OK, try running mri_label2vol --seg chuman_1_do.mgz --temp orig.mgz --regheader chuman_1_do.mgz --o chuman_1_do.conf.mgz Then load chuman_1_do.conf.mgz as a segmentation. doug
Anthony Dick wrote: > Sorry Doug--it seems I misspoke. > > The following works, as you predicted, and these are the files that > align in AFNI (had to convert chuman_1_do to .mgz): > > adick% tkmedit 01_do orig.mgz -overlay chuman_1_do.mgz -fthresh .5 > INFO: No registration type specified for overlay, assuming identity. > tkmedit: Trying to open ./chuman_1_do.dat > Reading /Applications/freesurfer/tktools/tkm_common.tcl > Reading /Applications/freesurfer/tktools/tkm_wrappers.tcl > Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl > Reading /Applications/freesurfer/tktools/tkUtils.tcl > > Loading the same file as a segmentation does not. This might give you > some different ideas. > > Anthony > > On 1/26/12 11:36 AM, Douglas N Greve wrote: >> What are the two things that align in AFNI? >> doug >> >> Anthony Dick wrote: >>> Hello Doug, >>> >>> Prof. Diedrichsen kindly shared the original brains he manually >>> parcellated that were used to create his probabilistic atlas >>> (http://www.icn.ucl.ac.uk/motorcontrol/imaging/propatlas.htm; see >>> the 2009 Neuroimage paper). So each brain had an anatomy and a >>> cerebellar parcellation, and these align in AFNI so I assumed there >>> wasn't anything special about the parcellation process. However, I >>> don't know the exact process he used to create them. So you're >>> right, there is likely some intermediate step that I am missing. My >>> goal here is to use them to create a training atlas for Freesurfer, >>> which (if it works) we would like to share with the community. So >>> all of your help here is appreciated! >>> >>> Here's where I am: The tkmedit command doesn't work (the cerebellum >>> ends up in the same place--see image). Here was the output--is there >>> a way to specify a registration file? Any ideas? Would knowing the >>> intermediate steps help, or is there a way for me to try to >>> troubleshoot this without bugging Prof. Diedrichsen? >>> >>> adick% tkmedit 01_do orig.mgz -overlay chuman_1_do_shft.nii -fthresh .5 >>> INFO: No registration type specified for overlay, assuming identity. >>> tkmedit: Trying to open ./chuman_1_do_shft.dat >>> Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl >>> Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl >>> Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl >>> Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl >>> >>> Thanks much for all the help so far, >>> >>> Anthony >>> >>> On 1/17/12 12:57 PM, Douglas N Greve wrote: >>>> >>>> Hi Anthony, there's something I don't understand here. You said >>>> that ahuman_1_do_shft.nii was used as input to to create >>>> chuman_1_do_shft.nii, but they have different sizes, so something >>>> else is happening along the way, and this is causing the problem. >>>> One thing you can try first is to load chuman_1_do_shft.nii as an >>>> overlay instead of a segmentation. The segmentations much be in >>>> voxel-for-voxel alignment or things will get messed up, so >>>> >>>> tkmedit 01_do orig.mgz -overlay chuman_1_do_shft.nii -fthresh .5 >>>> >>>> If this comes up in alignment, then Ithink I know where to go from >>>> there. >>>> doug >>>> >>>> >>>> Anthony Dick wrote: >>>>> I ran mri_info--results at the bottom. I also ran mri_convert, but >>>>> it did not save an output file (summary below). >>>>> >>>>> The tkmedit command is: tkmedit 01_do orig.mgz, and then File > >>>>> Load Segmentation to load chuman_1_do_shft.nii >>>>> >>>>> I am attaching images of the alignment in AFNI. It does not align >>>>> in mricron--I misspoke previously. >>>>> >>>>> adick% mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz >>>>> chuman_1_do_shft_new.nii >>>>> mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz >>>>> chuman_1_do_shft_new.nii >>>>> reading info from rawavg.mgz... >>>>> $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ >>>>> reading from chuman_1_do_shft.nii... >>>>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >>>>> volume sizes do not