Freesurfer April 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
217 discussions

Long-stream comparing differing resolutions
by Adam Martersteck 03 May '17

03 May '17

Dear FS Experts, I’m trying to compare multiple T1-weighted sequences taken across multiple scanners in the same day in 15 individuals using the longitudinal stream. One question we had was how different cortical thickness estimates would be using a 0.8mm^3 resolution vs. our standard 1mm^3 MPRAGE. Unfortunately, during the initial long-stream norm fusion, the –hires enabled 0.8mm data has a mismatch in dimensions compared to the standard 1mm data. Given this limitation -- what would be the best way to compare these two sequences? Thanks, Adam

2 2

Volume vs cortical thickness
by John Anderson 02 May '17

02 May '17

Dear Freesurfer experts, I highly appreciate if anybody clarify how Freesurfer calculate cortical thickness and gray matter volume. If the cortical thickness of e.g. precentral gurus is measured as the closest distance from the gray-white boundary to the gray-CSF boundray at each vertex on the tessellated surface (Fischl and Dale. 2000). How the gray matter volume for the precentral gyrus was measured? Thank you for any clarification! John

3 7

[FreeSurfer] cortical parcellation
by VA Research 01 May '17

01 May '17

Does freesurfer output individual roi volume masks for each of the cortical parcellations in aparc+aseg? thanks Joseph Veliz VA Hospital West LA

3 3

Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast
by Antonin Skoch 01 May '17

01 May '17

Dear Doug, the subject with leak of white surface outside brain (my first post with screenshots) is subject 1. Slice number (coronal) around 100. The subject in second post (with text below) is subject 2, slice number (coronal) also 100. I have processed the subjects with v 6.0 (in fact dev version from feb 2017, but this is irrelevant) with -cubic -no-mprage. It looks much like v5.3, i.e. the wm.mgz and surfaces are much better, but v5.3 looks still better, at least for subject 1. I have uploaded them as file v6.0_cubic_no_mprage.tar.gz to your ftp site. The optical difference in norm.mgz/brain.mgz between v5.3 and v6.0 with -cubic is very minor, but still there is some other thing which renders wm.mgz worse than with v5.3 for subject 1. The -cubic has profound effect, the images seem much smooth with lose of contrast without using -cubic. Regards, Antonin And what slice number? On 04/24/2017 11:16 AM, Douglas N Greve wrote: > Anonin, of the three subjects you sent, which one is shown in these > pictures? > > > On 04/19/2017 05:23 PM, Antonin Skoch wrote: >> Dear experts, >> >> I am sending just one more example to illustrate issue with white >> surface estimation in v6.0. See the attached screenshots: In v6.0 >> there seems to be insufficient contrast in brain.finalsurfs.mgz, so >> the white surface is leaking at three spots dramatically outwards >> towards pial surface. The white surface in v5.3 looks much more >> anatomically relevant in the same spot. >> >> Could you please comment on how to avoid such issues in v.6.0? >> >> Regards, >> >> Antonin Skoch

2 1

Hippo-subfiled Need Help
by Ramesh Babu 01 May '17

01 May '17

Dear Experts, I ave done hippocampal subfield segmentation by using 1x1x1 t1 scan. Please see the attached image and give your suggestions. It took nearly 7 hrs 10 min. to complete hippo-subfield segmentation for one scan by using the command recon-all -i grp205_t1.nii -s grp205 -sd grp205 -all Started at Wed Apr 26 11:03:34 IST 2017 Ended at Wed Apr 26 17:17:35 IST 2017 #@#%# recon-all-run-time-hours 6.234 recon-all -s grp205 finished without error at Wed Apr 26 17:17:35 IST 2017 done Then for hipposubfield, recon-all -s grp205 -sd grp205 -hippocampal-subfields-T1 I want to run for 40 scans grp-1 20 scans and grp-2 20 scans. How to modify in the command. Since it is taking long time I want to run 10 scans n give rest again 10 scans. Can I do so? I am15.6 GiB ram, Intel® Core™ i7-4790 CPU @ 3.60GHz × 8 processor, GeForce GT 610/PCIe/SSE2 graphic card.It is octa core processor. Can I run 8 analysis simultaneously (in 8 separate terminal?). Your suggestion will be helpful to me to proceed further. Thanks RB

