[Freesurfer] slice timing

Hi, I am running a pASL sequence with a TR = 3 sec and TI2 = 1.8. I am wondering when I do slice time correction does that move all slices to the mid of TR that is 1.5 s prior in time or, it moves them to the timing of the mid slice, which would be the mid of image acquisition aorund 0.6 sec prior

[Freesurfer] slice timing

y to make take into account the > fact that the slices are not uniform over the TR. You should contact the > list of the software you are using to get a definative answer. > doug > > > On 03/29/2013 11:37 AM, Meryem Ayse Yucel wrote: > > Hi, > > > > I am running

[Freesurfer] slice timing

y to make take into account the > fact that the slices are not uniform over the TR. You should contact the > list of the software you are using to get a definative answer. > doug > > > On 03/29/2013 11:37 AM, Meryem Ayse Yucel wrote: > > Hi, > > > > I am running

[Freesurfer] preproc-sess

Hi all, I am running: preproc-sess -s sess01 -fsd bold -fwhm 5 -stc up -per-run However at the end it did not create an output like fmcsm. I only have fmc.nii, fmc.up.nii and fmcpr.up.nii. Am I doing something wrong, or these outputs are smoothed too? Thanks, Meryem __

Re: [Freesurfer] preproc-sess

> Hi Doug, > > This is the terminal output. The output volumes don't seem to be smoothed. > > preproc-sess -s 8003 -fsd bold -stc up -fwhm 5 -per-run > -- > preproc-sess logfile is log/preproc-sess.8003.log > -

[Freesurfer] head surface

Hi freesurfer community, I am trying to get faces and vertices of the head surface mesh in Matlab. freesurfer_read_surf works perfectly when I extract faces and vertices for the pial surface (from lh.pial), but I get an "unknown magic number in surface file" error when I use the same function for

[Freesurfer] head surface

Hi Doug, I used mkheadsurf function. Meryem ___ 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 addresse

[Freesurfer] head surface

Sorry about that, here is the whole correspondance: Hi Doug, I used mkheadsurf function. Meryem Hi freesurfer community, I am trying to get faces and vertices of the head surface mesh in Matlab. freesurfer_read_surf works perfectly when I extract faces and vertices for the pial surface (from

[Freesurfer] (no subject)

Hi, I am trying to use selxavg3-sess function and getting this error. Below is the error I get. I actually have this fingertap.par file but freesurfer somehow does not see it. Any help would be appreciated. Thanks! Meryem Yucel PMI Lab Extension format = nii.gz ERROR: opening /autofs/space/m

Re: [Freesurfer] (no subject)

Hi, Now it seems to be working with the par file but I am getting this error. Any help will be appreciated. Thanks, Meryem Computing compensation for resdual AR1 bias 1 -0.5 -0.473129(t=0.192235) 2 -0.25 -0.238292(t=1.09283) 3 0 -0.00411884(t=1.27811) 4 0.25 0.228971

Re: [Freesurfer] (no subject)

g again. The above mkbrainmask command tells it to only > erode the mask by one voxel (the default in preproc-sess is 3 which is > removing all of them). > > doug > > > > Meryem Ayse Yucel wrote: >> Hi, >> >> Now it seems to be working with the par file but I am