Freesurfer January 2013

freesurfer@nmr.mgh.harvard.edu

111 participants
203 discussions

applying distortion correction output from epi_reg in fsl to freesurfer
by Ted Satterthwaite 04 Jan '13

04 Jan '13

Hi Bruce, Doug, and FreeSurfer Team, We have calculated coregistrations between bold timeseries and T1 images using BBR & distortion correction as implemented in the epi_reg utility in FSL5. We would like to map our functional timeseries to surface space for connectivity analyses (analagous to papers by Yeo & Buckner). Normally, without distortion correction, we would use tkregister tp convert the rigid body coregistration calculated in fsl by flirt(.mat) to a register.dat file, and then use mri_vol2surf to birng the data to surface space. However, with distortion correction, the coregistration between the epi & T1 is represented as a deformation field (_warp.nii.gz). Is there a way for FreeSurfer to read this warp and use the information? We could of course simply do a two-step registration by moving our epi data into T1 space first using FSL and then use FreeSurfer to get it to the surface, but that would involve an extra interpolation. Are the ways to do this in one step using our already-calculated & QA'd deformation fields from FSL? Thanks so much for your time & advice. Best, Ted Satterthwaite

2 4

bbregister error: no regisster.dat file
by Shukla,Priyank 04 Jan '13

04 Jan '13

Hi, My bbregistration finished with the warnning" --------------------------------------------------------------------------------------------- WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 -------------------------------------------------------------------------------------------- and does not create subj_RS_register.dat file... I thought, it is only warning so it should create the files. Here is the command, I run to do bbregistration, where ${sub} is substituted by subject number: -------------------------------------- bbregister --s ${sub}_FS --mov $main_path/$sub/${sub}.RS.mgz --reg ${sub}_RS_register.dat --init-fsl --bold --frame $framenum --nearest --o ${sub}.RS.template.mgz ------------------------------------------------------------------------- Thanks Priyank

2 1

FW: FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer
by Jeff Eriksen 04 Jan '13

04 Jan '13

FreeSurfer experts, I am trying to mark points on a surface in tksurfer, then obtain their original voxel coordinates. These are some of the problems I have encountered, and some of the instructions and examples I do not yet understand. -Jeff From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> Date: Thursday, January 3, 2013 6:27 PM To: Jeff Eriksen <eriksenj(a)ohsu.edu<mailto:eriksenj@ohsu.edu>> Subject: Re: [Freesurfer] FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer Can you cc the list so others can answer? Freeview can rotate.... On Jan 3, 2013, at 8:06 PM, Jeff Eriksen <eriksenj(a)ohsu.edu<mailto:eriksenj@ohsu.edu>> wrote: Bruce, This is what I get when I try to use tksurfer to open the scalp surface created with mkseghead: ********************************************************************************************* kje-macbook:mri jefferiksen$ tksurfer AIRC0001 lh seghead subject is AIRC0001 hemi is lh surface is seghead surfer: current subjects dir: /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/mri Reading image info (/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001) Reading /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/mri/orig.mgz surfer: Reading header info from /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/mri/orig.mgz ltMNIreadEx: could not open file /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/mri/transforms/talairach.xfm No such file or directory surfer: Talairach xform file not found (ignored) surfer: vertices=219128, faces=442484 MRISreadVertexPosition(/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/surf/lh.orig): could not open file /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/surf/lh.orig No such file or directory MRISreadOriginalProperties: could not read surface file /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/surf/lh.orig No such file or directory surfer: single buffered window surfer: tkoInitWindow(AIRC0001) surfer: using interface /Applications/freesurfer/lib/tcl/tksurfer.tcl Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... mrisReadTriangleFile(/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/surf/lh.white): surface doesn't match /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/surf/lh.seghead mrisReadTriangleFile failed. *********************************************************************************************** The surface displays, but when I click on a point it puts all 0.0s in the Vertex RAS fields. I presume this is because I have not specified a volume or transform. I am confused by the example given below which uses orig.mgz. I tried to substitute T1.mgz, but it still tries to use orig.mgz above. *********************************************************************************************** 1. I have a point on the surface and want to compute the CRS for voxel in the orig.mgz that corresponds to this point: VoxCRS = inv(Torig)*[tkrR tkrA tkrS 1]' where [tkrR tkrA tkrS] is the "Vertex RAS" as seen in the tksurfer Tools window (also output of mris_convert). Torig is the Vox2tkrRAS matrix obtained from "mri_info --vox2ras-tkr orig.mgz" (note: this is the same for all orig volumes). Test: click on a point in tksurfer. Use "Vertex RAS" to compute Vox2CRS. Round Vox2CRS to the nearest integer. Hit Save Point in tksurfer. In tkmedit, Goto Saved Point. Compare VoxCRS to "Volume Index". Note: you may need to use the "Volume RAS" from tkmedit in the computation above to get an exact match ************************************************************************************************ I tried mri_info --vox2ras-tkr T1.mgz and got a matrix, which I could use in Matlab to transform, but not without knowing the vertex RAS coordinates. Have I confused you enough? From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> Date: Wednesday, January 2, 2013 7:08 PM To: Jeff Eriksen <eriksenj(a)ohsu.edu<mailto:eriksenj@ohsu.edu>> Cc: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer Hi Jeff The coordinate conversions are documented on our wiki. Or you could do the marking in tkmedit or freeview which will show you voxel and surface RAS coords. There might also be an option to view them in tksurfer too, I can't remember (view->information or something like that) Cheers Bruce On Jan 2, 2013, at 7:43 PM, Jeff Eriksen <eriksenj(a)ohsu.edu<mailto:eriksenj@ohsu.edu>> wrote: HI, I created a scalp surface mesh with mkheadsurf. I need to mark or select some scalp surface points and obtain their MRI coordinates. That is, if my MRI is 256-cubed I need the (ix,iy,iz) MRI voxel coordinates closest to the scalp mesh point I mark, where these run from 1 to 256 (or 0-255 if you must). The tksurfer display shows several types of floating point coordinates, but they assume an origin in the center of the head somewhere. If I knew the MRI coordinates of this origin I could calculate the original MRI. Thanks, -Jeff _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@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.

2 1

motion correction
by O'Shea,Andrew 04 Jan '13

04 Jan '13

Hello, Our data set has two T1 weighted scans for some subjects but only one for others. Would you recommend running all subjects with no motion correction (1 scan input)? Also can files be mixed in the analysis that have had motion correction with those who have not? Thanks! -Andrew

2 1

qdec question
by Maria Jalbrzikowski 04 Jan '13

04 Jan '13

Dear Freesurfer users, I have a question regarding qdec and I would like your help. When conducting qdec analyses, is it possible to restrict the analyses to specific brain regions? I would like to limit my qdec analyses to brain regions typically associated with social cognition and have chosen these regions based on the existing literature. If so, could you tell me how this is done? Thank you so much for your help! Best, Maria -- Maria Jalbrzikowski, M.A. University of California, Los Angeles

3 2

ghosting problem in raw anatomical images
by Skyler Gabriel Shollenbarger 04 Jan '13

04 Jan '13

Hello, We want to create a surface model in freesurfer. Our raw spgr T1-anatomical images have a bad ghosting problem. We have attached a pic to show the prob. Is there any corrections that we can do to fix this? Thanks in advance! Skyler and Jon -- Skyler G. Shollenbarger Graduate Student - UWM Brain Lab Clinical Psychology & Neurospychology University of Wisconsin-Milwaukee CONFIDENTIALITY NOTICE! This email transmission may contain confidential and privileged client health information that may not be re-disclosed without further written authorization by the client. The information contained in this transmission is intended for the addressee only. If the receiver of this information is not the intended recipient or an agent responsible for delivering the information to the intended recipient, you are hereby notified that you have received this document in error. Review, copying, modification, or dissemination of this information under these circumstances is strictly prohibited. IF YOU HAVE RECEIVED THIS COMMUNICATION IN ERROR, PLEASE TELEPHONE US IMMEDIATELY. Thank You.

2 1

trac-all bval bvecs bedpostx not running
by Gerit Pfuhl 04 Jan '13

04 Jan '13

Dear all, despite reading the list and having tried various versions of the bvals and bvecs files, I still get the message in dtifit: Error: bvecs and bvals don't have the same number of entries. but it also says "trac-preproc finished without error" and the generated bvals and bvecs in folder dmri look similar to the ones from the tutorial (tab stop checked, everything done in Ubuntu, no OS Windows anywhere) but when I then try to run trac-all -bedp -c owndata the process finished after 1 min with 0 slices processes. I attach the bval and bvec files as they are from the scanner, as they are modified by me according to the tutorial instructions (1 column and 3 columns) and how they look after the cp command in the folder dmri (there is no error message during this step) Attached also the log file (error message on line 357). Regards Gerit Pfuhl

2 1

fscalc / mris_calc problem
by Fred Lado 03 Jan '13

03 Jan '13

Hi FreeSurfer Gurus, I am having difficulty invoking the 'upl' and 'lrl' operations in mris_calc. The following is the message I get for 'upl': /usr/local/freesurfer/bin/fscalc rh.dat.mgh upl 20 --o tmp.mgh freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Darwin Fred-Lados-MacBook-Pro.local 12.2.0 Darwin Kernel Version 12.2.0: Sat Aug 25 00:48:52 PDT 2012; root:xnu-2050.18.24~1/RELEASE_X86_64 x86_64 mri_convert rh.dat.mgh ./tmpdir.fscalc.5004/tmp.mgh mri_convert rh.dat.mgh ./tmpdir.fscalc.5004/tmp.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from rh.dat.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, -1) writing to ./tmpdir.fscalc.5004/tmp.mgh... ---------------------- mris_calc -o ./tmpdir.fscalc.5004/tmp.mgh ./tmpdir.fscalc.5004/tmp.mgh upl 20 Unknown operation upl failed. No such file or directory Fred Lado, MD PhD Director, Neurology Service - Moses & North Divisions Director, EEG Laboratory Associate Clinical Professor of Neurology Montefiore Medical Center 718-920-8499 office 718-324-3730 fax email: ladofred(a)gmail.com

3 4

Brain imaging PhD trainee project available at the Netherlands Institute for Neuroscience, Amsterdam, The Netherlands.
by Diederick Stoffers 03 Jan '13

03 Jan '13

Dear all, Please find attached a description of PhD trainee project available at the Netherlands Institute for Neuroscience, Amsterdam, The Netherlands, that I am posting on behalf of my group leader. Relevant keywords for this project are sleep, emotion, arousal, high-density EEG, fMRI, insomnia and internet. Cheers, Diederick

1 0

FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer
by Jeff Eriksen 02 Jan '13

02 Jan '13

HI, I created a scalp surface mesh with mkheadsurf. I need to mark or select some scalp surface points and obtain their MRI coordinates. That is, if my MRI is 256-cubed I need the (ix,iy,iz) MRI voxel coordinates closest to the scalp mesh point I mark, where these run from 1 to 256 (or 0-255 if you must). The tksurfer display shows several types of floating point coordinates, but they assume an origin in the center of the head somewhere. If I knew the MRI coordinates of this origin I could calculate the original MRI. Thanks, -Jeff

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 January 2013