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Nope that isn’t it. If he uses --premat it accepts affine matrices. Please use the --super flag in applywarp as I suggested in the first e-mail.
Peace,
Matt.
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Christine Zakrzewski
Sent: Wednesday, October 05, 2011 1:00 PM
Hey Daniel. Your linear transform probably has to be in NifTI format—ie, not <struc2diff.mat>, but < struct2diff.nii>.
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Daniel Cole
Sent: Wednesday, October 05, 2011 1:01 PM
To: [log in to unmask]
Subject: Re: [FSL] FLIRT - Nearest Neighbor option failing
Hello again,
I figured out how to generate the matrix using flirt but am now having trouble using applywarp. I decided it was better to get the seed masks into diffusion space so that my tracking outputs in diffusion space.
My code looks like this:
"flirt -in xxxx/T1_c_brain -ref xxxx_dwi.nii -omat struc2diff.mat"
"applywarp -i xxxx/StructuralMask.nii.gz -o xxxx/DiffusionOutput -r xxxx_dwi.nii --premat=xxxx_struc2diff.mat -s "
But when I open the output of applywarp I get nothing, 'fslstats output -M' gives me 0.
Is there something simple I'm missing?
Many thanks,
Daniel
On Tue, Oct 4, 2011 at 2:46 PM, Daniel Cole <[log in to unmask]> wrote:
Why didn't I think of this! For some reason I kept thinking you need the seed to be in diffusion space for probtracking...
My bedpost directory doesn't have a structural2diff.mat - is there an easy way to create this?
I know FLIRT creates one but I'm sure there's a better way.
Thanks so much!
Daniel
On Tue, Oct 4, 2011 at 2:37 PM, Matt Glasser <[log in to unmask]> wrote:
You should use applywarp --premat=<yourmat> with the --super flag set instead of FLIRT to resample the ROIs. However, why not just make use of the --xfm option of probtrackx to do this for you?
Peace,
Matt.
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Daniel Cole
Sent: Tuesday, October 04, 2011 1:24 PM
To: [log in to unmask]
Subject: [FSL] FLIRT - Nearest Neighbor option failing
Hello FSL list,
I have a rather odd issue that I was unable to find a solution to in the archives. I am attempting to linear register a structural ROI into a subject's native space for use in probabilistic tracking. However, when I attempt to use nearest neighbor interpolation my ROI disappears!
Some things you should know:
- My ROI is only 1 voxel thick.
- 157 voxels total (for this particular ROI)
- Registration with other subject's is fine.
This doesn't happen with all of my subject's but a good chunk of them are problematic. I'm guessing that somehow the voxels I've chosen for my ROI are being lost in the transformation from the high res to the diffusion image?
Is there a way to know this for sure?
Also, what would be the best way to account for this... make my ROIs thicker for all subjects?
Thanks so much!
Daniel
P.S. The code for trilinear/nearest neighbor is as follows.
Tri
"/RCBI/fsl/bin/flirt -in /Volumes/rcbiUsers/dcole/Broca/${sub}/t1/T1_c_brain.nii.gz -ref /Volumes/rcbiUsers/dcole/FSLProcessing/TBSS/${sub}/${sub}_dwi.nii -out /Volumes/rcbiUsers/dcole/FSLProcessing/TBSS4.1/Probabilistic/Masks/Handdrawn/${sub}LOperTriTest -omat /Volumes/rcbiUsers/dcole/FSLProcessing/TBSS4.1/Probabilistic/Masks/Handdrawn/${sub}LOperTriTest.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear
/RCBI/fsl/bin/flirt -in /Volumes/rcbiUsers/dcole/FSLProcessing/TBSS4.1/Probabilistic/Masks/Handdrawn/Structural/${sub}_LOper_struc.nii.gz -ref /Volumes/rcbiUsers/dcole/FSLProcessing/TBSS/${sub}/${sub}_dwi.nii -out /Volumes/rcbiUsers/dcole/FSLProcessing/TBSS4.1/Probabilistic/Masks/Handdrawn/${sub}LOperTriTest_shadowreg_${sub}_LOper_struc.nii -applyxfm -init /Volumes/rcbiUsers/dcole/FSLProcessing/TBSS4.1/Probabilistic/Masks/Handdrawn/${sub}LOperTriTest.mat -interp trilinear"
NN
"/RCBI/fsl/bin/flirt -in /Volumes/rcbiUsers/dcole/Broca/${sub}/t1/T1_c_brain.nii.gz -ref /Volumes/rcbiUsers/dcole/FSLProcessing/TBSS/${sub}/${sub}_dwi.nii -out /Volumes/rcbiUsers/dcole/FSLProcessing/TBSS4.1/Probabilistic/Masks/Handdrawn/${sub}LOperNNTest -omat /Volumes/rcbiUsers/dcole/FSLProcessing/TBSS4.1/Probabilistic/Masks/Handdrawn/${sub}LOperNNTest.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp nearestneighbour
/RCBI/fsl/bin/flirt -in /Volumes/rcbiUsers/dcole/FSLProcessing/TBSS4.1/Probabilistic/Masks/Handdrawn/Structural/${sub}_LOper_struc.nii.gz -ref /Volumes/rcbiUsers/dcole/FSLProcessing/TBSS/${sub}/${sub}_dwi.nii
-out /Volumes/rcbiUsers/dcole/FSLProcessing/TBSS4.1/Probabilistic/Masks/Handdrawn/${sub}LOperNNTest_shadowreg_${sub}_LOper_struc.nii -applyxfm
-init /Volumes/rcbiUsers/dcole/FSLProcessing/TBSS4.1/Probabilistic/Masks/Handdrawn/${sub}LOperNNTest.mat -interp nearestneighbour"
--
Daniel Cole
University of Rochester
Brain and Cognitive Sciences
--
Daniel Cole
University of Rochester
Brain and Cognitive Sciences
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