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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