Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30071 discussions

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* >

1 0

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* >

2 2

eTIV in SynthSeg
by Marco Ganzetti 01 Jul '25

01 Jul '25

External Email - Use Caution Dear, I would like to know how the eTIV is estimated in SynthSeg and SynthSeg+ . Is it a combination of CSF+ventricles+WM+GM masks? Or do you estimate is using the registration to MNI space approach? Best, Marco

2 3

FreeSurfer License Request
by 李xx 01 Jul '25

01 Jul '25

External Email - Use Caution Dear FreeSurfer Team, I previously submitted a license request but only received a mailing list notification. Could you please send me the license file directly? My details: - Full Name: Li Xuelian - Institution: University of Electronic Science and Technology of China (UESTC) - Intended Use: Academic Research Thank you! Best regards, Li Xuelian

1 0

FreeSurfer License Request
by 李xx 01 Jul '25

01 Jul '25

External Email - Use Caution Dear FreeSurfer Team, I am unable to complete the online registration due to reCAPTCHA issues. Could you please send me a FreeSurfer license file? My details: - Full Name: Li Xuelian - Institution: University of Electronic Science and Technology of China (UESTC) - Intended Use: Academic Research Thank you! Best regards, Li Xuelian

1 0

QC Synthseg
by Marco Ganzetti 30 Jun '25

30 Jun '25

External Email - Use Caution I would like to know how to interpret the QC output from the SynthSeg application. What do they mean and how they are computed? Marco

2 3

Please remove me from this email list
by Haniya Saleh 29 Jun '25

29 Jun '25

External Email - Use Caution Please remove myself (hsaleh(a)uoguelph.ca) from this email list. I get flooded with these emails at my work account and this was something I was assisting 3 years ago. There's no unsubscribe option that I can find. Warm Regards, Haniya Saleh ________________________________________________________________ Haniya Saleh | (She/Her) | Managed Desktops Analyst III – Client Productivity Computing & Communications Services (CCS) | University of Guelph Johnston Hall rm. 034 | 45 Trent Ln | Guelph, ON | N1G 1Y4 519-824-4120 Ext. 56713 | hsaleh(a)uoguelph.ca

2 1

SynthSR - T1 3D post-gadoinium vs. T2 FSE 4mm
by Diana Lorenzo 28 Jun '25

28 Jun '25

External Email - Use Caution Dear All, we are running a project on brain morphometry in a clinical sample without brain injury. For most patients, we have both: * T1W isotropic 1mm post-gadolinium * T2W TSE with 4mm axial slices We would like to obtain high-resolution T1 images with SynthSR followed by standard voxel-based and surface-based processing in CAT12. I am wondering which contrast is best suited for our purpose, also considering that our clinical sample has no brain injury and the only blood vessels are enhanced in post-gadolinium sequences. I made some attempts on both sequences for a couple participants and segmented them with CAT12. The overall image quality rating is almost identical. So is the estimate of total intracranial volume, with some differences in grey matter volume estimation (generally smaller in synthetized post-gado sequences vs synthetized T2) and CSF (generally bigger in synthetized post-gado). I haven't checked surface-based metrics. I am quite new to the field, and I really appreciate your help! Best, Lorenzo Lorenzo Diana, PhD PostDoc Advanced Imaging Research (AIR) Group Swiss Paraplegic Research Guido A. Zäch Strasse 4 6207 Nottwil, Switzerland

