Freesurfer June 2021

freesurfer@nmr.mgh.harvard.edu

97 participants
140 discussions

make other atlases compatible with freesurfer
by Roxana Namiranian 26 Jun '21

26 Jun '21

External Email - Use Caution Dear Friends, I want to use neonatal atlas in freesurfer which is compatible with brainVisa (available: https://secure-web.cisco.com/1xxPZ7hbZXB7YNzBLH04kH_oyg98giX78BB7hKRwAwIw9I…) How Can I use this atlas in freesurfer? (available files of this atlas are: label_?h.gii, template_?h.gii, template_?h.mesh, template_head.mesh, T1.nii, T2.nii, labeltable.csv) I am trying to do this using mris_ca_train, but it is challenging to provide suitable files needed for this function from the available files. Is there any other way to use this atlas in freesurfer? Thank you very much, best regards, Namiranian

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Changing script from tksurfer to freeview
by Marlene Staginnus 25 Jun '21

25 Jun '21

External Email - Use Caution Dear FreeSurfer Team, As part of the ENIGMA consortium, research groups that contribute data need to run certain standardized scripts to pre-process their data and create outputs for subsequent quality control using FreeSurfer. One issue that has recently occurred is that Mac users with a recent MacOS are no longer able to run one of the scripts that uses tksurfer to generate lateral and medial screenshots of the pial surface reconstructions. Reading previous posts in the mail archive, this seems to be due to recent versions of MacOS being unable to run 32-bit programmes like tksurfer and that users should either use Freeview for visualisation or revert to an older operating system. As the latter is not possible for some groups, we’ve been trying to edit the script by altering which programme it calls (e.g., freeview or tksurferfv instead of tksurfer) as well as other aspects of the script (e.g., -cmd instead of -tcl). However, so far, we have been unable to successfully amend the script. Would you have any pointers for us as to how to alter the script to call freesurfer whilst arriving at the same output (i.e., multiple screenshots of the external view of a subject’s brain)? Is there a way to script Freeview similar to using tcl in tksurfer? I have also attached the script in question to this email. The FreeSurfer versions used by the contributing research groups are 5.3 or 6.0. Thank you in advance for any advice you might have on this. Best wishes, Marlene

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Edits to White Matter (wm.mgz)
by Boa Sorte Silva, Narlon 25 Jun '21

25 Jun '21

External Email - Use Caution Dear FreeSurfer experts: I am working on a manual for my lab and I would like to clarify the two points below (to which I couldn’t find answers in the online FS content available): * When editing the wm.mgz fails, can control points (CPs) be used to correct pial errors cause by lesions (e.g., perivascular spaces, microbleeds, WMH). I understand the FS tutorial recommends against this, however at times it seems that only editing the wm.mgz will not be sufficient (Figure 1 below) * Should white matter voxels with 0 intensity in the wm.mgz (inside the white surface) be filled in, even when these voxels do not affect white matter surface segmentation whatsoever? (Figure 2 below). * Would the cerebral white matter volumetric data (wmparc.stats) be affected by these 0 intensity voxels? Thanks so much for you help! Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSFHR/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon [cid:0757C5B4-5E01-42A4-8BE6-6C5779C2D024][cid:E4FD3068-0778-4057-850B-40E9EB3318C8]

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Differences in FLAIR assisted pial segmentation from FS6.0 to FS7.1
by Fredrik Magnussen 25 Jun '21

25 Jun '21

External Email - Use Caution Dear FreeSurfer experts, We have processed UKB data with FLAIR assisted pial segmentation using FS7.1. The results differs quite a lot from using FLAIR assisted pial segmentation in FS6.0. For details please see the reported issue on the freesurfer github page: https://secure-web.cisco.com/1BsLOtOMPefP19V4jaUIGxvB6cloD65XJYgob0S0aurJu0…. Might be related to another issue reported here (though this is T2w assisted pial segmentation): https://secure-web.cisco.com/1ZD-HjicZD5y6JRb7Rg-7byCuNf0LNbmLLvFu37e46JHBZ…. The FS pial segmentation for UKB data is prone to include dura if only T1w data is used, so assisting with FLAIR is quite detrimental. Best regards, Fredrik Magnussen

