Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30129 discussions

Recon-all clinical vs. FS version 8.0.0
by Stefanie Bradley 02 Jul '25

02 Jul '25

External Email - Use Caution Hi there, I am analyzing some pediatric brains with clinical pathology, and I was wondering if I would expect a difference in the reconstructions from regular recon-all (Freesurfer version 8.0.0) vs. recon-all clinical, since they both use SynthSeg from what I understand? Thanks, Stefanie

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Re: Freesurfer Digest, Vol 257, Issue 14
by Sunniva Fenn-Moltu 02 Jul '25

02 Jul '25

External Email - Use Caution Please unsubscribe me! Dr Sunniva Fenn-Moltu (she/her) Postdoctoral Research Associate Department of Forensic and Neurodevelopmental Science Institute of Psychiatry, Psychology & Neuroscience King’s College London 16 De Crespigny Park, Denmark Hill, London, SE5 8AF ________________________________ From: freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: 02 July 2025 15:23 To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 257, Issue 14 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Recon-all clinical vs. FS version 8.0.0 (Iglesias Gonzalez, Juan E.) ---------------------------------------------------------------------- Message: 1 Date: Wed, 2 Jul 2025 14:23:09 +0000 From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Subject: [Freesurfer] Re: Recon-all clinical vs. FS version 8.0.0 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <PH0PR04MB83888D5F6E0D1EB14A99250EFD40A(a)PH0PR04MB8388.nam prd04.prod.outlook.com> Content-Type: multipart/alternative; boundary="_000_PH0PR04MB83888D 5F6E0D1EB14A99250EFD40APH0PR04MB8388namp_" Oh, I see. They are fairly different in the way that they try to place cortical surfaces. Recon-all uses T1 intensities directly, and only works with high-resolution near-isotropic T1w scans. Recon-all-clinical uses machine learning and is compatible with scans of any contrast and resolution, BUT is less accurate than recon-all if you actually do have 1mm T1 data. So, I would try recon-all first. Cheers, /Eugenio -- Juan Eugenio Iglesias https://secure-web.cisco.com/1K25c8GgtPaI1iQbFYGnNILxny8Ubj0djw1dmJIKkZgr4F…<http://secure-web.cisco.com/19dk633J8cDfEYmJaTrtHSBYKUttUKjsNwNDCuKAZXv-UO6…> From: Stefanie Bradley <stefanie.bradley(a)mail.utoronto.ca> Date: Wednesday, July 2, 2025 at 09:24 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Re: Recon-all clinical vs. FS version 8.0.0 External Email - Use Caution Hi Eugenio, Thanks for your response. I was more wondering if the standard recon-all pipelines (v8.0) are the same for recon-all clinical, since it seems like recon-all in version 8 uses Synthseg by default. My population is children aged 4-6 years old with cerebral palsy. The T1-weighted scans are MPRAGE, 0.8mm isotropic. Thanks, Stefanie ________________________________ From: Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Sent: Tuesday, July 1, 2025 8:35 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Re: Recon-all clinical vs. FS version 8.0.0 Dear Stefanie, What type of pathology are we discussing? What ages? What MRI sequence and resolution? Cheers, /Eugenio -- Juan Eugenio Iglesias https://secure-web.cisco.com/1HDqa2YX4Xwt8w_hiXJZ0lyV8Spi72Rzf-J41A6uWqy-QZ…<http://secure-web.cisco.com/19dk633J8cDfEYmJaTrtHSBYKUttUKjsNwNDCuKAZXv-UO6…> From: Stefanie Bradley <stefanie.bradley(a)mail.utoronto.ca> Date: Tuesday, July 1, 2025 at 5:49 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Recon-all clinical vs. FS version 8.0.0 External Email - Use Caution Hi there, I am analyzing some pediatric brains with clinical pathology, and I was wondering if I would expect a difference in the reconstructions from regular recon-all (Freesurfer version 8.0.0) vs. recon-all clinical, since they both use SynthSeg from what I understand? Thanks, Stefanie -------------- next part -------------- A message part incompatible with plain text digests has been removed ... 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Issue with TRACULA - failure Orient LAS
by Gabriella Monopoli 02 Jul '25

02 Jul '25

External Email - Use Caution Hi everyone, I hope this email finds you well. I'm trying to run TRACULA on a subject using FreeSurfer 8 (working on Ubuntu 22). However, when launching the first step of TRACULA (-prep), I encountered some issues with the creation of the dwi.bvecs file: after the LAS orientation, the dwi.bvecs file is empty. As a result, the symbolic links created afterward are incorrect, and the subsequent dtifit step produces empty files. After some attempts, I realized that the problem is caused by the fact that the orientLAS command fails, thus creating empty files. I wonder if anyone has ever encountered the same type of error and if they could help me solve it. I've attached the log file, the script, and the configuration file I used to this email. Best regards, Gabriella Monopoli

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Re: Updates/bug fixes available for the 8.0.0 release
by fsbuild 01 Jul '25

01 Jul '25

External Email - Use Caution  The freesurfer 8.0.0 patch archive is back online with a new update, and the script to download and run is now called fs800_updates.sh instead of fs8_updates.sh.  Please delete any copy of the old fs8_updates.sh script and download and use the fs800_updates.sh script in all of the example commands previously listed in the thread. - R.

