Freesurfer

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30128 discussions

Problem using my own mask in recon-all
by Jerome Maller 30 Dec '25

30 Dec '25

External Email - Use Caution Hi Freesurfer experts. I am trying to process a T1-MPRAGE 7T scan with 0.5mm isotropic resolution with the recon-all -highres flag. FS is struggling to make a good mask even though I’ve tried various combinations in the recon-all command (e.g. different -skullstrip -wsthresh numbers, -wsmore, different -watershed atlases). I have tried with and without neck removal (using FSL’s robustfov) as well as bias field correction (via SPM and also FSL’s FAST), and feeding in with and without the scan already brain extracted (via robex). I am now trying to feed in my pre-made mask using the -expert flag. * I have named my pre-made mask as brainmask.mgz and placed it in the directory where my t1.nii.gz is located * I have made a text file (called expert.opts) that contains: mri_mask brainmask.mgz My recon-all command calls the file using -expert expert.opts However, recon-all seems to ignore the calling of the expert.opts and so tries to make its own mask… So my question is: am I correctly using the =expert flag and expert.opts to use my pre-made brainmask.mgz? PS. I am using FS version 7.1 (as I am running Ubuntu 18.04 and can’t upgrade due to lots of other software running on the computer) Thankyou! Jerome --

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localGI recon-all failure related to cerebellum/dura inclusion (multiple subjects)
by 효원 29 Dec '25

29 Dec '25

External Email - Use Caution Hello FreeSurfer Developers, I am running recon-all with the -localGI option to compute local gyrification index (LGI). Across multiple subjects from the same dataset, the pipeline fails at different stages. Although the failure points differ, all errors appear to be related to *posterior fossa inclusion (cerebellum or dura)* in the filled or white matter volumes. Below I describe two distinct failure patterns observed in different subjects. *1) What I am trying to accomplish* I am running recon-all with -localGI to compute local gyrification index (LGI). The error occurs only in a specific subject. *2) Command I ran* recon-all -i {name of the nii files}.nii -s {name of the new file} -sd {directory of the new file} -all *3) Exact error output* *1) Failure pattern 1: filled volume stage* (*Subjects: SPR_023_gi, SPR_024_gi, SPR_025_gi, SPR_037_gi*) In these subjects, recon-all fails early at the mri_fill stage with the following error message: error: Please check filled volume. Cerebellum may be included. *2) Failure pattern 2: topology defect correction stage* *(1) Topology Abort* (*Subject: SPR_039_gi, SPR_052_gi, SPR_070_gi, SPR_071_gi, SPR_078_gi, ,SPR_082_gi, SPR_084_gi, SPR_085_gi, SPR_092_gi*) 1. SPR_039_gi An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. CORRECTING DEFECT 101 (vertices=11842, convex hull=2982, v0=103450) Abort The run terminates with: recon-all -s SPR_039_gi exited with ERRORS 2. SPR_052_gi In an additional subject (SPR_052_gi), recon-all also aborts during topological defect correction: CORRECTING DEFECT 26 (vertices=16843, convex hull=2967, v0=19098) Abort 3. SPR_070_gi CORRECTING DEFECT 11 (vertices=20829, convex hull=3275) Abort 4. SPR_071_gi CORRECTING DEFECT 83 (vertices=15893, convex hull=2782, v0=123875) Abort 5. SPR_078_gi CORRECTING DEFECT 0 (vertices=54094, convex hull=2051, v0=0) Abort 6. SPR_082_gi CORRECTING DEFECT 43 (vertices=13775, convex hull=2607, v0=41288) Abort 7. SPR_084_gi CORRECTING DEFECT 16 (vertices=14335, convex hull=4350, v0=21574) Abort 8. SPR_085_gi CORRECTING DEFECT 0 (vertices=18840, convex hull=3104, v0=591) Abort 9. SPR_092_gi CORRECTING DEFECT 19 (vertices=9080, convex hull=3587, v0=17615) Abort (2) Topology segfault(signal11) (*Subject: SPR_058_gi, SPR_063_gi,*) 1. SPR_058_gi An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. CORRECTING DEFECT 38 (vertices=15899, convex hull=3154) Command terminated by signal 11 2. SPR_063_gi CORRECTING DEFECT ... Command terminated by signal 11 *(3) LGI computation stopped due to topological defects* *(Subject: SPR_079_gi, SPR_136_gi)* 1. SPR_079_gi WARNING -- Problem for vertex iV = 20401, lGI value is aberrantly high (lGI=47.0556)... This may be caused by topological defects, check mris_euler_number on the pial surface. ERROR: compute_lgi did not create output file 'rh.pial_lgi.asc' 2. SPR_136_gi ERROR: compute_lgi did not create output file 'lh.pial_lgi.asc' *4) FreeSurfer version* freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b *5) Platform* OS: Ubuntu 20.04.1 LTS uname -a: Linux climb 5.15.0-139-generic #149~20.04.1-Ubuntu SMP Wed Apr 16 08:29:56 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux *6) recon-all.log* all files are attached to this email. Thank you very much for your time and help. Best regards, Hyowon Ju.

