[Freesurfer] percent signal change

, Mariam. Mariam Sood PhD student Department of Psychological Sciences Birkbeck, University of London ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e

Re: [Freesurfer] percent signal change

; > On 7/24/15 11:11 AM, Mariam Sood wrote: >> Dear Doug, >> >> I am using the FSL-Freesurfer pipeline, with single subject analysis done in >> Feat and group analysis done using mri_glmfit. Is there a way I can >> calculate percent signal change from the grou

[Freesurfer] reg-feat2anat problem

Hello, I am running reg-feat2anat and facing some problems. First I ran the command in its default mode using FSL initialisation reg-feat2anat --feat featdir.feat --subject s. That gave me a bad registration. There is a warning coming up WARNING: initial G-W contrast is negative, but expec

Re: [Freesurfer] reg-feat2anat problem

ll > have to bypass reg-feat2anat to create the registration. > > Unless you use --overwrite-exf2std, the exf2anat will not affect the exf2std > > doug > > > On 02/02/2014 05:59 PM, Mariam Sood wrote: >> Hello Doug, >> Thank you for your reply. I tried to i

[Freesurfer] FWHM in mri_glmfit-sim

Hi Doug, I have a few queries regarding FWHM used in multiple comparisons correction program mri_glmfit-sim My data at present is analysed in FSL & Freesurfer following the procedure in the link http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer. No volume based smoothing at

Re: [Freesurfer] FWHM in mri_glmfit-sim

: > > On 03/31/2014 10:05 AM, Mariam Sood wrote: >> Hi Doug, >> >> I have a few queries regarding FWHM used in multiple comparisons correction >> program mri_glmfit-sim >> >> My data at present is analysed in FSL & Freesurfer fo

Re: [Freesurfer] FWHM in mri_glmfit-sim

Thanks very much Doug. Mariam. On 1 Apr 2014, at 17:17, Douglas N Greve wrote: > > If I could not reanalyze the data, I would just follow the standard process. > doug > > On 04/01/2014 04:12 AM, Mariam Sood wrote: >> Hi Doug, >> Thank you for your advice. Would

[Freesurfer] nifti1Read(): unsupported slice timing pattern 5

Hello everyone, I was trying out FS-FAST tutorial with my set of images (converted to NIFTI from AFNI BRIK format using 3dAFNItoNIFTI). However, I get this error 'nifti1Read(): unsupported slice timing pattern 5 in … '. Looking at NIFTI.h, this value (#define NIFTI_SLICE_ALT_INC2 5) is added

[Freesurfer] mris_preproc

Hello All, I am trying to do a cross-subject surface based analysis of data analysed using FSL. I am following the instructions in the following tutorial link. http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer Each of my subject data comprises of two runs. My question is rel