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Saving ROIs on freeview
by Tina Thomas 24 Jun '21

24 Jun '21

External Email - Use Caution Hello, I am attempting to edit ROIs using Freeview, but when I save the label files, none of my edits are being saved. I am using a Mac. When I tried troubleshooting on a different computer (PC), I was able to save changes using the same methods. Could this be an issue with the version of Freesurfer (I'm using 6) or the computer I'm using? Is there another way to work around this issue? I also had an issue where when I used Freeview buttons to load an ROI, it wouldn't work unless I did it using code. Please let me know if this is something you have seen before or if you can help with this issue! Thank you, -Tina

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Longitudinal processing
by AJ 24 Jun '21

24 Jun '21

External Email - Use Caution Hi, After running longitudinal processing and creating base and long runs, When looking at volumes of various structures over time of the same subject, are the volumes not need to be corrected by eTIV since head size does not vary overtime? Many thanks for your input. Sincerely, AJ

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Fwd: Running FreeSurfer with fmriprep
by Rosalia Dacosta Aguayo 24 Jun '21

24 Jun '21

External Email - Use Caution Dear Freesurfer's experts, I have run recon-all all to one subject with fmriprep. The work finished without errors. However, after inspecting the results, I have seen that there are some *grey regions* (mainly frontal and temporal ones) that have not been fully covered. I wonder how I could proceed in order to improve the segmentation. Kind regards, Rosie

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Is hypointensities part of lh/rh cerebral white matter from aparc+aseg.mgz using mri_segstats
by miracle ozzoude 24 Jun '21

24 Jun '21

External Email - Use Caution Hello All, I was wondering if the Right/Left-Cerebral-White-Matter in the aparc+aseg.mgz contains WM hypointensities. mri_segstats --seg aparc+aseg.mgz -i dti_fa.nii.gz --sum dti_fa.stats --ctab FreeSurferColorLUT.txt Best, Paul

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Visualization of specific ROIs
by Jennifer James, MD 24 Jun '21

24 Jun '21

External Email - Use Caution Hello, We used FreeSurfer version 6.0 to extract thickness values and then used SPSS for statistical modeling. We found significant results in the thickness of the following two regions: *lh_G&S_cingul-Mid-Ant_thickness* *lh_S_front_middle_thickness* We want to make a simple figure showing just these two areas of the brain for visualization purposes only (similar to the attached figure). Could you let us know how we can make such an image in Freeview? Any help is highly appreciated! Best, Jennifer

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Seeing "Include the flag -cw256 with recon-all!" for HCP 7T data
by Soichi Hayashi 24 Jun '21

24 Jun '21

External Email - Use Caution Hello. I am having a problem running freesurfer on a HCP 7T data and I am wondering if someone from this mail list could help me out. I am trying to run freesurfer (v7.1.1) and I am seeing the following error message. **************************************** ERROR! FOV=268.800 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. **************************************** I am already passing -cw256 option. $ recon-all -i ../60ccadb32b8bed7302843abc/59a09e1d34ea2464e4d1bdcd/t1.nii.gz -subject output -all -parallel -openmp 8 -hires -cw256 -expert expert.opts The error message sounds like my -cw256 option is ignored, but I am not sure.. I see this at the top of the stdout log. INFO: hi-res volumes are conformed to the min voxel size Subject Stamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Current Stamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 INFO: SUBJECTS_DIR is /export/prod/60ccadb32b8bed493f843abb/60ccadbb2b8bed6894843ac0 Actual FREESURFER_HOME /usr/local/freesurfer Linux slurm9-compute3 4.15.0-126-generic #129-Ubuntu SMP Mon Nov 23 18:53:38 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux '/usr/local/freesurfer/bin/recon-all' -> '/export/prod/60ccadb32b8bed493f843abb/60ccadbb2b8bed6894843ac0/output/scripts/recon-all.local-copy' -cw256 option is now persistent (remove with -clean-cw256) /export/prod/60ccadb32b8bed493f843abb/60ccadbb2b8bed6894843ac0/output I believe "-cw256 option is now persistent" means that freesurfer is aware that I am setting this parameter? expert.opts is empty. I appreciate if you could assist me in troubleshooting this error message! Soichi

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Freesurfer June 2021