Re: [caret-users] metric user scale with fixed step size
Hi Donna, I am using the following setting is the palette file: 1. -> _br1 0.8333 -> _br2 0. -> _br3 0.5000 -> _br4 0. -> _br5 0.1666 -> _br6 The colorbar alwas has 5 steps, not six, and it is the first one that is missing. I tried extending and shrinking the scale in metric settings, but did not gain the extra step. I also tried adding a 0 in the palette file, but that did not change anything either. Caspar 2014-12-11 10:30 GMT-05:00 Caspar M. Schwiedrzik : > Hi Donna, > I followed your advice and compressed the scale into 0:1. > One more question: While the colors are displayed correctly now, is there > a way to change the number of steps that the colorbar shows? Somehow, it > always shows 5 discrete levels, but I would like to get 6. > Thanks, Caspar > > > 2014-11-25 18:57 GMT-05:00 Caspar M. Schwiedrzik < > cschwie...@rockefeller.edu>: > > Hi Donna, >> thanks for pointing out the palette file format. I have been playing >> around with this but am running into two strange issues. First, the I am >> getting a fairly weird display that differs markedly from the one I >> originally created in Freesurfer. For example, the maximal number appears >> much less frequently in Caret than in FS. I am not sure where that problem >> could arise (I am converting a w file into Caret format which for all other >> maps has worked just fine). Secondly, and this may or may not be related, >> the colorbar only displays one color, but all tickmarks. >> Any ideas? >> This is an excerpt from my palette file: >> >> _br1 = #7f >> _br2 = #ff3f00 >> _br3 = #efff0f >> _br4 = #1fffdf >> _br5 = #004fff >> _br6 = #8f >> >> ***PALETTES bluered [6+] >> 6.00 -> _br1 >> 5.00 -> _br2 >> 4.00 -> _br3 >> 3.00 -> _br4 >> 2.00 -> _br5 >> 1.00 -> _br6 >> >> Thanks, Caspar >> >> >> 2014-11-24 13:29 GMT-05:00 Caspar M. Schwiedrzik < >> cschwie...@rockefeller.edu>: >> >>> Hi! >>> I am trying to display some metric data that has a fixed, meaningful >>> step size. Specifically, my data ranges from 1 to 6 and I would like to >>> have each step (1,2,3,4,5,6) assigned a specific color, and no intermediate >>> steps (e.g., 1.5). Is that possible? >>> Thanks, Caspar >>> >>> >> > ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] metric user scale with fixed step size
You have six bins, like below, but compressed to 0:1? Hmmm. Scratching my head on that one. On Dec 11, 2014, at 9:30 AM, "Caspar M. Schwiedrzik" wrote: > Hi Donna, > I followed your advice and compressed the scale into 0:1. > One more question: While the colors are displayed correctly now, is there a > way to change the number of steps that the colorbar shows? Somehow, it always > shows 5 discrete levels, but I would like to get 6. > Thanks, Caspar > > > 2014-11-25 18:57 GMT-05:00 Caspar M. Schwiedrzik : > Hi Donna, > thanks for pointing out the palette file format. I have been playing around > with this but am running into two strange issues. First, the I am getting a > fairly weird display that differs markedly from the one I originally created > in Freesurfer. For example, the maximal number appears much less frequently > in Caret than in FS. I am not sure where that problem could arise (I am > converting a w file into Caret format which for all other maps has worked > just fine). Secondly, and this may or may not be related, the colorbar only > displays one color, but all tickmarks. > Any ideas? > This is an excerpt from my palette file: > > _br1 = #7f > _br2 = #ff3f00 > _br3 = #efff0f > _br4 = #1fffdf > _br5 = #004fff > _br6 = #8f > > ***PALETTES bluered [6+] > 6.00 -> _br1 > 5.00 -> _br2 > 4.00 -> _br3 > 3.00 -> _br4 > 2.00 -> _br5 > 1.00 -> _br6 > > Thanks, Caspar > > > 2014-11-24 13:29 GMT-05:00 Caspar M. Schwiedrzik : > Hi! > I am trying to display some metric data that has a fixed, meaningful step > size. Specifically, my data ranges from 1 to 6 and I would like to have each > step (1,2,3,4,5,6) assigned a specific color, and no intermediate steps > (e.g., 1.5). Is that possible? > Thanks, Caspar > > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] metric user scale with fixed step size
Hi Donna, I followed your advice and compressed the scale into 0:1. One more question: While the colors are displayed correctly now, is there a way to change the number of steps that the colorbar shows? Somehow, it always shows 5 discrete levels, but I would like to get 6. Thanks, Caspar 2014-11-25 18:57 GMT-05:00 Caspar M. Schwiedrzik : > Hi Donna, > thanks for pointing out the palette file format. I have been playing > around with this but am running into two strange issues. First, the I am > getting a fairly weird display that differs markedly from the one I > originally created in Freesurfer. For example, the maximal number appears > much less frequently in Caret than in FS. I am not sure where that problem > could arise (I am converting a w file into Caret format which for all other > maps has worked just fine). Secondly, and this may or may not be related, > the colorbar only displays one color, but all tickmarks. > Any ideas? > This is an excerpt from my palette file: > > _br1 = #7f > _br2 = #ff3f00 > _br3 = #efff0f > _br4 = #1fffdf > _br5 = #004fff > _br6 = #8f > > ***PALETTES bluered [6+] > 6.00 -> _br1 > 5.00 -> _br2 > 4.00 -> _br3 > 3.00 -> _br4 > 2.00 -> _br5 > 1.00 -> _br6 > > Thanks, Caspar > > > 2014-11-24 13:29 GMT-05:00 Caspar M. Schwiedrzik < > cschwie...@rockefeller.edu>: > >> Hi! >> I am trying to display some metric data that has a fixed, meaningful step >> size. Specifically, my data ranges from 1 to 6 and I would like to have >> each step (1,2,3,4,5,6) assigned a specific color, and no intermediate >> steps (e.g., 1.5). Is that possible? >> Thanks, Caspar >> >> > ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] metric user scale with fixed step size
Hi Caspar, If you converted from Freesurfer, rather than mapping independently in Caret, then this is puzzling. I believe mris_convert can now convert directly to GIFTI (.gii) format, and I suspect this route might be more reliable than converting .w to .metric. Have you tried this? Probably easy and worth a shot. As for the palete, your range needs to be compressed into the -1.0 to 1.0 range, or in your case 0 to 1. On Nov 25, 2014, at 5:57 PM, Caspar M. Schwiedrzik wrote: > Hi Donna, > thanks for pointing out the palette file format. I have been playing around > with this but am running into two strange issues. First, the I am getting a > fairly weird display that differs markedly from the one I originally created > in Freesurfer. For example, the maximal number appears much less frequently > in Caret than in FS. I am not sure where that problem could arise (I am > converting a w file into Caret format which for all other maps has worked > just fine). Secondly, and this may or may not be related, the colorbar only > displays one color, but all tickmarks. > Any ideas? > This is an excerpt from my palette file: > > _br1 = #7f > _br2 = #ff3f00 > _br3 = #efff0f > _br4 = #1fffdf > _br5 = #004fff > _br6 = #8f > > ***PALETTES bluered [6+] > 6.00 -> _br1 > 5.00 -> _br2 > 4.00 -> _br3 > 3.00 -> _br4 > 2.00 -> _br5 > 1.00 -> _br6 > > Thanks, Caspar > > > 2014-11-24 13:29 GMT-05:00 Caspar M. Schwiedrzik : > Hi! > I am trying to display some metric data that has a fixed, meaningful step > size. Specifically, my data ranges from 1 to 6 and I would like to have each > step (1,2,3,4,5,6) assigned a specific color, and no intermediate steps > (e.g., 1.5). Is that possible? > Thanks, Caspar > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] metric user scale with fixed step size
Hi Donna, thanks for pointing out the palette file format. I have been playing around with this but am running into two strange issues. First, the I am getting a fairly weird display that differs markedly from the one I originally created in Freesurfer. For example, the maximal number appears much less frequently in Caret than in FS. I am not sure where that problem could arise (I am converting a w file into Caret format which for all other maps has worked just fine). Secondly, and this may or may not be related, the colorbar only displays one color, but all tickmarks. Any ideas? This is an excerpt from my palette file: _br1 = #7f _br2 = #ff3f00 _br3 = #efff0f _br4 = #1fffdf _br5 = #004fff _br6 = #8f ***PALETTES bluered [6+] 6.00 -> _br1 5.00 -> _br2 4.00 -> _br3 3.00 -> _br4 2.00 -> _br5 1.00 -> _br6 Thanks, Caspar 2014-11-24 13:29 GMT-05:00 Caspar M. Schwiedrzik : > Hi! > I am trying to display some metric data that has a fixed, meaningful step > size. Specifically, my data ranges from 1 to 6 and I would like to have > each step (1,2,3,4,5,6) assigned a specific color, and no intermediate > steps (e.g., 1.5). Is that possible? > Thanks, Caspar > > ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] metric user scale with fixed step size
I think you should be able to write a palette like that: http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#paletteFile The palette file format was originally intended to be compatible with AFNI, which may have palette editing capabilities of which I am unaware. But if AFNI has updated their file format, it may no longer be readable by caret. Most people edit the palette file via text editor or have a script generate it. Make sure interpolation is toggled off on the Metric Settings menu. Another possibility is converting your "metric" data to paint (scalar vs integer values). Those formats are slightly different, but you could probably manage the conversion via text editor or script. If you go the paint route, then you'll also need an areacolor file. Attributes: Area Color can help you out there. On Nov 24, 2014, at 12:29 PM, Caspar M. Schwiedrzik wrote: > Hi! > I am trying to display some metric data that has a fixed, meaningful step > size. Specifically, my data ranges from 1 to 6 and I would like to have each > step (1,2,3,4,5,6) assigned a specific color, and no intermediate steps > (e.g., 1.5). Is that possible? > Thanks, Caspar > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
[caret-users] metric user scale with fixed step size
Hi! I am trying to display some metric data that has a fixed, meaningful step size. Specifically, my data ranges from 1 to 6 and I would like to have each step (1,2,3,4,5,6) assigned a specific color, and no intermediate steps (e.g., 1.5). Is that possible? Thanks, Caspar ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
