Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30128 discussions

Freeview questions
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 22 Sep '25

22 Sep '25

External Email - Use Caution Hi freeview developers - Still trying to make a rough transition from tkmedit to freeview. I have two questions: *I want to the recon brush to paint the main volume voxels from a secondary volume. Is there a possible way to do that in freeview without doing it one voxel at a time? Ex. I want to draw back voxels from the brainmask.mgz from the T1.mgz. *What are waypoints? I don't see any instructions on the wiki on how to take advantage of them - are they designed to supersede control points? Thanks. Victor Zeng Beth Israel Deaconess Medical Center Vial of Victory LLC -- ---------------------------------------------------------------------- PLEASE NOTE: This message is intended for the use of the person to whom it is addressed. It may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the intended recipient, your use of this message for any purpose is strictly prohibited. If you have received this communication in error, please delete the message and notify the sender so that we may correct our records. See our web page at http://secure-web.cisco.com/1an1yVo6v6mmRxVNWBlv4yPHWVxCUoCso9_-8NIHwNomwWY… for a full directory of Beth Israel Lahey Health sites, staff, services and career opportunities.

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Creating aparc+aseg files
by Chen Goldstein 22 Sep '25

22 Sep '25

External Email - Use Caution Hello, I’m working with data created using freesurfer, specifically aparc+aseg.mgz files (I’m using nii.gz). I was wandering if you can tell me what is the minimal way to create this file? I don’t want to run the whole Recon-All process and was wandering if there is a shorter way to create them, and if yes how long creating one scan might take? Thank you in advance.

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Questions for analyzing pediatric data
by Yoonho Hwang 22 Sep '25

22 Sep '25

External Email - Use Caution Dear FreeSurfer experts, Hello, I hope this message finds you well. I am planning to perform FreeSurfer analyses across a range of pediatric age groups. It is recommended to use the adult FreeSurfer pipeline for individuals aged 5 and older, and the infant FreeSurfer pipeline for those up to 2 years of age. Which pipeline should be used for analyzing pediatric subjects between the ages of 2 and 5? Additionally, could you recommend any papers that provide guidelines or age criteria for pipeline selection? Thank you very much! Sincerely, Yoonho

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Question about combining data from cohorts processed with different Freesurfer versions
by Stacey Schaefer 21 Sep '25

21 Sep '25

External Email - Use Caution Hello Freesurfer gurus, We have two samples of approximately n~125-150 whose T1s were collected on the same scanner with the same acquisiton, except for a difference in head coil (8 vs 32 channel) and processed with different Freesurfer versions (v5.3.0 and v. 6.0.0). Both also had the FreeSurfer segmentation of hippocampal subfields v 6.0.0 applied. We would like your guidance about combining their data if possible to maximize sample size. What would your suggestion be for hypothesis testing? Can we combine the samples - for example to test moderators of hippocampal x age relationships, using simply a covariate to account for the differences in acquisition/Freesurfer processing (in addition to the usual sociodemographic and estimated intracranial volume covariates)? OR is that problematic and would you instead suggest keeping them separate and using one as a replication sample? Thank you for your guidance! Stacey Stacey M. Schaefer, Ph.D. Leader of the MIDUS Neuroscience Project & Co-Leader of the MIDUS Admin Core MIDUS NEURO Keystone House 901 University Bay Dr Madison WI 53705

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Re: recon-all: expert options not applied to mris_inflate
by Su, Weizhong 21 Sep '25

