Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30133 discussions

trac-all bug: using #!/bin/sh instead of #!/bin/bash in scripts which use bash-only syntax extensions
by Parzer, Peter 24 Jan '17

24 Jan '17

Hi, there is a bug in the scripts bedpostx_mgh and fsl_sub_mgh. Both use code that do not conform to the standard shell syntax and work only with bash. This does not work in system that do not link /bin/sh to /bin/bash (as is the case in Ubuntu). Both scripts must use #!/bin/bash as the interpreter command in the first line. Peter

2 1

R: Re: recon-all -all FS6.0
by stdp82＠virgilio.it 24 Jan '17

24 Jan '17

Thanks! >----Messaggio originale---- >Da: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> >Data: 24-gen-2017 21.45 >A: <stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard. edu> >Ogg: Re: [Freesurfer] recon-all -all FS6.0 > >Hi Stefano > >that's a warning burried in the depths of some open source quasi-newton >optimization code that doesn't seem to matter - it can be safely ignored I >believe > >cheers >Bruce >On Tue, 24 Jan 2017, >stdp82(a)virgilio.it wrote: > >> Hi list,I wonder whether the recon-all -all processing are running >> correctly. >> I'm noting the follow lines >> Thanks >> >> Stefano >> >> nsamples 3243 >> >> Quasinewton: input matrix >> >> 1.05460 -0.04529 -0.00589 -5.39976; >> >> 0.04715 1.21082 0.14343 -52.53261; >> >> 0.00057 -0.10515 0.95251 8.62344; >> >> 0.00000 0.00000 0.00000 1.00000; >> >> IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR >> RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE >> INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = >> -0.0 tol 0.000010 >> >> Resulting transform: >> >> 1.05460 -0.04529 -0.00589 -5.39976; >> >> 0.04715 1.21082 0.14343 -52.53261; >> >> 0.00057 -0.10515 0.95251 8.62344; >> >> 0.00000 0.00000 0.00000 1.00000; >> >> >>_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >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 -all FS6.0
by stdp82＠virgilio.it 24 Jan '17

24 Jan '17

Hi list,I wonder whether the recon-all -all processing are running correctly.I'm noting the follow linesThanks Stefano nsamples 3243 Quasinewton: input matrix 1.05460 -0.04529 -0.00589 -5.39976; 0.04715 1.21082 0.14343 -52.53261; 0.00057 -0.10515 0.95251 8.62344; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.05460 -0.04529 -0.00589 -5.39976; 0.04715 1.21082 0.14343 -52.53261; 0.00057 -0.10515 0.95251 8.62344; 0.00000 0.00000 0.00000 1.00000;

2 1

Freesurfer 6.0 and ex-vivo T1
by Trisanna Sprung-Much 24 Jan '17

24 Jan '17

Hi there I am wondering if the Freesurfer 6.0 version is more flexible with the parameters used for ex-vivo scans other than what 5.3 required, as listed here https://surfer.nmr.mgh.harvard.edu/fswiki/ExVivo. We acquired some ex-vivo scans at 0.4mm iso but not with those above parameters. many thanks! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

2 2

How high resolution for -hires in FS6.0
by Alex Cohen 24 Jan '17

24 Jan '17

So what resolution would make sense to use? the release notes say <1.0mm but would 0.9mm isovol really cut it? -Alex ---------------------------------------------------------------- Alexander Li Cohen, M.D., Ph.D. E-mail: Alexander.Cohen2(a)childrens.harvard.edu (Medical/Science Email) E-mail: alexcohen(a)gmail.com (Lifetime Email) ----------------------------------------------------------------

2 5

Neighborhood of a vertex
by Onur Uğurlu 24 Jan '17

24 Jan '17

Hi all, I have a 'lh.thickness.asc' file which contains thickness values of each vertex. The format of the file is following; <vertex index> <x> <y> <z> <thickness> However, x,y,z are not integer. What is the unit of the x,y,z values in the file? I am trying to find all the neighborhood of any given vertex as x,y,z -> x+1,y,z etc, can you suggest a method for this problem. Sincerely yours, Onur

2 10

Extracting significant clusters after qdec analyses
by Katherine Damme 24 Jan '17

24 Jan '17

Hello Everyone, Is there a way to extract the significant clusters as masks from significant group comparisons using qdec? All I can seem to find is mri_glmfit-sim which doesn't quite replicate the QDEC FDR 0.05 output and doesn't seem to make anything that I could extract as a label, or hand drawing an ROI. I am working with a longitudinal model of cortical thickness, and would like to extract the average thickness of each significant cluster to understand the change in thickness. Thank you. Kate Damme

3 5

FS6 recon-all hangs at mris_fix_topology
by Hibert, Matthew Louis 24 Jan '17

24 Jan '17

Hi Freesurfer Devs, I'm trying to re-process a subject who had a right temporal lobectomy using FS6 but the recon hangs at the mris_fix_topology step, saying "XL defect detected...". It continues to use a CPU for several days if allowed, but does not actually progress from that point. This scan was able to be processed in both stable 4 and stable 5.3. I've attached the recon-all log from the recon using the Martinos installation of "stable6". Any suggestions? Thanks, Matt

2 3

REPOST: Regarding: Habenula ROI
by Dr Sampada Sinha 24 Jan '17

24 Jan '17

Dear freesurfer experts, Is it possible to create Habenula as region of interest from fsaverage (orig.mgz images) using tkmedit? I will be using following links to guide me for creating Habenular region of interest. Hope my question is answered since the next question is related to this please. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI_tktools http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/ FreeSurferColorLUT Thanks for your help. Kind regards, Sampada -- Sampada Research medical scientist (B) Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 , Uttar Pradesh India -- Sampada Research medical scientist (B) Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 , Uttar Pradesh India

2 1

Some questions about coordinate systems
by Hsin-Tsung Lee 24 Jan '17

24 Jan '17

Dear Freesurfer experts: My project objective is to build 3D reconstruction of brain with inserted electrodes. I want register the Brian volume of CT and MR via freesurfer. The registration result looks great when I used th "mri_coreg" instruction, but when I tried to use the information in lta data to register by myself, some trouble happens. The LTA data -------------------------------------------------------------------------------------------------------------------------------------------------------------- # transform file p19_movCT2refMR.lta # created by caca on Tue Jan 24 17:45:08 2017 type = 0 # LINEAR_VOX_TO_VOX nxforms = 1 mean = 0.0000 0.0000 0.0000 sigma = 10000.0000 1 4 4 4.795561134815216e-01 -1.318652089685202e-02 -2.057363465428352e-02 1.383309745788574e+01 1.247252989560366e-02 4.785549342632294e-01 -6.737518310546875e-02 1.315915203094482e+01 1.107159163802862e-02 3.306149691343307e-02 9.974335432052612e-01 -6.133582305908203e+01 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 src volume info valid = 1 # volume info valid filename = patient19CT.nii volume = 512 512 228 voxelsize = 4.873275756835938e-01 4.873275756835938e-01 9.999971985816956e-01 xras = -9.993908405303955e-01 -0.000000000000000e+00 3.489949554204941e-02 yras = -0.000000000000000e+00 1.000000000000000e+00 -0.000000000000000e+00 zras = 3.489949554204941e-02 0.000000000000000e+00 9.993908405303955e-01 cras = 7.397460937500000e-02 -1.105121917724609e+02 1.181088867187500e+02 dst volume info valid = 1 # volume info valid filename = patient19MR.nii volume = 256 256 192 voxelsize = 1.015599966049194e+00 1.015599966049194e+00 1.000001072883606e+00 xras = -1.000000000000000e+00 -0.000000000000000e+00 0.000000000000000e+00 yras = -0.000000000000000e+00 1.000000000000000e+00 -0.000000000000000e+00 zras = -0.000000000000000e+00 -0.000000000000000e+00 1.000000000000000e+00 cras = 3.934204101562500e+00 2.904579925537109e+01 1.511990356445312e+01 subject unknown ------------------------------------------------------------------------------------------------------------------------------------------------------------------- First I thought the 4x4 matrix is the affine matrix (type = VOX_TO_VOX) 4.795561134815216e-01 -1.318652089685202e-02 -2.057363465428352e-02 1.383309745788574e+01 1.247252989560366e-02 4.785549342632294e-01 -6.737518310546875e-02 1.315915203094482e+01 1.107159163802862e-02 3.306149691343307e-02 9.974335432052612e-01 -6.133582305908203e+01 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 After I studied the document "FS Coordinates (PDF)" at the following URL : http://freesurfer.net/fswiki/CoordinateSystems there are some question : I thought in my case correspond to the page 3 condition "Two Fields of View, Two Coordinate Systems" But I am not sure that that does the affine matrix above is the vox_to_vox matrix or not. If it is, could I use it directly to compute the corresponding voxel location between 2 volume? or I need additional coordinate transfer? Sincerely, Hsintsung

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