#contents
Suppose we have the following three data.
:| High resolution anatomical data ('''''anat.high.vmr''''')
:| Low resolution anatomical data ('''''anat.low.vmr''''')
:| EPI data ('''''epi.fmr''''')
* Make a transformation file for the epi data [#o5b2dd38]
In this step, we will make a transformation file ('''''.trf''''' file).
This '''''.trf''''' file adjusts the epi image to have the same directions as the high resolution anatomical image.
+ Open the '''''anat.high.vmr''''' file
+ In "3D Volume Tools" dialogue, choose "Coregistration" and click "Select FMR..." to open '''''epi.fmr''''' file for FMR-VMR coregistration.
#ref(Fig1.png,left,30%)
&br;Press "Align".&br;-> You will see "FMR-VMR Coregistration" dialogue, high resolution anatomical image and epi image.
+ In the "FMR-VMR Coregistration" dialogue, check the "Flip slice order" option. Then choose "Source Options" and click "To SAG".
+ Choose "Source Options" and click "To SAG".
+Rotate the view by clicking the "Rotation buttons" to adjust the current sagital view to the sagital view of the anatomical data.&br;Press "OK".
#ref(tosag.jpg,left,60%)
&br;-> Now, you can check the epi image and high resolution anatomical image have roughly the same direction.
#ref(Fig2.png,left,30%)
+Select "Manual alignment..." for initial Alignment then press "Run IA". You will get a transformation file, '''''epi-TO-anat.high_IA.trf'''''.
&br;
&color(blue){''※If there is a gap between the center of low resolution anatomical image and the center of epi image...''};~
+ Calculate the distance between these two centers (low resolution anatomical data and epi data) from pss value [cm].~
+ Input the distance to the transformation matrix file, '''''epi-TO-anat.high_IA.trf''''', in [mm].~
　　↓'''''epi-TO-anat.high_IA.trf''''' file~
#ref(trf.png,left,90%)
*CoordinateSystem
0: BV internal [X: anterior -> posterior, Y: superior -> inferior, Z: right -> left]
1: BV-system [X: right -> left, Y: anterior -> posterior, Z: superior -> inferior]
2: Talairach [X: left -> right, Y: posterior -> anterior, Z: superior -> inferior]
Later on, use this new transformation matrix file as a '''''epi-TO-anat.high_IA.trf''''' file.
* Registration between high and low resolution anatomical data [#t70f6665]
Since the epi image has low resolution, we align the low resolution anatomical image instead of the epi image to high resolution anatomical image and make a transformation file. We will use this file for epi image - high resolution anatomical image coregistration.
* Preprocessing :High resolution anatomical data [#jc775835]
+Open the '''''anat.high.vmr''''' file.
+In the "3D Volume Tools" dialogue, select "Talairach".
+Press "Find AC Point" and you will see "Find AC Point" dialogue. Move the cross to the AC point and click "OK".
+Press "Find AC-PC Plane..." Since the cross is located at AC, rotate the plane to find PC. When you find AC-PC plane, click OK".
#ref(Fig3.png,left,30%)
+Press "Transform" and then click "GO".&br;-> You will get '''''anat.high_ACPC.vmr''''' and '''''anat.high_ACPC.trf''''' files.
* Preprocessing :Low resolution anatomical data [#q7e33fe5]
In this process, we will make the low resolution anatomical image to have the same view as the high resolution anatomical image for later alignment.
+Open '''''anat.low.vmr''''' file.
+Select "Spatial Transf" and click "To Sag" if the SAG view of the '''''anat.low.vmr''''' dataset does not show sagittal plane.
#ref(tosag_anat.jpg,left,70%)
+Click "Iso-Voxel" and you will see "Iso-Voxel Transformation" dialogue. Check the Source voxel size is correct and press "OK".&br;-> You will get '''''anat.low_SAG_ISO.vmr''''' file.
+Open '''''anat.high.vmr''''' file
+In the "3D Volume Tools" dialogue, choose "Coregistration" and click "Select VMR..." button to select '''''anat.low_SAG_ISO.vmr''''' file for VMR-VMR coregistration. &br;Press "Align..." then "GO" in the "VMR-VMR Coregistration Options" dialogue.
#ref(Fig4.png,left,70%)
+Select "Spatial Transf" and click "Save .TRF" to save the parameter file for this spatial transformation.&br;-> You will get the '''''anat.high_Man.trf''''' file.
* *Talairach transformation (if necessary) [#r22e41b4]
:|#You can skip this part if you don't need the data in Talairach space.
+Open the '''''anat.high_ACPC.vmr''''' file.
+Select "Talairach" in the "3D Volume Tools".
+Click the list box in the "Talairach proportional grid reference points" and you will see eight reference points (AC, PC, AP, PP, SP, IP, RP, and LP).
+Select each point and move white cross to that point on the image to define the locations of all reference points.&br; Click the "Set point" each time when you define the point as the current location of the white cross.
+After you define every reference points, click the "Save .TAL..." to save parameters. Click the "ACPC -> TAL..." then "Go". &br;-> Now you have '''''anat.high_TAL.vmr''''' and '''''anat.high_ACPC.tal''''' files.
* Registration between the epi and high resolution anatomical data [#n0982cc3]
+Open the '''''anat.high.vmr''''' file.
# Open the ''anat.high_ACPC.vmr'' file if you want to check the image in Talairach space.
+Click "Analysis" and select "create 3D-Aligned Time course (VTC) data...".
#ref(VTCfCr.png,right,around,70%)
+Click the "Browse..." to select the '''''epi.fmr''''' file for "Functional slice-based data file (FMR)"
+Select the identify matrix file, '''''epi-TO-anat.high_IA.trf''''', for "FMR -> VMR coregistration file 1, i.e. header-based (_IA.TRF)".
+Select '''''anat.high_Man.trf''''' file for "FMR -> VMR coregistration file 2, i.e. intensity-based fine-tuning (_FA.TRF)".&br;Choose "yes" to the dialogue box asking "Do you really want to use it for FMR-TOVMR initial alignment?".&br;
#You can skip the following two steps if you don't need the image in Talairach space.
+Select '''''anat.high_ACPC.trf''''' file for "AC-PC translation/rotation file - Talairach, step 1 (_ACPC.TRF)".~
+Select '''''anat.high_ACPC.tal''''' file for "Cerebrum border file for scaling - Talairach, step 2 (.TAL)"&br;~
+Press "GO". When the process is done, you will get the '''''epi.vtc''''' file.~
+Click the "Analysis" then select "Link 3D Time Course (VTC) File..."
+Press the "Browse" to choose the aligned file, '''''epi.vtc''''' and click "OK".
+On the "3D Volume Tools" dialogue, choose "Spatial Transf" and press "Show VTC Vol" and after a while, you will see the image aligned epi image.
+Click the "Blend2" and you can check if the epi image are correctly aligned to anatomy image.
#ref(blend.png,left,90%)