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by 田质文 15 Aug '25

15 Aug '25

External Email - Use Caution I need to get the license.txt,please. 广东省智能科学与技术研究院田质文实习生

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Missing endif in recon-all-clinical.sh
by Sebastian Rodrigo 14 Aug '25

14 Aug '25

External Email - Use Caution Dear FreeSurfer Guru, in case you don't already know, "endif" missing after line 185 within recon-all-clinical.sh. Best regards Sebastian

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TIV estimation from Fastsurfer
by Marco Ganzetti 13 Aug '25

13 Aug '25

External Email - Use Caution Dear, I would like to know how to extract the total intracranial volume after running Fastsurfer. The aseg.stats file only report the following regions: # Measure Mask, MaskVol, Mask Volume, 1378561.000000, mm^3 # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1112716.172377, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1095647.392151, mm^3 # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 966887.205081, mm^3 # Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 949818.424855, mm^3 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 58370.262413, mm^3 # Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere cerebral white matter volume, 235981.558256, mm^3 # Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere cerebral white matter volume, 231717.193880, mm^3 # Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral white matter volume, 467698.752136, mm^3 I don’t see any eTIV. Regards Marco

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Permission Request to Publish FreeSurfer MNI Template Rendering under CC BY
by Matic Kadiš 11 Aug '25

11 Aug '25

External Email - Use Caution Dear FreeSurfer Team, I am a co-author on a manuscript currently in revision for Scientific Reports. One of our figures includes the attached image, which was generated in FreeSurfer (version 7.4.1) from the MNI152 template brain using the default Desikan–Killiany atlas, with the insula highlighted and inflated. The journal requires explicit written permission from the copyright holder to publish this image under a Creative Commons Attribution (CC BY 4.0) license in all formats (print and digital). Their requirements are: * The permission must be in English. * It must explicitly grant Springer Nature Limited permission to publish the image under a CC BY 4.0 open access license. * It must cover publication in all formats (print and digital). * It must be signed by the copyright holder. Could you please confirm whether MGH / the FreeSurfer team holds the copyright for the MNI template and atlas rendering, and if so, provide a signed permission letter meeting these conditions? I am happy to provide any additional details you need. Of course, a different approach to how you usually handle requests like that is also acceptable. Thank you very much for your time and assistance. Best regards, Matic Kadiš [https://secure-web.cisco.com/1iyBRIi0eNVnfRGRv5UF8xLktnjxF21sPChWICxSp1ZNeh… asist. Matic Kadiš, mag. psih. Asistent | Assistant Univerza v Mariboru | University of Maribor Filozofska fakulteta | Faculty of Arts Oddelek za psihologijo | Department of Psychology Koroška cesta 160, 2000 Maribor, Slovenija E: matic.kadis1(a)um.si

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Help
by Gantz, Abbey 10 Aug '25

10 Aug '25

External Email - Use Caution Hello, I’m just contacting to ask for advice with the use of recon-all on a participant that has an abnormally structured brain, specifically a compressed Anterior temporal lobe. Recon-all finished without error, but didn’t completely encapsulate the anatomy properly. I ran recon-all using this code: recon-all -s omni07 -i /mnt/sml_share/OMNI/derivatives/fpp/sub-omni0 7/anat/sub-omni07_space-individual_res-1_desc-preproc_Tlw.nii.gz -all -deface -T2 /mnt/sml. share/OMNI/derivatives/fpp/sub-omni07/anat/sub-omni07_space-individual_res-1_desc-preproc_7 2w.nii.gz -T2pial The final recon-all brain mask.mgz file came out like this: [cid:10e2f9c0-f6e6-4f8f-bf38-405a0b106646] Questions: 1. Are there flags to or steps to manually adjust surface place for such cases? 2. Would you recommend disabling certain steps/running in stages to improve the outcome? Thank you for your help, and let me know if there is anything else I can provide to clarify the issue Abigail Gantz PhD Student | Social Memory Lab Tulane Department of Psychology agantz1(a)tulane.edu

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Issue with Pial and WM Surface Distortion
by Mahta Abbaspour 10 Aug '25

10 Aug '25

External Email - Use Caution Hello FreeSurfer team, While performing QC on my recon-all output, I spotted an issue in a scan where the pial surface intersects with the white matter surface, causing distortions across several slices in that region. I overlaid the filled.mgz and white matter segmentation, and the area appears to be fully filled in both masks, so I'm not quite sure why the surfaces are inaccurate here. I'd appreciate any insights and the best way to edit this. I've attached a few example slices below for reference. [image: image.png] [image: image.png] [image: image.png] [image: image.png]

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Consistent Dura Inclusion in QC
by Mahta Abbaspour 10 Aug '25

10 Aug '25

External Email - Use Caution Hello Freesurfer team, I'm currently performing QC on the FreeSurfer outputs and noticed that in many scans, there’s consistent inclusion of dura near the occipital lobe and cerebellum, spanning approximately 10–40 slices sometimes. No dura is included in the anterior or middle slices. I had two questions: - Do you have any idea why this might be happening? The pial and white matter surfaces look fine throughout. - What would be the best way to address this? Should I manually remove the dura and regenerate the surfaces — though this is quite labor-intensive, especially when it affects many slices — or should I consider adjusting the -h parameter for more aggressive skull stripping? However, brainmask also look fine in all other regions. I’ve attached a screenshot from one of the slices for reference. I’d appreciate any suggestions you might have. Thank you. [image: image.png]

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License not received after confirmation
by 강다정 07 Aug '25

