Thanks Doug! just editing to correct a minor error in the last question: > 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 anatomicals are LIA and freesurfer diffusion are LAS, 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
On Thu, Jan 9, 2014 at 6:48 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > > 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. > >
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