Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30066 discussions

N3 options (was: [Freesurfer] parameters for N3 correction)
by Sebastian Moeller 03 Nov '06

03 Nov '06

Hi List, On 3. Nov 2006, at 19:48 Uhr, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 10 > Date: Fri, 03 Nov 2006 13:48:18 -0500 > From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] parameters for N3 correction > To: Chacko Cherian <chacko_cherian(a)yahoo.com> > Cc: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <1162579698.27296.26.camel(a)minerva.nmr.mgh.harvard.edu> > Content-Type: text/plain > > also, the command: > > recon-all -s <subjid> -nuintensitycor > > will run just that stage. > Something relted on the topic of N3. Using the default settings with surface coils (RX and TX through the same coil in our case) ends up looking ugly no matter the number of -nuiterations specified in recon-all. Hacking mri_nu_correct.mni to include "-iterations 150 -stop 0.0001" in the invocation of nu_correct, ends up with better results. Just as the N3 documentation recommends for surface coils ;). Now would it be possible to get a "-surfacecoil" argument for mri_nu_correct.mni (or even better recon_all via the experts options mechanism?) included into the distribution. If yes I would be willing to hack something up (at least including this properly into mri_nu_correct.mni). This might be helpful for other surface coil users out there... ahoi & sorry -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

3 6

parameters for N3 correction
by Chacko Cherian 03 Nov '06

03 Nov '06

Hello users, Is there any information available regarding the parameters used for N3 correction in the autorecon process? Thanks, Chacko.

4 3

Doubt on spherical coordinates
by jorge luis 03 Nov '06

03 Nov '06

Hello all I would like to know what kind of coordinates (RAS, Talairach, Spherical) are saved in the AsCII file resulting from: mris_convert lh.sphere.reg lh.sphere.reg.asc I could not find correspondence among the resulting coordinates and those that are shown in Tksurfer. If they are not the spherical ones, how can I get an ASCII file with the spherical coordinates ( XYZ) or (Rho,Theta) in order to work on the spherical world? In advance Thank you a lot ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

3 4

freesurfer course
by Nicolas Cherbuin 01 Nov '06

01 Nov '06

Dear Freesurfers, I am trying to plan international travel for next year. Can somebody inform me of when the next freesurfer courses will take place in 2007? Thanks Nic

2 1

mris_anatomical_stats error
by Johannes Klein 01 Nov '06

01 Nov '06

Hi everyone, I'm trying to calculate surface areas for some labels I've drawn on an averaged subject created with mrake_average_surface, and mris_anatomical_stats seems the way to go. Unfortunately, it needs a file called wm.mgz, which doesn't exist for my averaged subject. The mri subdir contains T1, brain, mni305.cor and orig.mgz, but no wm.mgz. Is there a way to create this file from the data I've got? Thanks for your help, Johannes

4 4

recon-all autorecon2 error.
by Mithra 31 Oct '06

31 Oct '06

Hello, I ran autorecon1 this step worked fine. The transform obtained from this step looked good. When I run autorecon2, I get a segmentation fault error. Can anybody tell me whats wrong. Thanks a whole bunch. Error: Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86 _64 x86_64 x86_64 GNU/Linux WM removal version #------------------------------------- #@# EM Registration Tue Oct 31 14:32:46 CST 2006 /usr/pubsw/freesurfer/subjects/sub02/mri mri_em_register -mask brainmask.mgz nu.mgz /usr/pubsw/freesurfer/average/RB_all _2006-02-15.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/pubsw/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type average std = 7.4 using min determinant for regularization = 5.5 0 singular and 1662 ill-conditioned covariance matrices regularized reading 'nu.mgz'... Segmentation fault Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86 _64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Oct 31 14:32:57 CST 2006

2 1

mri_convert options
by Derin Cobia 31 Oct '06

31 Oct '06

Hi, Currently we've been converting from .img to .mgz format using the following syntax: mri_convert -TI 20 -te 4 -tr 9.7 -flip_angle 0.174532925199433 -ot mgz s1501p.img mri/orig/001.mgz It came to my attention today that the values we used for TI, TE, and TR are all actually in ms, and correspond to the Siemen's Vision use of the terms TI and TR for the MRPAGE sequence. This is quite different from how TI and TR are used for the MPRAGE sequence on the Symphony, Sonata, and Trio Siemens platform. Furthermore, we have actually been applying these values to Vision FLASH data as well, for which TI is irrelevant, and the TR and flip were different. Basically, we have just been confused in our use of mri_convert. So, this raises a couple questions: 1) Are the TI, TE, TR and flip parameters important to mri_convert? How are they used? Are they used in any manner in the subsequent Freesurfer processing stream? We wonder if they are not important, since the current documention lists TR as an option, but doesn't mention TI, TE, or flip as options. 2) If these parameters are important in some manner how would the use of such grossly incorrect values affect the results? So basically, we are wondering what parameters, if any, are truly necessary as part of mri_convert? And do we (gasp) need to consider rerunning the stream from stage 1... Thanks! Derin

2 1

automatic processing
by Nicolas Cherbuin 31 Oct '06

31 Oct '06

Hi, I have to process more than 500 good quality scans (1mm isotropic) for an epidemiological study and have limited time resources. Initial processing of 20 scans seems promising but I am new to freesurfer and therefore I am not quite sure how significant small defects might be in the big picture (where they will be averaged over a large number of subjects). I would be interested to hear the experience of others in using autoreconall for processing most scans and only reprocessing a small portion of scans with obvious substantial defects (mostly on the inflated surface). With good quality scans would most people reprocess most scans? Thanks for sharing your experiences. Nic

2 1

ROI group analysis
by Cameron Ellis 31 Oct '06

31 Oct '06

Hi, I am trying to run mri_volcluster on a group ROI and am having some trouble. I was hoping someone had suggestion. I created individual ROIs and wanted to average them to obtain a group ROI. I ran isxavg-re-sess for each ROI but there is no registration file for mri_volcuster to reference. Have I hit a dead end? Does anyone know another way of creating a group ROI that I can apply the mri_volcluster command to? Thanks, Cameron

2 2

Morphological measures
by Juergen Haenggi 31 Oct '06

31 Oct '06

Dear Freesurfer users after running Freesurfer, I got 11 colums (without structure name) in the recon_all.log file with the different morphological indices: e.g. 208 122 451 3.056 0.740 0.125 0.024 2 0.6 15 0.179 G_cingulate-Isthmus but actually there should be only 9 colums (without structure name). further I am confused because in another subject there are only 10 colums (without structure name) e.g. 188 124 272 2.121 0.641 0.107 0 18 1.966 0.12 G_cingulate-Isthmus and in the second example, the 7th colum (Gaussian curvature) is always zero!!! What happens? Thanks in advance for clarification Best regards Juergen ---------------------------------------------- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931 Lenggstrasse 31, 8032 Zurich 0041 44 384 26 10 (office phone) 0041 76 445 86 84 (mobile phone) 0041 44 384 26 86 (fax) H 115 (office room number) juergen.haenggi(a)bli.unizh.ch (division email) http://www.dpr.unizh.ch/ (division website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------

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