Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

subject IDs for qdec
by Helen Beaumont 20 Dec '18

20 Dec '18

External Email - Use Caution Please, what format should the subject IDs have for qdec. At the moment my subjects IDs are alphanumeric (e.g. h00013), and although the SUBJECTS_DIR is set correctly, the files are not being found. I have changed the first to numeric only (024), but it is also not found. I attach the .dat file, and below is the error when I try to load the table: Data table /media/QuantimaPoP/Humans_AllProcessed/FS_for_qcache/qdec/qdec.table.dat loaded. SUBJECTS_DIR is '/media/QuantimaPoP/Humans_AllProcessed/FS_for_qcache' Verifying subject data.sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '024' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'h00025' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number Thanks for any help Helen Beaumont PhD Manchester NeuroImaging

1 0

Re: [Freesurfer] FreeSurfer: trouble processing subjects
by Diamond, Bram Ryder 20 Dec '18

20 Dec '18

Hi Andrade, I'm adding the FreeSurfer support list so other can benefit. To answer your question, you would use the first dicom from the diffusion scan... but since you don't have the dicoms that won't work. You can combine all of the DTI nifty files into one multi-frame diffusion 4d volume using mri_concat. mri_concat /path/to/all/IXI025-Guys-0852-DTI-??.nii.gz --o /output/path/dti.mgz Then run dt_recon using dti.mgz as your input. cd /path/to/desired/subjects/dir export SUBJECTS_DIR=$(pwd) dt_recon --b /path/to/bvals.txt /path/to/bvecs.txt--i /path/to/dti.mgz --s andrade --o /path/to/desired/diffusion/output Let me know if this works. Best, Bram Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598 ________________________________________ From: Renew Andrade <andraderenew(a)yahoo.com> Sent: Thursday, December 20, 2018 10:12:31 AM To: Diamond, Bram Ryder Subject: Re: FreeSurfer: trouble processing subjects External Email - Use Caution I don'tknow if I understand right. I don't have a dicom format file for dtrecons. What I have is nii.gz all that I gave you. In case I need to do dcmunpack either way I need to do dtrecons for each of those dcmunpack or just the first one? Sent from my iPhone > On 20 Dec 2018, at 15:46, Diamond, Bram Ryder <BRDIAMOND(a)mgh.harvard.edu> wrote: > > Hi Andrade, > > You should be submitting the IXI025-Guys-0852-T1.nii.gz for recon-all. This seems to be working fine with freesurfer v6.0 on my machine. > > cd /path/to/desired/subjects/dir > export SUBJECTS_DIR=$(pwd) > recon-all -i /path/to/IXI025-Guys-0852-T1.nii.gz -s andrade -all > > For the diffusion scan, you will want to run it through dt_recon. If you have the raw dcms, it would easiest to use one of those as input rather than combine all of your directions into one multi-frame volume. You can run unpacksdcmdir to get the first dcm of the diffusion scan. > > cd /path/to/desired/subjects/dir > export SUBJECTS_DIR=$(pwd) > unpacksdcmdir -src /path/to/dicom/dir -targ /path/to/desired/log/output/ -scanonly unpack.log > dt_recon --b /path/to/bvals.txt /path/to/bvecs.txt--i path/to/first/diffusion/dicom.dcm --s andrade --o /path/to/desired/diffusion/output > > I hope this helps. > > Best, > Bram > > Bram R. Diamond, BSc > Research Technician II > Laboratory for Computational Neuroimaging > Martinos Center for Biomedical Imaging > Massachusetts General Hospital > 149 13th Street > Charlestown, MA 02129 > (p): 617-726-6598 > > > ________________________________________ > From: Renew Andrade <andraderenew(a)yahoo.com> > Sent: Wednesday, December 19, 2018 3:13:18 PM > To: Diamond, Bram Ryder > Subject: Re: FreeSurfer: trouble processing subjects > > External Email - Use Caution > > I sent you the whole information but the problem rises in processing with recon-all the DTI files. > > Sent from my iPhone > >> On 19 Dec 2018, at 16:54, Diamond, Bram Ryder <BRDIAMOND(a)mgh.harvard.edu> wrote: >> >> Good morning, Andrade. >> >> I received a message from Bruce that suggests you are having trouble processing a few of your subjects. We received the following file from you via the Martinos Center FileDrop: >> IXI025-Guys-0852-DTI-16.nii.gz >> IXI025-Guys-0852-DTI-14.nii.gz >> IXI025-Guys-0852-DTI-15.nii.gz >> IXI025-Guys-0852-DTI-13.nii.gz >> IXI025-Guys-0852-DTI-12.nii.gz >> IXI025-Guys-0852-DTI-10.nii.gz >> IXI025-Guys-0852-DTI-09.nii.gz >> IXI025-Guys-0852-DTI-11.nii.gz >> IXI025-Guys-0852-DTI-08.nii.gz >> IXI025-Guys-0852-DTI-07.nii.gz >> IXI025-Guys-0852-DTI-05.nii.gz >> IXI025-Guys-0852-DTI-06.nii.gz >> IXI025-Guys-0852-DTI-04.nii.gz >> IXI025-Guys-0852-DTI-03.nii.gz >> IXI025-Guys-0852-DTI-02.nii.gz >> IXI025-Guys-0852-DTI-01.nii.gz >> IXI025-Guys-0852-DTI-00.nii.gz >> bvecs.txt >> bvals.txt >> IXI025-Guys-0852-T1.nii.gz >> >> They seem to be a separated diffusion scan (along with bvec and bcal files), and a T1. In order for me to help you, I need to know what exactly you are having trouble with. >> >> Thanks, >> Bram >> >> >> Bram R. Diamond, BSc >> Research Technician II >> Laboratory for Computational Neuroimaging >> Martinos Center for Biomedical Imaging >> Massachusetts General Hospital >> 149 13th Street >> Charlestown, MA 02129 >> (p): 617-726-6598 >> >> >> >> 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. >> > >

