Re: [Freesurfer] How to deal with labels and structural data

Hi Silas what do you want to do with the labels? As for whether to do it on fsaverage or individuals, you could start with fsaverage and map it to your other subjects and see how accurate it looks cheers Bruce On Tue, 21 Jul 2015, Silas wrote: Dear Freesurfer team, I've created my own

Re: [Freesurfer] mri_watershed mask and skull surfaces

Hi Sam if you want us to help you, you need to provide us with the full command line and screen output (at least!) cheers Bruce On Tue, 21 Jul 2015, Sam Zorowitz wrote: Hi all, I am using mri_watershed to create skull surfaces for a cohort of subjects for whom we were unable to collect a

[Freesurfer] if: Expression Syntax

Hi there, When running selxavg for the following session: nmasa_031_130412 The following error message was generated: Error using MRIread (line 76) ERROR: cannot determine format of /autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm (MRIread) Error

[Freesurfer] R: Re: R: R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity

My concern is whether this command line is correctfcseed-config -segid 1 -seg ROI_MASK. -fsd rest -mean -cfg mean.ROI_MASK.configfcseed-sess -s SessXXX -cfg mean.ROI_MASK.configThank youStefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 20-lug-2015 19.17 A:

[Freesurfer] paradigm file

Hello, I'm working on fMRI analysis on flattening brain by using FSFAST tool. In our data, subjects play game: Matrix reasoning. How can I set up the paradigm file if the duration stimulus depends on the Time response of each subject following each trial. Thanks !! Trinh

[Freesurfer] QA measures mgz

Excellent, thank you for sharing! I have one more question. When running the mri_cnr function I tried using a number of different .mgz files with varying results, which would you recommend for the most accurate gm/wm and gm/csf CNR? Best, KZ

Re: [Freesurfer] if: Expression Syntax

what environment are you running in? ie, dev or stable? On 7/21/15 2:12 PM, Morenikeji Adebayo wrote: Hi there, *When running selxavg for the following session:* nmasa_031_130412 * * *The following error message was generated:* * * Error using MRIread (line 76) ERROR: cannot determine format

[Freesurfer] Question about pial surface correction through Freesurfer

Hi, I am trying to manually correct some segmentation errors through Freesurfer. In particular, I have noticed a number of areas where the pial surface appears to miscalculated and is excluding chunks of grey matter. I tried using control points to push the pial surface out, and this helped

[Freesurfer] About reference to zgees_ and ztrsen_

Hi, I actually come across this problem twice both when trying to compile on a armv7 machine and an ordinary Centos 6.6 intel machine. The error shows up when compiling the package mri-robust-register:MyMatrix.cpp:54 I understand the error comes from the zgees_ and ztrsen_ functions

Re: [Freesurfer] About reference to zgees_ and ztrsen_

I was able to get around that issue by installing the following packages: lapack-devel.x86_64 liblapack-devel.x86_64 For more information, see the following page: http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page -Zeke On 07/21/2015 04:50 PM, Matthew, L. Wong wrote:

Re: [Freesurfer] help on mris_preproc

Hi Doug, Thanks. I was able to resolve this issue now. David -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, July 20, 2015 3:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re:

[Freesurfer] mri_convert command line did not provide output file

Hi list,mri_convert command line did not provide output file.This error was produced during the first computations of trac-all -prep command line. Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] mri_watershed mask and skull surfaces

Hi all, I am using mri_watershed to create skull surfaces for a cohort of subjects for whom we were unable to collect a FLASH sequence. To improve the estimation of the inner skull layer, I would like to use edited brainmasks. However whenever I supply the -mask flag, and only when I supply -mask

[Freesurfer] How to deal with labels and structural data

Dear Freesurfer team, I've created my own labels using tksurfer and common anatomical guidelines - and my next step is to apply these labels to my subjects and analyze (ROI) cortical thickness or volume (first of all), functional data and myelination data.1 - Do you suggest drawing a label on

Re: [Freesurfer] How to deal with the distortions of EPI images when applying the parcellated results of T1 images?

Hi Bingjiang did you acquire any field maps? If so, you can them to undistort the EPIs cheers Bruce On Tue, 21 Jul 2015, Bingjiang Lyu wrote: Dear all, I've got the automaticlly parcellated 'aparc.a2009s+aseg.nii' file for individual T1 image, and I want to calculate functional

Re: [Freesurfer] How to deal with the distortions of EPI images when applying the parcellated results of T1 images?

If you did collect field maps, you can use epidewarp.fsl to create a voxel shift map (the only output of epidewarp.fsl that you need; you'll need to FSL to run that program), then use bbregister with the --vsm option to register your func to the struct, then use mri_vol2vol with the --vsm

Re: [Freesurfer] How to deal with labels and structural data

On 7/21/15 10:04 AM, Silas wrote: Dear Freesurfer team, I've created my own labels using tksurfer and common anatomical guidelines - and my next step is to apply these labels to my subjects and analyze (ROI) cortical thickness or volume (first of all), functional data and myelination data.