Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

Start a nNew thread

Problem with uploading Cluster Simulation data
by carina＠van-vlodrop.de 10 Jun '14

10 Jun '14

1 0

A question about mri_glmfit-sim --3spaces
by 王晗 09 Jun '14

09 Jun '14

Hi,all: I was using mri_glmfit-sim for multiple correction,but I'm wondering if --3paces could influence the correction result. From the website I saw the explanation below: mri_glmfit-sim --glmdir my-glm.wls --cache 3 pos --cwpvalthresh .0166 Using a cluster-wise p-value threshold of p < .0166 corrects across all three spaces for p<.05 (ie, .0166 = .05/3). This corrections for a whole brain (ie, lh, rh, and subcortical) analysis. Also,from the help document I saw: --3spaces : additional Bonferroni correction across 3 spaces (eg, lh, rh, mni305) So, I'm wondering if the command: ' mri_glmfit-sim --glmdir my-glm.wls --cache 3 pos --cwpvalthresh .0166 ' same with the command: ' mri_glmfit-sim --glmdir my-glm.wls --cache 3 pos --cwpvalthresh .0166 --3spaces ' or same with the command: ' mri_glmfit-sim --glmdir my-glm.wls --cache 3 pos --cwpvalthresh .05 --3spaces '. If there is anyone know this question clearly, please reply me. Many thanks. Best regards. Han

2 2

Re: [Freesurfer] Seg fault (fwd)
by Nick Schmansky, MGH 09 Jun '14

09 Jun '14

Gillian, This tkmedit crash problem is a strange one. Something must have changed, and I’ll try to suggest some things to try. Was your .cshrc file changed? Anything added to it that might change LD_LIBRARY_PATH s? What is the output if you run: otool -L `which tkmedit.bin` it should be something like this (although my system is 10.9.3, Mavericks): /Applications/freesurfer/tktools/tkmedit.bin: /usr/pubsw/packages/tcltktixblt/current/lib/libtk8.4.dylib (compatibility version 8.4.0, current version 8.4.0) /usr/pubsw/packages/tcltktixblt/current/lib/libtcl8.4.dylib (compatibility version 8.4.0, current version 8.4.0) /opt/X11/lib/libGLU.1.dylib (compatibility version 1.3.0, current version 1.3.0) /opt/X11/lib/libGL.1.dylib (compatibility version 1.2.0, current version 1.2.0) /opt/X11/lib/libX11.6.dylib (compatibility version 10.0.0, current version 10.0.0) /opt/X11/lib/libXmu.6.dylib (compatibility version 9.0.0, current version 9.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.3) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 125.2.11) /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 7.9.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 830.0.0) did any of the files in /opt/X11 change recently? Did you recently update XQuartz? what version are you using? I use v2.7.5. open Applications/Utilities/XQuartz to find out. I just now opened XQuartz and see that it is prompting me to upgrade to 2.7.6 and also that there is a checkbox to ‘Automatically download and install updates in the future’. Perhaps that was set for you (if you suddenly have version 2.7.6). If so, go to the XQuartz site and get v2.7.5. Although after I updated to v2.7.6, tkmedit still works for me, but I’m using Mavericks. Can you try creating a new user account and try freesurfer using that? perhaps some config thing happened in your regular account. Lastly, if all else fails, I’d suggest removing Freesurfer and XQuartz and reinstalling. Perhaps some files got corrupted on the disk. Nick >> >> ---------- Forwarded message ---------- >> Date: Fri, 30 May 2014 16:32:11 +0000 >> From: "Cooke, Gillian" <gcooke(a)illinois.edu> >> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >> To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] Seg fault >> >> It is happening with all subjects that I've loaded this week, but this >> is my second pass through checks on this data - so all have previously >> loaded successfully. >> >> On May 30, 2014, at 11:24 AM, Douglas N Greve wrote: >> >>> >>> It might be the data you are trying to load in. Does it happen with >>> other subjects or volumes? >>> >>> On 05/30/2014 12:17 PM, Cooke, Gillian wrote: >>>> Thanks for the quick responses. >>>> I'm using version 10.7.5 - I purposely haven't updated this as we've been analysing a large set of intervention data. >>>> I'm also using freesurfer-Darwin-lion-stable-pub-v5.3.0 - again we've been consistent with this and have run everything in this version. >>>> I'm still using the same machine, I'm writing to a large server so there is plenty of space. >>>> The only updates I've installed since I last used Freesurfer successfully are safari and iTunes, and I was getting this error before that installation. >>>> >>>> On May 30, 2014, at 11:04 AM, Bruce Fischl wrote: >>>> >>>>> Hi Gillian >>>>> >>>>> what changed? Did you upgrade a video driver? Use a new machine? Update the operating system? Run out of disk space? Something is different.... >>>>> >>>>> Bruce >>>>> On Fri, 30 May 2014, Cooke, Gillian wrote: >>>>> >>>>>> Hi, >>>>>> I've been working with Freesurfer for years and have suddenly been getting >>>>>> this fault: >>>>>> tkmedit started: Fri May 30 10:08:23 2014 >>>>>> /Applications/freesurfer/tktools/tkmedit.bin ACCE633_1 brainmask.mgz >>>>>> -aux T1.mgz -surfs >>>>>> $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ >>>>>> Set user home dir to /Users/gilliancooke >>>>>> Set subject home dir to /Volumes/HealthAging/ACCE/Freesurfer/ACCE633_1 >>>>>> Using interface file /Applications/freesurfer/tktools/tkmedit.tcl >>>>>> Segfault >>>>>> Setting global interpreter >>>>>> xDebug stack (length: 2) >>>>>> 01: main() >>>>>> 01: Setting global interpreter >>>>>> 00:Z K <zkaufman(a)nmr.mgh.harvard.edu> >>>>>> 00: >>>>>> Any suggestions? >>>>>> Many thanks, >>>>>> Gill >>>>>> _____________________ >>>>>> Gillian Cooke, Ph.D. >>>>>> Postdoctoral Research Associate >>>>>> Lifelong Brain & Cognition Lab >>>>>> Beckman Institute >>>>>> University of Illinois, Urbana >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it is >>>>> addressed. If you believe this e-mail was sent to you in error and the e-mail >>>>> contains patient information, please contact the Partners Compliance HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in error >>>>> but does not contain patient information, please contact the sender and properly >>>>> dispose of the e-mail. >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> >

1 0

Using Gender as a Covariate in glm_fit
by Thomas DeRamus 09 Jun '14

09 Jun '14

Hello, I am performing an mri_glmfit analysis between my control and my clinical group, and I'm including age and total intracranial volume in the model. However, I'd like to regress out the effects of gender, and I'm curious if the best approach to do this is to group my subjects by their gender (i.e. Have Class: MaleClinical, FemaleClinical, MaleControl, Female Control), or to add gender as a factor in the model (Make Variables: Age, ICV, and gender [ coded as 0 for female and 1 for male]). My clinical population is primarily a male disorder (we have close to 10 females out of at total of 114 participants), so I feel like splitting them into groups would make a huge difference just based on that, and I'd honestly rather regress out the effects of gender rather than analyze them as variables of interest. Please let me know what you think at your earliest convenience. -Thomas

1 0

Re: [Freesurfer] free-surfer longitudinal Qdec table
by Martin Reuter 09 Jun '14

09 Jun '14

Hi Anna, Fsid is the cross sectionall name without the .long. Best martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Anna Jonsson <ajonsson09(a)gmail.com> Date:06/04/2014 7:22 AM (GMT-05:00) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] free-surfer longitudinal Qdec table Hi, I would like to make my freesurfer longitudinal qdec table for the to use in the lme matlab tools. However, does the fsid need to refer to the longitidunally derived subject; eg XXX.long, or the cross-sectionally derived subject, eg XXX. Im not sure based on the specification online. Kind Regards Anna

2 1

3dvolreg Error for preproc-sess
by Nitenson, Adam 09 Jun '14

09 Jun '14

Hi all, I'm running version 5.2 off-site, and I keep running up against an error for preproc-sess. From my SUBJECTS_DIR, I am running preproc-sess -fsd bold -s 608_Sess1 -fwhm 5 -per-run which provides the following error: 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr ERROR: 3dvolreg.afni Invalid null command. I found this old communication https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28736.html in which this user had the same problem. I found 3dvolreg.afni in the Freesurfer "bin" folder and copied to to my AFNI folder, but I still get the same error when running preproc-sess, even with 3dvolreg.afni now in the AFNI cluster. Any idea what the problem might be? Best, Adam Nitenson

3 4

Quality control of the splitting of midline structures?
by Jensen, Sarah 09 Jun '14

09 Jun '14

Dear Freesurfers, I have a question about whether it is possible to check how well each participant in my study lines up with the Freesurfer template in order to check how midline structures were split. I am concerned about how well my ACC ROIs line up with the midline of the brain, and would like to check for cross-hemisphere contamination along the medial wall. I am particularly interested in detecting any potential residual rotation along the Y axis. I have projected cortical ROIs onto the cortical surface of the average brain using the mri_vol2surf function and then used annotation files for the left and right hemisphere to project my ROIs from the average template into participant's native space using the mri_surf2surf function. My question is whether it is possible to get an image of how well the fully segmented Freesurfer image lines up with the template? Preferably in an axial view with both hemispheres visible. Thanks in advance! Sarah? Sarah K. G. Jensen Ph.D. Student Department of Psychology Institute of Psychiatry King's College London E-mail: sarah.jensen(a)kcl.ac.uk Phone: 075 2789 3171

2 3

Unpacking Problem
by Emad Ahmadi 08 Jun '14

08 Jun '14

Hello, I’m trying to unpack and run recon-all on a set of MEMPRAGE images we’ve obtained in Lunder 6 scanner (Siemens Skyra), but recon-all is giving me errors. I’ve attached for the scan.info file (outputted by unpacksdcmdir), the unpack.config file that I used to unpack the MEMPRAGE images, and the recon-all.log file containing the error that recon-all command gives me. I’m running recon-all on in MEMPRAGE3 folder containing MEMPRAGE_IPAT3 RMS images. Please let me know if I have to provide any further info about this problem. Thank you very much for your help, Emad Emad Ahmadi, MD ----------------------------------------------- Postdoc Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad(a)nmr.mgh.harvard.edu

2 1

neocortical gray matter
by Elisabetta del Re 08 Jun '14

08 Jun '14

Dear Freesurfer team, what is the best measure for neocortical gray matter from the FS output? Thank you so much, best, Elisabetta

2 1

freeview permission error
by Andrews, Derek 08 Jun '14

08 Jun '14

Hello Freesurfer community, Unfortunately I am having an issue with saving a point set (control point manual edits) within FreeView. I get the error "Could not save point set. Check console for more information.", the console readout states "Permission Denied". I have looked through past threads to try and address this and have not had much luck. I have included a screen shot. Thank you for your support. Best, Derek ________________________________ Derek Sayre Andrews, MSc PhD Candidate & Student Forum PGR Co-Chair Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, King's College London Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews(a)kcl.ac.uk

2 1

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