Create exp4 …. to exp9 (if not exist) (using command cexp(i)) • Go to expN by typing jexpN or clicking the “expN” button on center top (N >3) • Run “dj_psggen” in command line to compile psg. • Run “dj_cc(0)” in command line to compile related bin files. • Open one of example .fid data set from djSWIFTpkg in expN.

  5. h. Open one of example .fid data set from djSWIFTpkg in expN • i. Run “seqgen” in command line to compile the sequence.

  6. g. Click “nogo” button on right panel to do gocheck. • h. Click “djDisp” button (located nearby Start button) to check if bin files installed correctly: The k-space sampling trajectory should appear on the screen. • .

  7. i. plan the future experiment by using Plan option • j. after setting required FOV parameters, save the plan by clicking rx button

  8. k. set the flip angle • l. run the SWIFT by clicking djgo button

  9. run SWIFT • When acquisition is finished save the data by clicking “djsvf”; • Choose/change the server name used for recon using parameter serverName. (e.g. serverName = ‘yourservernameforrecon’); • click “recon_SWIFT” button:> the background reconstruction will be started; In the body of saved .fid data a new directory will be created and when the recon finished .nii image files (nifty format) will be created. • Some more information you can find at djSWIFTpkg/cmrr/doc file.

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