You can tell the order from the orientation string. For example PIL means coronal (P-A), axial(I-S) and sagittal (L-R).

Ruopeng

On Aug 29, 2019, at 12:12 PM, Hoke, Harris <hhoke@g.harvard.edu> wrote:

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 <hhoke@g.harvard.edu> 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 <rpwang@nmr.mgh.harvard.edu> 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 <hhoke@g.harvard.edu> 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 <hhoke@g.harvard.edu> 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
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer