Thanks, problem solved! Leah.
> On Mar 25, 2019, at 2:35 PM, Timothy Coalson <tsc...@mst.edu> wrote: > > 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 > <mailto:mmorenoort...@icloud.com>> wrote: > Thanks for your response. The image is now cropped, image attached. > > Leah. > > <image.png> > > ******************************************* > 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 <mailto:mm4...@cumc.columbia.edu> > >> On Mar 24, 2019, at 10:58 PM, Glasser, Matthew <glass...@wustl.edu >> <mailto: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 >> <mailto:mmorenoort...@icloud.com>> >> Date: Sunday, March 24, 2019 at 9:54 PM >> To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>> >> Cc: HCP Users <hcp-users@humanconnectome.org >> <mailto: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 <mailto:mm4...@cumc.columbia.edu> >> >>> On Mar 24, 2019, at 10:47 PM, Glasser, Matthew <glass...@wustl.edu >>> <mailto:glass...@wustl.edu>> wrote: >>> >>> Not negative. >>> >>> Matt. >>> >>> From: Marta Moreno <mmorenoort...@icloud.com >>> <mailto:mmorenoort...@icloud.com>> >>> Date: Sunday, March 24, 2019 at 9:45 PM >>> To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>> >>> Cc: HCP Users <hcp-users@humanconnectome.org >>> <mailto: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 >>>> <mailto: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 >>>> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno >>>> <mmorenoort...@icloud.com <mailto:mmorenoort...@icloud.com>> >>>> Date: Sunday, March 24, 2019 at 6:40 PM >>>> To: HCP Users <hcp-users@humanconnectome.org >>>> <mailto: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 <mailto:HCP-Users@humanconnectome.org> >>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> <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. 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