Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

Re: [Freesurfer] data from different MRI scanner
by Bruce Fischl 01 Sep '16

01 Sep '16

Hi rujing that can be tough. If all your group1 are on one scanner and all group2 are on the other how can you tell the difference between a group effect and a site effect? At the very least you should scan some people on both scanners. cheers Bruce On Wed, 31 Aug 2016, charujing123 wrote: > Hi all > I collected two groups: each participant in group A collected from site 1; > Part of group B collected from site 1 and part of group B collected from > site 2. Can I compare the cortical thickness between these two groups > directly? > thanks. > rujing > > 2016-08-31 > > ____________________________________________________________________________ > charujing123 > >

1 0

Pial refinement with FLAIR
by Eelco van Duinkerken 01 Sep '16

01 Sep '16

Dear all, Sorry for spamming, as I have posted this message about 2 weeks ago, but didn't receive an answer just yet. I probably did something wrong :). I've been preprocessing, in FS5.3, 3T GE data in controls, obese and diabetes patients and adding the available flair to do the pial refinement as follows: recon-all -i t1 -s participant -all -FLAIR flair -FLAIRpial This works excellent for most of the scans. Unfortunately, for some scans adding the flair leads to some interesting refinements, either extending outside of the brain.mgz or going deep into the white matter. I didn't notice any misregistrations of the flair to the T1 scan when checking the bb-registration. I have added some screenshots and the recon-all.log files. The red lines represent the pial with the flair refinement, and the blue lines the pial without the refinement. As you can see, these interesting segmentations are not there when the flair is no used. Does anyone know what is going on? Thanks a lot, Eelco -- Eelco van Duinkerken, PhD Pontifícia Universidade Católica | Department of Psychology | R. Marquês de São Vicente 225 | Gávea, Rio de Janeiro - RJ | CEP 22451-900 | Brasil | E-mail: e.vanduinkerken(a)vumc.nl | Phone: +55-21-35271855 | http://lattes.cnpq.br/7180895567820901 & VU University Medical Center | Department of Medical Psychology | De Boelelaan 1117 | 1081 HV | Amsterdam | The Netherlands

3 3

inclusion of both T1 and T2 in a recon-all run
by Krieger, Donald N. 01 Sep '16

01 Sep '16

Dear list: What are the advantages of including a T2 scan when running recon-all -all ? Which results can it effect and to what extent? And how sensitive is freesurfer to artifacts in the T2 scan? Is there a good reference for this/ Thanks and best - Don

5 8

nu_correct crashed
by Fanny Munsch 01 Sep '16

01 Sep '16

Hi everyone, I just installed the latest version of Ubuntu (Ubuntu 16.04 LTS) and I reinstalled FreeSurfer (centos4). When I computed recon-all it exited with errors (nu_correct crashed). I have attached the .log files. I have already used FreeSurfer with older versions of Ubuntu and I have never had this error. Do you have any idea what needs to be done? Thanks a lot ----------------- Fanny Munsch PhD in Neurosciences Engineer in MRI post-processing

1 0

3 fixed factors and matrix design
by Shady Rahayel 01 Sep '16

01 Sep '16

Greetings, I want to design a matrix that contains 3 fixed factors. The first is diagnosis (3 levels), the second is gender (2 levels), and the last is imaging site (2 levels). However, the thing is that the imaging site factor only applies to only one level of the diagnosis factor (i.e. patients from the first level of the diagnosis factor were seen in 2 different imaging sites, whereas for the two other groups of patients the same imaging site was used). I have followed the tutorials but I still be am confused concerning how I should go about creating the design matrix with 3 fixed factors. Would it be: GroupDescriptorFile 1 Title xx Class Diagnosis1-Male-Site1 Class Diagnosis1-Female-Site1 Class Diagnosis1-Male-Site2 Class Diagnosis1-Female-Site2 Class Diagnosis2-Male-Site1 Class Diagnosis2-Female-Site1 Class Diagnosis3-Male-Site1 Class Diagnosis3-Female-Site1 Input etc etc... Afterwards, if I'm looking for a difference between Diagnosis1 and Diagnosis2, what would be the contrast? 0.25 0.25 0.25 0.25 -0.5 0.5 0 0 ? Thank you very much for your help, Shady -- *Shady Rahayel* Étudiant au Ph.D. en neuropsychologie R/I Université du Québec à Montréal Centre d'Études Avancées en Médecine du Sommeil Hôpital du Sacré-Coeur de Montréal