1 0

recon-all error : Too many intersected faces for face 120047 (60827, 60826, 59444)
by 허정선 20 Dec '18

20 Dec '18

External Email - Use Caution Hello Freesurfer developers I'm starting using FS and I have a problem running recon-all. #recon-all -s /usr/local/freesurfer/subjects/20180108 -all I've attached the output to a ERROR image file. We're doing on a GE scanner 3T, T1-FSPGR axial slices, 3D with a slice thickness of 2.0mm. freesurfer version : freesurfer-x86_64-unknown-linux-gnu-stable6-20170118 Any help is greatly appreciated. Thanks. Jeongson

2 1

surfreg cannot allocate memory
by Haoran Xu 19 Dec '18

19 Dec '18

External Email - Use Caution Hello FreeSurfer Developers, I am using surfreg to map one of my subject "subj001" to "fsaverage_sym" by these commands: surfreg --s subj001 --t fsaverage_sym --lh surfreg --s subj001 --t fsaverage_sym --lh --xhemi The first command worked well, however the second did not. It showed error: "znzTAGskip: tag=1952870258, failed to calloc 1768846336 bytes! Cannot allocate memory" Searched the archive but without good luck. Any suggestions? Appreciated! 1) FreeSurfer version: freesurfer-Linux-centos6_x86_ 64-stable-pub-v6.0.0-2beb96c. 2) Platform: UBUNTU 16.04 LTS with 23.5GB memory and 1.4TB available space. (With this, 1.7G should be fine.) 3) uname -a: Linux haoranPC 4.15.0-43-generic #46~16.04.1-Ubuntu SMP Fri Dec 7 13:31:08 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Regards, Haoran Xu

1 0

Postdoctoral Fellow at Northwestern's Alzheimer's Disease Center
by Adam Martersteck 19 Dec '18

19 Dec '18

External Email - Use Caution *Apologies for cross-posting* Northwestern University’s Mesulam Center for Cognitive Neurology and Alzheimer’s Disease is seeking candidates for a postdoctoral fellowship in Neuroimaging of Aging and Dementia. The fellow will focus on analyzing multimodal MR, amyloid PET, and tau PET data for our NIA-funded Alzheimer’s Disease Center. The fellow may develop, adapt, implement and/or optimize analysis pipelines for our newly funded AD Center Imaging Core, which will substantially contribute to imaging biomarker discoveries and enhance data sharing procedures. The fellow may participate in publications and presentations resulting from the work. The fellow will work with Dr. Rogalski (Imaging Core Leader) and her collaborators Dr. Todd Parrish (Director of the Center for Translation Imaging) and Dr. Lei Wang (Director of the Applied Computational Anatomy Lab). The Mesulam Center is located on the downtown campus, nestled between the Magnificent Mile and the city's beautiful lakefront. Successful candidates will have a PhD in neuroscience, physics, psychology, bioengineering or a related field. Experience with analysis of sMRI, DTI, rsfMRI and/or PET is required with a particular emphasis on multimodal approaches. Interested applicants should send a CV and cover letter stating experience and interests, 2-3 peer-reviewed publications, and at least two letters of recommendation. The start date is negotiable and the position will remain open until filled. Please send application materials to ADC(a)northwestern.edu.

