Freesurfer June 2025

freesurfer@nmr.mgh.harvard.edu

48 participants
57 discussions

Info about Cortical Parcellation Participants?
by Jamie Hanson 14 Jul '25

14 Jul '25

External Email - Use Caution Hello Freesurfer list- I had a (hopefully) quick question about the cortical parcellation manual labeling data... specifically, is there any information about race/ethnicity and education levels for these participants? It looks like from some past replies (in ~2009), the cortical labels were based on two sets-- one done by Rahul Desikan (~40 subjects) and the other by Christophe Destrieux (~24 subjects). I'm presuming it is these two papers: -Desikan, R. S., Ségonne, F., Fischl, B., Quinn, B. T., Dickerson, B. C., Blacker, D., ... & Killiany, R. J. (2006). An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. Neuroimage, 31(3), 968-980. -Destrieux, C., Fischl, B., Dale, A., & Halgren, E. (2010). Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. Neuroimage, 53(1), 1-15. If that's correct, those publications only list a bit about the participants' ages and sex. There's nothing about these other demographic factors, and I thought I would try to track that information. Thanks much in advance for the help, and all the best, Jamie. --- Jamie Hanson Associate Professor, Psychology Research Scientist, Learning Research and Development Center University of Pittsburgh

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longitudinal analysis on one subject
by Isabella Rossellini 13 Jul '25

13 Jul '25

External Email - Use Caution Hello Freesurfer users/experts, I am working with Freesurfer 7.4.1 on a MacStudio (macOS 15.2) and I would like to ask your opinion about the following. Basically, we had an anxiety treatment study and I would like to analyze one subject who has 5-time points (0, 3, 6, 9, 12) with a longitudinal pipeline, two-stage model. Is it possible to run this on one person only and see the changes between these time points? I have never done this before on one subject so I am not sure what the best approach would be to look at the changes. After running the longitudinal preprocessing (base, long), should I generate the tables of freesurfer parcellation/segmentation stats data (aparcstats2table, asegstats2table)? Or can I just follow the two stage model steps? Maybe glm only works on a group of subjects. https://secure-web.cisco.com/1iC7gpXrtEAUPrcmI22C302poe7thUhcUmsjgK95UydNOq… (We have 9 more subjects - 10 in total - so I was hoping to visualize the pattern of changes one by one, in each subject, since these patients showed different changes in anxiety based on self-reported questionnaires) Sincerely, Isa Rosselini

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Dealing with black-holes / editing surface
by Bartosz Kossowski 09 Jul '25

09 Jul '25

External Email - Use Caution I’m working with MRI data from individuals with multiple sclerosis (MS). I preprocess their scans using lesion filling in FSL, based on lesion masks prepared from FLAIR images. However, for some subjects with extensive lesions—particularly large black holes and/or juxtacortical lesions—the surface reconstruction remains inaccurate, even after applying lesion filling (and of course without it as well). I would like to manually correct the reconstruction in these problematic areas. I’ve tried adding control points directly inside the black holes (!) and also editing the *wm.mgz* by manually adding voxels, but it seems that directly editing the surface mesh would probably be more effective and less cumbersome. Is this feasible? Are there established tools or workflows that allow manual surface mesh correction in this context? Please note that in the example provided, there is an area where, despite the correct wm.mgz mask, the surface does not follow the mask boundary. Alternatively, I would appreciate any suggestions on other methods or pipelines that might be worth trying to improve surface reconstruction in such challenging cases. Thank you!

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PetSurfer surface-based SUVR
by Mia Anthony 07 Jul '25

07 Jul '25

External Email - Use Caution Hello FS, I have calculated regional SUVR and would like to calculate SUVR on the surface. I have followed the wiki tutorial, including PVC, through smoothing on the surface. The last commands I ran are: mris_fwhm --smooth-only --i all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz --fwhm 5 --o all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz --cortex --s fsaverage --hemi lh mris_fwhm --smooth-only --i all.rh.mgx.ctxgm.fsaverage.sm00.nii.gz --fwhm 5 --o all.rh.mgx.ctxgm.fsaverage.sm05.nii.gz --cortex --s fsaverage --hemi rh Do I need to run the mri_glmfit command? For example: mri_glmfit --y all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz --surface fsaverage lh --fsgd g1v0.fsgd mri_glmfit --y all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz --surface fsaverage rh --fsgd g1v0.fsgd Will the mri_glmfit output provide surface-based SUVR, or will I need to run additional commands after? Thank you, Mia

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Mask-to-eTIV > 1
by Krystalyn Edwards-Calma 06 Jul '25

06 Jul '25

External Email - Use Caution Aloha, I am using Version 7.4.1. After running recon-all for multiple subjects, I noticed the Brain mask is larger than the intracranial volume (Mask-to-eTIV > 1). I attempted multiple different skull stripping methods, however, the mask-to-eTIV is always > 1. Any suggestions on how to fix this? Mahalo for your help. Malama pono, Krystalyn Edwards-Calma

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QC recon- all and manual editing
by Mahta Abbaspour 06 Jul '25

06 Jul '25

External Email - Use Caution Hi, I recently attended your FreeSurfer course in June and found it incredibly helpful—thank you! I’m currently working on a research project on AD patients and have been performing quality control on my FreeSurfer outputs using version 8.0.0. I’d really appreciate your input on a few slices I came across, as I wasn’t sure whether they require manual correction. In this image, do you think the pial surface (red line) near both hippocampus (light blue) are undersegmented? [cid:1f744d31-7e4a-40c3-959e-09280cea965e] This is also another screenshot of the same brain. The pial surface on the left placed inside the WM surface. It's just 1-2 slices but I was wondering what's the best approach to these types of error. [cid:173d0154-9a5e-49f2-a430-c68849f64d80] Thank you for your time. Best

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ASLPrep Recon-all Error
by 岳昊 06 Jul '25

06 Jul '25

External Email - Use Caution Dear FreeSurfer Developers, I am a neuroscience student currently working on analyzing ASL MRI data using ASLPrep. I am encountering difficulties running recon-all during the preprocessing pipeline. Specifically, I am running the command recon-all, and the exact error message displayed is Cmdline: recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -rh-only -openmp 8 -subjid sub-OAS30001 -sd /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer Stdout: ERROR: Flag -rh-only unrecognized. I encountered an issue similar to one reported on GitHub, suggesting a FreeSurfer version incompatibility. Attempts to resolve this by using FreeSurfer version freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c and freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b did not resolve the original issue. Upgrading to FreeSurfer version freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 resulted in a complete failure of ASLPrep. For your reference, the following information may be relevant: 1).FreeSurfer Version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c, and freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b and freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460. 2).Platform: Red Hat Enterprise Linux 8.5 (Ootpa) 3).uname -a: Linux cn77042 4.18.0-348.cn.x86_64 #1 SMP Wed Sep 14 10:27:16 CST 2022 x86_64 x86_64 x86_64 GNU/Linux 4).recon-all.log and the crash file: Please find those files attached to this email. Any guidance you could provide in resolving this issue would be greatly appreciated. Thank you for your time and assistance. Sincerely, Hao Yue

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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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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

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

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Freesurfer June 2025