Freesurfer June 2017

freesurfer@nmr.mgh.harvard.edu

116 participants
186 discussions

recon-all on T1s without anterior coil
by Gullickson, James 12 Jun '17

12 Jun '17

Hello all, We have a subject whose T1s were collected without the anterior head coil engaged, due to a technical error. The posterior coil collected signal. This was on a Siemens Prisma 3T scanner. Would you expect Freesurfer to still be able to process/segment this data accurately, or is it a lost cause at this point? Thanks, James Gullickson

2 3

Re: [Freesurfer] Outputs from 5.3 to 6.0
by Antonin Skoch 12 Jun '17

12 Jun '17

Dear Manuel, I would chime in with my current experience with transfering v5.3 reconstructions to v6.0: The wm segmentation results (and therefore white/pial surfaces, apart from other things) are different between versions, especially in ambiguous areas and especially if there is a difference in interpolation during conform step (in v 6.0 the cubic interpolation is off; if it is off or on in v5.3 it depends on whether you used patched version of recon-all or not). It of course also depends on the quality of your data. In any case, my experience is, if you want to keep high quality of your results, you probably would need to re-inspect your data again and correct newly appeared errors in surfaces. Antonin Skoch all the edits will be taken into account regardless of what command line args you use On 6/9/17 3:08 AM, Manuel Delgado wrote: Dear all, Regarding this issue: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51931.html we have the same situation. We are going to reprocess data previously processed with FS 5.3. If we proceed with *recon-all -all *will all the edits be taken into account (i.e. skull strip, control points, wm and pial edits) or is it necessary to proceed with ordered steps (i.e -autorecon-pial, then -autorecon2-cp autorecon3, and so on)? Thanks in advance, Manuel

2 1

Statistical analysis
by Laura Ferrero Montes 11 Jun '17

11 Jun '17

Dear FS team, Thank you very much for your help. Just a few more questions. I want to perform a statistical analysis between two groups:controls and patients, using age and IQ as covariates. First I have to test if there is an interaction between group and covariate using DODS. My questions are: Q1) Do I have to test age and IQ separately, or together? Q2) In case that there is not interaction in any of the covariates, can I use the same FSGD file but do I have tu run it as DOSS? How it could be done? I would appreciate if you could give me some hints or examples about the matrices and contrast files that I must use. Thank you, All the best, Laura

3 10

cortical metrics description
by Aniqa Nisar 11 Jun '17

11 Jun '17

Hi All, Is there a full description on what these cortical metrics are and how are they derived ? How do I calculate sulcal depth ? Is it available already ? What does the ?h.curv mean ? Please suggest. Thanks Ani

2 1

mri_cvs_register error: Symbol not found: ___emutls_get_address
by Elijah Mak 10 Jun '17

10 Jun '17

Hi Freesurfer Developers, I am trying use mri_cvs_register but I ran into an error (Mac OS SIERRA 10.12.2). The log is pasted below. Logfile for mri_cvs_register Sat 10 Jun 2017 17:58:48 BST --mov 16084 $Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $ dhcp-10-240-198-151.cp.wireless.private.cam.ac.uk Darwin dhcp-10-240-198-151.cp.wireless.private.cam.ac.uk 16.3.0 Darwin Kernel Version 16.3.0: Thu Nov 17 20:23:58 PST 2016; root:xnu-3789.31.2~1/RELEASE_X86_64 x86_64 asegfname aseg Using m3z type morph files. mris_register -1 -dist 1.0 -inflated /Volumes/CITADEL/16084/surf/lh.sphere /Applications/freesurfer/subjects//cvs_avg35/surf/lh.sphere /Volumes/CITADEL/16084/surf/lh.cvs.tocvs_avg35.sphere.reg dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib I have also tried to update the freesurfer binaries with sudo -E fs_update but the problem persists. Thanks for looking into this! Best Wishes, Elijah

1 0

Re: [Freesurfer] Regarding: Group analysis of WMHs
by Elijah Mak 09 Jun '17

09 Jun '17

Hi Doug, I am referring to a rather old thread where you have provided some interesting suggestions to perform group-wise analysis of WMHs. I am trying to do something similar in patients and controls. First, mri_binarize was used to extract the individual WMH volumes from aseg.mgz. These volumes were subsequently warped into MNI305 space and smoothed (using mri_fwhm 8mm). The goal is to compare the spatial distributions of WMH between both groups. Finally, mri_concat --mean was used to visualise group averaged WMH volumes. The outputs can be found here: http://imgur.com/a/curYf Do these steps look alright? On a conceptual level, is it statistically valid to compare stacks of binarised lesion maps between groups (using mri_glmfit and then performing MC with FDR/mri_glmfit-sim)? On an individual level, I noticed that some WMH voxels show up inside the MNI305 ventricles for a few subjects. This happens despite a good-looking talairach registration. Thanks a lot for your time in advance and I’ll appreciate any thoughts you may have on this. Sincerely, Elijah Dr. Elijah Mak, Research Associate Department of Psychiatry, Old Age Psychiatry Group University of Cambridge Trinity College, CB21TQ, UK http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24

