Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30064 discussions

creating a cortical label using a 3D image ROI and calculating its volume and average thickness
by Yakupov, Renat /DZNE 23 Feb '24

23 Feb '24

External Email - Use Caution Dear Freesurfer users, I would like to do the following: - there is an ROI mask image file in the same space as the T1-weighted image - I would like to use that mask to define the borders of a cortical area - and then calculate volume and average thickness of the above defined cortical area I know that I can get a rough estimate of the volume by applying the ROI mask to the the aparc* file and calculating the number of voxels, but what I would really like to do is use the ROI mask to constrain the WM and pial surfaces to the volume inside the ROI and then calculate statistics using the surfaces approach. I also know that I can combine existing labels, but unfortunately this custom ROI contains parts of various cortical regions, not whole regions. Any advice would be appreciated! Best wishes, Renat.

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How to write rh.w-g.pct from recon-all stats output into a table
by ERNEST KISSI 23 Feb '24

23 Feb '24

External Email - Use Caution I processed several items of data. And I have rh.w-g.pct file in my stats folders. How can I get process this file to get table reading file? I tried to use asegstats2table and aparcstats2table but it didn’t work. Could you provide me with necessary information about getting of stats from rh.w-g.pct to table file like asegstats2table? Thank you.

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Using MRI_segstats to calculate grey matter intensity
by ERNEST KISSI 23 Feb '24

23 Feb '24

External Email - Use Caution Hello freesurfer Team, I have the grey matter segmentation from FSL and I have freesurfer recon-all output but the recon-all outputs do not have regional grey matter intensities. Can I use MRI_segstats to calculate the regional grey matter output using the FSL grey matter segmentation and the recon-all subject hemi parc and subject hemi labels to get the various brain parts and labels for the grey matter?

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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

2 1

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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