Re: [Freesurfer] mris_divide_parcellation replication

come to grab it and > take a look > > On Mon, 3 Feb 2014, Martin Luessi wrote: > >> I'm wondering about this as well. It would be great if someone who is >> familiar with the FreeSurfer code could explain the split algorithm. >> >> Best, >> >

Re: [Freesurfer] mris_divide_parcellation replication

I'm wondering about this as well. It would be great if someone who is familiar with the FreeSurfer code could explain the split algorithm. Best, Martin On 01/29/14 14:36, Christian Brodbeck wrote: > Dear Freesurfer developers, > > I am trying to replicate mris_divide_parcellation for mne-pytho

Re: [Freesurfer] convert FSL .mat matrix to TkReg-RAS space

er2 --mov flirtinputvol --targ flirtrefvol --fsl flirt.mtx --reg > register.dat > > > > > On 12/19/2013 01:33 PM, Martin Luessi wrote: >> Hi, >> >> I'm using FSL's mcflirt for motion correction with the "-mats" option to >> store a r

[Freesurfer] convert FSL .mat matrix to TkReg-RAS space

Hi, I'm using FSL's mcflirt for motion correction with the "-mats" option to store a registration matrix for each time point. In my application, I would like to use a one-step interpolation process to sample points from the freesurfer surfaces (e.g. white) from the 4D fMRI data. I tried to conver

Re: [Freesurfer] mris_fix_topology hangs (?)

artin On 11/07/13 11:17, Bruce Fischl wrote: > Hi Martin > > see my response to a similar question just a minute or two ago. This is > the same issue (a defect that is too big) > > cheers > Bruce > On Thu, 7 Nov 2013, Martin Luessi wrote: > >> Hi, >> >>

[Freesurfer] mris_fix_topology hangs (?)

Hi, I'm running recon-all on a subject from the human connectome project, and for some reason "mris_fix_topology" seems to be hanging, or at least it has been using 100% of a CPU for more than 24h with no new output. Is this normal or is there a way to fix this problem? Best, Martin PS: I'm

Re: [Freesurfer] Extract voxel time series from subcortical segmentation (without averaging)

hub.com/nipy/nipype/blob/master/examples/rsfmri_preprocessing.py#L219 > > cheers, > > satra > > > On Tue, Nov 5, 2013 at 5:30 PM, Martin Luessi > mailto:mlue...@nmr.mgh.harvard.edu>> wrote: > > Hi, > > I have fMRI data which has been co-registered wi

Re: [Freesurfer] Extract voxel time series from subcortical segmentation (without averaging)

> funcroi will be the ntimepoints by nroivoxels matrix that you are > looking for > > doug > > > On 11/05/2013 05:30 PM, Martin Luessi wrote: >> Hi, >> >> I have fMRI data which has been co-registered with the FS reconstruction >> using "bbregister&q

[Freesurfer] Extract voxel time series from subcortical segmentation (without averaging)

Hi, I have fMRI data which has been co-registered with the FS reconstruction using "bbregister". I would like to extract the voxel time series for the voxels in the subcortical labels from the "aseg" subcortical segmentation. I know that "mri_segstats" can be used with the "--avgwf" option to

Re: [Freesurfer] RAS coordinates in tksurfer and matlab

>> Alfred 9-441C, SMH >> 1216 Second St. SW >> Rochester, MN 55902 >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/lis

Re: [Freesurfer] How can I get 300 dpi resolution or about when saving tiff files in tksurfer?

t;> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > > > ___