Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30066 discussions

vertex coordinates and thickness in mgh file
by Giuliano Giari 18 Jul '17

18 Jul '17

Dear Freesurfer users, i have to run vertex by vertex analysis of cortical thickness across subjects. As of now i have processed my data using the recon-all command and then the mris_preproc (separately for each hemisphere). I have now two .mgh file but i don’t know where to find the info that i need, namely the cortical thickness at each vertex and their coordinates. Thank you, Giuliano

2 1

TalAviQA and mris_jacobian
by Helfand, Alexander I 17 Jul '17

17 Jul '17

Hi FreeSurfer Team, I was hoping I might be able to get some information about TalAviQA. I have read that this number is a spatial correlation between the input image and the image transformed to the Talairach atlas. Is that correct? Can you tell me any more about how this correlation is calculated? I hope this isn't a silly question, but besides the Euler numbers and the mris_jacobian command, are there any other quantitative metrics of how much warping was necessary for a particular subject's recon-all? Also, are there multiple ways to run mris_jacobian such that you can get information beyond lh/rh.white.preaparc? Might you be able to offer any hints as to other files to feed the mris_jacobian command besides 'mris_jacobian ../surf/l(r)h.white.preaparc ../surf/l(r)h.sphere.reg ../surf/l(r)h.jacobian_white' Finally, is there a complete set of documentation somewhere for the QA Tools package of scripts? Are these scripts up to date and compatible with Freesurfer 6? https://surfer.nmr.mgh.harvard.edu/fswiki/QATools suggests that v1.1 came out in 2012 and the current release for download is v1.2... Thanks for your time, thanks for your efforts creating and maintaining Freesurfer! Alex

2 1

spmregister
by John Anderson 17 Jul '17

17 Jul '17

Dear Freesurfer experts, I want to derive registration matrix between pcasl image and the structural space in Freesurfer (i.e. orig.mgz) If I open orig.mgz and the pcasl image in Freesurefr I see overlap between the images (attached Figure1). When I use "spmregister" as follow: spmregister --mov perfusion_calib.nii.gz --s SUBJ --reg reg.dat --fsvol orig --o CBF_T1.nii Then visualize "CBF_T1" using freeview I see mis-registration (attached Figure2) Please what I am doing wrong? Thank you for any guidance Jon

2 4

qcache ERROR on longitudinal image processing with FreeSurfer v6.0
by Lisa Delalande 17 Jul '17

17 Jul '17

Hello everyone, I'm using the new version of FreeSurfer processing with longitudinal image processing. And at the step -base after a recon-all processing i would like to make a qcache processing but it doesn't work... "cannot find [...]/template_1-01VALAL/surf/lh.w-g.pct.mgh" (See in attachment longitudinal image processing withFSv6.0 first and FSv5.3). Thanks in advance, Best regards, Lisa

2 1

Custom Annotation: 1st Annot Visible in TKSurfer but not Freeview
by Ursula Tooley 17 Jul '17

17 Jul '17

Hi FreeSurfer Experts, I’ve created a custom annotation file in MATLAB, using read_annotation.m and write_annotation.m, relabeling the Glasser parcellation regions. It seems to display as expected in tksurfer and tkmedit, but in freeview the first annotation is completely transparent (see images below), although if I hover my mouse over the area, it’s labeled with the correct struct_name. I’ve changed the alpha value in the annotation file and see no difference in freeview, and also given some previous listserv posts tried changing the RGB values for that first annotation in colortable.table. View in tksurfer: tksurfer fsaverage lh inflated -annotation my_annotation.annot View in freeview: freeview $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=my_annotation.annot Any help would be greatly appreciated. I’m running FS 6.0, Freeview V2, this occurs both locally on my OSX El Capitan and on an HPC running Linux Centos. Thanks in advance, Ursula --- Ursula Tooley Ph.D. Student Neuroscience Graduate Group University of Pennsylvania utooley(a)gmail.com 202.413.5627

2 1

Re: [Freesurfer] FS Version 6 Long Processing
by Allison Rainford 17 Jul '17

17 Jul '17

Hi FreeSurfer Team, My lab has recently begun editing longitudinal data in version 6 and have found that we cannot use the same flags for -autorecon2 as we did when running longs in version 5.1. Typically, after making any necessary edits to a long, we run -autorecon2-pial -autorecon3. This flag hasn't been successful in version 6, producing an error message that the flag is unrecognized. Because we still only require some brainmask edits on the longs, we would like to know how we can continue to run these to process only pial. All help is greatly appreciated! Allison

3 2

SPMPainting
by Geng Shuang 17 Jul '17

17 Jul '17

I am confused that how to align the brain.img with my functional data in spm... https://surfer.nmr.mgh.harvard.edu/fswiki/SpmPainting Best wishes! 1. Convert the brain.mgz volume to analyze: mri_convert $SUBJECTS_DIR/subjectname/mri/brain.mgz brain.img 2. Align brain.img with your functional data in spm (eg, func.img) ____________________________________________________________________________ Irene Geng Institute of Cognitive Neuroscience East China Normal University

2 2

Re: [Freesurfer] Freesurfer pipeline for infant
by Lilla Zollei 17 Jul '17

17 Jul '17

Hi Gianluca, For your younger ages, this is the wiki that I would check: https://surfer.nmr.mgh.harvard.edu/fswiki/ChildBrainManualEdits We will look into the stats file. Best, Lilla On Tue, 11 Jul 2017, Gianluca Sforza wrote: > Hi Lilla,is there a range of age I should possibly take more care of with the FS outputs? > Should I refer to the advices on this page http://freesurfer.net/fswiki/FsTutorial/TroubleshootingData > > I take the opportunity to report a small issue in the format of the stat files rh.aparc.stats & lh.aparc.stats > While parsing those files, I found that a comma is missing after the field `CortexVol’ on the Measure Cortex row. > Please double check it; I am using last ver. 6 of FS. > > > sincerely > gianluca >

1 0

Pediatric Atlas/Template
by Jessica Reynolds 17 Jul '17

17 Jul '17

I am wondering whether there are still plans to implement a pediatric atlas/template? I’m working with children aged 3-6 years. Thanks in advance, Jess.

2 1

vertex-wise contra-lateral mapping on an ico surface
by Burke Rosen 14 Jul '17

14 Jul '17

Hello, I've created single subject surfaces sampled in ico7 space with make_average_subject --ico with a single input subject. Because of the ico7 sampling, both hemispheres have the same number of vertices. I am interested in the index-to-index mapping between equivalent contra-lateral vertices. How do I compute this mapping? Thank you, -Burke Rosen

1 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