Freesurfer April 2023

freesurfer@nmr.mgh.harvard.edu

80 participants
105 discussions

Issue with running recon-all on Synthsr output
by hmarzban＠student.ubc.ca 04 Apr '23

04 Apr '23

External Email - Use Caution Dear developers, I recently ran Synthsr on one of my images and now I am attempting to run recon-all. The output states that it finished without any errors in just 0.006 hours, but I am unable to proceed with the processing. Have any of you encountered this issue before? I would greatly appreciate your recommendations on how to proceed. (I am confident that there are no issues with the Freesurfer version and recon-all, as I have successfully run a 3T MP-RAGE image) Thank you Hengameh

2 1

Which motion correction parameters are used in FSFAST?
by Andy Kim 03 Apr '23

03 Apr '23

External Email - Use Caution Dear FreeSurfer Developer, Hi. Thanks to FreeSurfer, I could perform surface-based activation analysis with FSFAST. Now I want to do surface-based functional connectivity analysis. For the sake of consistency, I want to use the same nuisance regressors as used in FSFAST. Unfortunately I'm stuck in motion correction parameters. According to https://secure-web.cisco.com/10LyHLSQ2Psfux7V-2TqU0TpTUpRE9gROQ8dm_KryluL_Q…, motion correction parameters are stored in mcprextreg. Since there are 6 columns, I guess they are 3 translations and 3 rotations. On the other hand, none of them are in mcAll, X.mat. What are the 18 motion correction parameters in X.mat? and which motion correction parameters are used as nuisance regressors in FSFAST? Thanks in advance. Kind regards, Andy (Junghyun) Kim

2 8

Finding non-contiguous labels within an annotation
by Colleen Hughes 03 Apr '23

03 Apr '23

External Email - Use Caution Hello, I have an fsaverage5 parcellation/annotation based on Schaefer 200 (attached). The parcel boundaries are supposed to be adjusted iteratively resulting in 200 contiguous parcels with new boundaries. In this person, it is clear from plotting in freeview that 1 vertex from a visual parcel migrated to be surrounded by the SOM (blue) and VAN (violet) network on the lateral side (same hemisphere). This doesn’t happen in all subjects, so I’d like to write a function to find this and similar parcels that are not contiguous in a more automated fashion. So far, I’ve used the matlab read_annotation.m function to count vertices per parcel but that’s not quite right because it treats all vertices with the same label as the same thing. Not sure if there is a way to identify neighboring vertices so I can see if any have the same label (contiguous) or not. I investigated mri_surfcluster but I’m not sure how to make it treat the annotation as the input. Perhaps there is a way to project the values (1-200) associated with each label to their vertices. And then mri_surfcluster requires contiguity so it may identify if there is a mismatch between the expected # of parcels and observed # of clusters. I am using freesurfer 7.3.2, Matlab 2020a, M1 iMac. Any thoughts on how to identify non-contiguous vertices within a parcellation? Thank you, Colleen -- Colleen Hughes, PhD Postdoctoral Researcher Laboratory of Brain and Cognition Montreal Neurological Institute-Hospital McGill University

2 1

Re: [Freesurfer] moving results from fsaverage space to subject space
by Douglas N. Greve 03 Apr '23

03 Apr '23

Hi Jennifer, remember to send questions to the freesurfer list, thanks! Answers below On 4/3/2023 4:01 AM, Jennifer Kilmer wrote: > > External Email - Use Caution > > Hi Douglas, > > Thank you for your response. I have a few more questions; > > We can do the analysis in the surface space, but how could we move the > results from the surface space (FS average) to the original subject > volumetric space? Do you need to go to fsaverage space? If all you want to do is the surface-based smoothing, then you can do it in the native space, then use mri_surf2vol to map it back into the volume. Run it with --help. Use method2 with --fillribbon and --surfval as your surface pet data. > > "Why not map the individual to fsaverage space and do the comparison > there?" > We already do that in MNI space using volume smoothing and go back to > the individual subject space. We want to use the surface smoothing as > it's "... constrained to be only within cortical GM" (PMC4008670). As > we have to compare also with volumetric maps from electrophysiology > data, we need to go back to the individual volumetric space. > > > I hope this clears things up, please let me know if there is anything > we can try to achieve this. > > Jennifer

1 0

Is it possible to add additional T1 scans to improve surfaces/segmentation
by Michael Mc Laughlin 01 Apr '23

01 Apr '23

External Email - Use Caution I am working with standard neuro radiological MRI scans. These typically have something like this:: a) T1 headscout volume: 1.6mmx1.6mmx1.625mm 160x160x128 b) T1 se tra 0.72x0.72x5.2 320x320x30 c) T2 tse tra scan 0.72x0.72x5.2 320x320x30 d) T2 FLAIR (dark fluid) scan 0.58x0.58x5.2 460x460x30 c) T1 tse sag 0.72x0.72x5.2 320x320x30 c) T2 tse sag 0.72x0.72x5.2 320x320x30 I have found that the best results are obtained if I do the following: i) Start with the T1 headscout volume: 1.6mmx1.6mmx1.625mm This produces poor pial results but much better than using the T1s with a small number of slices. ii) Add in the flair data: Use -FLAIR and -autorecon3 with a FLAIR MRI scan This dramatically improves the pial surfaces and they look almost normal iii) Add some T2 data. This give more improvement of the pial surfaces See attached image for how the cortex looks after these stages My questions are: *1) How can I add in the data from the higher resolution T1 scans? (with only 30 slices)* *2) If I add a second T2 scan with -T2 -T2pial -autorecon3 will the results improve even more?* Regards, Michael

3 4

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer April 2023