Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

talairach.lta manual alignment
by Mark Plantz 21 Feb '14

21 Feb '14

Hello freesurfers, I recently attempted to fix the talairach.lta file from a bad recon-all run for one of my subjects. I originally thought that the second pass of recon-all would automatically load this talairach file. However, it looks like the talairach alignment keeps restarting each time recon-all is run. I couldn't seem to find a recon-all flag to manually send the program this new talairach.lta.reg.dat file. Has anyone else encountered this type of problem? My command line is as follows: tkregister2 --mov /Applications/freesurfer/subjects/CMH-9018/mri/brainmask.mgz --targ /Applications/freesurfer/subjects/fsaverage/mri/brainmask.mgz --lta /Applications/freesurfer/subjects/CMH-9018/mri/transforms/talairach.lta --reg /Applications/freesurfer/subjects/CMH-9018/mri/transforms/talairach.lta.reg.dat --s CMH-9018 Thanks in advance! - Mark

2 1

bug in dwri-motion
by Gerit Pfuhl 21 Feb '14

21 Feb '14

Dear Tracula Experts, after careful checking we still cannot run trac-all -qa or dwri-motion as the command always returns: could not open bvals but the same file is flawlessy opened/retrieved in version 5.2. [cat bvals is fine, trac-all -prep in 5.2. runs fine, trac-all -prep in 5.3 returns could not open bvals] Kind regards Gerit Pfuhl

2 9

Neuroimaging Postdoctoral Research Position in Mild Traumatic Brain Injury and Posttraumatic Stress Disorder
by Scott Hayes 21 Feb '14

21 Feb '14

*Neuroimaging Postdoctoral Research Position in Mild Traumatic Brain Injury and Posttraumatic Stress Disorder* Memory Disorders Research Center and Translational Research Center for TBI and Stress Disorders The Boston University Memory Disorders Research Center and the Translational Research Center for TBI and Stress Disorders are seeking an advanced postdoctoral fellow with expertise in Magnetic Resonance Imaging. The postdoctoral fellow will work closely with neuropsychologists and neuroscientists on a clinical research program aimed at elucidating the neural and cognitive sequelae of posttraumatic stress disorder and blast-induced traumatic brain injury in returning Veterans, as well as cognitive and neural change subsequent to exercise training. The candidate will receive advanced training in multi-modal imaging (fMRI, diffusion tensor imaging, volumetric and surface-based analyses, ASL) and the use of cognitive and MRI outcome measures subsequent to exercise intervention in Veterans with mTBI and PTSD. Dr. Scott Hayes will be the primary mentor, and the fellow will also collaborate with an interdisciplinary team including Drs. Mieke Verfaellie, David Salat, Daniel Forman, and Jasmeet Pannu Hayes. The successful candidate will have a doctoral degree in cognitive neuroscience, neuropsychology, biomedical engineering, or a closely related field, and substantial experience in MRI data acquisition and analysis. Candidate should have expertise working with MRI analysis software such as AFNI, FSL, SPM, or FreeSurfer, as well as familiarity with unix and Matlab. Experience interpreting neuropsychological and/or exercise physiology data and previous work with clinical populations are also desirable. The postdoctoral fellow will interact with several research groups at VA Boston studying TBI and PTSD in returning veterans. The candidate should have a keen interest in developing an independent research career. The starting date is flexible. A minimum two-year commitment is required. Salary for highly qualified candidates may be up to $52,000. U.S. citizenship is required for consideration. Potential applicants are encouraged to *immediately* email a letter describing research interests and experience and CV and should arrange to have three letters of recommendation emailed to Dr. Scott Hayes at smhayes(a)bu.edu Lab website: www.bu.edu/brainlab The Department of Veterans Affairs is an Equal Opportunity Employer. -- Scott M. Hayes, Ph.D. Memory Disorders Research Center Neuroimaging Research Center VA Boston Healthcare System Assistant Professor Department of Psychiatry Boston University School of Medicine

1 0

Neuroimaging Postdoctoral Research Position in Memory, Aging, and Alzheimer's disease
by Scott Hayes 21 Feb '14

