That looks like you cut off some brain tissue. I'm not really sure what your goal is here, but if you have images with different voxel sizes, what you may actually need to do is to resample an image (flirt, applywarp, or wb_command -volume-*-resample), and not crop it.
Tim On Sun, Mar 24, 2019 at 10:22 PM Marta Moreno <mmorenoort...@icloud.com> wrote: > Thanks for your response. The image is now cropped, image attached. > > Leah. > > > ******************************************* > Leah Moreno, PhD > Research Scientist > Division of Experimental Therapeutics > Department of Psychiatry > Columbia University Medical Center > 1051 Riverside Drive, Unit 21 > New York, NY 10032 > phone: (914) 218-7311 > email: mm4...@cumc.columbia.edu > > On Mar 24, 2019, at 10:58 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > > 0 66 to include all slices and probably 0 1 for timepoints tacked onto the > end. > > Matt. > > From: Marta Moreno <mmorenoort...@icloud.com> > Date: Sunday, March 24, 2019 at 9:54 PM > To: Matt Glasser <glass...@wustl.edu> > Cc: HCP Users <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] Topup_AP dimension issue > > Thanks for your response. Still seams to be empty. I have attached both > files into this email in case it helps. > > Leah. > > > > ******************************************* > Leah Moreno, PhD > Research Scientist > Division of Experimental Therapeutics > Department of Psychiatry > Columbia University Medical Center > 1051 Riverside Drive, Unit 21 > New York, NY 10032 > phone: (914) 218-7311 > email: mm4...@cumc.columbia.edu > > On Mar 24, 2019, at 10:47 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > > Not negative. > > Matt. > > From: Marta Moreno <mmorenoort...@icloud.com> > Date: Sunday, March 24, 2019 at 9:45 PM > To: Matt Glasser <glass...@wustl.edu> > Cc: HCP Users <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] Topup_AP dimension issue > > Thanks for your response. Do you mean running this?: fslroi > NTTMS_s037_181015_3T_SpinEchoFieldMap_AP_1.nii.gz test.nii.gz -16 96 -16 96 > 66 66 > > If that is the case the test file seams to be empty. > > Leah. > > > > On Mar 24, 2019, at 8:25 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > > Subtract 128 from 96 and then take half of that as your start and 96 as > your length. > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Marta Moreno < > mmorenoort...@icloud.com> > Date: Sunday, March 24, 2019 at 6:40 PM > To: HCP Users <hcp-users@humanconnectome.org> > Subject: [HCP-Users] Topup_AP dimension issue > > Dear Experts, > > Maybe a trivial question but how can I change the Topup_AP dimension' size > from 128 128 66 to 96 96 66? Using fslroi I am cutting the brain. > > Thanks, > > Leah. > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ------------------------------ > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > > > > > ------------------------------ > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > > > > > ------------------------------ > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
