Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30055 discussions

SegmentHA_T2: USE_T1 and T2 alignment in ADNI data
by AmirHussein Abdolalizadeh 09 Jul '25

09 Jul '25

External Email - Use Caution Dear FreeSurfer users/experts, I have two questions related to the manual of segmentHA_T2.sh pipeline written on the FreeSurfer's website, which I would like to apply to ADNI data. I couldn't find any solutions to that elsewhere. Regarding the data, T1s have a resolution of 1.2 x 1.05 x 1.05 and T2s have a limited FoV on Hippocampus/Amygdala with a voxel size of 0.4 x 2 x 0.4. I have two questions: 1. What value should I set for USE_T1? According to the manual on FreeSurfer's website: *"Using the main T1 is advised when the additional scan is of comparable resolution as the T1, or when the additional scan does not cover the whole hippocampal region - in that case, the T1 information will be critical to segment the hippocampal regions outside the field of view of the additional volume. Using the additional scan in isolation is advised when it is of higher resolution than the T1 while covering the whole hippocampi and amygdalae." *Based on this text and ADNI's high-resolution T2, what should I set USE_T1 to? 2. Regarding the additional scan, it is written that: *"In this case, the only requirement is that the additional scan is coarsely aligned to the main T1 scan." *What does it mean by "coarsely aligned"? Should I linearly register the T2 to T1? However, visualizing the T1 and T2 images overlaid on top of each other reveals that they are somewhat aligned, as both T1 and T2 were acquired in the same session; however, they are not as aligned as one would expect after a rigid transformation. Looking forward to your comments. Best, Amir

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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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Re: Freesurfer Digest, Vol 257, Issue 32
by James Hartzell 09 Jul '25

09 Jul '25

External Email - Use Caution please unsubscribe me James Hartzell, PhD(2x), EMBA Donostia-San Sebastián, Spain > On 9 Jul 2025, at 15:44, 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: mri_convert error: Floating point exception (core dumped) > (Huang, Yujing) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 9 Jul 2025 13:44:11 +0000 > From: "Huang, Yujing" <YHUANG43(a)mgh.harvard.edu> > Subject: [Freesurfer] Re: mri_convert error: Floating point exception > (core dumped) > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <SN6PR04MB48944C05656912922B19BA459D49A(a)SN6PR04MB4894.nam > prd04.prod.outlook.com> > Content-Type: multipart/alternative; boundary="_000_SN6PR04MB48944C > 05656912922B19BA459D49ASN6PR04MB4894namp_" > > We will investigate the issue further. > > From: Óscar Peña-Nogales <opennog(a)gmail.com> > Sent: Wednesday, July 9, 2025 3:00 AM > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] Re: mri_convert error: Floating point exception (core dumped) > > > External Email - Use Caution > Yes, that seems to execute the command correctly as in FS7.4.1. Is it however possible to modify something and execute it as it should be in FS8.0.0? > > Thanks > > On Mon, 7 Jul 2025 at 15:33, Huang, Yujing <YHUANG43(a)mgh.harvard.edu<mailto:YHUANG43@mgh.harvard.edu>> wrote: > Can you try ‘-dsold’ in FS8.0.0 instead? It should behave the same as ‘-ds’ in FS7.4.1 > > Yujing > > From: Óscar Peña-Nogales <opennog(a)gmail.com<mailto:opennog@gmail.com>> > Sent: Monday, July 7, 2025 7:27 AM > To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: [Freesurfer] mri_convert error: Floating point exception (core dumped) > > > External Email - Use Caution > Dear, > > I'm attempting to increase the resolution of an image but I get the following error when I run the mri_convert command: > > Command: > mri_convert -rt nearest -it nii -i XX.nii.gz -ds 0.2 0.2 0.2 -ot nii -o XX_sr_temp.nii.gz > Log: > reading from XX.nii.gz... > TR=10.01, TE=4.75, TI=0.00, flip angle=50.00 > i_ras = (-0.99768, -0.0561452, 0.0384932) > j_ras = (0.0571764, -0.998019, 0.026235) > k_ras = (0.036944, 0.0283751, 0.998914) > DownsampleFactor = 0.200000, 0.200000, 0.200000 > > Error: > Floating point exception (core dumped) > > I was not able to find any similar error on the mailing list. Does anyone have any thoughts on how to trouble-shoot this one? > > More info: > 1) FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a > 2) Platform: > Distributor ID: Ubuntu > Description: Ubuntu 22.04.5 LTS > Release: 22.04 > Codename: jammy > > 3) uname -a: Linux eec78b7407cc 6.8.0-60-generic #63~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Apr 22 19:00:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linu > > Note1: I also tried with FreeSurfer 7.4.1, and the command, with the same input data, works in that version. Nevertheless, I wanted to update to 8.0.0. > Note2: The same command does work on 8.0.0 when -ds >1 > > Thanks in advance. > Óscar > > _______________________________________________ > Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> > To unsubscribe send an email to freesurfer-leave(a)nmr.mgh.harvard.edu<mailto:freesurfer-leave@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/18r-mX7rYMTUSrHGb9Oq3HswRQqRic1c3I5A8Zfbjy4jan…<https://secure-web.cisco.com/1gpUbe4FVznzxjJNztWXHjiRUB0bqZe0MFTUsScr4IZ6a_…> > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1wrwX7KDxq5Ami71oWtsW0Fihzlv20-5ZW1arID7LEsWi8…<https://secure-web.cisco.com/178B-zhI0ShZzQF3qeDysqtzG8HdElMPFmXJKtMfIaNCR4…> <https://secure-web.cisco.com/1wrwX7KDxq5Ami71oWtsW0Fihzlv20-5ZW1arID7LEsWi8…<https://secure-web.cisco.com/178B-zhI0ShZzQF3qeDysqtzG8HdElMPFmXJKtMfIaNCR4…>> . >

