Hi Doug we got good results with the dit of the merged brik's Jon ----- Original Message ----- From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> To: "Jon Wieser" <wie...@uwm.edu> Cc: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> Sent: Thursday, April 11, 2013 11:22:13 AM Subject: Re: [Freesurfer] merging dti data
That might work. I think "motion" correction is going to be your biggest problem since the slabs were acquired at different times. On 04/11/2013 11:05 AM, Jon Wieser wrote: > 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. >> >> > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- 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
