the gradients were the same for each slab. What is the difficulty with runnning the merged brain halves in tracula?
I have another to do it that I am going to try. I made AFNI Brik's of the two slabs, and merged them together into one AFNI brik with the AFNI command 3dZcat. I made a nifti file from the merged afni brik. i will try running tracula on the merged nifti file.
Jon
----- Original Message ----- From: "Douglas Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, April 11, 2013 9:56:53 AM Subject: Re: [Freesurfer] merging dti data
yes, they work for whole brain, but not if you have two brain halves. You might be able to do something in matlab. I assume the gradient direction order was the same for both slabs? doug
On 4/11/13 10:36 AM, Jon Wieser wrote:
Those commands were given to me by Anastasia. they work fine for merging two whole brain datasets. jon
----- Original Message ----- From: "Douglas Greve" greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, April 10, 2013 10:13:05 PM Subject: Re: [Freesurfer] merging dti data
Hi Jon, I don't know how to make this work, but I'm sure that those commands will not do it. Sorry:( doug
On 4/10/13 1:13 PM, Jon Wieser wrote:
we captured some dti data. there were 2 runs. we acquired in the axial plane, 2mm slice thickness the first run captured the lower half of the brain, slice locations: I56-S20, and the second run captured the upper half of the brain S16-S92. i have made briks from each of these runs. I can convert the briks to nifti files I want to merge the nifti files together to analyze the data in tracula
In the past i have merged data from two dti runs, but each run have covered the entire brain, with the following commands
mri_convert MJ0001dti1+orig.BRIK MJ0001dti1.nii.gz mri_convert MJ0001dti2+orig.BRIK MJ0001dti2.nii.gz mri_concat --i MJ0001dti1.nii.gz MJ0001dti2.nii.gz --o MJ0001dti12.nii.gz
would it work to concat the two half brain niftis into one file and analyze that with tracula? (I will concat the bvec and bvals files too) would this cause problems doing it this way? Thanks Jon
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