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mri_convert error: Floating point exception (core dumped)
by Óscar Peña-Nogales 09 Jul '25

09 Jul '25

External Email - Use Caution Dear, I'm attempting to increase the resolution of an image but I get the following error when I run the mri_convert command: Command: *mri_convert -rt nearest -it nii -i XX.nii.gz -ds 0.2 0.2 0.2 -ot nii -o XX_sr_temp.nii.gz* Log: reading from XX.nii.gz... TR=10.01, TE=4.75, TI=0.00, flip angle=50.00 i_ras = (-0.99768, -0.0561452, 0.0384932) j_ras = (0.0571764, -0.998019, 0.026235) k_ras = (0.036944, 0.0283751, 0.998914) DownsampleFactor = 0.200000, 0.200000, 0.200000 Error: *Floating point exception (core dumped)* I was not able to find any similar error on the mailing list. Does anyone have any thoughts on how to trouble-shoot this one? More info: 1) FreeSurfer version:* freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a* 2) Platform: Distributor ID: Ubuntu Description: *Ubuntu 22.04.5 LTS* Release: 22.04 Codename: jammy 3) uname -a: *Linux eec78b7407cc 6.8.0-60-generic #63~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Apr 22 19:00:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linu* Note1: I also tried with FreeSurfer 7.4.1, and the command, with the same input data, works in that version. Nevertheless, I wanted to update to 8.0.0. Note2: The same command does work on 8.0.0 when* -ds >1* Thanks in advance. Óscar

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FreeSurfer Recon-all error : found no voxels matching id 1
by Khine, Win 08 Jul '25

08 Jul '25

External Email - Use Caution Hi FreeSurfer Developer, I am using FreeSurfer to analyse cortical thickness and ROIs volume. My input MRIs brain format is – nii.gz ( converted from T1 .dicom). I managed to run recon-all without any errors in some of my subjects. But, I am encountering the following error when I run recon-all on the other half of my subjects ( all are the same error) : Recon-all -s subject05_post exited with ERRORS. Error : found no voxels matching id 1 Found : 0 label voxels I have tried both watershed and no skull strip to tackle it. But it still finished with the same error. I have also tried running recon-all in separate stages – autorecon 1 , autorecon 2, autorecon 3 – the error seems to happen in autorecon 2 stage. I have searched the list, and no similar error was reported. Could you help me troubleshoot this error? ( I am also quite new to the field of MRI analysis and using FreeSurfer) I’m using FreeSurfer version 8.0.0 Platform – Mac OS Sequoia version 15.5 , Memory 36 GB, Storage – 370 GB Recon-all log : please see the attached. I have also attached the input nii.gz file to this email. Thank you. Yours sincerely, Dr Win Khine Clinical Research Fellow Imperial College London

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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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Re: Ubuntu 24 release
by fsbuild 07 Jul '25

07 Jul '25

External Email - Use Caution  We hope to have a development build for Ubuntu 24 in the near future. - R. On Jul 7, 2025, at 03:46, Alpay Özcan <ialpayozcan(a)gmail.com> wrote:        External Email - Use Caution        Hello,Any plans for compiling on Ubuntu 26.04? Thanks in advance... --  Alpay Özcan, D.Sc. Professor Electrical & Electronics Eng. Dept., Boğaziçi University Bebek Istanbul 34342 Türkiye Tel: +90 212 359 7427 (or 6414 for Dept.) _______________________________________________ Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1l2ZjAmSRBzEqngLJIi7nu56UGID6r3V7Bnda0i0LO_Rko…

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Re: Freesurfer installation help
by fsbuild 07 Jul '25

07 Jul '25

External Email - Use Caution  Try using the bash shell (by typing "bash" in the terminal window) and setup the environment with that instead of zsh. mymac[~] bash The default interactive shell is now zsh.To update your account to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit https://secure-web.cisco.com/1D7LUoH_cGGJxXRUBJGiZn5rlB8hoE9OQBmiNugxPvMyZ5… bash-3.2$ export FREESURFER_HOME=/Applications/freesurfer/8.0.0bash-3.2$ source /Applications/freesurfer/8.0.0/SetUpFreeSurfer.sh-------- freesurfer-macOS-darwin_x86_64-8.0.0-20250205-0f2bd3a --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/8.0.0FSFAST_HOME       /Applications/freesurfer/8.0.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/8.0.0/subjectsMNI_DIR           /Applications/freesurfer/8.0.0/mni if the above works you could try changing your default shell to bash with "chsh -s /bin/bash" - R.

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Re: Recon-all clinical vs. FS version 8.0.0
by Zollei, Lilla,Ph.D. 07 Jul '25

07 Jul '25

Hi Stephanie, How old are the subjects in your pediatric cohort? Lilla -------- Forwarded Message -------- Subject: [Freesurfer] Recon-all clinical vs. FS version 8.0.0 Date: Tue, 1 Jul 2025 21:48:43 +0000 From: Stefanie Bradley <stefanie.bradley(a)mail.utoronto.ca><mailto:stefanie.bradley@mail.utoronto.ca> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> 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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Ubuntu 24 release
by Alpay Özcan 07 Jul '25

07 Jul '25

External Email - Use Caution Hello, Any plans for compiling on Ubuntu 26.04? Thanks in advance... -- Alpay Özcan, D.Sc. Professor Electrical & Electronics Eng. Dept., Boğaziçi University Bebek Istanbul 34342 Türkiye Tel: +90 212 359 7427 (or 6414 for Dept.)

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