Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

postdoctoral fellow position for dementia research
by Anqi Qiu 14 Oct '10

14 Oct '10

Postdoctoral Fellow Position on Dementia NeuroImaging Job description: National University of Singapore (NUS) is a leading global university centred in Asia. It offers a global approach to education and research, with a focus on Asian perspectives and expertise. Computation functional anatomy laboratory at NUS (http://www.bioeng.nus.edu.sg/cfa) focuses on brain and cognition studies using neuroimaging techniques. Our group is leading the dementia neuroimaging project in Singapore. The project involves multi-modal MRI techniques, including resting fMRI, HARDI, and ASL. We are looking for a research fellow who is interested in multi-modal MRI studies in dementia, especially, who is interested in developing anatomical and functional connectivity methods or investigating anatomical and functional connectivity in dementia. We offer high salary with medical and other benefits. Requirements: Ph. D or MD Background on Alzheimers disease or vascular disease research is preferable but necessary Knowledge in statistical analysis is necessary Good communication and writing skills in English language If you are interested in the jobs listed below, please send your CV to Dr. Anqi QIU Division of Bioengineering National University of Singapore Email: bieqa(a)nus.edu.sg Phone: +(65) 6516 7002

1 0

Mapping labels to the RH on Macs
by Tessa Harrison 14 Oct '10

14 Oct '10

Dear FreeSurfers, I am running FS 4.5 or FS 5.0 on Mac OS X 10.6.4 -Intel (see attached screenshot). I am not able to map RH labels created in fsaverage to the RH of any of my subjects. LH labels map to the LH from qdec "Map Label to All Subjects" option and from the command line with no problem. However, when I try to map RH labels (that map correctly to the RH in fsaverage) to individual subjects, the command appears to work (no error messages), but something goes wrong. It appears that the label is actually mapped to the LH because when I pull it up on the RH in an individual subject it looks like scattered dots (see attached image). The same thing happens on another Mac in our lab. I have tried both FS 4.5 and 5.0 and the problem occurs in both versions. Could this be a bug in the Mac FS release? I did not find any mention of this problem in the archives. Thank you for you help! -Tessa

3 8

converting IMA files
by Lisa F. Akiyama 14 Oct '10

14 Oct '10

Hello, I am a Freesurfer newbie trying to use the mri_convert command to convert IMA format files to either nii or nifti1 format files. Whenever I run the command I get an error at the very end saying that it failed to write (please see below for the exact output error that was displayed). Any help would be greatly appreciated. Thank you in advance. Best, Lisa Akiyama % mri_convert -i $SUBJ_DIR/393-2-4.ima -ot nii -o 393-2-4.nii mri_convert -i /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima -ot nii > -o 393-2-4.nii $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima... rows = 256 cols = 256 TR=11.40, TE=4.40, TI=300.00, flip angle=15.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to 393-2-4.nii... niiWrite(): error opening file 393-2-4.nii ERROR: failure writing 393-2-4.nii as volume type 24 % mri_convert -i $SUBJ_DIR/393-2-4.ima -ot nifti1 -o 393-2-4 mri_convert -i /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima -ot > nifti1 -o 393-2-4 $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima... rows = 256 cols = 256 TR=11.40, TE=4.40, TI=300.00, flip angle=15.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to 393-2-4... nifti1Write(): error opening file 393-2-4.hdr ERROR: failure writing 393-2-4 as volume type 20

2 4

talairach transform error...
by Gonzalo Rojas Costa 13 Oct '10

13 Oct '10

Hi: I tried to process the T1 of a 7 month old patient with a big resection (see attached image)... I got the error: "#@# Talairach Failure Detection Wed Oct 13 13:21:39 CLST 2010 /usr/local/freesurfer/subjects/rivas_carmona_gabriel_13_10_2010/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux image 2.6.28-17-generic #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Wed Oct 13 13:21:39 CLST 2010" How can I process it ?... Sincerely, Gonzalo Rojas Costa

1 0

Job Opening, FreeSurfer Team, Software
by Nick Schmansky 12 Oct '10

12 Oct '10

Hello FreeSurfers, The always-busy FreeSurfer team is looking to add another team member with software skills to work in our lab. Our needs include someone to work on maintaining the existing software, to 'own' the build and release tasks, to maintain and create tests, to provide internal support to researchers within the center, to help others on the mailing list, to add to and improve our documentation, and to help in conducting courses. This opening is for someone with entry-level to five years of experience. Ideally, the candidate would have a computer science background, with C/C++ programming experience in Linux. Candidates from other backgrounds, such as psychology or cognitive science, but are comfortable with scripting or Matlab in Linux, and want to take-on a software role, will also be considered. If you are this person, or know of someone, please send a CV or resume to me at nicks(a)nmr.mgh.harvard.edu Sincerely, Nick Schmansky

1 0

Fwd: RE: password for windows ubuntu to share folders:
by Krish Subramaniam 12 Oct '10

