Freesurfer January 2021

freesurfer@nmr.mgh.harvard.edu

98 participants
132 discussions

FreeSurfer 7 vs FreeSurfer 6 surface differences
by Mike Schmidt 01 Mar '21

01 Mar '21

External Email - Use Caution I have written a script that reads the binary representations of the vertices and faces from FreeSurfer's surf/{l,r}h.pial files and saves them out unchanged to stl and obj file formats for 3D rendering. I have used it with FreeSurfer 6 and several MRI images, everything working fine. Processing the identical input, a single T1-weighted MPRAGE MRI, FreeSurfer 7 works great and finishes faster than FreeSurfer 6, but we see strange aliasing on the 3D objects. The aliasing is identical if I avoid all of my own code and use mris_convert (from either FreeSurfer version) to generate an stl file from the pial file. I've spent a lot of time debugging, messing with different materials and textures, generating vertex normals at different stages, but I can't find anything that makes any difference except the FreeSurfer version. I have seen several items in the release notes ( https://secure-web.cisco.com/1NYZrvHyVXqxTpZBiwiJ49J4EeeNWwqM6oBe0m-ipN8Gos…) that may be related, but I'm not sure how to go about investigating them. Left cortex images are included, with links if they don't show up in the email, of the same brain processed with FS6 and FS7. These are rendered in Firefox with the three.js library. FreeSurfer 6.0.0 works well with a smooth surface ( https://secure-web.cisco.com/1eQ5Q62ZQtG-RYtwAFFKvhYNEYp7A20Vte8M_v6fEXDVss…) This image is of surf/lh.pial with 149,968 vertices and 299,932 faces. [image: rh_pial_oblique_from_fs6.png] FreeSurfer 7.1.1 results in the same size and shape cortex, but renders strangely with mottled shading of triangles. ( https://secure-web.cisco.com/1JB4zyZhlTjmxoItAOFNb40IoMYhEZt8T-O0MINoKqg8cl…) This image is from the same T1 image as above, but processed with FS7, resulting in 147,292 vertices and 294,580 faces. [image: rh_pial_oblique_from_fs7.png] I'm out of ideas, and the only difference I can find is FreeSurfer version, so thank you to anyone who can point me in the right direction to fix this issue. Mike Schmidt

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data sharing of freesurfer processed data
by STACEY M SCHAEFER 04 Feb '21

04 Feb '21

External Email - Use Caution Does the freesurfer group have any recommendations or procedures for public sharing data that has been processed with freesurfer? In particular, procedures to automatically swap out participant IDs to anonymize the data? Stacey M. Schaefer, Ph.D. Center for Healthy Minds University of Wisconsin-Madison 625 W Washington Ave Madison WI 53703

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Hypothalamus segmentation - Freesurfer 7.1
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 02 Feb '21

02 Feb '21

External Email - Use Caution Dear Freesurfer experts, I am having some trouble getting the hypothalamus segmentation recognized on the command line for FreeSurfer 7.1.0. Is it even available for this version? If not, will it work on the 6.0 or the 7.1.1 version? Thanks and stay safe! All the best, Alex

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label to surface
by Sam W 02 Feb '21

02 Feb '21

External Email - Use Caution Hi, Is there a way to convert a label file into a surface/overlay? Thank you! Best regards, Sam

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recon all
by 郑凤莲 01 Feb '21

01 Feb '21

External Email - Use Caution Hi experts, We have segmented hippocampus using Freesurfer 6.0. I have a question that is there "head motion correct" in this step? If yes, how does it examined? I am looking forward to your reply. Thanks very much. Sincerely, Zheng | | 郑凤莲 | | 邮箱：zhengfenglian0105(a)163.com | 签名由网易邮箱大师定制

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Voxel-wise volumes vs APARC volumes
by Mark Wagshul 31 Jan '21