match >>>>> >>>>> chuman_1_do_shft.nii: (width, height, depth, frames) = (145, 136, >>>>> 102, 1) >>>>> >>>>> rawavg.mgz: (width, height, depth, frames) = (160, 256, 256, 1) >>>>> adick% >>>>> >>>>> >>>>> >>>>> Volume information for chuman_1_do_shft.nii >>>>> type: nii >>>>> dimensions: 145 x 136 x 102 >>>>> voxel sizes: 0.8083, 0.8083, 0.8083 >>>>> type: SHORT (4) >>>>> fov: 117.210 >>>>> dof: 0 >>>>> xstart: -58.6, xend: -58.6 >>>>> ystart: -55.0, yend: -55.0 >>>>> zstart: -41.2, zend: -41.2 >>>>> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip >>>>> angle: 0.00 degrees >>>>> nframes: 1 >>>>> PhEncDir: UNKNOWN >>>>> ras xform present >>>>> xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, >>>>> c_r = 6.6335 >>>>> : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, >>>>> c_a = 59.5238 >>>>> : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, >>>>> c_s = -0.5958 >>>>> Orientation : LPS >>>>> Primary Slice Direction: axial >>>>> >>>>> voxel to ras transform: >>>>> -0.8083 -0.0000 -0.0000 65.2384 >>>>> -0.0000 -0.8083 -0.0000 114.4912 >>>>> 0.0000 0.0000 0.8083 -41.8213 >>>>> 0.0000 0.0000 0.0000 1.0000 >>>>> >>>>> voxel-to-ras determinant 0.528187 >>>>> >>>>> ras to voxel transform: >>>>> -1.2371 0.0000 0.0000 80.7063 >>>>> 0.0000 -1.2371 0.0000 141.6368 >>>>> -0.0000 -0.0000 1.2371 51.7371 >>>>> 0.0000 0.0000 0.0000 1.0000 >>>>> >>>>> >>>>> >>>>>> >>>>> Volume information for orig.nii >>>>> type: nii >>>>> dimensions: 256 x 256 x 256 >>>>> voxel sizes: 1.0000, 1.0000, 1.0000 >>>>> type: UCHAR (0) >>>>> fov: 256.000 >>>>> dof: 0 >>>>> xstart: -128.0, xend: -128.0 >>>>> ystart: -128.0, yend: -128.0 >>>>> zstart: -128.0, zend: -128.0 >>>>> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip >>>>> angle: 0.00 degrees >>>>> nframes: 1 >>>>> PhEncDir: UNKNOWN >>>>> ras xform present >>>>> xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, >>>>> c_r = 6.5377 >>>>> : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, >>>>> c_a = 60.4280 >>>>> : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, >>>>> c_s = -1.5000 >>>>> Orientation : LIA >>>>> Primary Slice Direction: coronal >>>>> >>>>> voxel to ras transform: >>>>> -1.0000 0.0000 0.0000 134.5377 >>>>> 0.0000 0.0000 1.0000 -67.5720 >>>>> 0.0000 -1.0000 0.0000 126.5000 >>>>> 0.0000 0.0000 0.0000 1.0000 >>>>> >>>>> voxel-to-ras determinant -1 >>>>> >>>>> ras to voxel transform: >>>>> -1.0000 0.0000 0.0000 134.5377 >>>>> -0.0000 -0.0000 -1.0000 126.5000 >>>>> -0.0000 1.0000 -0.0000 67.5720 >>>>> 0.0000 0.0000 0.0000 1.0000 >>>>> >>>>> >>>>> >>>>>> >>>>> Volume information for rawavg.mgz >>>>> type: MGH >>>>> dimensions: 160 x 256 x 256 >>>>> voxel sizes: 1.0000, 1.0000, 1.0000 >>>>> type: FLOAT (3) >>>>> fov: 256.000 >>>>> dof: 0 >>>>> xstart: -80.0, xend: 80.0 >>>>> ystart: -128.0, yend: 128.0 >>>>> zstart: -128.0, zend: 128.0 >>>>> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip >>>>> angle: 0.00 degrees >>>>> nframes: 1 >>>>> PhEncDir: UNKNOWN >>>>> ras xform present >>>>> xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, >>>>> c_r = 6.5377 >>>>> : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, >>>>> c_a = 60.4280 >>>>> : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, >>>>> c_s = -1.5000 >>>>> >>>>> talairach xfm : >>>>> Orientation : LPS >>>>> Primary Slice Direction: axial >>>>> >>>>> voxel to ras transform: >>>>> -1.0000 0.0000 0.0000 86.5377 >>>>> 0.0000 -1.0000 0.0000 188.4280 >>>>> 0.0000 0.0000 1.0000 -129.5000 >>>>> 0.0000 0.0000 0.0000 1.0000 >>>>> >>>>> voxel-to-ras determinant 1 >>>>> >>>>> ras to voxel transform: >>>>> -1.0000 0.0000 0.0000 86.5377 >>>>> 0.0000 -1.0000 0.0000 188.4280 >>>>> -0.0000 -0.0000 1.0000 129.5000 >>>>> 0.0000 0.0000 0.0000 1.0000 >>>>> >>>>> >>>> >>>>> Volume information for ahuman_1_do+orig.BRIK >>>>> type: brik >>>>> dimensions: 160 x 256 x 256 >>>>> voxel sizes: 1.0000, 1.0000, 1.0000 >>>>> type: FLOAT (3) >>>>> fov: 256.000 >>>>> dof: 0 >>>>> xstart: -80.0, xend: 80.0 >>>>> ystart: -128.0, yend: 128.0 >>>>> zstart: -128.0, zend: 128.0 >>>>> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip >>>>> angle: 0.00 degrees >>>>> nframes: 1 >>>>> PhEncDir: UNKNOWN >>>>> ras xform present >>>>> xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, >>>>> c_r = 6.5377 >>>>> : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, >>>>> c_a = 60.4280 >>>>> : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, >>>>> c_s = -1.5000 >>>>> Orientation : LPS >>>>> Primary Slice Direction: axial >>>>> >>>>> voxel to ras transform: >>>>> -1.0000 0.0000 0.0000 86.5377 >>>>> 0.0000 -1.0000 0.0000 188.4280 >>>>> 0.0000 0.0000 1.0000 -129.5000 >>>>> 0.0000 0.0000 0.0000 1.0000 >>>>> >>>>> voxel-to-ras determinant 1 >>>>> >>>>> ras to voxel transform: >>>>> -1.0000 0.0000 0.0000 86.5377 >>>>> 0.0000 -1.0000 0.0000 188.4280 >>>>> -0.0000 -0.0000 1.0000 129.5000 >>>>> 0.0000 0.0000 0.0000 1.0000 >>>>> >>>>> >>>>> On 1/13/12 5:14 PM, Douglas N Greve wrote: >>>>>> Which volumes align in AFNI? The orig.mgz and >>>>>> ahuman_1_do_shft.nii? I'm guessing not. Try this instead: >>>>>> >>>>>> mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz >>>>>> chuman_1_do_shft_new.nii >>>>>> >>>>>> and see if you get alignment. If this does not work, make sure to >>>>>> send us the tkmedit command too. >>>>>> doug >>>>>> >>>>>> Anthony Dick wrote: >>>>>>> It was created from the ahuman_1_do_shft.nii volume, which was >>>>>>> what was input to recon-all in Freesurfer. And these volumes >>>>>>> (the overlay and underlay) align in other viewers (e.g., AFNI >>>>>>> and mricron). >>>>>>> >>>>>>> On 1/13/12 2:40 PM, Douglas N Greve wrote: >>>>>>>> What volume was human_1_do_shft.nii created from? >>>>>>>> >>>>>>>> Anthony Dick wrote: >>>>>>>>> Here is the command, in case I didn't run it right. >>>>>>>>> >>>>>>>>> adick% mri_convert chuman_1_do_shft.nii --in_like orig.mgz >>>>>>>>> chuman_1_do_shft_new.nii >>>>>>>>> mri_convert chuman_1_do_shft.nii --in_like orig.mgz >>>>>>>>> chuman_1_do_shft_new.nii >>>>>>>>> reading info from orig.mgz... >>>>>>>>> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >>>>>>>>> reading from chuman_1_do_shft.nii... >>>>>>>>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >>>>>>>>> volume sizes do not match >>>>>>>>> >>>>>>>>> chuman_1_do_shft.nii: (width, height, depth, frames) = (145, >>>>>>>>> 136, 102, 1) >>>>>>>>> >>>>>>>>> orig.mgz: (width, height, depth, frames) = (256, 256, 256, 1) >>>>>>>>> adick% >>>>>>>>> >>>>>>>>> >>>>>>>>> An image of the tkmedit output is attached. Thanks for any >>>>>>>>> suggestions. >>>>>>>>> >>>>>>>>> Anthony >>>>>>>>> >>>>>>>>> >>>>>>>>> On 1/13/12 2:15 PM, Douglas N Greve wrote: >>>>>>>>>> Try changing the header information in your parcellation, >>>>>>>>>> something like >>>>>>>>>> mri_convert yourparcellation.mgh --in_like orig.mgz >>>>>>>>>> yourparcellation.new.mgh >>>>>>>>>> doug >>>>>>>>>> >>>>>>>>>> Anthony Dick wrote: >>>>>>>>>>> Good question. The parcellation is created outside of >>>>>>>>>>> Freesurfer (the data were shared from another lab and I >>>>>>>>>>> don't know which program they used to create the >>>>>>>>>>> parcellation; of course I can find out if this would be >>>>>>>>>>> helpful). At any rate, the anatomy and parcellation align >>>>>>>>>>> when viewed in AFNI. >>>>>>>>>>> >>>>>>>>>>> Anthony >>>>>>>>>>> >>>>>>>>>>> On 1/13/12 2:11 PM, Douglas N Greve wrote: >>>>>>>>>>>> Hi Anthony, how are you creating the parcellation? Are you >>>>>>>>>>>> generating it off the orig.mgz? >>>>>>>>>>>> doug >>>>>>>>>>>> >>>>>>>>>>>> Anthony Dick wrote: >>>>>>>>>>>>> Hello, >>>>>>>>>>>>> >>>>>>>>>>>>> I am trying to train a cerebellar atlas based on 20 >>>>>>>>>>>>> manually parcellated cerebellums. I have run the >>>>>>>>>>>>> anatomical through freesurfer. When I try to load the >>>>>>>>>>>>> overlay (parcellation) in tkmedit, the underlay (e.g., >>>>>>>>>>>>> orig.mgz, T1.mgz) and the overlay (the parcellation) are >>>>>>>>>>>>> no longer in alignment. >>>>>>>>>>>>> >>>>>>>>>>>>> However, loaded in AFNI the underlay and overlay of course >>>>>>>>>>>>> align. Is there a quick fix to get them in alignment? >>>>>>>>>>>>> >>>>>>>>>>>>> Anthony >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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