Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30090 discussions

(no subject)
by Nicholas Paul Denisuk 09 Jul '13

09 Jul '13

Dear Freesurfer Users, I am trying to regress out the activity associated with button presses in my GLM analysis. How do I generate a nuisance regressor file analogous to a white matter regressor generated in functional connectivity (a one column time course file)? Thanks you, Nick

2 1

Subcortical volume stream
by Jim Monti 09 Jul '13

09 Jul '13

Hello, I would like to verify something regarding subcortical volume estimation in Freesurfer before we move forward with our analyses. From what I've read on the wiki and listserv, it seems the subcortical and cortical processing streams are largely independent. If one were only interested in subcortical volumes (e.g. hippocampus, striatum) is it sufficient to run recon-all -all on the participants, verify/correct any issues with the registration, verify that the segmentations look correct, and then move forward with statistical analyses on the subcortical volumes using aseg.stats, or will refinements in the surfaces (e.g. manually removing dura mater from the pial surface) have an effect on subcortical volume and thus it is necessary to check the surfaces as well, make the corrections, rerun autorecon 2 and 3, the and then perform stats on the subcortical volumes? Thank you in advance for your time. Sincerely, Jim Monti -- Jim Monti PhD Candidate 2012-2013 Beckman Institute Graduate Fellow Memory Systems Laboratory (http://msl.beckman.illinois.edu/) Psychology-Cognitive Neuroscience University of Illinois at Urbana-Champaign

1 0

Is this an example of pial surface extending into cerebellum?
by ye tian 09 Jul '13

09 Jul '13

Dear Freesurfers, Is the attached file an example of pial surface extending into cerebellum? Thank you very much! Sincerely, Ye

2 5

qdec control variable limitation
by Jiang Jiyang 09 Jul '13

09 Jul '13

Dear all, I am using qdec to do a shape analysis with 16 control variables. I was wondering if there is a limit on how many covariates can be used in qdec? Because it seems that I cannot select all my covariates in "nuisance factors". Thanks and regards, Jiyang

2 1

average/RB_all_2008-03-26.gca not found error
by Salil Soman 09 Jul '13

09 Jul '13

Hi, *Am running this command:* $FREESURFER_HOME/bin/recon-all -i 3DSPGR.nii.gz -s WCA_248_T1Q_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -use-cuda -all *And am get this out put / error:* Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221 Driver : 5.50 Runtime : 5.0 Acquiring CUDA device Using default device CUDA device: GeForce GTX 660 ======= NUMBER OF OPENMP THREADS = 50 ======= stable5 NVIDIA driver version info: NVRM version: NVIDIA UNIX x86_64 Kernel Module 319.32 Wed Jun 19 15:51:20 PDT 2013 ERROR: cannot find /usr/local/freesurfer/average/RB_all_2008-03-26.gca Any suggestions what I am doing incorrectly? Thank you, Sal

2 2

mri_cvs_register std:: bad_alloc
by Marcel Falkiewicz 09 Jul '13

09 Jul '13

Dear FreeSurfers, I'm trying to use mri_cvs_register, however the process can't complete and I get the following error: [...] loading transform id string = data size = 18728074 uilen = 6 loading transform id string = data size = 19845421 uilen = 6 loading transform id string = data size = 19120776 uilen = 6 loading transform id string = data size = 71 uilen = 7 loading transform id string = saveTransform code writing transform size = 117019458 saveTransform code writing transform size = 117019458 saveTransform code writing transform size = 16 saveTransform code writing transform size = 21339696 saveTransform code writing transform size = 21092930 saveTransform code writing transform size = 20795616 saveTransform code writing transform size = 20591898 saveTransform code requested buffer size = 436643894 Exception caught while saving morph ZlibStringCompressor::setBufferSize - Caught std::bad_alloc My command line was: mri_cvs_register --mov subject01 --mni --openmp 8 --m3d At the time of crash all RAM is consumed by createMorph process (10 GB). Is this crash related to the ammount of RAM on my machine (12 GB)? If so, how much RAM is needed to complete mri_cvs_register? Best regards, Marcel

2 2

custom fill function for matlab
by Catarina Rua 09 Jul '13

09 Jul '13

Dear freesurfer admin, I'm writing a piece of code in matlab based on freesurfer reconstructed brains generating series of labels to an annotation file. However, I wanted to include a process similar to the existing in tksurfer options in the 'custom fill' where you can fill in all vertices up to a label border/up to included paths. I have searched on the web for a piece of matlab code that would process this, but I coulnt seem to find it. Is there any quick way to do this? The basic idea is that I have a group of non-labeled vertices enclosed within a label, and I just want to 'fill" them with the same label as the label that surrounds it. Thank you very much in advance. I really do hope this can be possible! Cheers! Catarina Rua

4 3

how to use mris_register?
by fatma zribi 09 Jul '13

09 Jul '13

Dear Mr, When I execute mris_register to register one subject to a template., I have this message of error: mris_register -1 s000/surf/lh.sphere avg_all_subjects_SD/lh.reg.template.tif sphere_reg treating target as a single subject's surface... $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere... MRISread(s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere): could not open file No such file or directory mris_register: could not read surface file s000/surf/lh.sphere No such file or directory note that the file exist in the specifeid SUBJECT_DIR Thank you for your help Fatma

2 1

Re: [Freesurfer] Artefactual skull stripping for some subjects
by Tudor Popescu 09 Jul '13

09 Jul '13

Dear FSers, Still haven't got to the bottom of this, any suggestions would be much appreciated, thanks in advance! Tudor On 5 July 2013 17:26, Tudor Popescu <tudor3(a)gmail.com> wrote: > Hi everyone > > The skull-stripping step of recon-all must have gone bad for my sample, > because I noticed that there are artefacts (chips) in the brain-extracted > structurals of several of my subjects. Since I ran recon-all on all my > sample without having noticed this initially, this of course also lead to > the surfaces being created wrongly, i.e. following the wrong volumetric > information. > > I attach screenshots showing some of the more obvious artefactual skull > extractions, corresponding to subjects 04, 06 and 17, and also the > brain.mgz and T1.mgz for subject 17. > > FSL's BET extracted the skull with no problems from the same original > structurals, so I'm guessing it's maybe the case that I need to override > some parameters in recon-all in order for the initial recon-all to produce > good brain extractions? > > And by the way, I noticed that, in any one subject's folder, the images > /mri/T1.mgz, /mri/orig.mgz and /mri/orig/001.mgz all seem to contain the > subject's original structural scan. Why does this exist in 3 separate > copies, which also seem to be of different file sizes? The only difference > I can see between them is in terms of brightness correction... > > Many thanks! > > Tudor >

3 4

likelihood of identical subcortical volumes
by Satrajit Ghosh 08 Jul '13

08 Jul '13

2 4

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