Freesurfer December 2010

freesurfer@nmr.mgh.harvard.edu

92 participants
128 discussions

Using aseg to sample other image types
by Carl Anderson 06 Jan '11

06 Jan '11

Dear Freesurfer, I have co-registered a map of whole brain T2-relaxation time values to the corresponding aseg.mgz for this subject (see attached jpegs). Does a tool exist in freesurfer to enable regional sampling of T2 values from the T2-relaxation time map based on aseg? Thanks for any thoughts. Happy New Year. <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

3 3

Dipole localization
by Leonardo Barbosa 05 Jan '11

05 Jan '11

Hi, I'm trying to save the white matter surface as a gifti file so I can use it outside the freesurfer to implement an EEG dipole fitting, but I'm not sure if this is the best way to do it. I searched old posts in the list, but didn't find an answer. The problem is how to export the whole cortex, and not only one hemisphere. I'm using mris_convert subjects/subj1/surf/lh.white ~/subj1.lh.white.gii mris_convert subjects/subj1/surf/rh.white ~/subj1.rh.white.gii and trying to mix the two surfaces inside my program, but I guess it's not right, because the middle of the brain is opened. I have two closed surfaces, and I would like to have one close mesh, without creating new faces and ignoring vertices in the middle. Sorry i this is confusing, but the question is: Can I export one closed surface of the whole brain with freesurfer? Thanks in advance for any help... and Happy New Year! Leonardo Barbosa www.if.usp.br

4 7

Small bug in mri_probedicom
by Inge Amlien 03 Jan '11

03 Jan '11

Hi, trying to chuck together a script to do consistency checking for when our scans get off the scanner using mri_probedicom with the --compare flag. There is a small bug with the tag for software version, the program reports the tag for model twice. The tag for software version I believe should be (18,1020). eg. 0 Manufacturer (8,70) SIEMENS SIEMENS 1 Model (8,1090) Avanto Avanto 2 Software Version (8,1090) Avanto Avanto Merry xmas! Inge Amlien University of Oslo --------------------------------------------------------------------- Build stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 RedHat release: Red Hat Enterprise Linux Client release 5.5 (Tikanga) Kernel info: Linux 2.6.18-194.26.1.el5 x86_64 cmdline: mri_probedicom --compare 1.IMA 2.IMA

2 1

mri_vol2surf --cortex and --mask flags appear ineffective
by Michael Waskom 03 Jan '11

03 Jan '11

Hey developers, It seems as if the --cortex and --mask flags for mri_vol2surf are not doing anything. E.g., if I use the exact same command line: mri_vol2surf --hemi rh --o rh.w-cortex.nii.gz --out_type niigz --reg register.dat --reshape --projfrac-avg 0 1 .1 --mov cope2.nii.gz --cortex With and without "--cortex" and then diff the output, they are identical. When you load the overlay in tksurfer, the medial wall has values that are not 0. Here's my bugr data: FREESURFER_HOME: /software/Freesurfer/5.0.0 Build stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 Debian version: squeeze/sid Kernel info: Linux 2.6.31-22-generic x86_64 Best, Mike

2 1

Whole Surface SNR Calculation for Individual Functional Runs
by Adam Nitenson 03 Jan '11

03 Jan '11

Hello Freesurfers, We are beginning to perform QC on our subjects and want to look at signal to noise ratio. I've taken a look at the fsnr.nii overlay files, but we would like to be able to calculate a whole surface value for SNR for each functional run of each subject, so that we can exclude runs if that SNR values falls below our designated threshold. Is there a way to accomplish this? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

3 4

spikedet-sess buglet & solution
by Sebastian Moeller 03 Jan '11

03 Jan '11

Dear All I just noticed that spikedet-sess (for both FS 4.5 and 5.0) will error out if the mystudy/log directory does not yet exist. I think that would be easy to fix by including the following after line 72: if !(-e ./log) then mkdir -p ./log endif Best Sebastian -- Sebastian Moeller telephone: 626-807-5242 / 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 US CDMA: + 1 - 626 - 807 - 5242 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

2 2

(no subject)
by FIDEL ALFARO ALMAGRO 02 Jan '11

02 Jan '11

Happy holidays for those who celebrate it today, Hi. Is there any documentation on how to use mri_mark_temporal_lobe application and what is its output? I cannot find any. Thanks in advance.

4 7

cortical thickness of a ROI
by angela.favaro＠unipd.it 02 Jan '11

02 Jan '11

Dear all, I have not received any advice about this point. Can somebody help me? thank you! I followed the instructions found in Freesurfer tutorials ('cortical thickness of a volume-defined ROI'). However, in the point 4 of the procedure I am not able to change the --reshape default. My run is: mri_surf2surf --s subj001 --trgsubject fsaverage --hemi rh --sval rh.thickness --tval rh.thickness.fsaverage.mgh --reshape-factor 7 but it continues to create (like default) a reshape with 6. For this reason, I think, the following command: mri_segstats --seg $SUBJECTS_DIR/rh.fsaverage.mask21.mgh --in rh.thickness.fsaverage.mgh --sum segstats-mask21.txt give: ERROR: dimension mismatch between input volume and seg input 27307 1 6 seg 23406 1 7 What can I do to solve this problem? Thank you for your help! Angela Angela Favaro, MD, PhD, MSc Psychiatric Clinic Department of Neurosciences via Giustiniani 3 35128 Padova Italy

3 2

Interpreting results from Qdec
by Gallen, Courtney (NIH/NIDA) [F] 02 Jan '11

02 Jan '11

Hi, I'm currently running analyses in Qdec and have identified areas that show significant effects in my contrasts. I have two questions related to interpreting these results. 1. How can you interpret the effect in each "blob?" (i.e., which group has a greater cortical surface area, etc.). Right now, all I know is that there is an effect in certain areas. Can you export this data to get means and standard errors? 2. Is there a way to localize where these effects are? E.g., a tool that tells you this effect is located in __ area of the brain? Thanks in advance Courtney Courtney Gallen Post-baccalaureate IRTA Neuroimaging Research Branch National Institute on Drug Abuse (IRP) 251 Bayview Blvd Suite 200 Baltimore, MD 21224 Tel: (443) 740-2631

3 2

Smoothing fwhm.dat
by Joana Braga Pereira 02 Jan '11

02 Jan '11

Dear all, I have a question regarding smoothing in qdec. >From what i've understood from previous emails, for monte carlo simulations qdec calculates the best smoothing for your data set, saving it in the file fwhm.dat. How does it calculate this smoothing? Many thanks, Joana

2 1

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer December 2010