2 1

mri_glmfit: Cannot allocate memory
by Heidi Foo 01 Sep '16

01 Sep '16

Dear FreeSurfer team, I tried to run glm_fit to fit group membership. For this model, I have 3 diagnostic groups namely, HC, MCI, AD, and added lobar (Frontal, Parietal, Occipital, Temporal) WMH as the covariates. My contrasts are as follow: Group membership: 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0; 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 Frontal/Parietal/Occipital/Temporal MCI_HC: 0 0 0 -1 1 0 0 0 0 0 0 0 0 0 0 Frontal/Parietal/Occipital/Temporal MCI_AD: 0 0 0 -1 1 0 0 0 0 0 0 0 0 0 0 Frontal/Parietal/Occipital/Temporal AD_HC: 0 0 0 -1 0 1 0 0 0 0 0 0 0 0 0 However, I got the error message that matlab element type is not a matrix and another error that it cannot allocate memory. Attached the error log and the command for your reference. I am not sure what went wrong, any help will be great. Many thanks, Heidi

1 1

About TRACULA results
by Kang, XJ 31 Aug '16

31 Aug '16

Hi, I am trying to computer the changes of cortical parcellations and fiber pathways using FreeSurfer v5.3 and Tracula (2014/05/26 update) . I copied the anatomical and DWI images from the same scan session into five directories. Run recon-all and trac-all on the 5 same data sets, in order to check thereproducibility of the analysis. Here are what I got: the /Desikan/-Killiany parcellations in both GM and WM, and the subcortical structures, repeat well. No difference found in volume or size of those structures. However, the volume and averaged DTI parameters of the fiber pathways, which found in the file ~/sub/dpath/*_PP_avg33_mni_flt/pathstats.overall.txt, varies for the 5 sets. tracula.conf files were copied from ~/freesurfer/bin/dmrirc.example. The changes are calculated in percentage by (S1-S0)/((S1+S0)/2)*100%. For example, the changes of averaged FA between the 5 data sets are : S1-S0, S2-S0, S3-S0, S4-S0 Corpus Callosum - Forceps Major , -1.1 , 6.0 , 0.5 , 1.3 , Corpus Callosum - Forceps Minor , 0.1 , 0.0 , -1.6 , 0.0 , Right Anterior Thalamic Radiations , 0.1 , -1.0 , 0.5 , 0.9 , Right Cingulum - Angular Bundle , -4.8 , -2.0 , -1.5 , 3.8 , Right Cingulum - Cingulate Gyrus Endings , 0.5 , -0.9 , 0.4 , -2.3 , Right Corticospinal Tract , 1.9 , 0.6 , -2.2 , 1.4 , Right Inferior Longitudinal Fasciculus , -2.2 , -0.8 , -1.3 , 3.0 , Right Superior Longitudinal Fasciculus - Parietal Endings , 0.8 , -0.4 , -1.2 , 0.2 , Right Superior Longitudinal Fasciculus - Temporal Endings , -4.9 , -0.6 , -2.6 , -1.3 , Right Uncinate Fasciculus , 0.5 , 1.6 , -0.9 , 3.5 , Even larger changes for the volume of the pathways: S1-S0, S2-S0, S3-S0, S4-S0 Corpus Callosum - Forceps Major , 2.2 , -33.7 , -12.3 , 1.1 , Corpus Callosum - Forceps Minor , 11.9 , 4.8 , 0.6 , 7.2 , Right Anterior Thalamic Radiations , -8.9 , 2.2 , -12.5 , 7.5 , Right Cingulum - Angular Bundle , -38.1 , 41.6 , 34.8 , 8.6 , Right Cingulum - Cingulate Gyrus Endings , 24.4 , 33.1 , 21.3 , 17.5 , Right Corticospinal Tract , 9.8 , -3.0 , 2.2 , 19.5 , Right Inferior Longitudinal Fasciculus , 7.2 , 24.1 , -7.3 , 23.8 , Right Superior Longitudinal Fasciculus - Parietal Endings , 17.2 , 10.2 , 25.1 , 9.9 , Right Superior Longitudinal Fasciculus - Temporal Endings , 15.4 , 3.4 , -3.1 , -11.5 , Right Uncinate Fasciculus , 13.3 , -1.2 , 16.4 , -3.4 , Any expert has the experience on these? Thank you for your help. XJ Kang

