Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

recon-all Segmentation Error
by Boa Sorte Silva, Narlon 20 Nov '24

20 Nov '24

Hi there, Hope all is well Is there any preprocessing or additional steps within FreeSurfer that could help with issues like the ones in the images attached (aside from manual edits)? Granted this is an example of a sample of older individuals with marked neurodegeneration. Nárlon Cássio Nárlon C Boa Sorte Silva, PhD (He, Him, His) Postdoctoral Fellow Centre for Aging SMART, Vancouver Coastal Health Research Institute Djavad Mowafaghian Centre for Brain Health, Vancouver Coastal Health Research Institute Department of Physical Therapy, University of British Columbia +15196944893 https://secure-web.cisco.com/1WOyPTiy1S37KSd-TKeW2x9b9p4Iz3oChJj2C73O4_E4Rm… https://secure-web.cisco.com/11fPHF_NbaiAS9OznZllbCbArfM8-LaAlHeQDjv3l-NN6e… External Email - Use Caution

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mri_vol2surf error: GM estimation couldn't find enough samples
by Lee, Hansol 20 Nov '24

20 Nov '24

Dear FreeSurfer developers, I am attempting to use “mri_vol2surf” command to project output from diffusion MRI models (e.g., DTI) onto the cortical surface. The registration between the diffusion MRI and anatomical space was performed using “bbregister”, and the projection works well for different --projfrac values (e.g., 0 to 1 from the white matter surface). However, I encountered issues when attempting to use the “—projopt” option to account for partial volume effects. Specifically, I received the following errors: “reading gm volume fraction from /autofs/space/allegro_002/users/hlee/SANDI/pvf/Tract_HC_001_07222016/pvf.gm.mgz reading wm volume fraction from /autofs/space/allegro_002/users/hlee/SANDI/pvf/Tract_HC_001_07222016/pvf.wm.mgz reading csf volume fraction from /autofs/space/allegro_002/users/hlee/SANDI/pvf/Tract_HC_001_07222016/pvf.csf.mgz error: No such file or directory error: GM estimation at vno 0 couldn't find enough samples error: No such file or directory error: GM estimation at vno 1 couldn't find enough samples error: No such file or directory error: GM estimation at vno 2 couldn't find enough samples error: No such file or directory error: GM estimation at vno 3 couldn't find enough samples error: No such file or directory error: GM estimation at vno 4 couldn't find enough samples error: No such file or directory error: GM estimation at vno 5 couldn't find enough samples error: No such file or directory” In the directory, I already have “pvf.gm.mgz”, “pvf.wm.mgz”, and “pvf.csf.mgz” files. I searched the archive and found a similar error reported in this thread: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg72784.html I would greatly appreciate any insights or suggestions to resolve this issue. Thank you in advance for your help! Best regards, Hansol Lee

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Help with mri_vol2surf incorrect surface generation
by Pandey, Shraddha 20 Nov '24

20 Nov '24

External Email - Use Caution We are experiencing issues with `mri_vol2surf` generating an incorrect surface for the `Paramagnetic.nii` volume. Although the registration file (`volume_transform.dat`), created using `bbregister`, appears accurate, the output surface file (`Paramagneticsurface.mgh`) does not look correct. Specifically, some voxel values in the cortical areas are incorrectly predicted as zero. Command: ```bash input_volume=Paramagnetic.nii output_surface=Paramagneticsurface.mgh output_reg_file=volume_transform.dat mri_vol2surf --mov "$input_volume" --reg "$output_reg_file" --hemi lh --projfrac 0.2 --o "$output_surface" ``` Any guidance on resolving this issue with the surface generation would be greatly appreciated.

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mri_coreg error: could not open brainmask.mgz file to register PET image with anatomical
by Lai, Ian M. 20 Nov '24

20 Nov '24

External Email - Use Caution Trying to run this command: mri_coreg --s 002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501 --mov 002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/pet/template.nii.gz --reg 002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/pet/template.reg.lta Receiving this output and error: $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /blue/babajani.a/SharedFolder_SDT_Fall24/MRI_FreeSurfer_Outputs/ADNI_FreeSurferResults/002_S_0413/MPRAGE_SENSE2/2011-06-16_12_36_58.0/I240808 cmdline mri_coreg --s 002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501 --mov 002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/pet/template.nii.gz --reg 002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/pet/template.reg.lta sysname Linux hostname login9.ufhpc machine x86_64 user ianlai dof 6 nsep 2 cras0 1 ftol 0.000000 linmintol 0.001000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Seed 53 Reading in mov 002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/pet/template.nii.gz Reading in ref /apps/freesurfer/7.4.1/subjects/002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/mri/brainmask.mgz error: mghRead(/apps/freesurfer/7.4.1/subjects/002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/mri/brainmask.mgz, -1): could not open file I am able to manually download the brainmask.mgz file from that directory and open it in MRIcroGL, wondering what could be the issue here? Also dealing with a separate issue where when doing mri_gtmpvc \ --i 002_S_0413_MPRAGE_SENSE2_2011-06 16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/pet/002_S_0413.nii.gz \ --reg 002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/pet/template.reg.lta \ --psf 6 \ --seg 002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/mri/gtmseg.mgz \ --default-seg-merge \ --auto-mask 1 .01 \ --mgx .01 \ --km-ref 46 47 \ --km-hb 11 12 50 51 \ --no-rescale \ --o 002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/gtmpvc.kmref-46-47.kmhb-11-12-50-51-output, The output in the gtmstats file seems to be exactly the same when changing km-ref from 7 8 46 47 to 46 47, which I have also attached. Have never done this before so no idea if these values are in a range that seems reasonable or if it means we are providing it a blank file. Any help would be appreciated, Ian. 1) FreeSurfer version: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 2) recon-all.log: see attached

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How to interpret the vertex-wise area metric?
by Alex 20 Nov '24

20 Nov '24

External Email - Use Caution Dear FreeSurfer experts, I have a question about the interpretation of the vertex-wise area metric. For instance, if Vertex A had a larger area than Vertex B, then what's the difference between Vertex A and Vertex B biologically?  Based on my simple (probably wrong) understanding of the surface reconstruction process, the initial surface was created based on the GM-WM boundary voxels, in which the face of a voxel was divided into two triangles and the area of the triangles was equal. But after the refinement of the initial surface, the triangle area was not uniform any more. So what factors may explain the expansion or contraction of the surface triangles? I believe these factors may help me understand the vertex-wise area metric. Maybe I should treat the vertex and the triangles around it as a whole, which is the unit of comparison. For instance, the Vertex A having a larger area means the area of triangels around Vertex A is larger. This kind of interpretation would make the comparsion between Vertex A and B biologically meaningless. From another perspective, in the voxel-based morphometry (VBM), the voxel size is fixed and the volume is the proportion or probability of GM (or other tissue types) in the voxel. In the surface case, if the triangle size is kept fixed, the area is proportial to the number of triangles, which is conceptually similar to the VBM approach. Why FreeSurfer did not choose this kind of approach? Sorry if this question is not reasonable, as I did not have a strong technical background. Best, Yang Hu

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trac-all errors
by Alberto Benelli 20 Nov '24

20 Nov '24

External Email - Use Caution Dear freesurfer experts, I am trying to run trac-all -prep -c /Users/albertobenelli/tracula.config and getting the attached error. Do you have any ideas on how to solve the problem? Thank you, Alberto

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Synthmorph Deformations -Separating Components of Transforms
by Josh Lee 19 Nov '24

19 Nov '24

External Email - Use Caution Dear FreeSurfer People, I am hoping to use Synthmorph in a VBM or DBM like longitudinal analysis where I register timepoints to a template. Typically in VBM/DBM type analyses we decompose the affine and nonlinear transforms. The advantages of the joint registration approach may be that its high performance symmetry lessens the need to create an unbiased middle template of the timepoints. However, it produces a single deformation field comprising both affine and nonlinear deformations. I thought I could initialize using an affine, but it seems doing so still produces a deformation image comprising both affine and nonlinear transforms. It seems I have two options. 1) Somehow use the affine matrix to subtract (somehow) the affine component from the deformation field. 2) Perform deform only registration on an affine transformed image, in which case creating a template is probably needed. Juan Iglesias provided code to me once that suggested I compute the Jacobian of the full field, take the logarithm, and subtract the average (which Dr. Iglesias assured me is the contribution of the affine part). However, I am really unsure if that perfectly removes the 12 dof affine components, not that I doubt his expertise, I'd just like a second opinion :) On a side note, I just bought a gpu for the lab with 16Gb, vram and I'm really regretting not moving that up to one with 24Gb vram.