2 3

Re: [Freesurfer] recon-all with error (mris_curvature -w lh.white.preaparc)
by Antonin Skoch 30 Apr '17

30 Apr '17

Dear fwd9707, see these threads: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52560.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51797.html Antonin Skoch Dear all I performed the recon all in virtualbox (with centos 7), and there error and can not continue,the error information is that :#@# Curv .H and .K lh Sat Apr 29 21:06:24 CST 2017 /media/sf_VM_ShareFolders/Freesurfer_results/Sub_001/surf mris_curvature -w lh.white.preaparc total integrated curvature = 2.136*4pi (26.843) --> -1 handles ICI = 184.8, FI = 2061.6, variation=32051.104 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux localhost.localdomain 3.10.0-514.16.1.el7.x86_64 #1 SMP Wed Apr 12 15:04:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s Sub_001 exited with ERRORS at Sat Apr 29 21:06:26 CST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting need your help ,thank you very much

1 0

recon-all with error (mris_curvature -w lh.white.preaparc)
by fwd9707＠sina.com 30 Apr '17

30 Apr '17

Dear all I performed the recon all in virtualbox (with centos 7), and there error and can not continue,the error information is that :#@# Curv .H and .K lh Sat Apr 29 21:06:24 CST 2017 /media/sf_VM_ShareFolders/Freesurfer_results/Sub_001/surf mris_curvature -w lh.white.preaparc total integrated curvature = 2.136*4pi (26.843) --> -1 handles ICI = 184.8, FI = 2061.6, variation=32051.104 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux localhost.localdomain 3.10.0-514.16.1.el7.x86_64 #1 SMP Wed Apr 12 15:04:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s Sub_001 exited with ERRORS at Sat Apr 29 21:06:26 CST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting need your help ,thank you very much

1 0

perform group analysis on user defined maps
by Ladan Shahshahani 29 Apr '17

29 Apr '17

Dear experts, I have preprocessed my functional data using FSFAST. I have calculated an index for each of my ROIs' vertices in matlab, and then created a map for each hemisphere and subcortical regions using MRIwrite. I want to perform group analysis on these maps. I also want to apply cluster-wise multiple comparison correction. Since I have not defined an analysis using mkanalysis-sess, I do not know how to use isxconcat-sess and mri_glmfit. How should I perform this analysis? Bests, Ladan

2 1

FS-Fast's 'subject to fsaverage' registration files?
by Patrycja Naumczyk 29 Apr '17

29 Apr '17

Hello FS experts, I have a question regarding FS-Fast processing. I have performed (successfully!) an FS-Fast single subject analysis. The results look fine in the fsaverage space, but I'm interested in viewing them in the subject space. Are the registration files used along the processing pipeline (EPI->T1->fsaverage) stored anywhere (so far I only found the EPI->T1 and T1->talairach files), so I can use them? Or do I need to create new registration files (bbregister/tkregister2)? Best regards, Patrycja

4 7

How to get SUVR images with cerebellar GM reference?
by Shane Schofield 29 Apr '17

29 Apr '17

Hello PetSurfer and Freesurfer Developers, I am using PetSurfer to obtain PVC SUVR images . I have already used mri_concat to derive the mean images over three acquisitions (template image). After gtmseg amd mri_coreg, I want to get the SUVR map with whole cerebellum as the reference (instead of the pons). How could this be done? What can I modify in mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o gtmpvc.output to achieve this goal? Thank you.

3 3

← Newer
1
2
3
4
5
6
7
...
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 April 2017