Freesurfer September 2021

freesurfer@nmr.mgh.harvard.edu

76 participants
107 discussions

Repeated measures analysis
by Abbie Taing 08 Oct '21

08 Oct '21

External Email - Use Caution Hi all, I have a between subjects factor (3 groups) and within subjects factor (3 stimuli type). I am interested in comparing cortical volume differences between groups and stimuli (i.e. group x stimulus interaction). What pipeline can I use to examine this? Many thanks, Abbie

2 1

SAMSEG output orientation not the same as input images
by daedalus39＠aol.com 08 Oct '21

08 Oct '21

External Email - Use Caution We have recently installed FS-7.1 and have tested a few “ADNI” images with SAMSEG. The process runs to completion, but the output (seg.mgz) appears upside-down and rotated about 90 about the X-axis. We are passing seg.mgz through BrainStorm to create NiFTI images. We do not believe that this is a BrainStorm issue inasmuch as the same images run through recon-all (fully separate proc) yield output images in the same orientation as the original images. I found a thread from 2012 with a similar output orientation issue, but the I did not see a response that resolved this. Any solution or insight would be greatly appreciated Sincerely,Randolph Andrews (PS. listserv item from 2012)Re: [Freesurfer] integrating FSL and FreesurferChris Filo Gorgolewski Tue, 09 Oct 2012 01:03:57 -0700https://http://secure-web.cisco.com/1bJm-kJVNOrTUaWjoqVk32d_m43kHXTpDrk8lcY-0m9IZL70ouR0Amj-rARrWUqpHqs37bd05gpqsZ5ysfX2IwhyEvB-jtySLbpgfVIwI9odls_4K82Kvhw3QUndLV0gJI7R_qOETwN5R8IsMiDFIovreM-3E6uNLDr9ua3ZEczUFu9zQt9L__yWHK3owmBE4NgW7-Jnn33sNGKV7QlzDb88gcre-4JwPKkrKdRylwImRU0aoDyCaRRFgoCRV_0jNFU_SZCrwzKcpPOyFWMzFRA/http%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg24896.html

3 3

non-brain tissue segmentation from T1-w images
by Banik, Rana 08 Oct '21

08 Oct '21

External Email - Use Caution Hello All, I am a beginner in freesurfer. Was looking for resources to perform volumetric segmentation(not surface mesh) for non-brain tissues like Muscle-skin, fat from T1-w MR images. Is that feature available in freesurfer? I have used FSL for WM, GM, CSF segmentation. Also looking to protect the inter-subject variability without registering the head volumes to MNI or another atlas. -Rana

2 1

Missed grey matter of sulci
by McKavanagh, Andrea [amckav] 04 Oct '21

04 Oct '21

External Email - Use Caution Hi all, I am having a problem with some post recon-all edits. The white matter in some of my scans has been over estimated in the aparc+aseg file, labelling some of the white matter (e.g by the lingual gyrus) as hypointensities and/or missing out many sulcui entirely (figure 1). However, the wm.mgz file is accurate picking up only the correct white matter in these areas (figure 2). This is happening, on most of the scans I have processed with recon-all. I am using Freesurfer 7.2.0 on Mac BigSur and have ran the same scans through previous version of Freesurfer (6/7.1) with the same problem occurring. I have read on the archives this has previously been a bug in another version, is this the case here? Or is there another correction step I could try? Any suggestions are welcome :) Thanks, BW Andrea [cid:9B03F6B2-0EEC-4035-8303-7364C1852FBF][cid:7C1283D9-0375-4187-A927-0CFB4B6BD5A9]

2 2

inter-hemispheric registration
by Yu-Chi Chen 03 Oct '21

03 Oct '21

External Email - Use Caution Dear FreeSurfer experts, My current analysis is for analyzing the vertices of the cortical surfaces. I'd like to have the same vertice numbers of the left and right hemispheres and also to retain as much asymmetric feature as possible. I first created the xhemi by using the xhemireg Next, I registered the right hemisphere white surface to the /xhemi/rh.white as following: mri_surf2surf --hemi rh \ --srcsubject ${SUBJECT} \ --trgsubject ${SUBJECT}/xhemi \ --srcsurfval ${SUBJECT}/xhemi/surf/rh.white \ --tval ${SUBJECT}_reg.rh.white But this failed. Could you teach me how to revise the code or is there any other suggestion? Thank you very much. Kind regards, Edward