12 Oct '10

Hi, Also if feel the need to enable the root account for some reason, you can do sudo passwd root and enter a new password to begin using the account. -Krish -------- Original Message -------- Subject: RE: [Freesurfer] password for windows ubuntu to share folders: Date: Tue, 12 Oct 2010 10:58:37 -0500 From: Eggebrecht, Adam <eggebrechta(a)mir.wustl.edu> To: Krish Subramaniam <krish(a)nmr.mgh.harvard.edu> Ah, excellent. Thank you, Krish! -Adam Adam T. Eggebrecht, Ph.D. Dept. of Radiology Washington University School of Medicine St. Louis, MO 314-362-6942 ________________________________________ From: Krish Subramaniam [krish(a)nmr.mgh.harvard.edu] Sent: Monday, October 11, 2010 4:36 PM To: Eggebrecht, Adam Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] password for windows ubuntu to share folders: Hi Adam By default, the root account is locked in Ubuntu. See https://help.ubuntu.com/community/RootSudo You can do admin things by using "sudo" and entering the password when it prompts you. Krish On 10/11/10 5:32 PM, Eggebrecht, Adam wrote: > Hello Krish, > > Yes, that is the version of FreeSurfer. Alas, the password will not get me root access. > > -Adam > > Adam T. Eggebrecht, Ph.D. > Dept. of Radiology > Washington University School of Medicine > St. Louis, MO > 314-362-6942 > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] On Behalf Of Krish Subramaniam [krish(a)nmr.mgh.harvard.edu] > Sent: Monday, October 11, 2010 4:12 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] password for windows ubuntu to share folders: > > Hi Adam > > Is this for the FreeSurfer 5.0.0 virtual machine? The password is > "freesurfer" ( without the quotes ). > > Cheers > Krish > > On 10/11/10 4:43 PM, Eggebrecht, Adam wrote: >> The README file explains how to gain access to a USB device, not how to internally mount the shared folder. >> The only ways I know how to finish mounting a shared folder include using root access. >> I tried brain2009 and other similar strings, but have had no luck cracking into root yet. >> >> Any other suggestions for the root password in the Ubuntu release? >> >> Many thanks, >> -Adam >> >> >> Adam T. Eggebrecht, Ph.D. >> Dept. of Radiology >> Washington University School of Medicine >> St. Louis, MO >> 314-362-6942 >> ________________________________________ >> From: Pedro Paulo de Magalhães Oliveira Junior [ppj(a)netfilter.com.br] >> Sent: Monday, October 11, 2010 12:39 PM >> To: Eggebrecht, Adam >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] password for windows ubuntu to share folders: >> >> It's in the README >> >> As far as I remember is brain2009 >> --------------------------------------------------------------------- >> Pedro Paulo de Magalhães Oliveira Junior >> Diretor de Operações >> Netfilter& SpeedComm Telecom >> -- www.netfilter.com.br<http://www.netfilter.com.br> >> -- For mobile: http://www.netfilter.com.br/mobile >> >> >> >> >> On Mon, Oct 11, 2010 at 14:15, Eggebrecht, Adam<eggebrechta(a)mir.wustl.edu<mailto:eggebrechta@mir.wustl.edu>> wrote: >> Hello there, >> >> I am using FreeSurfer in my XP box within its Ubuntu Virtual Box. >> It appears that everything is working just fine. >> I would like to make changes to the guest OS but need the password to do so. >> Can I please get this password? I am having trouble mounting my data folders to the guest OS without password or root privileges. >> >> Many thanks! >> -Adam >> >> >> Adam T. Eggebrecht, Ph.D. >> Dept. of Radiology >> Washington University School of Medicine >> St. Louis, MO >> 314-362-6942 >> >> The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. >> >> _______________________________________________ >> 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. >> >> >> >> The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. >> >> _______________________________________________ >> 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 > > The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > > The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

1 0

Able to use bbregister to move from conformed space to diffusion space?
by Tanner,Jared J 12 Oct '10

12 Oct '10

Hi, Is there a way to use bbregister to register a FreeSurfer image (e.g., rawavg.mgz) to a diffusion image from the same participant? In other words, is there a way to specify --mov rawavg.mgz and make the target (template) image a b0 diffusion image? Or at least to perform an inverse transform on the rawavg image after registering the b0 to the rawavg? I plan on trying mris_cvs_register but I was wondering if bbregister can do what I want. I've used flirt, fnirt, and SyN registration methods but flirt isn't quite accurate enough for intra-subject, multi-modal registration, fnirt is better but still has troubles with cortical regions, and SyN has been too variable with results. Thank you, Jared Tanner PhD Candidate Clinical & Health Psychology University of Florida

3 2

mri_label2label problem
by Ritobrato Datta 12 Oct '10

12 Oct '10

Hello All, I hand drew a label on subject X's inflated surface using the tools in tksurfer outlined in http://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide/TkSurferWorkingWithD…, then I applied the label to Subject Y using mrilabel2label specifically - mri_label2label --srclabel ROI-subjX.label --srcsubject SubjX --trglabel ROI-subjY.label --trgsubject SubjY --regmethod surface --hemi lh The problem is on surface of subject Y, when I upload the label, I see these holes inside the label (please see figure attached). Can anyone tell how do I get rid of them ? Thanks much Ri

2 1

QDEC Design tab interface options
by Jay Ives 12 Oct '10

12 Oct '10

Hi, I am wondering what is going on "under the hood" when one makes a choice under the Design tab in the Measure (Dependant Variable) box for Measure. For example if one chooses "Volume" instead of Thickness, what exactly is being used as volume? Where does the information on volume come from? I am hoping the answer will be the volume associated with each vertex, but where is this information? Thanks....J

3 2

Left-Right Concern
by Jay Ives 11 Oct '10

11 Oct '10

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