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Re: [Freesurfer] Freesurfer tutorial troubles
by fsbuild 18 Nov '24

18 Nov '24

External Email - Use Caution The tutorial data exercises are not entirely up to date with the just announced beta release.   For now you could try running a pre 8.X stable dev build fromhttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/stable/- or for your M2 Mac, you would download and install,https://secure-web.cisco.com/1EHRZsiHuqZq__miKwcpbBYt0uQDNvI4V5qJK8… Before installing that dev build package I would remove your current install by running the following from the terminal$ cd $FREESURFER_HOME$ sudo bash uninstall.sh … answer the prompt to remove … - R. On Nov 18, 2024, at 16:37, Marcin Stański <marcin_stanski(a)hotmail.com> wrote:        External Email - Use Caution          <recon-all.log>_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/14F9RgT-BxqTI5c0ZHPStC12BkXBT3nknrz8Lwqv50daLL…

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Freesurfer tutorial troubles
by Marcin Stański 18 Nov '24

18 Nov '24

External Email - Use Caution Dear Freesurfer developers, I have no previous experience in Freesufer and I am trying to go through the tutorial before analyzing my own data. I’m working on the dataset you shared on your website. I work on MacBook Pro Apple M2 Pro 32 GB Sonoma 14.2.1. My Freesurfer version is 8.0.0 beta. I set environmental variable FS_ALLOW_DEEP to 1 as suggested. The dataset was one from the tutorial. The directory name was practice_with_data/dicoms I ran recon-all command: recon-all -all -i I49 -s Subj001 Freesurfer had worked for a time but eventually it came up with a message: (0) INVALID_ARGUMENT: input must be 4-dimensional[1,72,72,72,24] [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]] [[unet/unet_bn_down_0/FusedBatchNormV3/_16]] (1) INVALID_ARGUMENT: input must be 4-dimensional[1,72,72,72,24] [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]] 0 successful operations. 0 derived errors ignored. [Op:__inference_predict_function_1146] ERROR: Darwin 192.168.1.14 23.2.0 Darwin Kernel Version 23.2.0: Wed Nov 15 21:55:06 PST 2023; root:xnu-10002.61.3~2/RELEASE_ARM64_T6020 arm64 recon-all -s Subj001 exited with ERRORS at Mon Nov 18 21:41:39 CET 2024 label, surf, tmp, touch and trash in Subj001 are empty. I checked the mailing list but I couldn’t find any hint.. Please find attached recon-all.log file. I would be very grateful for your help! Marcin Stański Poznań University of Medical Science Department of General Radiology and Neuroradiology Poznań, Poland

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Re: [Freesurfer] Synthstrip error in FS v. 8.0.0 beta
by fsbuild 18 Nov '24

18 Nov '24

External Email - Use Caution Hello Adam, Sorry for the delay in getting back to you. If possible, I would do “sudo apt install ./freesurfer_ubuntu22-8.0.0-beta_amd64.deb” so that you end up with FREESURFER_HOME=/usr/local/freesurfer/8.0.0-beta and so that the linux install tools will have installed any missing packages on your system.  Then try putting SUBJECTS_DIR to be under a non-system subdirectory, e.g., “mkdir $HOME/subjects” and then “export SUBJECTS_DIR=$HOME/subjects”.   The recon-all command should be run with normal user (non-root, non-sudo) privileges. - R. On Nov 6, 2024, at 13:51, Raikes, Adam C - (adamraikes) <adamraikes(a)arizona.edu> wrote:        External Email - Use Caution        Hello Developers, I was attempting to test out the beta version of 8.0.0 and I recognize that this is on-going development. I installed it in a Singularity image running Ubuntu 22.04. Getting recon-all to run at all requires setting an environmental variable (FS_ALLOW_DEEP=1), which I did and recon-all launches. However, it crashes very quickly. In short, orig/001.mgz is created and then it immediately attempts to run mri_synthstrip on orig.mgz, which does not exist yet. See attached logs. Adam C. Raikes, PhDImaging Projects ManagerCenter for Innovation in Brain ScienceUniversity of Arizona <recon-all.log>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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