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.
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.
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
I tried switching the coordinate triplets for the sagittal and coronal viewport commands, and it looks like it's working again! Thank you! 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
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 192voxel 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: 3.000000ras 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 1.0000voxel-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 1.0000On 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
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 mailto: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 mailto: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 mailto:hhoke@g.harvard.edu> wrote:
correction: the output of uname -a should be Linux ncfood02.rc.fas.harvard.edu http://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 mailto: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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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@nmr.mgh.harvard.edu
-
Hoke, Harris -
Ruopeng Wang