Freesurfer February 2024

freesurfer@nmr.mgh.harvard.edu

58 participants
83 discussions

formula calculating percent signal change
by Tina Zahrie 23 Feb '24

23 Feb '24

External Email - Use Caution Hi all, How is the percent signal change calculated within a ROI? What is the formula for it? Thanks, Tina

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psf formula PET SURFER
by Federica Di Antonio 23 Feb '24

23 Feb '24

External Email - Use Caution Dear experts, I'm employing PETsurfer for partial volume correction. Could you share the definition or formula you use to define the psf (flag --psf of mri_gtmpvc) that is used to correct the PET image? I understand that it is an isotropic gaussian filter, but could you maybe provide the precise formula you employ or the reference you refer to? Thank you so much for your kindness and availability, Federica Di Antonio

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ERROR: awk -f in Talairach registration and multibyte conversion failure; possibly due to region settings?
by Mohn, Johannes Julius 23 Feb '24

23 Feb '24

External Email - Use Caution Dear Freesurfer Developers, I installed Freesurfer 6.0.0 fresh on a Macbook Pro (2021) with M1 chip running macOS Monterey 12.5. I tried to run recon-all on both on the bert data shipped with freesurfer and my own brain data in .nii.gz format (standard T1 sequence). Both process start fine but abort at the exact same step with an error in Talairach registration. The command I use is: $> recon-all -i sub-20190911.nii.gz -s jjm -all SUBJECTS_DIR is set correctly; sub-20190911 exists. I receive the following error: ERROR: awk -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk /Users/jjm/sci/freesurfer_data/bert/mri/transforms/talairach_avi.log failed! The contents of the talairach_avi.log are as follows: awk: towc: multibyte conversion failure on: ' ' input record number 86, file /Users/jjm/freesurfer_data/jjm/mri/transforms/talairach_avi.log source line number 8 For better diagnostics, I'm attaching the recon-all.log and talairach_avi.log and avi_QA.log. Interestingly, in previous attempts to run recon-all, I had received the same error with multibyte conversion failure on 'Ù' and later on 'ö'. I suspected that at some level this is related to language and region settings on my machine. Therefore, I changed region from Germany to United Kingdom and keyboard from German QWERTZ to US keyboard layout (language has always been English on my machine). As a result the reported error regarding multibyte conversion changed from 'Ù' / 'ö' to now ' ', but the error stubbornly persists. Are there any known issues with running Freesurfer on particular region/language/keyboard settings? Thank you in advance for help in debugging this. Best regards, JJ __________ Johannes Julius Mohn Doctoral candidate Max Planck School of Cognition<https://secure-web.cisco.com/19jWGTQ9dwmh-_dPrP9eYtOCqIlpsSLcrob7locC4sg0-s…> Institut für Medizinische Psychologie Charité – Universitätsmedizin Berlin Campus Charité Mitte | Luisenstr. 57 | 10117 Berlin T +49 030 450 529 213 johannes.mohn(a)charite.de<mailto:johannes.mohn@charite.de> http://secure-web.cisco.com/1Fmh9RNa1Lp2C3p3fMNDLavMb1aZuOMd8wv3n950I6oYSLt…<http://secure-web.cisco.com/1Fmh9RNa1Lp2C3p3fMNDLavMb1aZuOMd8wv3n950I6oYSLt…>

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aseg QA questions
by Sarah Skinner 23 Feb '24

23 Feb '24

External Email - Use Caution Question 1 - We found a few voxels that are labeled as the right choroid-plexus, but it is nowhere near the rest of the structure. See attached image. Is this a problem? If yes, what is the best way to fix this? Question 2 - The right-lateral-ventricle appears to be separated into 2 unconnected areas. We are assuming this is okay, but we wanted a second opinion. See attached image. Thanks! Sarah Skinner Research Specialist Institute on Aging University of Wisconsin-Madison

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Cortical WM parcellation for DKT atlas?
by Hamied Haroon 23 Feb '24

