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.
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