Re: freeview -ss orientation inconsistencies - Freesurfer

1 Jul 2025

      External Email - Use Caution
Hi Ruopeng,
I have tried:
freesurfer/7.3.2
freesurfer/8.1
freesurfer/dev-20250521-bad34cc
The command is (the mirroring occasionally occurs in the axial and coronal
views):
if ! [ -f "${OUTDIR}/pngs/${elec1label}_electrode_parc_T1_sag.png" ]; then
freeview -v ${t1img}:colormap=grayscale:grayscale=25,99.5:percentile=yes
$OUTDIR/wb_parcellations_upsample_${klevels[0]}.nii.gz:colormap=lut:lut=$colors
$OUTDIR/wb_parcellations_upsample_${klevels[1]}.nii.gz:colormap=lut:lut=$colors
$OUTDIR/wb_parcellations_upsample_${klevels[2]}.nii.gz:colormap=lut:lut=$colors
${elec1file}:colormap=binary:opacity=0.85 -viewport sagittal -viewsize 280
285 -slice $x $y $z -cc -zoom 2 -ss
${OUTDIR}/pngs/${elec1label}_electrode_parc_T1_sag.png
fi
if ! [ -f "${OUTDIR}/pngs/${elec1label}_electrode_parc_T1_ax.png" ]; then
freeview -v ${t1img}:colormap=grayscale:grayscale=25,99.5:percentile=yes
$OUTDIR/wb_parcellations_upsample_${klevels[0]}.nii.gz:colormap=lut:lut=$colors
$OUTDIR/wb_parcellations_upsample_${klevels[1]}.nii.gz:colormap=lut:lut=$colors
$OUTDIR/wb_parcellations_upsample_${klevels[2]}.nii.gz:colormap=lut:lut=$colors
${elec1file}:colormap=binary:opacity=0.85 -viewport axial -viewsize 280 285
-slice $x $y $z -cc -zoom 2 -ss
${OUTDIR}/pngs/${elec1label}_electrode_parc_T1_ax.png
fi
if ! [ -f "${OUTDIR}/pngs/${elec1label}_electrode_parc_T1_cor.png" ]; then
freeview -v ${t1img}:colormap=grayscale:grayscale=25,99.5:percentile=yes
$OUTDIR/wb_parcellations_upsample_${klevels[0]}.nii.gz:colormap=lut:lut=$colors
$OUTDIR/wb_parcellations_upsample_${klevels[1]}.nii.gz:colormap=lut:lut=$colors
$OUTDIR/wb_parcellations_upsample_${klevels[2]}.nii.gz:colormap=lut:lut=$colors
${elec1file}:colormap=binary:opacity=0.85 -viewport coronal -viewsize 280
285 -slice $x $y $z -cc -zoom 2 -ss
${OUTDIR}/pngs/${elec1label}_electrode_parc_T1_cor.png
fi
*Ania Holubecki*
On Tue, Jul 1, 2025 at 12:33 PM freesurfer-request@nmr.mgh.harvard.edu
wrote:
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Today's Topics:

Re: freeview -ss orientation inconsistencies (Wang, Ruopeng)
(Wang, Ruopeng)

Message: 1
Date: Tue, 1 Jul 2025 17:32:35 +0000
From: "Wang, Ruopeng" RWANG4@mgh.harvard.edu
Subject: [Freesurfer] Re: freeview -ss orientation inconsistencies
        (Wang, Ruopeng)
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Message-ID: 6145982B-4844-456B-B96E-A1AA0BA3B874@mgh.harvard.edu
Content-Type: multipart/alternative;
        boundary="_000_6145982B4844456BB96EA1AA0BA3B874mghharvardedu_"
Would it be possible to share the command that produced the error? Also,
can you confirm what version of freeview it was? Was it 8.1 or the latest
dev?
Ruopeng
On Jul 1, 2025, at 11:37 AM, Ania Holubecki <ania.holubecki@gmail.com
mailto:ania.holubecki@gmail.com> wrote:
    External Email - Use Caution

Hi,
I spoke too soon - using the developmental version of freesurfer did not
work. A reminder of the issue below:
I have a script that utilizes the -ss flag on the freeview command to take
axial, sagittal, and coronal screenshots iteratively. I have multiple
images loaded into freeview at a time for each screenshot, and most of the
loaded images are the same across all the screenshots, except for one
spherical ROI that is only the same within a given sagittal/axial/coronal
set.
I have been encountering a problem where some of the screenshots are
horizontally mirrored (left-hemisphere/right hemisphere flipped) in
comparison to the rest of the images. This happens the most often for the
coronal screenshot, but has also occurred for the axial screenshot. The
spherical ROIs for which this mirroring occurs is not consistent - every
time I run the script, it's a different set that's horizontally mirrored.
Ania Holubecki
On Tue, Jun 3, 2025 at 11:10 AM Ania Holubecki <ania.holubecki@gmail.com
mailto:ania.holubecki@gmail.com> wrote:
Hi Ruopeng,
I tried the two latest versions installed on our computing cluster:
freesurfer/7.3.2
freesurfer/8.1
The most recent development version worked - thanks so much!
Ania Holubecki
On Thu, May 15, 2025 at 9:10 AM <freesurfer-request@nmr.mgh.harvard.edu
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Today's Topics:

freeview -ss orientation inconsistencies (Ania Holubecki)
Re: freeview -ss orientation inconsistencies (Wang, Ruopeng)
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(Iglesias Gonzalez, Juan E.)
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and Buckner 2011 (Douglas N. Greve)
Re: Question on Samseg Basic and Samseg for MS lesions
(Douglas N. Greve)

Message: 1
Date: Tue, 13 May 2025 15:23:26 -0500
From: Ania Holubecki <ania.holubecki@gmail.commailto:
ania.holubecki@gmail.com>
Subject: [Freesurfer] freeview -ss orientation inconsistencies
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
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Hi,
I have a script that utilizes the -ss flag on the freeview command to take
axial, sagittal, and coronal screenshots iteratively. I have multiple
images loaded into freeview at a time for each screenshot, and most of the
loaded images are the same across all the screenshots, except for one
spherical ROI that is only the same within a given sagittal/axial/coronal
set.
I have been encountering a problem where some of the screenshots are
horizontally mirrored (left-hemisphere/right hemisphere flipped) in
comparison to the rest of the images. This happens the most often for the
coronal screenshot, but has also occurred for the axial screenshot. The
spherical ROIs for which this mirroring occurs is not consistent - every
time I run the script, it's a different set that's horizontally mirrored.
Has anyone encountered this issue and has a way to guarantee the
orientation of the screenshot? Any tips are greatly appreciated!
Best,
*Ania Holubecki*