Re: [Freesurfer] Hemodynamic Lag Shift

2018-03-28 Thread Douglas N. Greve
You can use the -delay flag in mkanalysis-sess doug On 03/28/2018 05:35 PM, Sarah Cole wrote: > Hi Doug, > > I have a block design experiment. After analyzing the data and > plotting the response magnitude across the TRs, we see that there is a > systematic lag in the response. For example,

[Freesurfer] Hemodynamic Lag Shift

2018-03-28 Thread Sarah Cole
Hi Doug, I have a block design experiment. After analyzing the data and plotting the response magnitude across the TRs, we see that there is a systematic lag in the response. For example, in a 16s block (TR=2s), at TR-1 and TR-2 the response goes down and then starts rising from TR-3. This is

Re: [Freesurfer] Brain volumetry: vessels

2018-03-28 Thread Douglas N. Greve
It is not so specific. It is really just a marker for very dark voxels usually in subcortical gray On 03/28/2018 02:32 AM, Patrik Krumpolec wrote: > Good morning! > I want to ask what type of brain vessels include structure "vessel" > (left and right) in result stats file from brain volumetry

Re: [Freesurfer] LME univariate data

2018-03-28 Thread Diers, Kersten /DZNE
Hi  sorry for the delayed response, I was not able to reply during the last week. You are right that the F-test provided in the LME toolbox initially does not provide information about the direction of the effects. You could do the following: First, it is always useful to plot the data to get

Re: [Freesurfer] convert labels to volume in MNI?

2018-03-28 Thread Douglas N. Greve
what is your freeview command line? In the mri_label2vol command below, where does the label come from? On 03/28/2018 01:11 PM, gj wrote: > Hi, > > I loaded the 2mm MNI152 template and the mri_label2vol outputs in > mricron, and I saw that the labels are completely outside the template. > So, I

Re: [Freesurfer] Information on FS-FAST

2018-03-28 Thread Douglas N. Greve
I'm not entire sure what you are asking. We do not have actual segmentations for 601-628. You can do FC in FSFAST, see http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough On 03/28/2018 12:54 PM, Piero Chiacchiaretta wrote: > > Hi list, > > > 601-628 labels in

Re: [Freesurfer] convert labels to volume in MNI?

2018-03-28 Thread gj
Hi, I loaded the 2mm MNI152 template and the mri_label2vol outputs in mricron, and I saw that the labels are completely outside the template. So, I know now to use freeview rather than the deprecated tkmedit so I can also load the original atlas labels to check against (using the 2mm MNI152

[Freesurfer] Information on FS-FAST

2018-03-28 Thread Piero Chiacchiaretta
Hi list, 601-628 labels in FreeSurferColorLUT or labels obtained by Buckner’s parcellation could be used in FS-Fast to assess the FC of each subfield? The labels should be spatially registrated in a specific space before to procede with FS-FAST? Thanks in advance, Piero Piero

[Freesurfer] Brain volumetry: vessels

2018-03-28 Thread Patrik Krumpolec
Good morning! I want to ask what type of brain vessels include structure "vessel" (left and right) in result stats file from brain volumetry measurement by freesurfer: artery, vein or booth? Thank You very much! patrik krumpolec ___ Freesurfer mailing