Re: [Freesurfer] shift to account for hemodynamic response

Thank you so much. On Fri, Feb 9, 2018 at 11:48 AM, Douglas Greve wrote: > It is already built into the HRF model. If you need to shift them more or > less than what is in the model, that can be accommodated. If you use the > -spmhrf option, then you will get the same

[Freesurfer] V1 functional ROI

Dear Dr. Douge, I am a little bit confused about creating function ROI in V1. Basically, I have some localizers that for some ROIs I need to find activated neurons in a specific contrast in native space and then create that ROI and map it to my experimental scans and extract their voxel data. I

[Freesurfer] FIR analysis

Hi experts, I was wondering if there is any tutorial or example on FIR analysis. I don't know where to start. I need to look at the time course of some voxels. I have a localizer session and the main experiment. I am intending to find the ROIs in the localizer scans and then extract their time

[Freesurfer] Goodness of fit

Hi Doug, I have used spmhrf 0 in my FS-FAST analysis. I was wondering if there is any way to check the variance explained and fits on the model? Thank you, -S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Goodness of fit

> > On 02/20/2018 12:07 PM, Sarah Cole wrote: > > Hi Doug, > > > > > > I have used spmhrf 0 in my FS-FAST analysis. I was wondering if there > > is any way to check the variance explained an

[Freesurfer] Creating ROI on the functional map

Hi, I was wondering if this method is still applicable in version 6 https://surfer.nmr.mgh.harvard.edu/fswiki/CreatingROIs I cannot seem to find any of the options for creating an ROI. Thank you, S ___ Freesurfer mailing list

[Freesurfer] Percent Signal Change

Hi, Could someone please let me know how to get the percent signal change for raw signal intensity? I think the cespct.nii.gz gives me the contrast as %. However, I am not sure about dividing h.nii and h-offset.nii. What are they? Thank you ___

Re: [Freesurfer] Percent Signal Change

coefficients) that > is included for backwards compatibility. What do you mean by % signal > change? Do you want the raw waveform as a percent? > > > On 02/15/2018 01:52 PM, Sarah Cole wrote: > > Thank you, Doug. > > > > Sorry for not being clear. Could you please

Re: [Freesurfer] Percent Signal Change

N Greve <gr...@nmr.mgh.harvard.edu > wrote: > It divides the contast (ces) by voxel-wise mean. I'm not sure I > understand your quesstion about h and h-offset > > > On 02/15/2018 01:04 PM, Sarah Cole wrote: > > Hi, > > > > Could someone please let me kn

[Freesurfer] key nSliceGroups unrecognized, line 11, skipping

External Email - Use Caution Hi, I know this is not an error but just a comment. But may I know what this means: "*key nSliceGroups unrecognized, line 11, skipping"* I tried to look for line 11 in matlab scripts but they are mainly commented out. Thank you, Sara

[Freesurfer] Fwd: Freeview update on Mac

, Sarah On Tue, Feb 27, 2018 at 11:40 AM, Hoopes, Andrew <ahoo...@mgh.harvard.edu> wrote: > Hi Sarah, I updated the wiki page. We actually just put up a standalone, > dev freeview app today. > > best > Andrew > > > On February 27, 2018 at 11:38:57 AM, Sarah Cole (coleashle

[Freesurfer] Freeview update on Mac

Hi Doug/Zeke, Could you please update the page for freeview update on Mac- if it is available. https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Thanks, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Creating ROI on the functional map

I apologize. I was wrong. Thanks, S On Mon, Feb 26, 2018 at 5:16 PM, Sarah Cole <coleashle...@gmail.com> wrote: > It doesn't work on tksurfer. But it's ok. > > So Doug, is this the latest tutorial: https://surfer.nmr.mgh. > harvard.edu/fswiki/FsTutorial/MultiModalFmriI

Re: [Freesurfer] Canonical HRF shape generated by FSFAST

Just one clarification, this is for first level analysis (individual subjects). Thanks On Wed, Apr 11, 2018 at 9:54 AM, Sarah Cole <coleashle...@gmail.com> wrote: > Hi Doug, > > At the end of my FSFAST analysis, I would like to plot the Canonical HRF > shape generated by FSFAS

[Freesurfer] Canonical HRF shape generated by FSFAST

Hi Doug, At the end of my FSFAST analysis, I would like to plot the Canonical HRF shape generated by FSFAST for my events. I have found this thread: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-July/031902.html but I am not sure if I understand this line:

[Freesurfer] FSFAST, Beta values and Percent Signal Change questions

Hi Doug, I need your recommendations on two topics. I really appreciate your help. 1.) I have two runs of the same experiment, each for about 12 minutes. These 2 runs are different only in the presentation order of the stimuli. I also have one localizer session which first, I calculated my

Re: [Freesurfer] Hemodynamic Lag Shift

ing to do. can you send a picture? the default > lag is TR/2 > > On 3/29/18 2:30 PM, Sarah Cole wrote: > > Thanks, Doug. > > I added (-4s) delay and plotted the data but I got the same delay as no > shift. Also I did (+4) delay and lost most of the activation. > > Do y

[Freesurfer] Hemodynamic Lag Shift

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] Hemodynamic Lag Shift

u 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

Re: [Freesurfer] Percent Signal Change

rite(s,'percentchange.nii.gz') > > > > On 02/15/2018 02:03 PM, Sarah Cole wrote: > > Yes, that's exactly what I am looking for. Raw waveform as a percent. > > > > On Thu, Feb 15, 2018 at 1:00 PM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr

Re: [Freesurfer] Hemodynamic Lag Shift

Please ignore my previous post. I was wrong on so many levels! Thanks S On Fri, Mar 30, 2018 at 8:34 AM, Sarah Cole <coleashle...@gmail.com> wrote: > Hi Doug, > > Sure. I have attached an excel sheet. > I have averaged the signal magnitude across 16 blocks of objects, and 16

Re: [Freesurfer] Creating ROI on the functional map

w > instead), but I think it should still work > > > On 02/23/2018 05:16 PM, Sarah Cole wrote: > > Hi, > > > > I was wondering if this method is still applicable in version 6 > > https://surfer.nmr.mgh.harvard.edu/fswiki/CreatingROIs > > > > > > I