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If the related packages have been installed, the fslview can show the color bar automatically? Mingxia On Thu, Feb 7, 2013 at 12:35 AM, Stephen Smith <[log in to unmask]> wrote: > Right - unfortunately it seems that too often people with the > Debian/Ubuntu distribution don't end up taking a complete distribution of > FSL. You need to ask your admin to install all of the FSL-related packages. > > Steve. > > > > On 7 Feb 2013, at 08:32, zhang mingxia wrote: > > I am using the server. It's the Debian GNU/Linux system. > > Mingxia > > > On Thu, Feb 7, 2013 at 12:27 AM, Stephen Smith <[log in to unmask]>wrote: > >> Which distribution of FSL are you using - maybe Ubuntu? >> >> >> On 7 Feb 2013, at 08:24, zhang mingxia wrote: >> >> I ls $FSLDIR/etc/luts, only these: >> ramp2.gif render1.map render2.lut render2t.map render3t.lut >> renderhsv.lut >> ramp.gif render1t.lut render2.map render3.lut render3t.map >> renderjet.lut >> render1.lut render1t.map render2t.lut render3.map renderhot.lut >> rendersea.lut >> >> Anyway, if I used the colorbar_maker.nii.gz provided by Jeanette, does >> any one know whether it's right to set min=90*.95 and max=90 (threshold >> p>.95 for TBSS results)? >> >> Thanks! >> >> Mingxia >> >> >> On Wed, Feb 6, 2013 at 11:54 PM, Stephen Smith <[log in to unmask]>wrote: >> >>> It should be there - it is in my copy of FSL - though you need the >>> proper English spelling of colour >>> >>> Cheers. >>> >>> >>> >>> On 7 Feb 2013, at 07:45, zhang mingxia wrote: >>> >>> Hi Mark, >>> >>> Sorry I didn't understand you. You meant we already have this in $FSLDIR/etc/luts? >>> I didn't find colorbar.nii.gz in the $FSLDIR/etc/luts >>> >>> Mingxia >>> >>> >>> On Wed, Feb 6, 2013 at 11:26 PM, Mark Jenkinson < >>> [log in to unmask]> wrote: >>> >>>> Hi, >>>> >>>> Everyone should have a version of this image (though with different >>>> dimensions, to make it look more like a thinner bar) in >>>> $FSLDIR/etc/luts/colourbar.nii.gz >>>> >>>> All the best, >>>> Mark >>>> >>>> >>>> >>>> On 7 Feb 2013, at 03:42, Jeanette Mumford <[log in to unmask]> >>>> wrote: >>>> >>>> Here's a link to the file. I didn't explicitly say it, but you'd load >>>> it in fslview, etc. >>>> >>>> http://mumford.fmripower.org/colorbar_maker.nii.gz >>>> >>>> Jeanette >>>> >>>> On Wed, Feb 6, 2013 at 8:53 PM, Chou Paul <[log in to unmask]>wrote: >>>> >>>>> Dear Jeanette >>>>> >>>>> Could you also provide me this file too? Thanks ! >>>>> >>>>> Best >>>>> >>>>> Paul >>>>> >>>>> ------------------------------ >>>>> Date: Wed, 6 Feb 2013 19:43:19 -0600 >>>>> From: [log in to unmask] >>>>> Subject: Re: [FSL] question about making color bar >>>>> To: [log in to unmask] >>>>> >>>>> >>>>> Hi, >>>>> >>>>> I have a nifti image that I made using some instructions that (I >>>>> think) Mark posted on the list a while ago. It simply creates a nifti >>>>> image that goes from 1 to 90 and you can choose the color option of your >>>>> choice and then take a snapshot for a DIY colorbar that you can then stick >>>>> onto your figure in photoshop. I'll send it directly to your email, since >>>>> it likely will be rejected by jiscmail. >>>>> >>>>> Cheers, >>>>> Jeanette >>>>> >>>>> On Wed, Feb 6, 2013 at 7:21 PM, zhang mingxia < >>>>> [log in to unmask]> wrote: >>>>> >>>>> Dear FSL expertise, >>>>> >>>>> I want to show the color bar in my figure of the TBSS results. I >>>>> read the email about the same question and understood "slicer" could do >>>>> that (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;d7372159.0810). >>>>> But it's 6 year ago's email. I think the slicer should be improved for >>>>> these 6 years and I can not understood the option of -s, -u, -z in the >>>>> example in the email. >>>>> >>>>> Anyway, I have the TBSS_tfce_corrp_tstat1.nii.gz file, it will be >>>>> displayed in "Red" with the threshold of .95 to 1. How can I get the color >>>>> bar for this figure? And, what's the code name in the $FSLDIR/etc/luts for >>>>> other color like the Blue, Green and Yellow? >>>>> >>>>> Thanks in advance! >>>>> >>>>> Mingxia Zhang >>>>> >>>>> >>>>> >>>> >>>> >>> >>> >>> >>> --------------------------------------------------------------------------- >>> Stephen M. Smith, Professor of Biomedical Engineering >>> Associate Director, Oxford University FMRIB Centre >>> >>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >>> +44 (0) 1865 222726 (fax 222717) >>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve >>> >>> --------------------------------------------------------------------------- >>> >>> >>> >>> >> >> >> >> --------------------------------------------------------------------------- >> Stephen M. Smith, Professor of Biomedical Engineering >> Associate Director, Oxford University FMRIB Centre >> >> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >> +44 (0) 1865 222726 (fax 222717) >> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve >> >> --------------------------------------------------------------------------- >> >> >> >> > > > --------------------------------------------------------------------------- > Stephen M. Smith, Professor of Biomedical Engineering > Associate Director, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 (fax 222717) > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > --------------------------------------------------------------------------- > > > >