2 3

methodological questions for manuscript
by Jacobs H (NP) 09 Jun '17

09 Jun '17

Hi! For my manuscript, the journal wants me to answer some questions on the methods that I used and I want to make sure I am giving correct information on how FreeSurfer calculates hippocampal volumes. Would it be possible to check my 4 answers and let me know if these are accurate? Question: How were the data normalized/standardizes? Answer: T1 data was intensity normalized using FreeSurfer's mri_normalize script Question: Describe the template used for normalization/transformation Answer: All data was kept in subject-specific space, no templates were used. FreeSurfer, volumes are defined in several steps during which a high-dimensional non-linear registration is done to the MNI305 template to increase the accuracy of the segmentation and to facilitate the segmentation and tissue-probability assessment for region labeling. Volumes of the hippocampus are ultimately extracted from a subject-specific subcortical volumetric atlas (aseg) in 1mm isotropic space. Question: Describe your procedure for artifact and structured noise removal Answer: The standard preprocessing pipeline of FreeSurfer incorporates motion correction, intensity correction and skull-stripping. Question: how are anatomical locations determined? Answer: In FreeSurfer a subject-independent probabilistic atlas (hand labeled atlas by neuroanatomists on a training set) and subject-specific measured values. Subject-specific segmentations of the hippocampus are based on these probabilities and on the white and pial surfaces. Many thanks! All the best Heidi

2 2

Cortical thickness_Group analysis
by Ali Radaideh 09 Jun '17

09 Jun '17

Dear FS experts, I am trying to analyse the cortical thickness for a group of MS patients and healthy controls. I have followed the instructions on how to perform group analysis but I am still unable to achieve what I am looking for. I am trying to produce a significance map to show the cortical areas that are statistically different between MS and healthy controls (in terms of cortical thickness). Would it be possible please to show you the matrix (fsgd) and contrasts files that I have used in my analysis? Best regards and many thanks in advance, Ali -- *Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite University, Zarqa, JordanW.phone +962 5 3903333 ext.5422, 5355, 5364Email: ali.radaideh(a)hu.edu.jo <ali.radaideh(a)hu.edu.jo>* *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*

3 6

Question regarding Qdec in Cortical thickness and Ventricular Volume Analysis
by Tamara Tavares 09 Jun '17

09 Jun '17

Hello, I have ran my data through the default recon-all processing stream and am planning on analyzing ventricular volume and cortical thickness. I was wondering whether I need to use the Qdec to complete the ventricular volume and cortical thickness analysis, or can I export the data (txt files found in the stats folder) and complete the analysis on any statistical program such as SPSS or STATA? I also noticed that Qdec needs to have the data smoothed before analyzing cortical thickness or other surface information. Why does the data need to be smoothed after being ran through recon-all and before analysis? Does the smoothing just need to occur if I am running the analysis via Qdec or do I need to complete the smoothing before analyzing the data on any statistical program? Thank you in advance for your help! Best, Tamara

3 2

Re: [Freesurfer] Question regarding Qdec in Cortical thickness and Ventricular Volume Analysis
by Tamara Tavares 09 Jun '17

09 Jun '17

Hi Douglas, The message stream indicates you replied to my email but I don't see your response in the email thread. I am not sure what happened. Can you please reply again? Thank you, Tamara On 6/6/17 11:50 AM, Tamara Tavares wrote: > Hello, > > I have ran my data through the default recon-all processing stream and > am planning on analyzing ventricular volume and cortical thickness. I > was wondering whether I need to use the Qdec to complete the > ventricular volume and cortical thickness analysis, or can I export > the data (txt files found in the stats folder) and complete the > analysis on any statistical program such as SPSS or STATA? you can export > > I also noticed that Qdec needs to have the data smoothed before > analyzing cortical thickness or other surface information. Why does > the data need to be smoothed after being ran through recon-all and > before analysis? Does the smoothing just need to occur if I am running > the analysis via Qdec or do I need to complete the smoothing before > analyzing the data on any statistical program? The data does not necessarily need to be smoothed, but people usually do because it improves stats. But I thought you were doing an ROI analysis based on the first question > > Thank you in advance for your help! > > Best, > Tamara >

1 0

← Newer
1
...
11
12
13
14
15
16
17
18
19
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 June 2017