07 Aug '25

External Email - Use Caution Dear FreeSurfer team, I successfully confirmed my email address for FreeSurfer license registration, but I have not received the license.txt file yet. Could you please send it again? My registered email: doramisister(a)naver.com Affiliation: Yonsei Unsiversity Yoon lab Thank you very much. Best regards, Dajeong Kang

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Discrete pial surface
by Yujia Huang 06 Aug '25

06 Aug '25

External Email - Use Caution Hi Freesurfers, I have a question reagrding to how the pial surface is generated. For an oversimplified description, I assume each subject's pial surface was initially created with a spherical shaped 3D-topology model. Then each verticie on the sphere is assigned to specific location of the pial surface to cover the subject's brain. If that is the case, then I don't understand the result illustrated below in the figure. The figure is showing anatomical T1w image overlay with left and right pial surface from recon-all (command used at the end), while the red cross is targeting a pial surface located within cortical region. Although there is some mis-segmentation error nearby, I don't see the pial surface inside of the cortical region is connecting to any outer surface when I move the image slice back and forth. Is this allowed or even possible if the initial spherical surface can generate such discrete surface that is disconnected from the whole outer brain region? [cid:20a64222-bc84-4c74-9935-ffd295eac833] Does anyone know what is the cause of this and how to trouble shoot? Thanks in advance! 1. Freesurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 2. Platform: Ubuntu 24.04.2 LTS 3. uname -a: Linux hawaii 6.11.0-26-generic #26~24.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Apr 17 19:20:47 UTC 2 x86_64 x86_64 x86_64 GNU/Linux 4. Command and steps used for recon-all: * recon-all -autorecon1 -s <subj_id> -i <mp2rage_input> * check and verify skull strip quality * recon-all -autorecon2 -autorecon3 -s <subj_id> Best, Yujia Huang Research Engineer Advanced Imaging Research Center UT Southwestern Medical Center 2201 Inwood Rd. Dallas, TX, USA, 75390 Office: 214.645.5241 Pronouns: He, Him, His ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Re: Reading mca-dura.both-lh.nstd21.fhs.h5 error
by fsbuild 05 Aug '25

05 Aug '25

External Email - Use Caution   This looks like a file system access/permissions problem, i.e., the hdf5 python code being run from where freesurfer is installed, namely the code in /usr/local/freesurfer/8.1.0/python/lib/python3.8/site-packages/h5py/_hl/files.py claims it cannot see or read the file via the absolute path /models/mca-dura.both-lh.nstd21.fhs.h5 Such an error might occur if /models/mca-dura.both-lh..nstd21.fhs.h5 is not a valid hdf5 file, or /models is a mount point or soft link in your computers file system.  It does however look like some previous code was able to open /models/mca-dura.both-lh.nstd21.fhs.h5 and load in the weights. You could try cd’ing to /usr/local/freesurfer/8.1.0/python/lib/python3.8/site-packages and see if you can read the file, i.e., “cat /models/mca-dura.both-lh.nstd21.fhs.h5”.  I would at least try re-locating that model file to be under a known path where you always have read/write permission like your home directory. - R. /usr/local/freesurfer/8.1.0/python/scripts/mri_sclimbic_seg --model /models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /data2/FST1T2Res/002_S_0295_006/mri/tmp.mri_mcadura_seg.271283/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 1 --fov 72 --i /data2/FST1T2Res/002_S_0295_006/mri/tmp.mri_mcadura_seg.271283/invol.lh.crop.nii.gz --o /data2/FST1T2Res/002_S_0295_006/mri/tmp.mri_mcadura_seg.271283/seg.lh.mgz Keeping anterior commissure in vols and stats Using CPU Using 1 thread(s) Loaded lookup table /data2/FST1T2Res/002_S_0295_006/mri/tmp.mri_mcadura_seg.271283/dumca.lh.ctab Loaded population stats /usr/local/freesurfer/8.1.0/models/sclimbic..volstats.csv nb_labels 2 inshape (72, 72, 72) features 24   (None, 72, 72, 72, 1) Loading weights from /models/mca-dura.both-lh.nstd21.fhs.h5 -----------------------     segmenter = LimbicSegmenter(model_file=model_file,   File "/usr/local/freesurfer/8.1.0/python/scripts/mri_sclimbic_seg", line 425, in __init__     self.model.load_weights(model_file, by_name=True)   File "/usr/local/freesurfer/8.1.0/python/lib/python3.8/site-packages/keras/src/utils/traceback_utils.py", line 70, in error_handler     raise e.with_traceback(filtered_tb) from None   File "/usr/local/freesurfer/8.1.0/python/lib/python3..8/site-packages/h5py/_hl/files.py", line 562, in __init__     fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)   File "/usr/local/freesurfer/8.1.0/python/lib/python3..8/site-packages/h5py/_hl/files.py", line 235, in make_fid     fid = h5f.open(name, flags, fapl=fapl)   File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper   File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper   File "h5py/h5f.pyx", line 102, in h5py.h5f.open FileNotFoundError: [Errno 2] Unable to synchronously open file (unable to open file: name = '/models/mca-dura.both-lh.nstd21.fhs.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) -- This is a copy of a message which has been originally sent to: "To" field: freesurfer(a)nmr.mgh.harvard.edu The message has been sent by https://secure-web.cisco.com/1K-uMBwgIPgOmDbmGlFSw0j7kzReQeeg5ieEo0Di0x-0Ti… and the used account name was: SSL  

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