How to make a fixel mask based on a GM or WM mask rather than whole brain


#1

Hi experts,

I am doing the FBA analysis following the tutorial.

Because I am interested in the white matter fibres across the hippocampus, thalamus, amygdala, cerebellum regions. Then I just want to do the FBA analysis based on these whiter matter fibres rather than whole brain white matter.

I wonder if I can make a fixel mask based on gray matter atlas (the atlas includes some interest of regions, such as, hippocampus, thalamus, amygdala, cerebellum)? Then I can do fixelcfestats based on the fixel mask that I made?

Or if I can use fod2fixel to make a fixel mask based on whiter matter mask?
Thanks,
Elvira


#2

Hi Elvira,

fixelcfestats has the command-line option -mask, which enables statistical inference to be performed only within a subset of fixels contained in the template. This strictly needs to be a fixel mask, not a voxel mask. Therefore, if you have voxel-based definitions of regions that you wish to test, you can use the voxel2fixel command to “project” the values from a voxel mask down to the underlying fixels: If a voxel is highlighted in the mask, then all fixels within that voxel will take a value of 1, whereas if a voxel is not highlighted in the mask, then all fixels within that voxel will take a value of 0.

Ultimately, all the fixelcfestats -mask option is looking for is a value of 1 for fixels that should be tested, and a value of 0 for those that should not. How you choose to derive these values is up to you and your particular experiment; but the voxel2fixel command is likely a good starting point.

Rob


#3

Hi Rob,

voxel2fixel SLF2mr_synants.mif fixel_mask new_voxelfixel slf -info

SLF2mr_synants.mif is the voxel mask. I have already register it to voxel_mask file (which is the output of step 13: fixel2voxel).
fixel_mask is the folder that includes directions.mif and index.mif (which is the output of step13: fod2fixel).
new_voxelfixel is the output folder
slf is the output file’s name

I run this code. But it failed. Could you please help me to figure out the problem?

voxel2fixel: [INFO] opening image “SLF2mr_synants.mif”…
voxel2fixel: [INFO] image “SLF2mr_synants.mif” opened with dimensions 146x178x147, voxel spacing 1.25x1.25x1.25, datatype Float32LE
voxel2fixel: [INFO] opening image “fixel_mask/index.mif”…
voxel2fixel: [INFO] image “fixel_mask/index.mif” opened with dimensions 146x178x147x2, voxel spacing 1.25x1.25x1.25x1, datatype UInt32LE
voxel2fixel: [. ] copying fixel index and directions file into output directory…
voxel2fixel: [INFO] opening image “fixel_mask/index.mif”…
voxel2fixel: [INFO] image “fixel_mask/index.mif” opened with dimensions 146x178x147x2, voxel spacing 1.25x1.25x1.25x1, datatype UInt32LE
voxel2fixel: [INFO] creating image “new_voxelfixel/index.mif”…
voxel2fixel: [INFO] image “new_voxelfixel/index.mif” created with dimensions 146x178x147x2, voxel spacing 1.25x1.25x1.25x1, datatype UInt32LE
voxel2fixel: [INFO] opening image “fixel_mask/index.mif”…
voxel2fixel: [INFO] image “fixel_mask/index.mif” opened with dimensions 146x178x147x2, voxel spacing 1.25x1.25x1.25x1, datatype UInt32LE
voxel2fixel: [INFO] opening image “fixel_mask/directions.mif”…
voxel2fixel: [INFO] image “fixel_mask/directions.mif” opened with dimensions 158463x3x1, voxel spacing 1.25x1.25x1.25, datatype Float32LE
voxel2fixel: [INFO] opening image “fixel_mask/index.mif”…
voxel2fixel: [INFO] image “fixel_mask/index.mif” opened with dimensions 146x178x147x2, voxel spacing 1.25x1.25x1.25x1, datatype UInt32LE
voxel2fixel: [INFO] opening image “fixel_mask/directions.mif”…
voxel2fixel: [INFO] image “fixel_mask/directions.mif” opened with dimensions 158463x3x1, voxel spacing 1.25x1.25x1.25, datatype Float32LE
voxel2fixel: [INFO] creating image “new_voxelfixel/directions.mif”…
voxel2fixel: [INFO] image “new_voxelfixel/directions.mif” created with dimensions 158463x3x1, voxel spacing 1.25x1.25x1.25, datatype Float32LE
voxel2fixel: [done] copying fixel index and directions file into output directory
voxel2fixel: [INFO] creating image “new_voxelfixel/slf”…
voxel2fixel: [ERROR] unknown format for image “new_voxelfixel/slf” (no file extension specified)
voxel2fixel: [ERROR] error creating image “new_voxelfixel/slf”

Thanks,
Elvira


#4

Hi Rob,

voxel2fixel SLF2mr_synants.mif fixel_mask new_voxelfixel slf.mif

I just try to add slf.mif, then it works. The below is the figure of slf.mif

Thanks,
Elvira