2 3

Freesurfer installation help
by Jarrar, Nadine 27 Jun '25

27 Jun '25

Good afternoon, I hope this finds you well. I am a research assistant at MGH, recently took the freesurfer course in June, trying to install it on an arm64 M3 chip Mac (OS Sequoia 15.5), 24GB RAM/memory. I followed the online installation guides and troubleshooting for V8.0.0, yet am getting stuck at the "setup and configuration" step: I successfully installed the freesurfer package file but when I enter the commands in a terminal window to "source the freesurfer environment", the terminal either says "zsh: parse error near '\n'" or it says "source: no such file or directory: /Applications/freesurfer/SetUpFreeSurfer.sh". I copy and pasted the full terminal content below (including the error messages). I looked at older online tutorials for installation, one of them had me load a tab in freeview after installation, before sourcing the environment in a terminal. When I tried to load any volume onto freeview, the app immediately quit and generated an error report. Since the same issue happened repeatedly, I copy and pasted the full error report to a word document attached to this email. Do you have any tips, recommendations, or ideas of what could be going wrong with my setup and configuration? Are there any videos I can consult online, or someone I could speak with to get assistance on my specific errors? Thank you for your time! Have a good weekend. Best, Nadine Terminal message: Last login: Fri Jun 27 11:50:08 on ttys000 nadinejarrar@MGB033764 ~ % export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh source: no such file or directory: /Applications/freesurfer/SetUpFreeSurfer.sh nadinejarrar@MGB033764 ~ % export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh source: no such file or directory: /Applications/freesurfer/SetUpFreeSurfer.sh nadinejarrar@MGB033764 ~ % export FREESURFER_HOME=/Applications/freesurfer/8.0.0 source $FREESURFER_HOME/SetUpFreeSurfer.sh export: not valid in this context: /Applications/freesurfer/SetUpFreeSurfer.sh nadinejarrar@MGB033764 ~ % >.... Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/8.0.0 FSFAST_HOME /Applications/freesurfer/8.0.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/8.0.0/subjects MNI_DIR /Applications/freesurfer/8.0.0/mni ... install either the Matlab R2014b or R2019b runtime environment ... $ which fs_install_mcr /Applications/freesurfer/8.0.0/bin/fs_install_mcr $ sudo FREESURFER_HOME=$FREESURFER_HOME $FREESURFER_HOME/bin/fs_install_mcr R2019b <output deleted> ... set LD_LIBRARY_PATH to point to The Mathworks libraries ... $ export LD_LIBRARY_PATH=$FREESURFER_HOME/MCRv97/runtime/maci64:$FREESURFER_HOME/MCRv97/bin/maci64:$FREESURFER_HOME/MCRv97/sys/os/maci64:$FREESURFER_HOME/MCRv97/extern/bin/maci64 zsh: parse error near `\n' nadinejarrar@MGB033764 ~ % export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh source: no such file or directory: /Applications/freesurfer/SetUpFreeSurfer.sh nadinejarrar@MGB033764 ~ %

1 0

Updates/bug fixes available for the 8.0.0 release
by fsbuild 27 Jun '25

27 Jun '25

External Email - Use Caution Some updates/bug fixes are available for an existing installation of the Freesurfer 8.0.0 release.  The list of files you can update along with a brief comment about the change(s) are: $FREESURFER_HOME/bin/csvprintScript changed to use python3 - values for eTIV should no longer be misreported as 0.00 for data processed with the recon-all command $FREESURFER_HOME/bin/recon-allFixes for options -autorecon1, -nonuintensitycor.  Add flag -no-fix-ga to turn off fixing of gyrus ambiens part of the cortex label. $FREESURFER_HOME/bin/gtmseggtmseg now uses samseg by default $FREESURFERR_HOME/bin/xhemiregModifications to make xhemireg work with 8.0. $FREESURFER_HOME/bin/xcerebralseggtmseg now uses samseg by default $FREESURFER_HOME/bin/post-recon-allgtmseg now uses samseg by default $FREESURFER_HOME/python/packages/gems/SamsegLongitudinal.pyfix parameters to surfa.image.transform() $FREESURFER_HOME/etc/recon-config.yaml Added option -no-fix-ga to turn off fixing of gyrus ambiens part of the cortex label. Please note THESE UPDATES DO NOT CHANGE THE OUTPUT OF THE recon-all COMMAND. If these updates are of interest to you, then please go the 8.0.0 download URL,https://secure-web.cisco.com/15mh8yOb2RWi2iQyUfX1LgM0gB5PobUejtWnQDIeOm… and download the fs8_update.sh script. On MacOS run the script as follows,$ sudo FREESURFER_HOME=/Applications/freesurfer/8.0.0  bash  fs8_updates..sh On CentOS and Rocky8 Linux run the script as follows,$ sudo FREESURFER_HOME=/usr/local/freesurfer/8.0.0-1  bash  fs8_updates.sh On Ubuntu Linux run the scripts as follows,$ sudo FREESURFER_HOME=/usr/local/freesurfer/8.0.0  bash  fs8_updates.sh You will be prompted on the command line as to whether or not you want to install each file, including displaying the description of the change(s) listed above.

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer