Re: [Freesurfer] How to threshold an input mutli-volume?
Thank you in advance for your help. We installed the freesurfer on a ubuntu 8.04 i686 machine. On Wed, Jul 8, 2009 at 9:57 AM, Bruce Fischl wrote: > I guess it would be pretty easy to fix to work on multi-frame images. What > hardware/software platform are you using? > > Bruce > > On Tue, 7 Jul 2009, [UTF-8] ?? wrote: > > Hi, all. >> Can mri_threshold threshold an input mutli-volume file? With a seven >> volumes NIFTI file, all voxels other than in the first volume are set to >> zero. In addition, the help for mri_threshold options is very limited. >> There >> is nothing about the options. >> >> Usage: mri_threshold [options] >> This program will threshold an input volume >> >> Where do I get more detailed description? >> Best Regards. >> >> -- Albert Lab of Complex System and Artificial Intelligence, Institute of Automation,Chinese Academy of Sciences(CASIA) Beijing, 100190,P.R.CHINA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] How to threshold an input mutli-volume?
Hi, all. Can mri_threshold threshold an input mutli-volume file? With a seven volumes NIFTI file, all voxels other than in the first volume are set to zero. In addition, the help for mri_threshold options is very limited. There is nothing about the options. Usage: mri_threshold [options] This program will threshold an input volume Where do I get more detailed description? Best Regards. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] How to "Fitting Tensors" in dt_recon?
Thank you very much. In fact, I want to insert the bet module before calculating the tensor, eigvals, eigvecs, fa, ra etc in dt_recon. I also know mri_glmfit can create glm-related images. But I can't find the tensor calculation in (mri_glmfit --y $fec --glmdir $OutDir --dti $bvals $bvecs). On Tue, Jul 7, 2009 at 12:36 AM, Douglas N Greve wrote: > It just takes the log of the input and constructs a design matrix from your > bvals and bvecs, then fits a glm. > > doug > > ?? wrote: > >> Hi, All. >> The related item of "Fitting Tensors" is listed from the dt_recon. >> >> # Fit tensors >> echo "#...@#---" | tee -a $LF >> echo "Fitting Tensors" | tee -a $LF >> date | tee -a $LF >> >> set cmd = (mri_glmfit --y $fec --glmdir $OutDir); >> if($#bvals == 0) then >> set cmd = ($cmd --dti $infodump) >> else >> set cmd = ($cmd --dti $bvals $bvecs) >> endif >> >> However, I can't find any description about this argument(--dti) in >> mri_glmfit. Did the mri_glmfit call the dtifit to fit the tensor from fsl?If >> not, what is it? >> >> -- >> Albert >> Lab of Complex System and Artificial Intelligence, >> Institute of Automation,Chinese Academy of Sciences(CASIA) >> Beijing, 100190,P.R.CHINA >> >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > -- Albert Lab of Complex System and Artificial Intelligence, Institute of Automation,Chinese Academy of Sciences(CASIA) Beijing, 100190,P.R.CHINA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] How to "Fitting Tensors" in dt_recon?
Hi, All. The related item of "Fitting Tensors" is listed from the dt_recon. # Fit tensors echo "#...@#---" | tee -a $LF echo "Fitting Tensors" | tee -a $LF date | tee -a $LF set cmd = (mri_glmfit --y $fec --glmdir $OutDir); if($#bvals == 0) then set cmd = ($cmd --dti $infodump) else set cmd = ($cmd --dti $bvals $bvecs) endif However, I can't find any description about this argument(--dti) in mri_glmfit. Did the mri_glmfit call the dtifit to fit the tensor from fsl?If not, what is it? -- Albert Lab of Complex System and Artificial Intelligence, Institute of Automation,Chinese Academy of Sciences(CASIA) Beijing, 100190,P.R.CHINA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
