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" <gr...@nmr.mgh.harvard.edu> To: "Jon Wieser" <wie...@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" <gr...@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 >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