31 Jan '21

External Email - Use Caution Dear Freesurfer experts, I'm stuck on something which I think has to do with how Freesurfer calculates volumes, but can't quite wrap my head around it, hopefully you can enlighten me. I have already produced robust results for our data using region-based cortical volumes, using aparcstats2table. This is in a group of 55 healthy older adults, modeling is using linear mixed effects models. All volumes were normalized with the eTIV. We were hoping on exploring the same models with voxel-wise analyses, and are getting wildly different results. Data were created using mri_preproc, resampled onto fsaverage, and my assumptions was that because of this resampling, we should NOT be normalizing these values to the eTIV. The same regions which were highly significant on the region-based analyses and now not significant at all, and other regions are now showing up as significant. Just as a sanity check, I attempted to reproduce the region-based analyses with these data using the following simple (I thought!) procedure: 1) Created an mgz mask of the region I'm interested in, using mri_annotation2label and mri_label2label 2) Read my volume data (#subjects x #vertices) into Matlab 3) Read my mask into Matlab (yes, I know I can probably do this in Freesurfer, but I'm more comfortable with Matlab!) 4) Multiply them together and take the sum across vertices. 5) Feed the resultant data back into my LME model. Two things are puzzling to me. 1) The highly significant results from the old LME are no longer significant (at the moment, only checked for two of the cortical regions), and 2) The correlation between these new data and the aparc volume are OK, although far from perfect (R2 ~ 0.86). So, I'm obviously missing something here. What is the difference between the two volume calculation methods which could explain these discrepancies? Any help with this would be MOST appreciated! Best, Mark [cid:image004.jpg@01D6F59B.DA0205F0] ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einsteinmed.org<mailto:mark.wagshul@einsteinmed.org> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

2 4

Tkregister2 resolution difference
by Shi, Yuelin 31 Jan '21

31 Jan '21

External Email - Use Caution Dear FreeSurfer, Hi, I'm Yuelin, a graduate student from Caltech. I came across an issue using the Tkregister2 registration GUI: the target scan are always rendered with much lower resolution than the movable scan. This difference in resolution makes it almost impossible to registering details. I wonder if this is a known issue and is there any way to solve that? Any information will be very helpful! Our lab currently uses version "freesurfer-local-build-dev-20200114" (this is what's shown with the "recon-all version" command, but should be 7.0 or 7.1), I also checked some older versions we used before and the same issue exists. Thanks, Yuelin

2 3

Fw: Freesurfer recon all
by Paul, Rahul 29 Jan '21

29 Jan '21

________________________________ From: Paul, Rahul Sent: Thursday, January 28, 2021 3:52 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer recon all Hi, I just started working on the freesurfer software. I was trying to use recon-all command but there was an output saying XL error detected, and it remained same for more than 6 hours or so. Any idea how I can fix it? Bdw i stopped it running after 8 hours or so. I am using a T1-MRI scan. I am using a MacBook pro (8GB RAM). I am attaching a screenshot and the command I used can be seen in the bottom of the screenshot. Thank you, Rahul Paul

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Parallel computing for recon-all
by Wei Shao 29 Jan '21

29 Jan '21

External Email - Use Caution Hi, Freesufer experts My name is wei shao, I have a few questions regarding the parallel computing of recon-all 1 According to documents, freesurfer is OpenMP code , I use -openmp 8 flag like: recon-all -alli -i input.file -s output.file -openmp 8 to tun the recon command on a server, but it doesn't work for me (the running time is very similar for the same subject). Cloud you tell me what is wrong? 2 Can Freesufer take advantage of several GPUs? 3 Is it possible to open few threads to run recon-all on different sections parallelly? Best, Wei

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FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing
by Loreto, Flavia 29 Jan '21

29 Jan '21

External Email - Use Caution Dear FreeSurfer Experts, I am writing to kindly follow-up on my below query. Is there any chance you could assist me? Thank you. Kind regards, Flavia From: "f.loreto(a)imperial.ac.uk" <f.loreto(a)imperial.ac.uk> Date: Monday, 18 January 2021 at 13:19 To: "Freesurfer(a)nmr.mgh.harvard.edu" <Freesurfer(a)nmr.mgh.harvard.edu> Subject: Recon-all error: CTABWriteFileASCII; could not open file for writing Dear FreeSurfer Experts, Version: FreeSurfer 7.0 Platform: Bash remotely through High Performance Computing (HPC) on a MacOS Mojave We are trying to run recon-all on T1 images but the job stops with the following error: Reading annotation /rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 error: Permission denied error: CTABwriteFileASCII(/tmp/mri_segstats.tmp.APC001.lh.176.ctab): could not open for writing Could you please help us figuring out where is the problem? I am attaching the script we are running and the recon-all log for one of our analysed subjects. Thank you for your help. Kind regards, Flavia

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Freesurfer January 2021