Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30089 discussions

overlapping labels
by David Grayson 06 Jul '12

06 Jul '12

Hi freesurfers, Can a .annot file include labels with overlapping vertices? If not, then when using mris_label2annot, how does freesurfer decide which label to assign the vertices to? Thanks, David

2 1

Image resolution and reliability of freesurfer measurements
by carolina.mr 05 Jul '12

05 Jul '12

2 1

multiple correction
by Meng Li 05 Jul '12

05 Jul '12

Hi, all, I have some questions about the multiple correction in qdec. I performed group analysis using qdec. There are 5 factors in the qdec.table.dat file: 1 discrete, 4 continuous variables (covariates). When I tried to perform the multiple correction, Whether I can choose one of two ways (the fdr and monte carlo null-z simulation) only. And if I use monte carlo null-z simulation, I have to pre-run mri_glmfit-sim 10000? Thanks, Meng -- ++++++++++++++++++++++++++++++ Meng Li major：Developmental and educational psychology South China Normal University Zhongshan Avenue West 55, Tianhe District Guangzhou 510631 P. R. China Tel: +86 (0)13824486409 ++++++++++++++++++++++++++++++ 李盟华南师范大学发展与教育心理学专业地址：广东省广州市天河区中山大道西55号邮编：510631 电话： 13824486409 (手机, 广州) +++++++++++++++++++++++++

2 1

Parallel vs. Sequential part
by Akio Yamamoto 05 Jul '12

05 Jul '12

Freesurfer experts, I have been working on openmp parallelization of Freesurfer programs. I'd like to know the ratio of sequential processing parts (which are essentially impossible to be parallelized) to the total amount of processing in order to calculate the theoretical limit of performance improvement rate. Have you ever made an estimate of the ratio between sequential and parallel processing segments, especially for ca_reg and em_reg? Thanks, Akio

3 5

label transformation to MNI space
by Linda Douw 05 Jul '12

05 Jul '12

Hi all, I am trying to transform some labels from the aparc to masks in MNI space. Ideally, I would like to do this for each subject in my study individually (using their own rawavg.mgz and labels), but for now I started out with fsaverage. I first converted the label file into a nifti: mri_label2vol --label ./fsaverage/label/lh.entorhinal.label --subject fsaverage --temp ./fsaverage/mri/brainmask.mgz --o lh_entorhinal.nii.gz --identity And then put the nifti file containing the label into MNI space: mri_vol2vol --mov lh_entorhinal.nii.gz --targ MNI152_T1_2mm.brain.nii.gz --o lh_entorhinal_MNI.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat But when I open lh_entorhinal_MNI.nii.gz with fslview, the location is completely wrong. I checked the location with tkregister as well: tkregister2 --mov lh_entorhinal_MNI.nii.gz --reg /$FREESURFER_HOME/average/mni152.register.dat But here the entorhinal was also in the wrong place. Do you know how to fix this? Thanks, -- Linda Douw, PhD.

4 7

Re: [Freesurfer] Hippocampal segmentation doubts
by Gabriel Gonzalez Escamilla 05 Jul '12

05 Jul '12

1 0

qdec covariate interact with a factor
by Emilia Lentini 04 Jul '12

04 Jul '12

Hi. I would like to test the effect of a covariate that interact with a factor. Eg. I have group (XX and XY) as fixed factors, and a ROI thickness (L Fusiform) as covariate. Now I would like to calculate the "correlation LFusiform for XX - correlation LFusiform for XY". Is this possible by using qdec? If so, how should I proceed? Best regards, Emilia

2 1

Hippocampal segmentation: version needed
by lorenzo pasquini 04 Jul '12

04 Jul '12

Dear Freesurfer experts, I used freesurfer v4.3.0 on anatomical data (T1). I am trying to segment hippocampal subfields with the following command: recon-all -s subjname -hippo-subfields unfortunately I get the following error: ERROR: Flag -hippo-subfields unrecognized I have already the files aseg.mgz, nu.mgz, talairach.xfm Does this error occur because I am using an old Freesurfer version? If this is the case which is the optimal version to run hippocampal segmentation? Should I process my whole data again with the newest version? Unfortunately I did not find any convincing answer from the posting list where I had the impression that version 5.1 is facing some problems regarding hippocampal segmentation. Thank you very much and kind regards, Lorenzo Pasquini

2 1

Extraction Longitudinal Stats
by Dídac Vidal 04 Jul '12

04 Jul '12

Hi everybody, I have a question about FS longitudinal post-processing. Currently I obtained some corrected results comparing a Control vs. an Experimental group (pre-post). What i would like to know is if there's a thinning in the control group or a increase in the thickness of the experimental group. I tought in create a label and extract the individual values of both timepoints and then do a t test in order to see if the mean differs to 0. How I can do that?; There is an easier way to do it? Thanks in advance -- Dídac Vidal Piñeiro Dept. Psychiatry and Clinical Psychobiology Faculty of Medicine University of barcelona

4 8

Post-Doctoral position in Computational Morphometry – University of Geneva
by Narly GOLESTANI 04 Jul '12

04 Jul '12

Post-Doctoral applications are invited at the Department of Clinical Neuroscience at the University of Geneva, in collaboration with the Swiss Institute of Technology (EPFL) in Lausanne, Switzerland. Projects will include the development of new data-driven computational morphometry methods for analysis of structural magnetic resonance imaging (MRI) data, and application of these to large datasets in the context of normal variability, disease, and expertise. Candidates should have a degree in Biomedical Engineering, Computational Neuroscience, or a related field with a strong mathematical and computational background. Ideally they should have experience in brain image analysis, pattern recognition, machine learning, statistics as well as excellent programming skills. We offer a starting salary of 68, 964 CHF/year. The position is available immediately, and applications will be considered until the position is filled. Informal inquiries can be addressed to Narly Golestani (Narly.Golestani(a)unige.ch) Applications including a CV, a statement of research interests, and the names and full contact details of three referees should be sent to: Narly.Golestani(a)unige.ch.

1 0

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