21 Sep '25

External Email - Use Caution Hi Yahia, I faced same issue when using mris_inflate expert option. Do not use this option for Freesurfer v8.1.0 until FS developer team fixes this problem. Best, Wayne From: "Mokli, Yahia" <yahia.mokli(a)psychiat.med.uni-giessen.de> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, September 4, 2025 at 8:53 AM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] recon-all: expert options not applied to mris_inflate [CAUTION: Non-UBC Email] External Email - Use Caution Hello FreeSurfer Team, What I am trying to accomplish: I am running a full recon-all (-all) and trying to control the number of inflation iterations via an expert options file containing: "mris_inflate -n 30" FreeSurfer version and platform: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed Running inside Docker based on Ubuntu 22.04 Command I ran: recon-all -i /data/test/sub-0113_t1_axisAlign.nii.gz -s sub-0113 -all -hires -parallel -openmp 16 -expert /data/test/expert_inflate30.opts Error/output seen: During the Inflation1 stage, the log shows mris_inflate being invoked without the -n flag and with a bare “30” argument: mris_inflate -no-save-sulc 30 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Shortly after, recon-all exits with ERRORS. The recon-all.log file have these lines at the end: #@# Inflation1 lh Thu Sep 4 13:54:46 UTC 2025 /data/subjects/sub-0113/scripts mris_inflate -no-save-sulc 30 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #----------------------------------- #@# Inflation1 rh Thu Sep 4 13:54:46 UTC 2025 /data/subjects/sub-0113/scripts mris_inflate -no-save-sulc 30 ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 4083 of (4083 4086) to complete... Waiting for PID 4086 of (4083 4086) to complete... mris_inflate -no-save-sulc 30 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading 30 ** failed to open GIFTI XML file '30.gii' mrisReadGIFTIdanum: ERROR reading gifti 30.gii [INFO] read, cannot find 30, trying 30.gii ... error: No such file or directory error: mris_inflate: could not read surface file 30 mris_inflate -no-save-sulc 30 ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading 30 ** failed to open GIFTI XML file '30.gii' mrisReadGIFTIdanum: ERROR reading gifti 30.gii [INFO] read, cannot find 30, trying 30.gii ... error: No such file or directory error: mris_inflate: could not read surface file 30 PIDs (4083 4086) completed and logs appended. Linux 4fa29909686b 6.8.0-78-generic #78-Ubuntu SMP PREEMPT_DYNAMIC Tue Aug 12 11:34:18 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-0113 exited with ERRORS at Thu Sep 4 13:54:46 UTC 2025 Troubleshooting already tried: - Recreated the expert file to ensure ASCII hyphen and LF newline: printf 'mris_inflate -n 30\n' > /data/test/expert_inflate30.opts - Resumed with overwrite -xopts-overwrite -expert /data/test/expert_inflate30.opts - Verified that mris_inflate accepts -n 30 manually:: /usr/local/freesurfer/8.1.0/bin/mris_inflate -no-save-sulc -n 30 in.surf out.surf - Other expert options (e.g., “mris_smooth -seed 9999”) are honored and appear correctly in the log Is there a known issue in FreeSurfer 8.1.0 on Ubuntu 22.04 where expert options for mris_inflate are not applied? What is the recommended way to ensure -n 30 is honored? Thank you for your help. Best regards, Yahia Mokli

