Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

Can find "mri_WMHsynthseg" command in freesurfer 7.4.1
by Byripudi Naveen Kumar ed20d402 28 Jun '24

28 Jun '24

External Email - Use Caution Dear freesurfer experts, I was trying to use synthseg for segmenting and parcellating a heterogeneous brain with lesions. It is advised in the freesurfer synthseg webpage to use mri_WMHsynthseg command for these cases. How ever when I tried to run the command, it shows that command not found. I checked mri_synsthseg command works. What shall I do to resolve this? Is there a way to install the mri_WMHsynthseg or is it part of some existing commands? Regards, Naveen Kumar

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Inquiry about alpha inflation in multiple comparison
by Emma Harper 28 Jun '24

28 Jun '24

External Email - Use Caution Dear Freesufer teams, Does anyone have any recommendations to correct for alpha inflation when doing the multiple comparisons in freesurfer? We are trying to avoid using the Bonferroni Correction so any recommendations for ways beside that would be greatly appreciated. Thanks, Emma Harper

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FreeSurfer atlases
by Savoia, Alice (Stud. FPN) 28 Jun '24

28 Jun '24

External Email - Use Caution Hello, I am looking for a freesufer standard atlas for hippocampal subfields (to be used for a DTI pipeline in FSL) but I cannot find it in fsaversage/label. Does anyone have any suggestion? Thank for the help, Alice

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Error saying cannot find my file for recon-all
by Lydia Luck 28 Jun '24

28 Jun '24

External Email - Use Caution Hello- I am trying to do recon-all on my brain MRI and I’ve rewritten it so many times I have absolutely no clue what is going wrong. Ultimately, the main error message I’m getting is that my file is not found. I’ve tried typing out the complete path, made multiple different folders, renamed the file and the folders, changed the file type, changed the location of the folder, exited terminal and tried again, switched to the other user on the computer (got the same error) even restarted my computer, etc. Kind of at a loss at this point. I am using a Mac with an M1 chip and the 7.4.1 version This is my current line of commands: export FREESURFER_HOME=/Applications/freesurfer/7.4.1 source $FREESURFER_HOME/SetUpFreeSurfer.sh export FS_LICENSE=/opt/freesurfer/license.txt export SUBJECTS_DIR=$Users/lydialuck/3DBRAIN recon-all -s lydiasbrain -i $Users/lydialuck/3DBRAIN/struct.nii.gz -parallel -all And then getting this back: ERROR: cannot find /lydialuck/3DBRAIN/struct.nii.gz Darwin Blazes-MBP.lan 23.4.0 Darwin Kernel Version 23.4.0: Wed Feb 21 21:44:06 PST 2024; root:xnu-10063.101.15~2/RELEASE_ARM64_T8103 arm64 recon-all -s lydiasbrain exited with ERRORS at Thu Jun 27 01:13:56 EDT 2024 If you could help me figure this out that would be great; I’ve probably spent well over 6 hours now trying different things. Thanks so much, Lydia

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The file absence problem of the recon-all -all output
by Quanjiang Liu 28 Jun '24

28 Jun '24

External Email - Use Caution Hi, I ran the recon-all -all command successfully. But the lh.seghead and rh.seghead didn't appear in my output folder. The attachment is the process record. Can you help to solve it? Sorry to bother. Best

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Inquiry About Using Freeview's ROI/Voxel Edit Tool on Surface File
by Dai, Y. (Yuxuan) 27 Jun '24

27 Jun '24

External Email - Use Caution Dear Freesurfer support team, Hope this email finds you well. I am writing to ask about using Freeview's ROI/Voxel edit tool on the surface file. To be more specific, my situation is that I need to customize regions of interest by manually drawing areas on the surface file and then storing the selected voxels, and I'm wondering if it's possible to do so with Freeview. I have found some previous scripts suggesting that this can be done using tksurfer. However, I understand that tksurfer has been deprecated for quite some time, and we are also eager to transition to a more updated tool. Yet, compared to tksurfer, freeview seems to be less flexible in terms of surface editing. It appears that I cannot find a surface operation tool in freeview that is similar to tksurfer. Moreover, tksurfer accepts customized parameter recipes (such as revphaseflag, usefdr, fthresh, etc.), configured through a .tcl file, but this option is no longer functional in freeview. If I want to continue using my old tksurfer configuration for surface display, is there a way to translate all those options to freeview? Thanks for your assistance in advance. Best, Yuxuan