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To unsubscribe from FreeSurfer Mailing List
by Khine, Win 27 Dec '25

27 Dec '25

External Email - Use Caution Hi, I want to unsubscribe from FreeSurfer Mailing list, please. I previously subscribed to FreeSurfer Mailing list to ask questions for support and I am getting enormous amounts of emails from the FreeSurfer Mailing list, hence I would like to unsubscribe as soon as possible please. Thank you. Warm regards, Win

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To unsubscribe from FreeSurfer Mailing List
by Khine, Win 27 Dec '25

27 Dec '25

1 0

Expert option is not appropriately reflected in recon-all
by Ikko Kimura 23 Dec '25

23 Dec '25

External Email - Use Caution Dear FreeSurfer Developers, I'm trying to run recon-all using freesurfer 8.0.0. with the command "recon-all -s ${sub} -i ${sub}_T1w.nii.gz -T2 ${sub}_T2w.nii.gz -T2pial -all -qcache -hires -expert expert," and writing to you because I got the following error: ------------------ mris_inflate -no-save-sulc 25 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading 25 ** failed to open GIFTI XML file '25.gii' mrisReadGIFTIdanum: ERROR reading gifti 25.gii [INFO] read, cannot find 25, trying 25.gii ... error: No such file or directory error: mris_inflate: could not read surface file 25\00 Command exited with non-zero status 255 -------------------- I added "mris_inflate -n 25" as expert option, and, as far as I see, this error happened because recon-all does not reflect the expert option properly (should be "mris_inflate -no-save-sulc -n 25 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix" not "mris_inflate -no-save-sulc 25 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix"). I could run exactly the same recon-all command without error using freesurfer 7.4.1. Could anyone kindly guide me on how to solve this issue? Best regards, Ikko ------------------- Ikko Kimura ikkok(a)drcmr.dk Postdoctoral researcher Neurophysics Group DRCMR, Copenhagen University Hospital - Amager and Hvidovre

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Implementing the Glasser Atlas on Processed Participants
by Carly McIntyre-Wood 23 Dec '25

23 Dec '25

2 2

Recon failing: normal vector of length zero at vertex NNNNN with N faces
by Sambamoorthy, Sowmya 23 Dec '25

23 Dec '25

External Email - Use Caution Hello! Need help getting past these errors (attached recon log) for reference. Many of my brains are throwing errors like below: "normal vector of length zero at vertex 101440 with 6 faces first tangent vector of length zero at vertex 101440" Last few lines of recon.log below: [cid:image001.png@01DC27E0.966D3810] Any help appreciated! Thank you in advance for your support. --Sowmya

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GLM on runs with different conditions
by Xu, Yaoda 23 Dec '25

23 Dec '25

External Email - Use Caution Hi there, I have a large number of conditions to include in a study, like 60. So I split the conditions into multiple runs, with 40 conditions per run, say run 1 with conditions 1 to 40, run 2 with conditions 21 to 60, and run 3 with conditions 1 to 20 and 41 to 60. Can I put all three runs in a run list and run a single GLM with 60 conditions? Normally, I would have the same number of conditions in each run when I put a bunch of runs together in a single GLM to increase SNR. In this case, different runs would share some of the conditions, but not all conditions appear in each run. I just want to make sure that it is OK to run a GLM like this and get a valid beta estimate for each of the 60 conditions. Thanks a lot. Yaoda Xu

2 1

make_average_subject
by Don Hagler 23 Dec '25

23 Dec '25

External Email - Use Caution We have used make_average_subject to resample the white and pial surfaces of an individual subject to ico 7 to produce surface coordinates in the standard tessellation, allowing for group analyses of cortical shape. It may be worth noting that we temporarily replace the talairach.xfm in the subject’s mri/transforms directory with an identify matrix so that the resampled surfaces have the same position and shape as the native surfaces but with the standard ico 7 tesselation. This resampling procedure works great with FreeSurfer version 5.3, but as of version 6.0 or 7.1.1, when a single subject is supplied to make_average_subject, it runs for a while but then eventually produces an error like this: nframes = 1 Computing std/var across frames ERROR: cannot compute std from one frame ERROR: make_average_surface While we can continue doing this resampling step using FS 5.3 (e.g., after running the initial recon with 7.1.1), we would like to stop relying on this very old version. Is there an alternative approach to re-tesellation of an individual subject’s surfaces into ico? Or could a future release of FreeSurfer include a modification to make_average_surface to allow it to once again handle a single subject as input?

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PETSurfer v8.1.0 vs 7.x.x — missing pons in gtmseg.ctab and rescale issue in mri_gtmpvc
by Carme Uribe 23 Dec '25

23 Dec '25

External Email - Use Caution Hi all, I’m running into an issue after upgrading from FreeSurfer 7.1.2 to 8.1.0 when using PETSurfer. In v7.1.2, the gtmseg.ctab included the *pons (Id 174)*, which allowed the subsequent mri_gtmpvc step to perform the default *rescale normalization based on pons intensity*. However, in v8.1.0, the pons no longer appears in the gtmseg.ctab. Since the rescale step still expects that region by default, the pipeline fails when trying to normalize by the pons. From the release notes I see that gtmseg now uses SAMSEG by default, and I suspect that this change may have modified how subcortical or brainstem structures are handled. Also, any chance the gtmseg step could add other regions typically used as reference (e.g., wm/whole cerebellum, centrum semiovale) maintaining the aseg and aparc parcellations from FS? Thanks very much in advance for your help, Carme

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