MRI DATA PROCESSING. Compiled by: Nicolas F. Lori and Carlos Ferreira. Introduction

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1 MRI DATA PROCESSING Compiled by: Nicolas F. Lori and Carlos Ferreira Introduction Magnetic Resonance Imaging (MRI) is a clinical exam that is safe to the patient. Nevertheless, it s very important to attend to some safety rules. These rules refer to the magnetic field being always on, and magnetic field attracting metalic objects; thus maybe putting at risk the life of the patients. The interactions between magnetic field and some devices (like pacemakers) must be taken into consideration. In case of doubt, ask the MR technician for clarifications. After a screening of the patient based in the security rules, it is possible to enter the scanner room and lay down the patient so that the exam can be performed. After laying down the patient and closing the scanner room door, it s time to initiate the exam. It is necessary to register the patient, then select all the necessary sequences and, at last, the data information collected by the MRI exam must be stored in an archiving system. The Siemens data will typically be acquired on a Siemens Trio system using TIM. Anatomical notations: PT (planum temporale), HG (Heschel gyrus), PP (planum polare), IFG_pt (inferior frontal gyrus, pars triangularis), IFG_po (inferior frontal gyrus, pars opercularis), and STG (superior temporal gyrus). Obtaining MRI data To register the patient you must follow these guidelines: Menu Patient Register (enter the follow information): Patient name Patient ID Date of Birth Sex and age Height and weight Referring physician Requesting physician Admission ID Accession Number Request ID Request Procedure(s) Study comment Patient position Institution name Performing physician MRI operator

2 After enter all this information press Exam and a new window will open. In this window it is necessary to confirm weight, patient name and patient position in order that there is no mistake with the identification of the patient. If everything is correct, press OK and a window where sequences can be chosen will open automatically. In this window the selection of sequences used on the exam is made. For a typical functional MRI exam with diffusion sequence four sequences must be used. They are the Localizer, the MP-RAGE, the BOLD and the Diffusion sequences. 1. To select Localizer sequence Region: Head Exams: Bold Programs: localizer, t1_mpr_ns_sg, ep2d_bold_moco_3d, ep2d_diff_3scan_trace 2. To select MP-Rage sequence Region: Head Exams: Bold Programs: t1_mpr_ns_sg, 3. To select BOLD sequence Region: Head Exams: Bold Programs: ep2d_bold_moco_3d To select Diffusion sequence Region: Head Exams: Bold Programs: ep2d_diff_3scan_trace After selecting this sequences press the «button and the sequences will be launched. Localizer will start automatically, the other sequences will prompt MR user to type in some extra parameters. Although there are many parameters that can be changed below are the ones that normally can be changed. EXPLAIN WHAT EACH PARAMETER IS MP-RAGE (t1_mpr_ns_sg): TR (repetition time): time interval between successive excitation pulses (usually expressed in milliseconds); Can be used TR like 10 ms. TE (Echo time): time interval between an excitation pulse and data acquisition (defined as the collection of data from the center of k-sapce), usually expressed in milliseconds; Can be used TE like 5 ms. Flip angle: the change in the precession angle of the net magnetization following excitation; Can be used flip angles like 10º. Slice thickness: size of the slice (usually expressed in millimetres); Can be used slice thickness like 3 mm

3 Gap: distance between slices (usually in millimetres); typical values 0-1 mm. Number of slices: the total number of slices to be acquired; Typical number of slices acquired Number of excitations: how many times each line of k-space data is acquired during the scan. Matrix size: determine how many voxels are acquired in each dimension; Typical matriz size used 256x256. Field-of-view (FOV): describes the extent of the imaging volume within a slice (usually expressed in centimetres). Typical FOV used 24x24cm. BOLD (ep2d_bold_moco_3d): TR (repetition time): typical values 2000 ms. TE (Echo time): typical values ms. Flip angle: typical value 90º. Slice thickness: typical values 4-5mm. Gap: typical values 1-2 mm. Number of slices: typical values Matrix: typical values 256x256. Field-of-view (FOV): typical values 24x24cm. Diffusion (ep2d_diff_3scan_trace): TR (repetition time): TE (Echo time): Flip angle: Slice thickness: Number of slices: Gap Number of excitations: Matrix: Field-of-view (FOV): b-factor: the degree of diffusion weighting applied within a pulse sequence (in provides the number of directions of diffusion measured). After selected all the desirable parameters, just press the OK button and the sequence will be automatically launched. After the sequences finished and all desirable data obtained it s necessary to store the exam. To store it select in Menu Transfer the desirable option: Menu Transfer Archive to (to store the exam in local database) Send to (to store the exam in network database) Export to (to store the exam in cd/dvd)

4 From Analyze mask to Analyze ROI Uses: Brainsuite, Analyze, mricro and rview. mricro and rview are co-registration tools that enable the co-registration of MRI images. The detailed procedures on how to do the co-registration are available. But each group typically has its own co-registration procedures. Uses: Analyze Transforming 8 bit unsigned data to 16 bit signed data Click on FILE/SAVE AS, change parameters to below then SAVE %%If Analyze image still has anatomy in it: making a mask using Analyze

5 In Analyze LOAD: x2227hd_cor3_trf_acpc_righthemi_stg_v4_analyze_2diffusion_8bit.img Object Extractor View Size=Triple Generate Define Region Coronal (assuming this is the best orientation) Select slice using slider Left Click on region Set Thresh Max/Min until wanted ROI is selected %%Saving Analyze-segmented ROI as Trackvis-ready Analyze image SAVE AS Signed 16 bit Thresh: Min=22000: Defined using the segmment analysiss above Max=32767 File: SUP_TEMP_Left_Obj1_trl20_16b_cut_96_51_96_Transformed_v2 (.img/.hdr)

6 From Analyze ROI to DTI white matter fibers Uses: Diffusion Toolkit Generation of white matter fiber tracks [Press RUN] Files created are.trk files. An example of a: trk file is dti_pair9a_ang50.trk

7 Uses: Trackvis To load the trk go to FILE and click on OPEN TRACK To select anatomy click on the face with green plus

8 To or draw ROIs click on ROI. Options: Ball, Hand Draw, Analyze image; scene Example: Analyze image/mask example Example: Handrawn

9 Generate tracks passing Handrawn region: Click SELECT NEW TRACK GROUP PS: can also be done with Analyze images/masks Tracks Passing in Handrawn ROI PS: Can also be done with Analyze images/masks Click on Track of ROI then Toggle ROI and select different ROI

10 Tracks passing in two ROI. COLOR CODE: solid red; Slice Opacity reduced Example of ROIs obtained using Brainvox Color Code: HG-Red, IFG_po-Green, IFG_pt-Blue, PT-Yellow, PP-Magenta.

11 Tracks from left to right HG: missed it by about 1 voxel Two Heschl gyrus connect through Splenium of Corpus Callosum Yellow fibers pass through left HG, while Blue fibers pass through right HG. Yellow fibers pass medial of the right HG, and blue fibers do not reach left HG. The failure of the blue fibers to reach left HG is likely due to crossing fibers. The average fractional anisotropy (FA) for the yellow bundles is 0.31±0.15 and for the blue bundle is 0.32±0.17.

12 Example of statistic table in Tackvis (yellow fiber bundle) Detail of right Heschl Gyrus Both Fiber track bundles that go towards the Heschl gyrus on the opposite Hemisphere pass on the vicinity of the Splenium of the Corpus Callosum (the most posterior portion of the Corpus Callosum). It was therefore hand-drawn brown ROI containing the two most anterior vertical column voxels of the Corpus Callosum in a Sagital slice (lower left square in image below). Using that brown ROI it was then possible to better select white matter fiber bundles that are likely responsible for connection the two Heschl gyri. To maximize the quality of fiber track curvature a 2 nd order Runge-Kutta stepping procedure is used ( -rk2 Additional Option in the Tracking portion of Diffusion Toolkit).

13 Fibers from HG passing in posterior Corpus Callosum: Water concentration background Fibers from HG passing in posterior Corpus Callosum: Fractional Anisotropy background Yellow Fiber: FA=0.55±0.05, Blue Fiber: 0.54±0.05, Expected: 0.50±0.02 (Shimoni 1999)

14 White Matter fibers from IFG_po (green) appear to go mostly above and below PT (yellow) but not to PT. This not going to PT is more marked in the left cortex (orange) than in the right (pink).

15 White matter connection between IFG_po_R and PT_R Statistics of White matter connection between IFG_po_R and PT_R FA= 0.45±0.02

16 Q-Ball 256 Directions White Matter Fiber Tracking

17 The two figures above are an example of the results that can be obtained by the Q-ball white matter fiber tracking TrackVis program. The diffusion MRI data used to obtain the fiber tracking results above was obtained at the Dana and David Dornsife Cognitive Neuroscience Imaging Center, and it consisted of 256 non-co-linear diffusion sensitizing gradient orientations with b=5000. The fiber tracks were obtained using the orientation distribution functions obtained from a Q-Ball treatment of the diffusion data. The tracks displayed are those passing in the displayed Coronal slice. Q-Ball white matter fiber tracking enables the visualization of fibers crossing within the same voxel as can bee seen by the crossing of fibers in the figure below, which is simply a zoom of the figure above.

18 BOLD FUNCTIONAL MRI DATA PROCESSING Although there are many different types of software packages that can be used in processing BOLD functional MRI (fmri) data, the most common are SPM, BrainVoyager, FSL and FreeSurfer. Each software package has its won set of advantages and disadvantages. Use of multiple software packages is encouraged, but our laboratory (IBILI) uses BrainVoyager more than any other. The Users Guide to BrainVoyager is very selfexplanatory, and can be downloaded from their website: The downloaded file is in pdf format, and is named: BVQXGettingStartedGuide_v2.5 If you have any difficulty in getting this file, please let us know and we will provide you that pdf file. Examples of the kind of images that you can get using BrainVoyager are: 1. Inputting MRI data: 2. Specifying the simulation protocol you used: 3. Obtaining BOLD signal based on protocol used: 4. Averaging BOLD data based on protocol used: 5. Overlaying BOLD data in Anatomical MRI: 6. Automatic Cortex Segmentation: 7. Cortical Inflation and Flattening: 8. Overlay of BOLD activation in flat Cortex:

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