Hi Anastasia, it worked perfectly and I could run probtrack between my anatomical seed and using waypoints from Tracula tracts.
I have another doubt right now. The probabilities in each new tract are very different. I divided every value with waytotal using fslmaths -div in order to normalize them, and obtained something like this: subject: S_20, Max Value after normalizing with waytotal: 0.75533 subject: S_23, Max Value after normalizing with waytotal: 0.27883 subject: S_25, Max Value after normalizing with waytotal: 0.60251 subject: S_27, Max Value after normalizing with waytotal: 0.32355 Should I consider the same absolute value for all tracts in order to threshold them or should I threshold all tracts independently with the 20%? I want to check visually the existence of the tract between the anatomical and the tract, with the same probability across subjects, and afterwards obtain the FA values in order to correlate with behavior. Thanks again! Gari On Mon, Jan 13, 2014 at 7:55 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Gari - Yes, fslmaths should be able to do it, with -thrp 20. > > a.y > > > On Mon, 13 Jan 2014, Garikoitz Lerma-Usabiaga wrote: > > 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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