Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Caudate segmentation and exporting ROIs
by Paula Banca 29 Jan '12

29 Jan '12

Dear Freesurfer's, I'm wondering if it is possible to use FreeSurfer to do the caudate segmentation automatically. I'm asking that because I did all my fMRI data analysis in BrainVoyager and currently I need to run more statistical analysis in this specific region (caudate). For that I need to have this ROI. However, to create it manually in BV I would need a lot of time. I'd like to check if there is a possibility to create this ROI automatically,using Freesurfer, and then export it to BV in order to finish my functional analysis there. Do you think this can be done ? Thanks in advance! All the best, Paula

2 1

mris_anatomical_stats: no smoothing effect when using ?h.area file as target
by Jürgen Hänggi 29 Jan '12

29 Jan '12

Dear FS experts I have done group comparisons wrt thickness, surface area and volume. The found clusters were written out as annotations, transformed into each individual space, and then the corresponding values were extracted. When using mris_anatomical_stats, values are different for thickness and volume maps depending whether I used the --nsmooth 15 option or not. So good so far. However, when using the same command (see below) for ?h.area files, extracted values are the same whether or not I used the --nsmooth 15 option. mris_anatomical_stats -a rh_area_parietal_insular.annot -t rh.area -nsmooth 15 -f subject/stats/output.stats subject rh It seems that the --nsmooth 15 option in mris_anatomical_stats does not affect (smooth) the area maps that were used to extract the values. Is this what one has to be expected? Or is it something like a bug? Thanks in advance Best regards Jürgen Hänggi ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

1 0

'::conj' has not been declared
by Hazard, E. Starr 28 Jan '12

28 Jan '12

Folks, I am doing my best to follow these instructions from : http://surfer.nmr.mgh.harvard.edu/fswiki/Devel My gcc is 4.4.6 Is there a way to avoid the error below or must I install gcc 3.4.6 as per the MNI readme? cd EBTKS-1.4-src; \ make; \ make install; make[1]: Entering directory `/home/hazards/COMPILE3/FreeSurf_Support/mni/EBTKS-1.4-src' make all-am make[2]: Entering directory `/home/hazards/COMPILE3/FreeSurf_Support/mni/EBTKS-1.4-src' if /bin/sh ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -msse2 -mfpmath=sse -MT Matrix.lo -MD -MP -MF ".deps/Matrix.Tpo" \ -c -o Matrix.lo `test -f 'templates/Matrix.cc' || echo './'`templates/Matrix.cc; \ then mv ".deps/Matrix.Tpo" ".deps/Matrix.Plo"; \ else rm -f ".deps/Matrix.Tpo"; exit 1; \ fi g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -msse2 -mfpmath=sse -MT Matrix.lo -MD -MP -MF .deps/Matrix.Tpo -c templates/Matrix.cc -o Matrix.o In file included from templates/Matrix.cc:3567: templates/MatrixSpec.cc: In member function 'Mat<Type>& Mat<Type>::conj() [with Type = std::complex<double>]': templates/MatrixSpec.cc:405: error: '::conj' has not been declared make[2]: *** [Matrix.lo] Error 1 make[2]: Leaving directory `/home/hazards/COMPILE3/FreeSurf_Support/mni/EBTKS-1.4-src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/hazards/COMPILE3/FreeSurf_Support/mni/EBTKS-1.4-src' make[1]: Entering directory `/home/hazards/COMPILE3/FreeSurf_Support/mni/EBTKS-1.4-src' if /bin/sh ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -msse2 -mfpmath=sse -MT Matrix.lo -MD -MP -MF ".deps/Matrix.Tpo" \ -c -o Matrix.lo `test -f 'templates/Matrix.cc' || echo './'`templates/Matrix.cc; \ then mv ".deps/Matrix.Tpo" ".deps/Matrix.Plo"; \ else rm -f ".deps/Matrix.Tpo"; exit 1; \ fi g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -msse2 -mfpmath=sse -MT Matrix.lo -MD -MP -MF .deps/Matrix.Tpo -c templates/Matrix.cc -o Matrix.o In file included from templates/Matrix.cc:3567: templates/MatrixSpec.cc: In member function 'Mat<Type>& Mat<Type>::conj() [with Type = std::complex<double>]': templates/MatrixSpec.cc:405: error: '::conj' has not been declared make[1]: *** [Matrix.lo] Error 1 make[1]: Leaving directory `/home/hazards/COMPILE3/FreeSurf_Support/mni/EBTKS-1.4-src' make: *** [ebtks] Error 2