21 Feb '14

*Neuroimaging Postdoctoral Research Position in Memory and Aging* Memory Disorders Research Center and Neuroimaging Research Center VA Boston Healthcare System The Boston University Memory Disorders Research Center and Neuroimaging Research Center at VA Boston Healthcare System are seeking an advanced postdoctoral fellow with expertise in Magnetic Resonance Imaging and human memory. The candidate will receive advanced training in multi-modal imaging (fMRI, diffusion tensor imaging, volumetric and surface-based analyses, ASL) in young adults, older adults, and patient populations (Mild Cognitive Impairment and medial temporal lobe amnesics). Studies will focus on human memory, age- and AD-related changes in memory and the brain, and individual differences (e.g., in cardiovascular fitness) that attenuate age-related decline. Dr. Scott Hayes will be the primary mentor, and the fellow will also collaborate on projects with Drs. Mieke Verfaellie and David Salat. The successful candidate will have a doctoral degree in cognitive neuroscience, neuropsychology, biomedical engineering, or a closely related field, and substantial experience in MRI data acquisition and analysis (fMRI preferred, but applicants with experience using other imaging modalities would also be considered). Candidate should have expertise working with MRI analysis software such as AFNI, FSL, SPM, or FreeSurfer, as well as familiarity with unix and Matlab. Experience interpreting neuropsychological data, and previous work with aging or clinical populations are also desirable. The postdoctoral fellow will interact with several research groups at VA Boston examining memory, age and AD-related changes in cognition and the brain and will be part of a rich and stimulating intellectual environment. The candidate should have a keen interest in developing an independent research career. The starting date is flexible. A minimum two-year commitment is required. Salary for highly qualified candidates may be up to $52,000. U.S. citizenship is required for consideration. Potential applicants are encouraged to *immediately* email a letter describing research interests and experience and CV and should arrange to have three letters of recommendation emailed to Dr. Scott Hayes at smhayes(a)bu.edu Lab website: www.bu.edu/brainlab The Department of Veterans Affairs is an Equal Opportunity Employer. -- Scott M. Hayes, Ph.D. Memory Disorders Research Center Neuroimaging Research Center VA Boston Healthcare System Assistant Professor Department of Psychiatry Boston University School of Medicine

1 0

ocn?
by Yang, Daniel 21 Feb '14

21 Feb '14

Dear FreeSurfers, I obtained a file from cluster analysis, called "cache.th20.pos.sig.ocn.mgh" Can you tell me what OCN stand for? And what is this file for? I tried to view it but was unable to see anything. Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang(a)yale.edu

2 2

interpretation of a 3-way interaction
by Yang, Daniel 21 Feb '14

21 Feb '14

Dear FreeSurfers, I have two discrete and binary factors (Dx: patients vs. controls; Sex: female vs. male), one continuous variable (Age), one nuisance factor (IQ). If there is a 3-way interaction of Dx x Sex x Age, regressing out IQ, is the following interpretation correct? Red/yellow: In females (vs. males), the Age effect of cortical thickening is stronger in patients (vs. controls). Blue/cyan: In females (vs. males), the Age effect of cortical thinning is stronger in patients (vs. controls). Note. by stronger, I mean greater magnitude without sign. Thanks, Daniel

3 3

continusous x continuous interaction?
by Yang, Daniel 21 Feb '14

21 Feb '14

Dear FreeSurfer Experts, In the example here: http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V, it describes the testing of the main effects of two continuous variables. In order to test the interaction effect, I think we can form an interaction term like age x weight as the third covariate, that is, Regressor1: All ones. Codes intercept/mean for Main Regressor2: age for each subject. Codes age slope for Main Regressor3: weight for each subject. Codes weight slope for Main Regressor4: age x weight for each subject. Codes age x weight interaction effect and then specify a contrast [0 0 0 1]? Is that the way to go? Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang(a)yale.edu

2 1

Segmentation process
by Saurabh Thakur 21 Feb '14

21 Feb '14

Hi Freesurfer expert, Thanks for all your help, I have explored the tkmedit ,tksurfer and freeview. How to move ahead with segmentation task. I looking forward to create my own .aseg file for sub cortical region. Is it possible...? And if possible,please share major breakpoint of the process. Thanks in advance. cheers Saurabh Thakur,

2 1

viewing corrected result error
by charujing123 20 Feb '14

20 Feb '14

Hi all, I try to see the cluster wised result by typing "freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=./Diff-CON-IA-Intercept-thickness/mc-z.neg.sig.cluster.mgh:overlay_threshold=2,5:annot=./Diff-CON-IA-Intercept-thickness/mc-z.neg.sig.ocn.annot",but it feedback some error infomation as below: Did not find any volume geometry information in the surface ԥhreading colortable from annotation file... colortable with 1 entries read (originally none) colortable with 1 entries read (originally none) Thanks. All the best 2014-02-20 charujing123

2 2

questions of clusters defined and sign of the threshold in simulation
by charujing123 20 Feb '14

20 Feb '14

Hi FS experts and users, May I ask some questions about clusterwise correction for multiple comparisons? 1,In mri_glmfit-sim command, there is a --sim(--sim nulltype nsim threshold csdbase) option. Choose the voxel/vertex-wise threshhold used to define clusters. This will be -log10(p), where p is the p-value. Eg, to use all voxels/vertices with p < .01, then set the threshhold = 2.I want to know what is meaning of "using all voxels with p < 0.01". Does it mean that considering all voxels whose p value below 0.01 in every iterations. Then it generates some clusters in every iteration. Is it right? 2,Also there is a --sim-sign option in this command. I want to know meaning of the sign: abs,pos,neg.Does it represent one- and two-tailed tests? Thanks. All the best. Rujing Zha 2014-02-20 charujing123

2 2

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