Thanks Anastasia, I finally got it, I had to do mri_vol2vol twice to have it in the diffusion space.
I have an additional question: I want to create waypoint masks for probtracx from Tracula tracts (for example, uncinate). Should I use mri_binarize on path.pd.nii to create the mask? Should I use 20% of the maximum value as the threshold in order to do so? (a little help with the command line will be greatly appreciated) thanks again! Gari On Sun, Jan 12, 2014 at 3:08 AM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Has mri/hippo_subfield_in_diffusion_space.nii been actually transformed > to diffusion space by applying the anatorig2diff transformation? I'm > assuming that your diffusion data is not 0.5mm resolution? You can search > for the name of the transformation in trac-all.log to see examples of how > it is applied to volumes. > > On Sat, 11 Jan 2014, Garikoitz Lerma-Usabiaga wrote: > > Hi Anastasia,the problem is with mri/hippo_subfield_in_ >> diffusion_space.nii, >> >> which originally is mri/hippo_subfield.mgz, the output of running >> recon-all >> -hippo-subfields. So as far as I understand it is not in anatomical space, >> according to MRI info, it is (one example): >> - LIA >> - 85x97x141 >> - 0.5x0.5x0.5 >> >> So, how could I convert it to the diffussion space in FSL format in order >> to >> be able to use it in probtrackx? >> Should I do 2 steps or 3 steps? >> 1.- mri_convert to anatorig space (brainmask.mgz space, LIA, 256x256x256) >> 2.- anatorig2diff in order to change to FSL format and to diffusion >> space? >> (3.- would be the previous one in two steps, first from anatorig to anat >> and >> then from anat to diff) >> >> Any indication of the best programs to do all the change will be >> appreciated >> (I've seen in trac-all.log that mostly fsl programs are being used to do >> the >> flips, and then tkregister2 and bbregister for the registrations) >> >> Thanks for the help! >> Gari >> >> >> >> On Sat, Jan 11, 2014 at 1:31 AM, Anastasia Yendiki >> <ayend...@nmr.mgh.harvard.edu> wrote: >> >> Hi Gari - So if I understand correctly, your inputs to >> probtrackx are: >> mri/hippo_subfield_in_diffusion_space.nii >> dmri.bedpostX/merged >> dmri.bedpostX/nodif_brain_mask >> >> If these all come from the output of tracula, aren't these all >> in LAS orientation? >> >> a.y >> >> On Thu, 9 Jan 2014, Garikoitz Lerma-Usabiaga wrote: >> >> Hi Anastasia,I want to use a hippocampal subfield as >> a seed in FSL. I am having problems understanding >> how >> to change spaces around... >> >> 1.- Is this command ok? >> mri_vol2vol --mov dmri/dtifit_FA.nii.gz --targ >> mri/hippo_subfield_in_anatomical_space.mgz --inv >> --interp >> nearest --o >> mri/hippo_subfield_in_diffusion_space.nii --reg >> dmri/xfms/anatorig2diff.bbr.dat --no-save-reg >> >> 2.- I would like to visualize it in freeview in >> anatomical space to check if it is ok, if I load >> nu.mgz and >> hippo_subfield_in_anatomical_space.mgz and then load >> hippo_subfield_in_diffusion_space.nii with the >> registration file dmri/xfms/anatorig2diff.bbr.dat, >> should I visualize it ok? >> If I don't register it, they show to be displaced >> (more than expected). >> >> >> 3.- Afterwards I want to run probtracx with the >> following command (my doubt is mainly about the >> files to >> use, since FSL files are RAS, freesurfer anatomical >> are LIA and freesurfer diffusion are LIA, are all >> the >> files in the same format and FSL is ok with it?): >> /usr/local/fsl/bin/probtrackx --mode=seedmask >> -x mri/hippo_subfield_in_diffusion_space.nii -s >> dmri.bedpostX/merged -m >> dmri.bedpostX/nodif_brain_mask -o >> fdt_paths_hippo_subfields >> --dir=FSL_ConnResults_Hipp -c 0.2 -S 2000 >> --steplength=0.5 -P 5000 --opd >> >> many thanks! >> Gari >> >> >> >> >> 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. >> >> >> >>
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