Freesurfer March 2017

freesurfer@nmr.mgh.harvard.edu

148 participants
263 discussions

Average myelination within ROI
by SHAHIN NASR 06 Jul '17

06 Jul '17

Hi Surfers, I want to measure the average amount of myelinations within my ROI(s), I have already generated my myelination maps on surfaces (e.g. lh.myelin_ProjFrac0p5.nii ). Then I used mri_segstats as below: mri_segstats --i lh.myelin_ProjFrac0p5.nii --slabel SBJ_001 lh lh.V1 --sum V1_Stats.txt --accumulate but the numbers don't make any sense. For instance: # ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 125261 82573.4 Seg0000 110280.4453 0.2922 -5.5000 51.0000 56.5000 2 1 1138 764.8 Seg0001 941.0988 0.1572 0.2675 1.4203 1.1527 How can mean=941.0988 when the max=1.4203 ??? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

2 1

Re: [Freesurfer] TRACULA tract reconstruction
by Antonin Skoch 12 May '17

12 May '17

Dear Joelle, regarding the conversion to .bvecs, could you please show the example of difference between bvecs converted by mri_convert of FreeSurfer and mrconvert of mrtrix3? Do you have most recent version of mrtrix3? There have been a quite extensive discussion on implementation of FSL .bvec convention in mrtrix3 in spring 2016: http://www.mrtrix.org/2016/04/15/bug-in-fsl-bvecs-handling/ However, there have been quite a big effort to settle this issue and I am pretty convinced that the recent versions should have this issue resolved. Maybe you can also post this to the mrtrix community forum, they are usually responding very quickly and each post gives detailed attention. Regards, Antonin Skoch ??Dear Tracula experts, I am applying Tracula on a longitudinal data set, and have some questions I am hoping you could help me with: Firstly, upon visual inspection, several tracts appear to be quite messy, or small (on the default freeview threshold) for most subjects. However, the -stat step from Tracula does not necessarily flag these tracts as outliers. What is then the best way to decide whether tracts are not correctly reconstructed and need to be rerun separately once more? Can I rely on the flagged outliers? Or should I rerun all the tracts that do not look ok after visual inspection? And in the last case, for tracts that look small, are they considered as correctly reconstructed if looking ok at lower thresholds than the default of freeview? Second, concerning the rerunning of poorly reconstructed tracts, I was wondering if there might be a more automated way to configure the dmrirc file in order to adapt it for each subject/each tract to rerun (and its corresponding control points). Third, I was wondering if there is a recommended software for obtaining bvecs and bvals. For the moment I used mrconvert (from MRtrix, using the -export_grad_fsl option) and the new mri_convert from freesurfer 6.0. As they give different outputs, I was wondering if this may impact the reconstruction. Lastly, would you recommend using freesurfer 5.3 or 6.0 for applying the longitudinal stream of Tracula? Related to this, is it recommended to use the same freesurfer version to obtain the long/base images, and to run Tracula? Thank you for your time, Best regards, Joëlle van der Molen

4 16

Qdec 1.5
by Duy Nguyen 28 Apr '17

28 Apr '17

Dear FS Expert I am doing analysis from the group_analysis_tutorial data to practice and learn. However, I come across the error window like it shows on the attached picture (please see the attachment) when I press the button "Generate Stats Data Table." Please help me how can I can find the file aseg.volume.stats.dat. If the file does not exist, how can I create one? Thank you for your response. Any help would be appreciated!!! *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme(a)gmail.com <duy.nguyenbme(a)gmail.com>*

3 7

Interaction effects in QDEC
by Heidi Foo 26 Apr '17

26 Apr '17

Hi all, I was wondering how I could test for interaction effects between a categorical variable and a continuous variable using QDEC. Is there a way to do so? Thank you. Best Regards, Heidi Foo

2 4

mri_cvs_register failure from missing shared lib
by Michael Waskom 25 Apr '17

25 Apr '17

Hi, I had mri_cvs_register die on me when it couldn't find a shared library. Relevant bit is (full log is attached): mris_resample: error while loading shared libraries: libboost_program_options.so.5: cannot open shared object file: No such file or directory Freesurfer bugr info: -------------------- FREESURFER_HOME: /hsgs/software/freesurfer/5.3.0 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: Red Hat Enterprise Linux Server release 6.3 (Santiago) Kernel info: Linux 2.6.32-358.6.2.el6.x86_64 x86_64 ---------------------- Any thoughts on how to proceed? Thanks! Michael

3 4

Multiple comparisons
by Laura Ferrero Montes 22 Apr '17

22 Apr '17

Dear FS team, I would like to correct for multiple comparisons after I run command-line GLM analysis on stats tables. I would like to make a second level analysis between a control group and an autism group. I would like to know if there is a command-line in FreeSurfer or if there is any program or toolkit in Matlab that allows to do that. Thank you, Laura

3 6

mri_concat pet images into 1 template image
by Shane S 12 Apr '17

12 Apr '17

Hello Freesurfer, I have 3 PET images per individual. I am learning PetSurfer based on the Greve et al., 2014 paper. On the PetSurfer link, there are 2 methods. mri_convert pet.nii.gz —frame frameno template.nii.gz or mri_concat pet.nii.gz --mean —0 template.nii.gz What are the differences? My files are listed as subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz —mean —o template.nii.gz” correct? Thank you for helping. Best Wishes, S -- Shane Schofield

3 7

glmfit mismatch between X and C with same no of columns
by Clara Kühn 12 Apr '17

12 Apr '17

Dear Freesurfer experts, I'm trying to run a repeated measures anova as described here: https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova I have 40 subjects with 2 time points each, so it's quite a large matrix. When running the mri_glmfit command I get the following error: ERROR: dimension mismatch between X and contrast /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx X has 41 cols, C has 81 cols I'm not sure what to do as the matrix and the contrast (see attachments) actually have the same amount of columns... Any help would be much appreciated, thank you! Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

3 19

Mri_convert defaults to trilinear interpolation if "--like" option is used, regardless of "-rt nearest"
by Harris Hoke 10 Apr '17

10 Apr '17

I’m currently running freesurfer 6.0.0, and I’ve run into the same problem described in this thread on the archives <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43697.html> . Does anyone know if a fix exists? ~Harris

2 1

calculating geodesic distances between vertices
by Burke Rosen 10 Apr '17

10 Apr '17

I am interested in finding the distance between two vertices along the cortical surface. So far I have used two methods: (1) Compute the shortest path with a variant of Dijkstra's algorithm on the white surface. (2) Compute the great circle distance on the sphere surface. (as done by Risk et.al. 2016 Neuroimage) Method (1) is slow and will tend to overestimate distances as the path only goes along mesh edges. Method (2) is very fast and gives a true geodesic but gives a scaled result because the radius of sphere surface is arbitrary; also this method is subject to distortions introduced by the inflation algorithm. My current strategy is to perform a linear regression between the triangle face areas of the sphere and white surfaces. And then apply the coefficients to the sphere surface diameter before calculating geodesic distances. This yields a distance matrix with a similar pattern to the Method (1) at about 62% scale. That scale seems like it might be reasonable. However, the regression only explains ~58% of the variance. My hunch is that the rest is due to inflation distortions. Is there a better way of scaling the sphere surface? Or a way to inflate in such a way that inter-vertex distances are preserved? Or, more generally, what is a good method of computing geodesic distances on freesurfer surfaces. Thank you, Burke Rosen

3 2

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 March 2017