Freesurfer January 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
215 discussions

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

tksurfer vertex location
by Nabin Koirala 24 Jan '17

24 Jan '17

Dear freesurfer team, I was trying to obtain the values at a vertex in tksurfer and this is what is written in tksurfer manual. ....*At first, an empty plot will be displayed in a separate window. To generate a plot for a particular vertex, select a point by clicking on the parametric map at that vertex and the plot window will be updated accordingly.* But is it possible to enter the desired vertex and get the plot rather than trying to point the mouse to exact vertex and update the plot because it looks like I am not good at pointing mouse to exact vertex I want. Thank you and excuse me for the naive query. Best, Nabin

3 4

mri_vol2surf
by Zhivago 24 Jan '17

24 Jan '17

Hi, I do not have a good understanding of the mri_vol2surf command. 1) Can this only project the part of the volume that lies between the white & pial matter? 2) What is the default projection parameter that it uses? 3) Does projection always start from the white matter, i.e. is 0 the white matter surface? 4) What is the nature of the mgh file that is created by: mri_vol2surf --src mri/spmT_0002.img --regheader s04 --interp nearest --hemi lh --o lh.sig.mgh Thanks, Zhivago...

3 10

FreeSurfer Version 6
by Douglas N Greve 23 Jan '17

23 Jan '17

Dear Freesurfers, At long last, the new version of Freesurfer v6.0 is available for download! For a list of what it contains, see this page: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes To download it, see this page: http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall We are working to set up some mirrors, so it may be slow to download if lots of people try to download at once. And remember our home page is here: http://surfer.nmr.mgh.harvard.edu Our advice concerning your data and different freesurfer versions is the same: do not mix versions when processing a set of subjects in your project. Thank you to everyone who downloaded and tested the beta release of v6.0 and thank you for your patience in regards to this release. The Freesurfer Team -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

2 1

longitudinal stream v 5.3 - transfer edits of the wm.mgz from cross to base?
by Antonin Skoch 23 Jan '17

23 Jan '17

Dear experts, I am currently starting longitudinal analysis of data I previously corrected in cross-sectional stream (FreeSurfer v5.3). The analysis comprises quite large number of subjects - approx 150 subjects, each scanned twice. All subjects are already inspected and errors corrected in cross-sectional analysis. Some of them needed quite large edits, mainly to the wm.mgz and the whole process took large time. As I read the documentation, the wm.mgz edits in cross are not currently transferred to base. However, wm.mgz has to be correct in base in order to estimate surfaces correctly. From this it implies to me that I would need to edit all wm.mgz errors in base again. Do you think that it could be possible/reasonable to transfer some wm.mgz edits from cross to base, for example to make intersection of edits of all cross timepoints and to transfer it to the base? This could significantly reduce time spent on edits. Does it make sense? Regards, Antonin Skoch

2 1

Stable version of freesurfer 6.0
by miracooloz＠gmail.com 23 Jan '17

23 Jan '17

1 0

?h.pial_lgi does not look right
by Mihaela Stefan 23 Jan '17

23 Jan '17

Hello FreeSurfers, I successfully ran the command recon-all -s <subj> -localGI for one of my subjects. However, the resulted ?h.pial_lgi files don't look right to me. I am attaching a pic for the right hemi (I made sure the overlay is rh.pial_lgi). Can someone help me figure out what went wrong? Thank you! Mihaela

1 0

← Newer
1
...
6
7
8
9
10
11
12
...
22
Older →

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 January 2017