2 2

Satellite Symposia - Resting-State and Brain Connectivity Conference
by Anastasia Yendiki 31 Aug '16

31 Aug '16

Dear FreeSurfers - If you're attending the Resting-State and Brain Connectivity Conference in Vienna, you can now register for satellite symposia, including one on diffusion MRI. Hope to see you there! a.y ---------- We are pleased to inform you that registration for the six Satellite Symposia at the Resting-State and Brain Connectivity Conference is open! These specialised meetings will take place on Saturday, September 24th right after the Resting-State and Brain Connectivity Conference. So why not extend your stay in Vienna for the sake of maximizing knowledge gain, deepening the vivid scientific exchange and socializing with your community members? The Satellite Symposia will will cover diffusion MRI, optogenetics, PET/MRI, TMS/fMRI and predictive analyses of neuroimaging data. We made sure to provide a large selection of topics for our six Satellite Symposia, so that everyone gets to choose the most interesting on their behalf: * Symposium #1: Probing white-matter anatomy and microstructure with diffusion MRI * Symposium #2: Tackling connectivity using non-invasive brain stimulation (fMRI/TMS, tDCS, tACS) * Symposium #3: The Emerging Field of Predictive Analytics in Neuroimaging: Applications, Challenges and Perspectives * Symposium #4: Multi-modal fMRI from photons to protons * Symposium #5: Dynamic Functional Connectivity * Symposium #6: Network-Based Approaches for Neuroimaging: Graph Theory Techniques for Brain Connectivity Research http://www.restingstate.com/2016/satellite-symposia/ So don’t hesitate to register for a satellite symposium now! We look forward to welcoming you to Vienna in September 2016! On behalf of the local and international organizing committees Christian Windischberger Claus Lamm Rupert Lanzenberger Bharat Biswal Mark Lowe Christopher Pawela Martin Walter Susan Whitfield-Gabrieli

1 0

LGI problem
by Alan Francis 31 Aug '16

31 Aug '16

Hi Marie: I am trying to run the LGI algorithm on 32 brains. As shown in the archives, I set the environment (on tcsh) and provided the MATLAB pathway. [afrancis-mac:~] afrancis% setenv MATLABPATH /Applications/MATLAB_R2015a.app/ [afrancis-mac:~] afrancis% setenv PATH ${MATLABPATH}/bin:${PATH} I also do have the Image processing toolbox. I got the following error: Current: /Applications/freesurfer Previous: /cm/shared/freesurfer /Applications/freesurfer/subjects/DM99/surf #-------------------------------------------- #@# Local Gyrification Index lh Wed Aug 31 13:37:51 EDT 2016 \n mris_compute_lgi --i lh.pial \n ================= rm -Rf /Applications/freesurfer/subjects/DM99/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /Applications/freesurfer/subjects/DM99/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /Applications/freesurfer/subjects/DM99/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /Applications/freesurfer/subjects/DM99/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/Applications/freesurfer/subjects/DM99/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/Applications/freesurfer/subjects/DM99/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= < M A T L A B (R) > Copyright 1984-2015 The MathWorks, Inc. R2015a (8.5.0.197613) 64-bit (maci64) February 12, 2015 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. Academic License >> reading filled volume... closing volume... Undefined function 'fspecial' for input arguments of type 'char'. Error in make_outer_surface (line 31) Gaussian = fspecial('gaussian',[2 2],1); >> ERROR: make_outer_surface did not create output file '/Applications/freesurfer/subjects/DM99/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Darwin afrancis-mac.mclean.harvard.edu 14.5.0 Darwin Kernel Version 14.5.0: Thu Jun 16 19:58:21 PDT 2016; root:xnu-2782.50.4~1/RELEASE_X86_64 x86_64 recon-all -s DM99 exited with ERRORS at Wed Aug 31 13:38:36 EDT 2016 For more details, see the log file /Applications/freesurfer/subjects/DM99/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting thanks so much, best regards, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* Instructor - Imaging Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> afrancis(a)mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

1 0

problem with Qdecrc file
by Clara Kühn 31 Aug '16

31 Aug '16

Dear FreeSurfer experts, I'm trying to run a 2stage Model in QDEC but I have troubles with incorporating the .Qdecrc file. Sadly the option of spc etc doesn't show up the Design tab when I want to chose a measure. the file is in the same directory the table.dat file is in. What might be the problem? Thank you for your help! Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

3 6

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