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Measuring longitudinal changes in brain volume using SynthSeg
by Marco Ganzetti 01 Jul '25

01 Jul '25

External Email - Use Caution Does SynthSeg offer any functionality for estimating longitudinal changes in segmented brain volumes beyond simply subtracting values from two time points? Marco

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Re: freeview -ss orientation inconsistencies
by fsbuild 01 Jul '25

01 Jul '25

External Email - Use Caution We usually do not recommend using development builds instead of officially released builds with numbers, e.g., 8.0.0, because development builds can be unstable and may not entirely work - or work the same way - depending upon the day you happen to download a dev build.  However If you can try the latest development build from under,https://secure-web.cisco.com/1jq3XGGcHpTiWr_hdA87MKZEwqIqc5TaHaDuWhZ4… … which will echo a July 01 identifier (20250701) when you source the freesurfer environment,freesurfer-<os_arch>-dev-20250701-f62f34b … then that would help us to look at making a fix on top of the most recent code changes if your issue persists in that current dev build. - R.

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Re: freeview -ss orientation inconsistencies
by Ania Holubecki 01 Jul '25

01 Jul '25

External Email - Use Caution Hi, To clarify, I also tried a development build around the end of May when I first posted about this issue (freesurfer/dev-20250521-bad34cc). Does the development build that is currently there (dated today) contain an updated fix to this issue? *Ania Holubecki* On Tue, Jul 1, 2025 at 4:49 PM <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via email, send a message with subject or > body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > Today's Topics: > > 1. Re: freeview -ss orientation inconsistencies (fsbuild) > 2. Recon-all clinical vs. FS version 8.0.0 (Stefanie Bradley) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 01 Jul 2025 20:23:36 +0200 > From: fsbuild <fsbuild(a)contbay.com> > Subject: [Freesurfer] Re: freeview -ss orientation inconsistencies > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <52b66d0818f14b6dbb070d0b4ba95965(a)trashmail.com> > Content-Type: multipart/alternative; > boundary="_=_swift_1751394216_db214b4c34d05cc9b5bbc04bb0801152_=_" > > External Email - Use Caution > > If you downloaded something labelled with 8.1, you should delete it and > either use the development builds from, > https://secure-web.cisco.com/15RxK9bSzU8k6FeMdNbLLEWxJ9eqC8NUcpIHgEEoSw3r4_… > OR use the 8.0.0 releases from, > https://secure-web.cisco.com/1uAi36bt4wpXbEOWQNu5DvWB0yjpPPP-Tgs_0dXQoN7JFc… > - R. > >

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Re: freeview -ss orientation inconsistencies
by fsbuild 01 Jul '25

01 Jul '25

External Email - Use Caution If you downloaded something labelled with 8.1, you should delete it and either use the development builds from,https://secure-web.cisco.com/15RxK9bSzU8k6FeMdNbLLEWxJ9eqC8NUcpIHgEEoS… OR use the 8.0.0 releases from,https://secure-web.cisco.com/1uAi36bt4wpXbEOWQNu5DvWB0yjpPPP-Tgs_0dXQo… - R.

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Re: freeview -ss orientation inconsistencies
by Ania Holubecki 01 Jul '25

01 Jul '25

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(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via email, send a message with subject or > body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > Today's Topics: > > 1. Re: freeview -ss orientation inconsistencies (Wang, Ruopeng) > (Wang, Ruopeng) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 1 Jul 2025 17:32:35 +0000 > From: "Wang, Ruopeng" <RWANG4(a)mgh.harvard.edu> > Subject: [Freesurfer] Re: freeview -ss orientation inconsistencies > (Wang, Ruopeng) > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <6145982B-4844-456B-B96E-A1AA0BA3B874(a)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(a)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(a)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(a)nmr.mgh.harvard.edu > <mailto:freesurfer-request@nmr.mgh.harvard.edu>> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu<mailto: > freesurfer(a)nmr.mgh.harvard.edu> > > To subscribe or unsubscribe via the World Wide Web, visit > https://secure-web.cisco.com/18etaNoAf6rn3JfXyKeD62n31eK9EYchyntd-duo-OKaTp…< > https://secure-web.cisco.com/1R5CD0U5oUsF2bnqAnv5jl0Wac6h-u4Pkyv-NRURa-sEbY… > > > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu<mailto: > freesurfer-request(a)nmr.mgh.harvard.edu> > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu<mailto: > freesurfer-owner(a)nmr.mgh.harvard.edu> > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. freeview -ss orientation inconsistencies (Ania Holubecki) > 2. Re: freeview -ss orientation inconsistencies (Wang, Ruopeng) > 3. Re: Hippocampal Subvolumes Error -- segmentHA_T1_long > (Iglesias Gonzalez, Juan E.) > 4. Re: Run NextBrain on a high-res 3D dataset: tweaks required > for 200um on Edlow brain? (Iglesias Gonzalez, Juan E.) > 5. Re: Striatum and cerebellum parcellation stats from Choi2012 > and Buckner 2011 (Douglas N. Greve) > 6. Question on Samseg Basic and Samseg for MS lesions > (Stefano Cerri) > 7. Re: Question on Samseg Basic and Samseg for MS lesions > (Arianna Menardi) > 8. Re: Striatum and cerebellum parcellation stats from Choi2012 > and Buckner 2011 (Payam Sadeghi Shabestari) > 9. Re: Run NextBrain on a high-res 3D dataset: tweaks required > for 200um on Edlow brain? (Iglesias Gonzalez, Juan E.) > 10. Re: SegmentSubfieldsT1Longitudinal Error, Line 2136 -- Are > disorganized volumes usable? (Iglesias Gonzalez, Juan E.) > 11. Re: Hippocampal Subvolumes Error -- segmentHA_T1_long > (Nolan, Jackson) > 12. Re: Hippocampal Subvolumes Error -- segmentHA_T1_long > (Toms, Robert) > 13. mri segstats "masksign abs" syntaxis option (Gonzalo Rojas Costa) > 14. Re: Hippocampal Subvolumes Error -- segmentHA_T1_long > (Iglesias Gonzalez, Juan E.) > 15. Re: Striatum and cerebellum parcellation stats from Choi2012 > and Buckner 2011 (Douglas N. Greve) > 16. 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(a)gmail.com<mailto: > ania.holubecki(a)gmail.com>> > Subject: [Freesurfer] freeview -ss orientation inconsistencies > To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <CADR7LJVJ1hFA0tPR-W2uXnKwY4GGQoW= > vP983k6hL4uaqAr0wg(a)mail.gmail.com<mailto:vP983k6hL4uaqAr0wg@mail.gmail.com > >> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > 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* >

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Re: freeview -ss orientation inconsistencies (Wang, Ruopeng)
by Ania Holubecki 01 Jul '25

01 Jul '25

External Email - Use Caution 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(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://secure-web.cisco.com/1Yq7Py_bXFPwJtbCae2FbB6Z2B91e8p1k8W0NgJtdUmp3b… > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. freeview -ss orientation inconsistencies (Ania Holubecki) > 2. Re: freeview -ss orientation inconsistencies (Wang, Ruopeng) > 3. Re: Hippocampal Subvolumes Error -- segmentHA_T1_long > (Iglesias Gonzalez, Juan E.) > 4. Re: Run NextBrain on a high-res 3D dataset: tweaks required > for 200um on Edlow brain? (Iglesias Gonzalez, Juan E.) > 5. Re: Striatum and cerebellum parcellation stats from Choi2012 > and Buckner 2011 (Douglas N. Greve) > 6. Question on Samseg Basic and Samseg for MS lesions > (Stefano Cerri) > 7. Re: Question on Samseg Basic and Samseg for MS lesions > (Arianna Menardi) > 8. Re: Striatum and cerebellum parcellation stats from Choi2012 > and Buckner 2011 (Payam Sadeghi Shabestari) > 9. Re: Run NextBrain on a high-res 3D dataset: tweaks required > for 200um on Edlow brain? (Iglesias Gonzalez, Juan E.) > 10. Re: SegmentSubfieldsT1Longitudinal Error, Line 2136 -- Are > disorganized volumes usable? (Iglesias Gonzalez, Juan E.) > 11. Re: Hippocampal Subvolumes Error -- segmentHA_T1_long > (Nolan, Jackson) > 12. Re: Hippocampal Subvolumes Error -- segmentHA_T1_long > (Toms, Robert) > 13. mri segstats "masksign abs" syntaxis option (Gonzalo Rojas Costa) > 14. Re: Hippocampal Subvolumes Error -- segmentHA_T1_long > (Iglesias Gonzalez, Juan E.) > 15. Re: Striatum and cerebellum parcellation stats from Choi2012 > and Buckner 2011 (Douglas N. Greve) > 16. 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(a)gmail.com> > Subject: [Freesurfer] freeview -ss orientation inconsistencies > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CADR7LJVJ1hFA0tPR-W2uXnKwY4GGQoW= > vP983k6hL4uaqAr0wg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > 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* >

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