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21 Sep '25

External Email - Use Caution Hi Freesurfer community, I am currently trying to project 3D density maps in individual diffusion space onto the cortical surface (within individual space). I'm not sure which registration function to use to obtain the register.dat file required for mri_vol2surf . Does bbregister work for this situation? If so, assuming I create a registration from diffusion space (RASmm/ACPC) to fsnative, would the --mov file as the T1w in diffusion space – same affine as that of the diffusion data, and same resolution as diffusion data– (obtained from qsiprep) work with the target being the T1 in fsnative space? Or should I use another type of function such as tkregister2 or something like this? My current code is the following: template_file = op.join(bids_path, 'derivatives', 'qsiprep', participant, 'anat',f"{participant}_space-ACPC_desc-preproc_T1w.nii.gz") registration_file = op.join(out_dir, 'ACPC2fsnative_register.dat') # 1) Generate registration file .dat cmd = ["bbregister", "--s", participant, "--sd", fs_path, "--mov", template_file, "--reg", registration_file, "--init-fsl", "--t1" ] print("Running:", " ".join(cmd)) subprocess.run(cmd, check=True, env={**os.environ, "SUBJECTS_DIR": fs_path}) #2) Apply ACPC2fsNative registration and project density map to surface hemisphere = ['L', 'R'] roi = ['LeftMTxWMxLGN', 'RightMTxWMxLGN'] for h, hemi in enumerate(hemisphere): mask = roi[h] density_map = op.join(analysis_path, 'tdi_maps', 'dipy_tdi_maps', participant, f"{participant}_ses-concat_desc-{mask}_tdi_map.nii.gz") # density_img = nib.load(density_map) # print(density_img.affine) # Output file name out_file = os.path.join(out_dir, f"{participant}_hemi-{hemi} _space-fsnative_label-{mask}_tdi_on_surf.mgh") if hemi == 'L': hm = 'lh' else: hm = 'rh' # Build mri_vol2surf command cmd = [ "mri_vol2surf", "--mov", density_map, "--regheader", participant, "--hemi", hm, "--reg", registration_file, "--surf", "white", "--projfrac", "0", "--sd", fs_path, "--out", out_file ] # Run the command print("Running:", " ".join(cmd)) subprocess.run(cmd, check=True, env={**os.environ, "SUBJECTS_DIR": fs_path}) Thanks, Best, -Loïc

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Zero Values for SegmentedTotalIntracranialVol
by Carly McIntyre-Wood 21 Sep '25

21 Sep '25

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Trouble figuring out error
by Reyes, Nicholas 21 Sep '25

21 Sep '25

External Email - Use Caution Hello! I cannot seem to figure out the problem with this patient. I am newer to using freesurfer, so I am a little lost trying out what I've read in the documentation. Could you help give me some insight on figuring this out? Thank you in advance, Nicholas K. Reyes | B.S. in Neuroscience Neural Signals Processing and Modeling Lab The University of Alabama at Birmingham nkreyes(a)uab.edu<mailto:nkreyes@uab.edu> || 205-937-3421 Nicholas K. Reyes | UNP Major & BME Minor College of Arts and Sciences The University of Alabama at Birmingham nkreyes(a)uab.edu<mailto:nkreyes@uab.edu> || 205-937-3421

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Issue with Skull Strip when Original Volume is Cut at the Nose
by 이준혁 21 Sep '25

21 Sep '25

External Email - Use Caution Environment - OS: Ubuntu 22.04.5 LTS - FreeSurfer: 7.4.1 I'm running FreeSurfer (Ubuntu 22.04 version 7.4.1), and during the Autorecon1 preprocessing, I noticed that the result depends on whether the original 3D volume includes the full face or the nose part is cut. When you run a truncated picture rather than a full face as input, the Skull strip results are completely different. In this case, do you have any official recommendations for normal preprocessing? How should I proceed I will attach the original picture and the pre-processing result picture.

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hippocampal subfield segmentation
by Zehua Cui 21 Sep '25

21 Sep '25

External Email - Use Caution Hi all, We want to use Freesurfer's automatic hippocampal subfield segmentation flag using a T1 and T2 (high resolution hippocampal T2 sequence that is focused on the Medial Temporal Lobe and does not have full coverage of the brain). We previously ran recon-all with just the T1. Is it essential for us to re-run recon-all with both the T1 and the T2 as input or can we simply run the subfields flag and specify the T1 and T2 (which we copied over into the recon-all output directory) there? Will it make a big difference for the resulting subfield volumes? Thank you very much! -- Zehua Cui|崔泽华, Ph.D. Post-Doctoral Fellow Neurocognitive Development Lab 4094 Campus Drive, Biology/Psychology Building University of Maryland, College Park, MD 20742 Zoom Meeting ID: https://secure-web.cisco.com/1_DD2JIMsdFxT6lsQdL9CaK--HcIDgdBd5U8PGauw5NHp6…

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