Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Optseq - optimal parameters
by Ella Hinton 16 Jun '13

16 Jun '13

Hi all, I have been advised to use optseq to aid my event related fMRI design, specifically to help calculate stimulus order and timing. I've read the help in some detail but am still a little unclear on some of the appropriate values to input and indeed what values I am aiming for in the output. It'd be great if anyone can help out... Briefly, my study is a simple food cue reactivity study in which three different types of pictures (50 each) are presented for 3s each, in pseudo-random sequence. I now intend to include null events to optimise the spacing of the events to detect a difference between conditions, but also to provide a baseline for a 'sanity check' just in case. I am uncertain as to the value of psdwin and associated variables (PSD, min, max dPSD) - should I include a post-stimulus delay or should that be set to 0 as in most examples? Also what is the recommended psdwinMAX value for events of 3s? 12 or as much as 18 seconds to capture the whole haemodynamic response? Also I am not certain how to judge the resulting output. I understand I should maximise 'efficiency' but I can't find any advice as to what is a 'good' value of efficiency to aim for. Any advice here? Also should I be judging the sequence on any other values? So I have inputted the following and got a value of 2.586 for efficiency for the best sequence. Is this reasonable/sufficient? optseq2 --ntp 200 --tr 3 ---psdwin 0 12 3 --ev ev1 3 50 --ev ev2 3 50 --ev ev3 3 50 --nkeep 3 --o test6 --nsearch 10000 Many thanks in advance, Ella

2 1

SPM ROI to Cortical Thickness
by xiangbo_2010 15 Jun '13

15 Jun '13

Dear experts, I was wondering if anyone can advise on the best way to use an ROI mask created in SPM (XjView) to extract cortical thickness values in freesurfer. Though which was pointed out by reseachers, but I still can not know it. I hope some experts help me, Thanks! Bo Thank you in advance for your help!

2 2

Conversion
by Anna Josefson 15 Jun '13

15 Jun '13

Dear FreeSurfer users! I am new to Freesurfer, and I have succesfully managed to run recon-all on my data, for every subject. Now I plan to use the output - some of the different cortical and subcortical brain structures as ROI's in my SPM analyses. Then I would have to convert from freesurfer space to SPM space via the coordinates. And - I would also have to convert from .mgz to .nii data format. Does any have any tips on how to do this? Or a script? Kind Regards, Anna B. Josefson

3 4

Group Analysis Error
by Nooshin Zadeh 15 Jun '13

15 Jun '13

Dear FreeSurfer Group I wanted to Group Analysis with qdec. I have MRIs of one patient in two different dates and I wanted to do group analysis on them to see the changes. I have "gender", "age", and "diagnosis". In qdec deme, when I make the analysis based on "thickness", I receive the attached error. I do not know what is the reason. Any help and advice would be appreciated. Thanks, Nooshin

2 1

2013年6月15日 20:37:34 自动保存草稿
by xiangbo_2010 15 Jun '13

15 Jun '13

1 0

Installation Conflict
by Mark Plantz 14 Jun '13

14 Jun '13

Hello, I recently installed FreeSurfer on an OS x machine. After finishing the process, I received the following output: *Setting up environment for FreeSurfer/FS-FAST (and FSL)* *FREESURFER_HOME /Applications/freesurfer* *FSFAST_HOME /Applications/freesurfer/fsfast* *FSF_OUTPUT_FORMAT nii.gz* *SUBJECTS_DIR /Applications/freesurfer/subjects* *grep: Command not found.* *wc: Command not found.* *grep: Command not found.* *wc: Command not found.* *grep: Command not found.* *wc: Command not found.* *MNI_DIR /Applications/freesurfer/mni* */usr/local/fsl/etc/fslconf/fslmachtype.sh: line 14: uname: command not found* *FSL_DIR /usr/local/fsl* */usr/local/Applications/freesurfer: No such file or directory.* Why can the grep, wc, of MNI commands not be found? Also, when I type the command: *$FREESURFER_HOME/subjects* I receive the following error: /Applications/freesurfer/subjects: Permission denied. Any ideas on how to solve this problem? Is it a licensing issue? I have already created the .license file. Best, Mark Plantz

2 1

methods Q
by Joshua Lee 14 Jun '13

14 Jun '13

Hi Experts, I just wanted confirm my understanding that Freesurfer does not employ multi-atlas label fusion methods. Is this correct? Thanks, Best, Joshua - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805

2 2

Overlapping perirhinal and entorhinal ex-vivo labels
by Sasa Kivisaari 14 Jun '13

14 Jun '13

Dear FS experts, first I would like to thank you for the very nice perirhinal cortex ex-vivo label you provide in your latest releases! My question concerns the relationship between the ?h.perirhinal.label and the ?h.entorhinal_exvivo.label. Going over some brains in our data set, it looks to me that these two labels have some degree of overlap which often occupies the lateralmost ~1-2 mm of the parahippocampal gyrus crown and ~1-2 mm of the collateral sulcus medial wall, depending on the y-level and the brain. As I understand, these labels (unlike e.g. the labels in the aparc.annot) were created independently from one another thus allowing such overlap. I appreciate that given the transitional nature of the BA35, one would not expect to see a clear border between the two cytoarchitectonic areas. Still, I would like to inquire whether you have any information on which label is 'more reliable' and whether you have any insights as to how to best go about resolving this ambiguity? Thank you for your help in advance! Best, Sasa

2 3

Errors during test of Freesurfer installation
by Rando, Kenneth 14 Jun '13

14 Jun '13

I recently installed Freesurfer on a computer running Red Hat Enterprise 6 for which the updates are current. The first tests, involving freeview, tkmedit, and qdec all produce the error: libGL error: failed to load driver: nouveau. free view produces no other error messages, but tkmedit adds: Reading /usr/local/freesurfer/tktools/tkm_common.tcl Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/tktools/tkUtils.tcl qdec repeats the error followed by: Reading /usr/local/freesurfer/tktools/tkUtils.tcl Using /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl >From what I have discovered "nouveau" is the open source nvidia driver used now by RHEL6. Is the problem with nouveau, or with my Freesurfer installation? Thanks. Ken Kenneth Rando Research Assistant 2 203-974-7731 Yale OCD Research Clinic Yale University School of Medicine Connecticut Mental Health Center 34 Park Street, Room W309 New Haven, CT 06519

1 0

recon-all errors
by Linda Zhang 14 Jun '13

14 Jun '13

Dear all, I've been running recon-all (subj) -all for a group of subjects on Freesurfer v5.1.0 on Virtualbox. Three of them exited with errors, each one having a different error. I've attached the recon-all.logs. For napo0195, the problem may be with the wm.mgz as someone mentioned before, but I don't know what the issue might be for the other two subjects. Thanks for your help! Cheers, Linda

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