1 0

Unable to open tkmedit
by Daniel R. O'Young 28 Jan '12

28 Jan '12

I've been trying to open tkmedit but am continually getting an error ("GLUT: Fatal Error in tkmedit.bin: visual with necessary capabilities not found"). I'm using a machine with Ubuntu 11.04 that formerly ran tkmedit. The only suggestion I could find so far was this (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-May/014433.html) Has anyone else run into this error or solutions for it? Daniel O'Young droyoung(a)umd.edu<mailto:droyoung@umd.edu> DSCN Lab

1 0

Too many levels of symbolic links
by cloud.ctrl＠me.com 27 Jan '12

27 Jan '12

I have subjects exiting with errors and I'm not sure why. The best clue I have is a line indicating "Too many levels of symbolic links" and an inability to read lh.BA1.label. Here are the last few lines of output: SUBJECTS_DIR /Applications/freesurfer/subjects FREESURFER_HOME /Applications/freesurfer Loading source label. Too many levels of symbolic links ERROR reading /Applications/freesurfer/subjects/fsaverage/label/lh.BA1.label Darwin stat-240-26.sdsu.edu 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 recon-all -s GB exited with ERRORS at Thu Jan 26 00:29:32 PST 2012 Can anyone tell me what is happening here?

2 1

how can I view and process Freesurfer files using AFNI
by Rashmi Singh 27 Jan '12

27 Jan '12

Hello, I ran recon all on my subjects data which went well. Now I would like to use AFNI-SUMA to view it , how do I go about doing this. Thanks, Rashmi. ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

3 2

FreeSurfer download failed
by Browne, Aaron N 27 Jan '12

27 Jan '12

Hi! I would love to start using FreeSurfer and cannot download the software from your server. I am on a 32 bit GNU/Linux virtual machine running CentOS 5.7 and typed the following command: wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Linux… my output is: --2012-01-26 14:58:03-- ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Linux… => `freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz' Resolving surfer.nmr.mgh.harvard.edu... 132.183.202.158 Connecting to surfer.nmr.mgh.harvard.edu|132.183.202.158|:21... failed: Connection refused. I also tried clicking the download link in a firefox browser on my machine and got an "Unable to connect" error page. Did you move to a new server or something? Thanks for any help you can provide! Aaron Research Assistant Center for Autism Research The Children's Hospital of Philadelphia 3535 Market Street, Suite 860 Philadelphia, PA 19104 Phone: 267-426-4900 Fax: 267-426-7590 email: brownea(a)email.chop.edu<mailto:rileym1@email.chop.edu>

1 1

Two FS versions in different user accounts
by _andreia_＠sapo.pt 27 Jan '12

27 Jan '12

Hi everyone, I'm sorry to bring this question up again, but I'm thinking to install version 5.1 in the same computer where version 5.0 is installed. However I'm thinking of installing the new one in another user account that I've created only for this porpuse. My question is, can I install and work in the new user independently? This way I won't need to be changing the subjects dir and the freesurfer environment each time I want to work with 5.0 or 5.1, right? Advice needed =) Thanks, Andreia

2 1

Two FS versions in different user accounts
by _andreia_＠sapo.pt 27 Jan '12

27 Jan '12

1 0

HandDrawn & Aseg amygdala comparisons.
by Jamie Hanson 26 Jan '12

26 Jan '12

Hi Freesurfer list- I was trying to compare hand-drawn amygdalae and amygdala volumes generated by mri_ca_label/aseg (similar to what Morey et al., 2009 did) and wanted some advice. My amygdalae are drawn by hand in pathological plane, with a quite labor intensive tracing routine. And I wondered the best way to get my aseg volumes into that (path plane) space (b/c I didn't want to move the hand-drawn masks)? Initially, I just aligned my raw T1w to pathological plane T1s and ran recon-all on these images, but the bivariate correlations between automated aseg volumes and hand-drawn amygdala dropped a fair amount (r=.5 in raw space, to r=.3 in path plane). I presume the re-alignment to path plane is adding some additional smoothing (which lowers mri_ca_label accuracy?). I didn't think it would be a fair comparison to calculate dice-coefficients, intersection/union, etc. with aseg pathological plane amygdala (compared to my hand-drawn amygdala). Is the best practice to segment in original space, calculate the transform on the T1 from orig to path-plane, and then apply that transformation matrix to the aseg volume generated from the raw T1? Are there other suggestions? Any advice is greatly appreciated! Thanks much! Best, jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53705 Email: jamielarshanson(a)gmail.com Homepage: http://brainimaging.waisman.wisc.edu/~hanson/

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