Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

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

Using T2 or FLAIR data to improve pial surfaces
by Hengameh Marzbani 19 Dec '18

19 Dec '18

External Email - Use Caution Dear all I want to use T2 or FLAIR data to improve pial surfaces. I wonder, which one is better? using T2pial or FLAIRpial? Is there any difference in output? Thank you so much in advance for your time and help! Hengameh

1 0

Help with finding which functional areas house certain electrodes
by Sparsh Jain 18 Dec '18

18 Dec '18

External Email - Use Caution Hey Doug, We want to find the functional areas where each electrode is located in patients. At present, we are finding the electrode RAS coordinates manually using CT-MRI co-registration. We are then manually searching for these locations in Freeview using the aparc.a2009s+aseg ATLAS (generated during MRI reconstruction) on top of MRI volume. This is giving us the exact anatomical/functional area where the electrode belongs. However, this is a very tedious and time-consuming process and we need to do this for many patients. We were wondering if there is 1. A way to automate this process by possibly entering all coordinates and using the LUT and atlas files to get the areas easily for all points. 2. More importantly, could you tell us how to establish a method where we can dump the anatomical region coordinates to a file, and then find the nearest functional area to a particular electrode automatically? For example, if a point lies in a white matter area, can we implement a process to find which functional area (gray matter region, or say hippocampus for example) lies CLOSEST to this electrode point in the white matter region. Can we implement this automated process in an efficient manner for all the points at once? We usually have anywhere between 140 -170 sets of coordinates for each patient, and doing this by hand on freeview is not practical. Instead of finding where exactly all the points lie, we would like to create a 'table' of all anatomical areas and then find out which area of relevance lies closest to a particular point. Thank you Sparsh Jain

1 0

input segmentation masks in recon-all
by yao wu 18 Dec '18

18 Dec '18

External Email - Use Caution Dear Prof. Fischl, I hope to use Freesurfer to get some surface measures of brain structures. The 'recon-all' command will give the output of the surface measures when input the T1w MRI images. If my input files are the segmented binary masks (such as white matter or cortical grey matter masks) which do not need the segmentation-related steps in 'recon-all', which function/command I should use to get the surface measures of the left and right hemispheres (lh.curv, lh.inflated, lh.sphere, lh.sulc, etc.) and also the cortical thickness? Thank you so much! Regards, Yao

1 0

Hippocampus cortical layers division
by Yixin Ma 18 Dec '18

18 Dec '18

External Email - Use Caution Hi Freesurfer experts, I'm writing to ask if you have any suggestions on generating cortical layers for hippocampus subfield cortical regions with the help of freesurfer. When generating cortical layers for other neocortex brain region, the surface files for pial and white/gray matter interface surface are required. But we don't have that surface data for hippocampus subfield division. Is that possible that I can generate those files? Thank you for your help in advance. Yixin

2 1

VBM by freesurfer
by Maurizio Bergamino 18 Dec '18

18 Dec '18

External Email - Use Caution Hello, I am trying to run a VBM analysis by using the white matter and the grey matter masks from Freesurfer, because, often, other tools are not able to calculate a correct white matter and grey matter masks. When I have these masks, I have to apply them to my original T1 images. However, the original T1 is in different space. I can resample the ROIs (WM and GM) in order to apply them to my original T1, but my question is: Can I use the orig.mgz from Freesurfer as my T1 for VBM, or does it have different intensity from my real T1 acquisition? Thanks, Maurizio

2 2

1) single subject surface activation in volume space and 2) small volume correction
by Loeffler, Martin 18 Dec '18

18 Dec '18

External Email - Use Caution Dear experts, I'm running a sensory mapping experiment, which I would like to analyse in single subject space. Everything seems to be working fine (see code excerpt below). Now I'd like to do two additional things: 1) show the surface results in single subject volume space (as overlay on T1). 2) Limit my surface analysis to BA3b, using correction for multiple comparisons in that region only. I've read that this should be possible with monte carlo simulation, but can't figure out how to do this for one subject only. Any help is much appreciated! Best, Martin mkanalysis-sess -fsd bold -surface self lh -fwhm ${fwhm_par} -event-related -paradigm Onsets.par -nconditions 5 -spmhrf 1 -TR 1.5 -refeventdur 12 -hpf 0.01 -nskip 3 -polyfit 2 -analysis MR.lh -force -per-run mkcontrast-sess -analysis MR.lh -contrast digit1_lh -a 1 -c 0 #... bbregister --s $subj --mov f.nii.gz --init-fsl --int whole.nii.gz --t2 --reg register.partial.dat preproc-sess -s $subj -fsd bold -surface self lhrh -fwhm ${fwhm_par} -projfrac 0.5 -per-run -update -regfile register.partial.dat selxavg3-sess -s $subj -analysis MR.lh -force freeview -f ${ANAT}/${subj}/surf/lh.inflated:curvature_method=binary:overlay=${FUNC}/${subj}/bold/MR.lh/digit1_lh/sig.nii.gz

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