23 Feb '24

External Email - Use Caution Hello Freesurfer Gurus, Is it possible to obtain "wmparc" but for the DKT cortical atlas, please? Many thanks. Best wishes, Hamied Dr Hamied A Haroon [he/him/his], MSc, PhD, MInstP Research Fellow in Quantitative Biomedical MR Imaging The University of Manchester

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Manual/reproduce conform
by Dipterix Wang 23 Feb '24

23 Feb '24

External Email - Use Caution Dear FreeSurer Wizards, I'm trying to run the recon-all command on one of my template brains such that the resulting Norig and Torig are identical. I understand that fs always conforms the MRI to 256^3 before segmentation. I wonder if there is any way that I can resample the original MRI to achieve the same Norig and Torig? More specifically, currently the Torig (vox to tkrRAS) is [,1] [,2] [,3] [,4] [1,] -1 0 0 128 [2,] 0 0 1 -128 [3,] 0 -1 0 128 [4,] 0 0 0 1 If I resample the input image such that Norig (vox to scanRAS) equals this matrix, can I expect that "conform" does not change the orientation? Alternatively, is there any method I can use to "predict" or reproduce the Torig from the original MRI outside of FreeSurfer? Thanks, - Dipterix

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Getting from MNI152 to fsaverage
by Lauri Tuominen 23 Feb '24

23 Feb '24

External Email - Use Caution Dear experts, I am comparing freesurfer mri_vol2surf to nilearn surface.vol_to_surf. I am finding large differences so I just wanted to get this command absolutely right before making any sort of conclusions. I would love if someone could confirm this is ok: ``` mri_vol2surf --mov task-rest_space-MNI152NLin6Asym.bold.nii.gz \ --mni152reg \ --hemi lh \ --surf white \ --o lh.task-rest_space-fsaverage.bold.nii.gz ``` Also I get complains about source volume voxel size (2,2,2) being different from target voxel size (1,1,1). I did read somewhere that this warning can be ignored. Is that correct? fsfast pipeline seems to use default projection fraction 0.5, while the default in the above command is 0. Could someone explain me the reasoning behind this? I am wondering if I should be using 0.5 or 0 with my data. Thank you so much!! Lauri

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Freesurfer white matter overestimated
by Luisa Klahn 23 Feb '24

23 Feb '24

External Email - Use Caution Hello! I am processing structural data from a 3T scanner using Freesurfer version 7.3.2. For some subjects, the grey matter looks very thin, and the white matter looks overestimated. I'll attach screenshots of the brainmask, wm mask, and T1 including wm and pial surface lines. I have tried to set control points into the wm but this did not change the results. Does anyone have an idea? Would it be possible to change the intensity settings in the recon-all command? Thanks for helping! Luisa

2 1

Fixing intensity normalization issue which leads to gray matter classified as WM
by Maya Yablonski 23 Feb '24

23 Feb '24

External Email - Use Caution Hello, I am running freesurfer v7.3.2 reconall with -synthseg on a pediatric sample, and for one specific subject I keep getting a lot of gray matter classified as white matter, which leads to the ?h.white surfaces being too close to the pial surface. I have tried running with and without the --robust option but the issue recurs. Are there any expert options that I can play with before manually editing the WM.mgz? The issue is pervasive throughout the brain so will require heavily editing every single slice. The values for the misclassified gray matter are 85-97 in the brainmask.mgz and 100-110 in the WM.mgz and the T1 image looks ok by eye. When trying to run the same subject with the default pipeline (no synthseg), it crashes with the following error: reading 1 input volumes... logging results to talairach.log reading '/share/software/user/open/freesurfer/7.3.2/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 1 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'nu.mgz'... error: mghRead(/MYPATH/freesurfer/sub-2341/mri/brainmask.mgz, -1): could not open file error: mri_em_register: could not open mask volume brainmask.mgz. I wonder if there's any parameter I can tweak in the expert.opts? Thanks for any leads, Maya

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Grey Matter Intensities
by ERNEST KISSI 21 Feb '24

21 Feb '24

External Email - Use Caution Hi Freesurfer team, Recon-all output shows the white matter volumes and white matter intensities of different brain regions but only shows grey matter volumes. I want to know if there is a function or a flag to also get information on the regional grey matter intensities. Thank you.

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Freesurfer February 2024