Re: [Freesurfer] mri_convert ERROR: could not determine file

2013-09-26 Thread Emily Ward
(my trouble is with fslregister-sess though) On Thu, Sep 26, 2013 at 11:25 PM, Emily Ward wrote: > Hi Doug, > > Can you make that file available again? I am having a similar issue > > Thanks, > > Emily > > > On Mon, Jul 29, 2013 at 11:13 AM, Douglas Greve &g

Re: [Freesurfer] mri_convert ERROR: could not determine file

2013-09-26 Thread Emily Ward
Hi Doug, Can you make that file available again? I am having a similar issue Thanks, Emily On Mon, Jul 29, 2013 at 11:13 AM, Douglas Greve wrote: > > Hi Morgan, this is a problem with newer versions of csh -- they changed > the way that errors are reported. Try using this version > > ftp:

[Freesurfer] First-level analysis with continuous covariate

2011-10-16 Thread Emily Ward
How does one execute a first-level (subject-level) analysis with a continuous covariate? For example, in an event-related experiment presenting pictures of scenes, I have two conditions: environment (indoors/outdoors) and openness (a continuous rating obtained independently). I am interested in th

Re: [Freesurfer] roisummary-sess from binary mask

2011-02-10 Thread Emily Ward
omical space if you need to. > > > Emily Ward wrote: >> >> Hi Doug, >> >> I've been running: >> >> mri_cor2label --c s105/rois/RhFFA_sphere.nii.gz --id 1 --l >> s105/labels/RhFFA_sphere.label >> >> to generate my label from m

Re: [Freesurfer] roisummary-sess from binary mask

2011-02-09 Thread Emily Ward
t 11:18 AM, Douglas N Greve wrote: > You have to make it work with func2roi-sess. One way to do this is to create > a label file then use the -labelfile option to func2roi-sess. You can create > a label from a binary mask with mri_cor2label. Spec "--id 1" > > doug > > Emily W

[Freesurfer] roisummary-sess from binary mask

2011-02-08 Thread Emily Ward
Hello, I am trying to get a summary of beta value activation for a hand-drawn binary mask. This mask is a sphere, so it does not correspond to a particular anatomical label or functional contrast. Is there any way to apply roisummary-sess to this type fo binary mask (in nii or mgz format)? If not,

Re: [Freesurfer] Difficulty running FreeSurfer

2010-12-15 Thread Emily Ward
If you're having trouble pasting it in there, try: pico /$FREESURFER_HOME/.license (Press Crt-X to save) If there are permission problems, manually go to the folder info and change permissions at the bottom. On Wed, Dec 15, 2010 at 8:11 PM, Bruce Fischl wrote: > > Hi Nisser, > > put it in a fi

Re: [Freesurfer] beta.nii vs h.nii for beta value extraction

2010-12-10 Thread Emily Ward
file plus nuisance variables. > > doug > > Emily Ward wrote: > >> I want to look at the beta values for all my conditions, voxel-by-voxel >> (in a specific ROI). I have 180 conditions, and am not looking at a >> specific contrast. >> >> When I open th

[Freesurfer] beta.nii vs h.nii for beta value extraction

2010-12-09 Thread Emily Ward
oxel-by-voxel beta values? Thanks, Emily Ward ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If yo