2 1

MRI watershed error
by Gaurav Ambwani 27 Jun '24

27 Jun '24

External Email - Use Caution Dear Freesurfer developers, I took a 1mm T1 MRI of the MNI152 skull stripped it using HD brain extraction tool in 3D slicer, and then I registered it in fsl to a skull stripped version of a T1 weighted image of a Stroke patient (which I got from Openneuro). The purpose of doing this is to, get the aseg.mgz file and overlay that onto the MRI of the stroke patient. Previously I have taken the T1 1mm MNI image and received an aseg.mgz file which I have overlayed onto my MNI registered T1 weighted stroke MRI and that worked perfectly. However, This time I have taken the T1 1mm MNI image registered that to my stroke T1 MRI, and the registered image hasn't gone through freesurfer. I have attached the recon-all.log file in this email. Freesurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 Uname -a: Linux DESKTOP-HV9KQQ6 5.10.16.3-microsoft-standard-WSL2 #1 SMP Fri Apr 2 22:23:49 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Distributor ID: Ubuntu Description: Ubuntu 22.04.4 LTS Release: 22.04 Codename: jammy I am using a WSL in windows 11 (64 bit) Thank you, Best Wishes, Gaurav Ambwani.

3 9

Differences between lme_mass_fit_vw and lme_mass_fit_Rgw
by Dan Levitas 26 Jun '24

26 Jun '24

External Email - Use Caution Hello, I've been analyzing a dataset consisting of two groups (control, clinical), each with two timepoints (tp1, tp2), following FreeSurfer's LME longitudinal analysis pipeline, to assess cortical thickness differences. Given the relative simplicity of my data, I've only specified a single random effect (intercept). In the FreeSurfer section on spatiotemporal models, it begins with "*Spatiotemporal models are more powerful to detect effects in your data than traditional vertex-wise models when two or more random effects are included in the longitudinal statistical model.*" However, I've currently been using the spatiotemporal model approach (lme_mass_fit_EMinit, lme_mass_RgGrow, lme_mass_fit_Rgw) with the single random effect, but am curious if this is inappropriate and instead need to use the mass-univariate (lme_mass_fit_vw) workflow? Dan

2 2

Recon-all manual edits - multiple re-runs
by Blujus, Jenna 25 Jun '24

25 Jun '24

External Email - Use Caution Hi all, I have processed a set of T1w data through recon-all (v7.3.2) and am now making manual edits, if necessary. I have had a few cases where control points, wm.mgz, and brainmask edits are needed and incorporated via 'recon-all -autorecon2-cp -autorecon3 -s ${id}'. However, upon inspection of the updated outputs following the initial manual edits, further edits are required only to the wm.mgz to fix new topological errors. To incorporate the second round of wm edits, would I need to rerun recon-all from the control point stage to incorporate *all* edits (i.e., first round [control points, wm, brainmask]) or just from the wm stage with recon-all -autorecon2-wm -autorecon3 -s ${sid}? Essentially, I am asking if each time recon-all is re-run does it progressively build off of previous edits? Let me know if you need any clarification. Thanks in advance, Jenna

2 1

Registering Two Anatomical Images
by Andrew Jahn 25 Jun '24

25 Jun '24

External Email - Use Caution Hello, I have a raw anatomical image called raw.mgz, which I have manually annotated using Freeview; the resulting annotations are saved in a file called seg.mgz. I want to compare this to the annotations automatically generated by recon-all, so I ran the image through the recon-all processing stream. However, the original dimensions of the raw.mgz image are 256x209x256, and recon-all resamples the image to 256x256x256 resolution. If I want to compare the amount of overlap between my annotations and those generated by FreeSurfer - specifically, the aparc+aseg.mgz file created by recon-all - what is the best way to register the seg.mgz file to aparc+aseg.mgz? I looked through the documentation of mri_vol2vol, but I wasn't sure which registration file to use. Is it one of the transformation files contained in the "transforms" folder from the image that has been processed through recon-all? Thank you! -Andy

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