I just needed to modify the last set of coordinates for sagittal, and the first for coronal.
How can I tell which coordinate I should modify -- is it the Primary Slice Direction or the PIL orientation? freeview -v SUB/mri/orig/001.mgz -layout 1 -cc -nocursor -viewport sagittal -slice 127 127 80 -ss ~/snaps/T1_sag_1.jpg -noquit -viewport sagittal -slice 127 127 90 -ss ~/snaps/T1_sag_2.jpg -noquit -viewport axial -slice 127 80 127 -ss ~/snaps/T1_ax_1.jpg -noquit -viewport axial -slice 127 90 127 -ss ~/snaps/T1_ax_2.jpg -noquit -viewport coronal -slice 80 127 127 -ss ~/snaps/T1_cor_1.jpg -noquit -viewport coronal -slice 90 127 127 -ss ~/snaps/T1_cor_2.jpg -noquit -quit On Thu, Aug 29, 2019 at 10:45 AM Hoke, Harris <[email protected]> wrote: > Fixed, thank you so much! > > Here's that output: > > type: MGH > > dimensions: 240 x 256 x 192 > > voxel sizes: 1.000000, 1.000000, 1.000000 > > type: SHORT (4) > > fov: 256.000 > > dof: 0 > > xstart: -120.0, xend: 120.0 > > ystart: -128.0, yend: 128.0 > > zstart: -96.0, zend: 96.0 > > TR: 2300.00 msec, TE: 2.96 msec, TI: 900.00 msec, flip angle: > 9.00 degrees > > nframes: 1 > > PhEncDir: ROW > > FieldStrength: 3.000000 > > ras xform present > > xform info: x_r = 0.0468, y_r = -0.0119, z_r = -0.9988, c_r = > -0.0820 > > : x_a = -0.9976, y_a = 0.0510, z_a = -0.0474, c_a = > 10.6233 > > : x_s = -0.0515, y_s = -0.9986, z_s = 0.0095, c_s = > 20.6047 > > > talairach xfm : > > Orientation : PIL > > Primary Slice Direction: sagittal > > > voxel to ras transform: > > 0.0468 -0.0119 -0.9988 91.7159 > > -0.9976 0.0510 -0.0474 128.3579 > > -0.0515 -0.9986 0.0095 153.6901 > > 0.0000 0.0000 0.0000 1.0000 > > > voxel-to-ras determinant -1 > > > ras to voxel transform: > > 0.0468 -0.9976 -0.0515 131.6617 > > -0.0119 0.0510 -0.9986 148.0342 > > -0.9988 -0.0474 0.0095 96.2251 > > -0.0000 -0.0000 -0.0000 1.0000 > > On Thu, Aug 29, 2019 at 9:55 AM Ruopeng Wang <[email protected]> > wrote: > >> Hi Harris, >> >> The slice option tales arguments as the original col, row and slice. So >> they are not necessarily in Sagittal, coronal and axial order, depending on >> the original orientation of the volume. If you run mri_info on the volume, >> what does the orientation show? >> >> Best, >> Ruopeng >> >> On Aug 28, 2019, at 7:21 PM, Hoke, Harris <[email protected]> wrote: >> >> correction: >> the output of uname -a should be >> Linux ncfood02.rc.fas.harvard.edu 3.10.0-957.12.1.el7.x86_64 #1 SMP Mon >> Apr 29 14:59:59 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux >> Sorry for the confusion. >> >> >> On Wed, Aug 28, 2019 at 7:18 PM Hoke, Harris <[email protected]> wrote: >> >>> Freeview does not update in the viewer window to the correct slice >>> position when calling on viewport. This means instead of taking snapshots >>> of N slices of the brain from N specified slice coordinates, it takes the >>> same snapshot over and over again. >>> Originally, we found a workaround by disabling qt_setup in the freeview >>> tcsh script: >>> #source $FREESURFER_HOME/bin/qt_setup. >>> After this, it worked perfectly. Since then, it has stopped working >>> well. >>> >>> The error occurs for saggital and coronal views. (Axial works fine, for >>> some reason). I am using the stable release of freesurfer 6.0.0. The >>> problem still happens if I interleave axial/coronal/saggital viewport >>> commands, instead of running them together as below. The problem also >>> occurs using the development version of freesurfer from august 27th, >>> CentOS7 build (but only for sagittal and coronal; Axial works fine). >>> >>> freeview -cmd minimalcmd.txt >>> >>> minimalcmd.txt: >>> >>> freeview -v SUBDIR/mri/orig/001.mgz -layout 1 -cc -nocursor >>> >>> >>> -viewport sagittal -slice 80 127 127 -ss OUTDIR/T1_sag_1.jpg -noquit >>> >>> -viewport sagittal -slice 90 127 127 -ss OUTDIR/T1_sag_2.jpg -noquit >>> >>> >>> -viewport axial -slice 127 80 127 -ss OUTDIR/T1_ax_1.jpg -noquit >>> >>> -viewport axial -slice 127 90 127 -ss OUTDIR/T1_ax_2.jpg -noquit >>> >>> >>> -viewport coronal -slice 127 127 80 -ss OUTDIR/T1_cor_1.jpg -noquit >>> >>> -viewport coronal -slice 127 127 90 -ss OUTDIR/T1_cor_2.jpg -noquit >>> >>> >>> -quit >>> >>> In case it's useful: >>> >>> uname -a >>> >>> Linux ncfservice02 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7 19:03:37 >>> UTC 2018 x86_64 x86_64 x86_64 GNU/Linux >>> >>> >>> I'm unsure what else I can try or what other information I can provide. >>> Please let me know. >>> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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