Freesurfer March 2008

freesurfer@nmr.mgh.harvard.edu

55 participants
81 discussions

purpose of creating own "average subject"
by Michael Harms 28 Mar '08

28 Mar '08

Hello, There have been numerous posts recently related to the creation of a study specific "average subject". I have a question about the purpose/motivation of this for surface-stream analysis/visualization that I was hoping someone could clarify. Specifically, my understanding is that the annotation/labels for any derived study specific average subject are determined by the "buckner40" gcs file (for the case of the desikan atlas). And similarly, the average surface (e.g., white, pial) and curvature-format files (e.g., curv, sulc, thickness) are registered across subjects via sphere.reg, which is determined by ?h.curvature.filled.buckner40.tif? So, since the annotation and registration for any study specific "average subject" is going to be determined by the "buckner40" set of subjects regardless of the specific subjects in a particular study, what is the purpose, advantage, or necessity for creating a study specific average subject? Or stated differently, since the whole FS approach for registering surfaces (and by extension parcellating the cortex) is based on the assumption that the "buckner40" set of subjects is an appropriate registration and parcellation target for ALL studies, what is the point of creating a study specific average rather than using the default 'fsaverage' (which has the advantage of being created from the same set of 40 subjects that drive the registration itself)? Please help me understand what I'm missing here. thanks, Mike H. P.S. Am I correct in presuming that the same 40 subjects were used for the Desikan GCS atlas and for deriving the spherical registration (.tif) target? -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

2 4

Label boundary
by SHRIKANTH KULASHEKHAR 28 Mar '08

28 Mar '08

Hi, Is there any freesurfer utility to isolate/plot the vertices that form the boundary of any label ? If no, how can one go about doing this ? Thank you. Shriks Forgot the famous last words? Access your message archive online at http://in.messenger.yahoo.com/webmessengerpromo.php

2 1

Parcellation Protocol?
by Raymond Hill 27 Mar '08

27 Mar '08

Hello, We are trying to compare FreeSurfer's parcellation with what we do here manually. To that end, we were wondering if we could access a detailed protocol that was used to manually create the ROIs that went into the FS Parcellation atlas? We have examined the Desikan et al (2006) paper with the brief descriptions but these are not particularly detailed. If this is not possible, is there any way we could find out the ways in which this atlas diverges from the standard CMA? Thank you! Ray Hill

1 0

Talairach transformation
by Thomas Doering 27 Mar '08

27 Mar '08

Dear List, I got stucked when running the first recon step. There seems something wrong with the Tailarach Transformation step...But i don´t know how to fix it... I attached the recon-all file. Thanks for help, suggestions, etc. Cheers, Thomas

2 1

Cluster on Demand
by Pedro Paulo Oliveira Jr 26 Mar '08

26 Mar '08

Dear Freesurfers I was testing a Cluster-on demand, pay-per-hour-used service US based and it seems pretty good. I ran 100 recon-all in 33 hours!!! The cost of one hour of CPU is USD 0.77 The quote I received is a package of 200.000 hours / month with an hour priced as USD 0.25 cents This figure represents 5500 Freesurfer recon-all per month. If many people in the list are interested in sharing the expenses I think it would be a quick way to process tons of brains. The info I received is that this cluster is based in Florida and have 300 cpus Hope this helps, PPJ

3 5

Recon-all recent errors
by lbotelho＠nmr.mgh.harvard.edu 26 Mar '08

26 Mar '08

Hi, Since March, recon-all exits with errors on mris_extract_main_component. This happens when analyzing the same data with the same input commands used successfully prior to March. -------------------------------------------- >From the RECON-ALL.LOG: mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix ERROR: MRISread: file '../surf/lh.orig.nofix' has more faces than vertices! Probably trying to use a scalar data file as a surface! No such file or directory Linux node0241 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Tue Mar 25 12:43:45 EDT 2008 -------------------------------------------- >From RECON-ALL.ERROR: $Id: recon-all,v 1.179 2008/03/19 20:11:52 greve Exp $ /usr/local/freesurfer/dev/bin/recon-all PWD /autofs/space/heisenberg_005/users/lbotelho/subjects/DBS_C12_15T_r2repeat/scripts CMD mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix -------------------------------------------- I wonder if this may be related with the updated Freesurfer development version and about the best way to fix it. Thank you, Luis

2 1

qdec error finding files
by Mischka Gerken 24 Mar '08

24 Mar '08

Hello to all the kind people at FreeSurfer! We are having difficulty running qdec. After solving my issues loading tables, qdec is having difficulty loading certain files. Our current error is that qdec says it cannot find the lh.curv file for the fsaverage subject. -I have verified that this file exists, and that it exists in the proper location (same directory qdec indicates it is searching in) -we have exported the correct subjects directory (in BASH not TCSH) -everything else until that point seems to be ok. We have been able to run some analysis just fine, then others run into this error of not being able to find files (no clear pattern why, but very frequent). This is a very simple trial (11subjects in two groups, so just one discrete variable). We have made the average subject (exited without errors) We have run -qcache on all subjects very recently (2 days before analysis) Any thoughts on what we might be doing wrong? -Mischka

2 1

libXmu error on cluster
by Pedro Paulo Oliveira Jr 24 Mar '08

24 Mar '08

Hi, I ran 40 process and all finished with /b/03/netfi01/freesurfer/subjects/rodiguespierinam/scripts/recon-all.log:mri s_volmask.bin: error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory But in /usr/lib there is a libXmu.so.6 My questions are: 1) Anybody know why it failed? 2) If I fix this how can I run recon-all from this point? Thanks PPJ

3 3

Error on Spline Cubic Set
by Pedro Paulo Oliveira Jr 21 Mar '08

21 Mar '08

Anyone can shed a light? FS 4.0.2 i386 CentOS Fri Mar 21 20:11:45 EDT 2008 talairach_avi done #-------------------------------------------- #@# Talairach Failure Detection Fri Mar 21 20:11:46 EDT 2008 /b/03/netfi01/freesurfer/subjects/neliseoliveira/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.2855, pval=0.0254 >= threshold=0.0050) awk -f /b/03/netfi01/freesurfer/bin/extract_talairach_avi_QA.awk /b/03/netfi01/freesurfer/subjects/neliseoliveira/mri/transforms/talairach_av i.log TalAviQA: 0.97187 z-score: -1 #-------------------------------------------- #@# Intensity Normalization Fri Mar 21 20:11:46 EDT 2008 /b/03/netfi01/freesurfer/subjects/neliseoliveira/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.157 0.025 -0.069 -0.036; 0.081 0.971 0.642 1.728; 0.091 -0.685 1.159 -15.320; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 SPLINE_CUBIC_SET - Fatal error! The number of data points N must be at least 2. The input value is 1. Linux n122128 2.6.18-1.2798.fc6 #1 SMP Mon Oct 16 14:54:20 EDT 2006 i686 athlon i386 GNU/Linux recon-all exited with ERRORS at Fri Mar 21 20:11:51 EDT 2008

2 1

visualizing individual structures
by Thomas Thesen 21 Mar '08

21 Mar '08

Hi All, What is a good and straight-forward way to visualize individual structures based on the segmentation (e.g. hippocampus) and labels (e.g. aparc)? Is that possible with the Freesurfer tools? cheers, Thomas --------------------------------- Looking for last minute shopping deals? Find them fast with Yahoo! Search.

2 1

← Newer
1
2
3
4
5
6
7
8
9
Older →

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer March 2008