2 1

Control for eTIV on Voxelwise Wholebrain Analysis?
by Wakim, Kathryn-Mary 01 Oct '21

01 Oct '21

External Email - Use Caution Hi all, I'm currently running a voxelwise whole-brain analysis on my recon-all data using the procedure outlined here: https://secure-web.cisco.com/1ltFRrUt9VeFo_xsJaFu_MKrnVu0LBNxjHernMBBefXqT5… If I am performing this analysis on volume (not cortical thickness), do I need to include eTIV as a covariate in my FSGD file? Thanks! Kamy

2 1

What does Freesurfer do with a T2 if you do not use the t2pial flag
by Aaron Tanenbaum 01 Oct '21

01 Oct '21

External Email - Use Caution What does Freesurfer do with a T2 if you do not use the t2pial flag?

2 3

Color LUT after coregister and reslice aparc/aseg.nii
by Ryan Wales 01 Oct '21

01 Oct '21

External Email - Use Caution Hello, I'm using fmriprep's aparcaseg_dseg.nii (still FreeSurfer code, right?) to create ROI masks. I wish to coregister and reslice this segmentation file to match the native space for another image (PET), then extract SUVR values for each ROI. However, after coregistration, the lookup values are no longer faithful to their original values. Would there be a way to view or create a new color LUT that reflects that aparcaseg_dseg.nii map in a different space? Thank you, Ryan -- Ryan Wales (he/him), M.A. Ph.D. Candidate Integrative Neuroscience Psychology Department Stony Brook University E-mail: ryan.wales(a)stonybrook.edu <ryanwales(a)stonybrook.edu>

2 1

unpacking Diffusion data
by Nasiriavanaki, Zahra,M.D. 30 Sep '21

30 Sep '21

Hello Freesurfers, I have 6 runs of DTI data per subject in a sample of 50, and I want to unpack the dicoms, so it outputs the bval bvec values, to use in dt_recon. I realized I can use either dcm2nii or mri_convert to do this. Could you please let me know what the command should be? and also should I do it separately for each run? subject’s scan info is attached. I used the below command in dev environment but didn’t get any bval bvec values. mri_convert /${subj}/IMAGES/IM01113 /${subj}/DTI/IM_13.nii Appreciate your help. Mona 1 Localizer ok 512 512 13 1 IM00269 2 SagT2FLAIRSPACE ok 512 512 176 1 IM00273 3 SagT2FLAIRSPACE ok 512 512 171 1 IM02084 4 SagT1MPRAGE1mmiso_P3 ok 256 256 176 1 IM00449 5 SagT2FLAIRSPACE ok 512 512 227 1 IM02311 6 SagT1MPRAGE1mmiso_P3 ok 256 256 171 1 IM02482 7 SagT1MPRAGE1mmiso_P3 ok 256 256 239 1 IM02721 8 AxWaveSWI ok 288 252 88 1 IM00793 9 AxWaveSWI ok 288 252 88 1 IM00881 10 AxWaveSWI ok 288 252 81 1 IM00705 11 AxWaveSWI ok 288 252 88 1 IM00969 12 Diffusion ok 990 990 1 70 IM00970 13 Diffusion ok 110 110 74 1 IM01113 14 Diffusion ok 110 110 74 1 IM01187 15 Diffusion ok 110 110 74 1 IM01261 16 Diffusion ok 110 110 74 1 IM01335 17 Diffusion ok 110 110 1 74 IM01336 Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

3 7

Fill between two surfaces
by I. Kelleher-Unger 30 Sep '21

30 Sep '21

External Email - Use Caution Hi there, Apologies if this is a basic question: I have two surfaces and I would like to make a ribbon/mask of the area between the surfaces. How could I go about this? Is mris_fill the right tool to use? Thanks for your help! Isaac

2 3

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer September 2021