Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

dPSD and ev duration
by Ella Hinton 28 Jul '13

28 Jul '13

Hi Quick question - why must the duration of the EVs be an integer multiple of the dPSD, which is also tied to the TR? I have event duration of 3 seconds, but would like to reduce my TR from 3 down to 2.5, but I can't seem to input the correct numbers for optseq to help me. thanks in advance Ella

2 1

A question about coordinates
by jh kim 28 Jul '13

28 Jul '13

Dear experts I have a simple question. To my knowledge, Freesurfer uses Talrairach coordinates. After doing 10000 permutations, I found that the resulting file *.sig.cluster.summary contained MNIX, MNIY, MNIZ coordinates. Are these coordinates in MNI space? Thank you in advance for your answer. Kim

2 2

Combining non accelerated and accelerated MRIs
by Stéphane Poulin 28 Jul '13

28 Jul '13

Dear Freesurfer experts I am using Freesurfer to process part of the ADNI 2 database which includes non accelerated and accelerated images. Images have different voxel sizes. Is there any litterature to guide me what should I do, ie combining or not these scans. Stephane

2 1

FW: VMAC neuroimaging research analyst opening (fwd)
by Bruce Fischl 26 Jul '13

26 Jul '13

FYI From: Jefferson, Angela [mailto:angela.jefferson@Vanderbilt.Edu] Sent: Friday, July 26, 2013 9:36 AM Subject: VMAC neuroimaging research analyst opening Dear colleague, My laboratory at Vanderbilt has a neuroimaging research analyst II opening. If you have students or recent trainees who have 2 years of research experience or a master’s degree equivalent with programming or scientific computing skills who are interested in gaining some research experience in neuroimaging for a couple of years before attending graduate school, this opportunity would be a great fit (especially if they don’t mind relocating to Nashville). If you wouldn’t mind distributing the attached posting to potential candidates, I would very much appreciate it. Best regards, Angela Angela L. Jefferson, PhD Director, Vanderbilt Memory & Alzheimer’s Center Associate Professor of Neurology Vanderbilt University Medical Center 2525 West End Avenue, 12th Floor, Suite 1200 Nashville, TN 37203 www.vanderbiltalzheimers.com www.vanderbiltcognitiveaging.com

1 0

Freesurfer surface circle of pre-defined size
by sarahp＠nmr.mgh.harvard.edu 26 Jul '13

26 Jul '13

Hello Freesurfer Experts, We would like to use PySurfer's function plot_label_foci.py to automatically create circular labels of a pre-defined radius (eg. 14mm) on the fsaverage surface of freesurfer. What are the specified units of "n_steps" in the command line argument "utils.coord_to_label(subject_id, coord, label='coord', hemi='lh', n_steps=50"? Thank you, Sarah

2 1

qdec question: discrepancy in sig. clusters
by Maria Kharitonova 26 Jul '13

26 Jul '13

Hello, I have another newbie question. I'm running qdec, trying to compare cortical thickness in children with and without ADHD. However, I'm seeing a discrepancy between the clusters that are significant according to the terminal (after applying the Monte-Carlo simulation with default parameters; output below) and the ones that pop up when I hit "Find clusters and goto Max". For example, I'm seeing 4 regions in the terminal: medialorbitalfrontal, inferiorparietal, caudalmiddlefrontal, and precentral. However, when I hit "Find clusters and goto Max", I only see the Frontalpole. Using mri_surfcluster to extrat thickness measures only extracts it for the frontalpole, and not for the 4 ROIs listed in the terminal. I would like to be able to extract stats on those 4 that are listed in the terminal, if possible. Can you please help me reconcile the 2 types of output? Thanks! *** terminal output: # Input /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/FS_5.3_final/qdec/dx_age_icv_nuis_lh/rh-Diff-CONTROL-ADHD-Cor-thickness-age/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi rh # surface white # annot aparc # SUBJECTS_DIR /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/FS_5.3_final # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 4.75828 at vertex 134555 # Overall min -2.56762 at vertex 93241 # NClusters 4 # Total Cortical Surface Area 65020.8 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 4.758 134555 1015.59 8.7 58.2 -5.8 0.00010 0.00000 0.00020 1292 medialorbitofrontal 2 3.968 135840 466.91 40.0 -66.8 25.9 0.01790 0.01620 0.01960 750 inferiorparietal 3 3.954 115431 497.60 29.3 21.4 39.9 0.01150 0.01010 0.01290 900 caudalmiddlefrontal 4 3.242 133890 439.44 49.4 -5.1 22.0 0.02520 0.02320 0.02720 932 precentral Simulation complete.

2 1

retinotopy betas
by dgw 26 Jul '13

26 Jul '13

Hi, I am examining the affect a metal artifact has on fMRI data, and I am using Eccentricity mapping with the retinotopy analysis in FSFast. I was recently asked to switch from examining the difference in the fsig to examining the difference in the betas. I opened up beta.nii.gz and I can see that it has a size of: 1 #of vertices 1 39 Can you explain to me, how I figure out where each of the 39 come from (and possibly point me to which of these might be appropriate to use?)? Thank You, Dan

3 4

functional connectivity, group averages
by Mario Ortega 26 Jul '13

26 Jul '13

Hi Team, I have a question on making a group average of subjects for functional connectivity. In detail, I want to make a surface overlay that is the average correlation (r-value) of a certain subject group. What commands would be used for this? simply isxconcat-sess? I could not find much info on the FSFAST or Functional webpages. Thanks, Mario

2 1

HypoIntense Lesions
by Fotiadis, Panagiotis 26 Jul '13

26 Jul '13

Hi FreeSurfer Community, I was wondering whether there is an automatic tool that outlines the hypointense lesions in a SWI scan. Thank you, Panos

3 12

selxavg3-sess： Matlab cannot display graphics
by Wang Zhiwei 26 Jul '13

26 Jul '13

Hi all, When I run selxavg3-sess for any analysis, the following information is always appearing. Can you please give some suggestions how to fix that? Any thoughts would be very appreciated! ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. Warning: No window system found. Java option 'MWT' ignored. < M A T L A B (R) > Copyright 1984-2012 The MathWorks, Inc. R2012b (8.0.0.783) 64-bit (glnxa64) August 22, 2012 No window system found. Java option 'MWT' ignored. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> Thanks! James

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer