On 01/09/2014 12:45 PM, 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 That looks right, though I would use mri_label2vol as it will be more accurate than mri_vol2vol for segmentations. > > 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). Yes I think so.
I'll leave the last question to AY > > > 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 > > > _______________________________________________ > 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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
