Freesurfer

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17 participants
30129 discussions

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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(无主题)
by 杨曦 13 Jul '25

13 Jul '25

External Email - Use Caution confirm 753a2b9a8d41bc6d3374a035829cb9c09415518

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Scalebar on Flatmap
by Manenti, Giorgio 11 Jul '25

11 Jul '25

External Email - Use Caution Hi all, I’m wondering how to add an accurate scalebar (in cm) to my flatmap. Is this possible to do in Freeview, or are there other recommended tools or methods? Thank you in advance for your help! Best regards, Giorgio

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Freesurfer output. Segmentation fault (core dumped) during parcellation step
by Samantha Hendry 10 Jul '25

10 Jul '25

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run freesurfer on a resampled T1w scan and it has come up woth segmentation fault error at the stages of the atlas. This is the full error when I just run recon-all from the start: #@# Parcellation Stats lh Thu May 1 20:28:36 BST 2025 /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab FMS_0094 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/mri/wm.mgz... reading input surface /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/surf/lh.white... reading input pial surface /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/surf/lh.pial... reading input white surface /exports/eddie/scratch/shendry2/rerun_w0_cross_mixed_protocol_out/FMS_0094/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 182364 Total vertex volume 180081 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Segmentation fault (core dumped) I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Performed on MobaXterm on windows computer using eddie super computer and Edinburgh university 3) uname -a: Linux node1c26.ecdf.ed.ac.uk 5.14.0-427.33.1.el9_4.x86_64 #1 SMP PREEMPT_DYNAMIC Wed Aug 28 17:34:59 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Not sure if the above is fully correct. Any help would be greatly appreciated! Best wishes Samantha Hendry The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.

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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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