If I could use workbench I would but: a) I need surefit (or some other rapid way of making a macaque surface) b) I need the possibility of flatmaps c) many target users already know caret
d) and this is worth considering I can't really publish something that requires users to register at the human connectome project in that way. It's harmless, but superficially it looks weird. My co-authors would say no. So workbench is out. It still has a sparse feature set for primate stuff anyway. Even though it's very nice. If it did what I need I'd use it. I use it a lot personally now. On 30 May 2013 18:00, <[email protected]> wrote: > Send caret-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://brainvis.wustl.edu/mailman/listinfo/caret-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of caret-users digest..." > > Today's Topics: > > 1. Re: label volume mapping (Donna Dierker) > > > ---------- Forwarded message ---------- > From: Donna Dierker <[email protected]> > To: "Caret, SureFit, and SuMS software users" < > [email protected]> > Cc: > Date: Thu, 30 May 2013 08:31:14 -0500 > Subject: Re: [caret-users] label volume mapping > This post, along with Matt's earlier one triggered the important point > that the CIFTI file format is coming along very fast -- progressing quickly > from "nice idea in theory" to "David and Matt are using this all the time." > It's covers a lot of data types: > > > http://www.nitrc.org/plugins/mwiki/index.php/cifti:ConnectivityMatrixFileFormats > > While I still tend to be very caret5-centric, because I'm wrapping up a > multi-year project started in caret5, I know I need to start understanding > this stuff. > > > On May 29, 2013, at 10:40 PM, Colin Reveley <[email protected]> wrote: > > > thanks. > > > > It didn't occur to me to just open it. > > > > Sure enough the caret extensions are just text in there. > > > > That should provide a really simple solution, as long as the behavior is > predictable. > > > > Each user gets a novel volume. We can't keep header properties like this > between operations on the data. So it has to go through CARET first if we > want process it in that easy way, or else we have to build a header > ourselves which I'd feel safer with. > > > > But it looks nice thank you very much. I guess if we find we can't keep > it consistent in testing we'll maybe follow up. > > > > thanks again > > > > Colin > > > > > > On 30 May 2013 02:52, Colin Reveley <[email protected]> wrote: > > Hi - > > > > re: wb_command -volume-label-import > > > > what it appears to do is just vaporize the header. > > > > However, much could have gone wrong. The input volume is wholly > constructed in software (mainly imageJ and inhouse C) and is probably weird > (although it's been saved in CARET before trying to run this. I tried both > ways. header below has been through caret). and maybe I've got the format > of the label list wrong. > > > > I note that the output of the command is a float volume. I was pretty > sure paint volumes had to be unsigned char. I tried both float and uchar as > inputs anyway. > > > > my input header looks something like this. and my label file looks like > what follows under the header > > > > thanks for advice > > > > I appreciate it may not work. That is ok. It was a bit too good to be > true anyway. it doesn't dump core, or give an error (or any info at all). > it just thinks for a bit, removes most info from the header and outputs a > float volume > > > > actually there's probably a debug swtich. I'll look at that now. > > > > thanks, > > > > Colin > > > > sizeof_hdr: 348 > > data_type: > > db_name: > > extents: 0 > > session_error: 0 > > regular: r > > dim_info: 0 > > dim: 3 137 347 245 1 1 0 0 > > intent_p1: 0.000 > > intent_p2: 0.000 > > intent_p3: 0.000 > > intent_code: 1002 > > datatype: 2 > > bitpix: 0 > > slice_start: 0 > > pixdim: 1.000 0.250 0.250 0.250 0.000 0.000 0.000 0.000 > > vox_offset: 41760.000 > > scl_slope: 1.000 > > scl_inter: 0.000 > > slice_end: 0 > > slice_code: 0 > > xyzt_units: 0 > > cal_max: 0.000 > > cal_min: 0.000 > > slice_duration: 0.000 > > toffset: 0.000 > > glmax: 0 > > glmin: 0 > > description: > > aux_file: > > qform_code: 3 > > sform_code: 3 > > quatern_b: 0.000 > > quatern_c: 0.000 > > quatern_d: 0.000 > > qoffset_x: -2.750 > > qoffset_y: -48.750 > > qoffset_z: -26.500 > > srow_x: 0.250 0.000 0.000 -2.750 > > srow_y: 0.000 0.250 0.000 -48.750 > > srow_z: 0.000 0.000 0.250 -26.500 > > intent_name: > > magic: n+1 > > > > Intent Name: NIFTI_INTENT_LABEL > > Intent Parameters:Label index > > > > First Voxel XYZ (method 1): 0.000, 0.000, 0.000 > > Spacing: 0.250, 0.250, 0.250 > > > > QFORM: NIFTI_XFORM_TALAIRACH > > 1.000 0.000 0.000 0.000 > > 0.000 1.000 0.000 0.000 > > 0.000 0.000 1.000 0.000 > > 0.000 0.000 0.000 1.000 > > Orientation: Left to Right, Posterior to Anterior, Inferior to > Superior > > First Voxel XYZ (Method 2): -2.750, -48.750, -26.500 > > Spacing: 0.250, 0.250, 0.250 > > > > SFORM: NIFTI_XFORM_TALAIRACH > > 0.250 0.000 0.000 -2.750 > > 0.000 0.250 0.000 -48.750 > > 0.000 0.000 0.250 -26.500 > > 0.000 0.000 0.000 1.000 > > Orientation: Left to Right, Posterior to Anterior, Inferior to > Superior > > First Voxel XYZ (Method 3): -2.750, -48.750, -26.500 > > Spacing: 0.250, 0.250, 0.250 > > > > Data Type: NIFTI_TYPE_UINT8 > > > > Space Units: NIFTI_UNITS_UNKNOWN > > Time Units: NIFTI_UNITS_UNKNOWN > > > > Extension 1 before byte swap > > Size: 22816 > > Code: 4 > > Extension 1 after byte swap > > Size: 22816 > > Code: 4 > > AFNI extension: > > Extension 2 before byte swap > > Size: 18592 > > Code: 30 > > Extension 2 after byte swap > > Size: 18592 > > Code: 30 > > > > > > --- > > > > F3 > > 107 50 5 240 255 > > 8Bm > > 77 50 10 5 255 > > ABmc > > 31 50 10 155 255 > > Ig > > 51 50 30 115 255 > > G > > 161 50 30 140 255 > > Ld > > 119 50 40 45 255 > > LIPv > > 20 50 40 120 255 > > Ia > > 87 50 55 15 255 > > > > > > > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >
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