1 0

PNM Gui
by Meisler, Steven Lee 19 Dec '18

19 Dec '18

Hello FS team, When I try to run Physiological Noise Modeling through the PNM GUI, I get an error message saying that I don't have permission to run the script "_pnm_stage3." Do you know how I may remedy this? Thanks, Steven -------------- Steven L. Meisler, M.S.E. Clinical Research Coordinator II Laboratory for NeuroImaging of Coma and Consciousness<https://www.massgeneral.org/neurology/research/researchlab.aspx?id=1605> 175 Cambridge Street, Suite 300 Boston, MA 02114 smeisler(a)mgh.harvard.edu<mailto:smeisler@mgh.harvard.edu> | (617)-726-1884 https://www.linkedin.com/in/steven-meisler [cid:04197f41-dc6e-4901-a717-cbcdd99bfbe2]

2 2

Re: [Freesurfer] PNM Gui
by Hoopes, Andrew 19 Dec '18

19 Dec '18

Hi Steven, PNM is an FSL tool, not freesurfer, but if you’re having remote-access permissions issues it might be best to contact the martinos help desk. Are you setting “output basename” to a writable directory? best Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Meisler, Steven Lee" <SMEISLER(a)mgh.harvard.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, December 19, 2018 at 4:35 PM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] PNM Gui Hello Freesurfer developers, I just wanted to kindly follow up to my previous message. I'm working from a remote Martinos linux server, so I've found that sometimes I don't have proper permissions to run important scripts, such as the physiological noise modeling processing pipeline that I referenced in my first message. Thank you in advance for your assistance. Best, Steven ________________________________ From: Meisler, Steven Lee Sent: Tuesday, December 4, 2018 9:38:12 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: PNM Gui Hello FS team, When I try to run Physiological Noise Modeling through the PNM GUI, I get an error message saying that I don't have permission to run the script "_pnm_stage3." Do you know how I may remedy this? Thanks, Steven -------------- Steven L. Meisler, M.S.E. Clinical Research Coordinator II Laboratory for NeuroImaging of Coma and Consciousness<https://www.massgeneral.org/neurology/research/researchlab.aspx?id=1605> 175 Cambridge Street, Suite 300 Boston, MA 02114 smeisler(a)mgh.harvard.edu<mailto:smeisler@mgh.harvard.edu> | (617)-726-1884 https://www.linkedin.com/in/steven-meisler [cid:04197f41-dc6e-4901-a717-cbcdd99bfbe2]

1 0

mri_segstats more decimals?
by Winkelbeiner, Stephanie A 19 Dec '18

19 Dec '18

External Email - Use Caution Hi Freesurfer, Is there a way to print out more decimals with mri_segstats? The mean diffusivity values are very small and with only four decimals not really distinguishable from each other. Thanks for your help! Stephanie The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

2 2

Job positions available. Science Programmer and Head Engineer in neuroimaging lab (LCBC, University of Oslo, Norway).
by Dídac Vidal 19 Dec '18

19 Dec '18

External Email - Use Caution I am delighted to advertise the following positions on behalf of Prof Anders M Fjell: At the Center for Lifespan Changes in Brain and Cognition, University of Oslo, Norway, we have available two new positions for excellent candidates. The main aim of LCBC research is to explain, predict and promote cognitive function from birth to old age, in health and disease. 1) We offer a full-time permanent Scientific Programmer position ( https://www.jobbnorge.no/en/available-jobs/job/161563/scientific-programmer) The candidate needs to have a master’s degree or similar in a relevant field, such as informatics, bioinformatics, computer science, etc. The candidate will have the opportunity to work collaboratively in an active group and analyze cognitive measures, imaging of brain activity and structure (MRI), genetics, molecular biology, and registry information across large data sets. 2) We offer a position in neuroinformatics/ brain imaging position on the Lifebrain project as Head engineer/lab engineer ( https://www.jobbnorge.no/en/available-jobs/job/160891/position-in-neuroinfo…) The position is suited for a person with strong programming competence and interest in signal and image processing and requires a master’s degree in a relevant field. Imaging of the human brain by MRI and PET is central to LCBC research and included in all projects. Main tasks include data preprocessing and higher-level analyses; development and maintenance of the neuroimaging database and the processing pipeline; implementation and testing of new processing procedures. The appointment is for 1 year while the possibility of extension is pending on further external funding. The application deadlines are 04.01.2018. P.S. Interested candidates are welcome to contact Anders M Fjell a.m.fjell(a)psykologi.uio.no if they have questions. All the best, Dídac -- Dídac Vidal Piñeiro

1 0

Original Volume Space
by Zohreh Ganji 19 Dec '18

19 Dec '18

External Email - Use Caution Hi Please tell me how do I use recon-all withkeeping original space without resampling?

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