Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30085 discussions

?h.aparc.annot data for N27 brain?
by John Sheppard 24 Jan '10

24 Jan '10

Hi all, I am curious if there is any way to get a copy of the ?h.aparc.annot (label) data for the Colin N27 brain? I wish to use these annotation data for my analysis, but need the original ..annot files as I need to translate the annotation data into my standard mesh space that I am doing my group analysis with. The folks at AFNI put out a zipped archive with surface data for N27, but this archive didn't include original ?h.aparc.annot files that I could work with (only some type of processed data in niml format that I wasn't able to convert to a standard 1D file for mapping purposes). I am following up with AFNI as well but haven't heard back yet. Thanks very much, John Sheppard -- John P. Sheppard Undergraduate Student Departments of Biomedical Engineering & Statistics Research Assistant Department of Communication Sciences & Disorders Northwestern University E-mail: john-sheppard(a)northwestern.edu Phone: +1 630 957 8321 Address: 1927 Sherman Ave, Unit G Evanston, IL 60201, USA

2 1

painting polar angle retinotopy with abblocked design
by Natalia Zaretskaya 22 Jan '10

22 Jan '10

Hi all, hi Doug, I am analysing polar angle retinotopy with abblocked design, but can not figure out how to paint the output of sfa-sess correctly, so that I see something reasonable. I know that my analysis generally worked fine, because when I can view the phase.nii overlay, and it looks quite polar. It's just that it is not thresholded. I would really appreciate a hint! Best regards, Natalia

2 1

bad ADNI data results
by Guang Zeng 22 Jan '10

22 Jan '10

Hi, there, I sent about 50 ADNI data to FreeSurfer pipeline last week, I found half of them have bad segmentation and parcellation results. I think most of them have the same type of errors and may because of the skull-stripping results are wrong. Could you please help me check the attached pics, see if I am correct. And please give me some suggestions to fix this problem. I really appreciate your help! Thanks a lot! Guang _________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/196390706/direct/01/

1 0

Sever problem
by Jürgen Hänggi 22 Jan '10

22 Jan '10

Dear FS experts I tried to download the Mac distributions of FS, but there seems to be a server problem, although the Linux distributions can be downloaded. Thanks Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

2 1

Orientation of 001.mgz versus raw dicom data
by yzhangd＠artsci.wustl.edu 21 Jan '10

21 Jan '10

I have run the following command to create a 001.mgz file from raw *.dcm data: recon-all -s <subjid> -i <path to *.dcm data> The output 001.mgz file is not in the same native space as the original *.dcm data. Could anyone tell me what space the 001.mgz file is in? Does the above command change the orientation (i.e does it rotate/translate) besides simply converting from .dcm to 001.mgz thanks a lot yuning

3 2

license problem
by Guang Zeng 21 Jan '10

21 Jan '10

Hi, there, I installed FreeSurfer under my local directory few months ago. Last week, I copied all the FreeSurfer folder under my local directory (include .license file) to the /home directory of our group, so everyone can use it. However, it turns out that they can not use it even they can see the .license in the /home directory through their machine. So do I need reinstall Freesurfer under our /home directory, instead of just copy? Thanks! Guang _________________________________________________________________ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/196390708/direct/01/

1 0

commandline tools to create .mgh files from .nii files.....
by Ritobrato Datta 21 Jan '10

21 Jan '10

Hello All, Are there commandline tools to take processed functional data in .nii format and overlay it on the inflated or spherical surface and output a .mgh file ? I want to specify the registration method as "Calculate identity matrix" Thanks Rito

2 1

mri_vol2surf
by 丽孔 21 Jan '10

21 Jan '10

Hello developer, I want to change a structure MRI (*.img) into two surface files (*_R.w and *_L.w). I first use mri_convert to change *.img to *.mgh ; then use mri_vol2surf to change a *.mgh file to two surface files *_L.w and *_R.w. But here I meet a problem: I don’t know how to get the register.dat file. I search many documents about this problem, But still didn’t find a method for this problem. Expecting freesurfer advancer give me some instructions! Any help will be appreciated! Best regards! karry ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/

2 1

Flip surface model
by Jürgen Hänggi 21 Jan '10

21 Jan '10

Dear FS experts As far as I know from Doug, there are preliminary tools for flipping a surface model (reversing left and right hemisphere) http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11896.html Because these tools are not yet available I would like to know whether you would recommend to flip the raw MR image and the running recon-all on this flipped MR image. Thanks in advance Best regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

3 2

flag error
by Buchmann Andreas 21 Jan '10

21 Jan '10

Dear Freesurfer Experts, after a new installation of freesurfer, the command "tkmedit" worked, but with the command "recon-all -i ... -s ..." we ran into the following error: Flag i unrecognized. i /Users/michael/Desktop/K01.img s K01 Darwin Macintosh-3.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 recon-all exited with ERRORS at Thu Jan 21 08:17:06 CET 2010 Any suggestions, what the problem might be? Best regards and thanks in advance Andreas

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