Re: [Freesurfer] Re: Re: Re: Re: Re: Time Series to Surface

What do I put for the email to send to? freesurfer@nmr.mgh.harvard.edu and freesurfer-boun...@nmr.mgh.harvard.edu said it was not a valid account From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas Greve

Re: [Freesurfer] Re: Re: Re: Re: Time Series to Surface

Can you upload the volume (img and hdr) here: https://gate.nmr.mgh.harvard.edu/filedrop2 On 4/6/18 12:24 PM, Crawford, Anna wrote: 1227 frames Thanks, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu on

Re: [Freesurfer] Re: Re: Re: Re: Time Series to Surface

1227 frames Thanks, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas Greve Sent: Friday, April 6, 2018 12:14 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re:

Re: [Freesurfer] Re: Re: Re: Time Series to Surface

How many frames are in your input file? Eg, if you run mri_info on it? On 4/6/18 12:05 PM, Crawford, Anna wrote: > I just opened freeview and loaded everything in the GUI. I did not use the > command line to open it. I do not see a slider bar. > > Thanks, > Anna >

Re: [Freesurfer] Re: Re: Re: Time Series to Surface

I just opened freeview and loaded everything in the GUI. I did not use the command line to open it. I do not see a slider bar. Thanks, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas Greve

Re: [Freesurfer] Re: Re: Time Series to Surface

what is your freeview command line? Do you see a "frame" slider bar? On 4/6/18 10:46 AM, Crawford, Anna wrote: > I tried without --init-fsl and adding in the --projfrac 0.5 for mri_vol2surf, > but I am still not able to view the time course. > > Thanks, > Anna >

Re: [Freesurfer] Re: Re: Time Series to Surface

I tried without --init-fsl and adding in the --projfrac 0.5 for mri_vol2surf, but I am still not able to view the time course. Thanks, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas Greve

Re: [Freesurfer] FSGD design for multi-centre study

Create a separate class for each combination of diagnosis, sex, and center, then create contrasts that average over center. On 4/6/18 7:11 AM, C.P.E. Rollins wrote: > Dear Freesurfer Developers, > > I'd like to do a standard CT analysis (patients vs. controls, covaried > for age and sex) on

Re: [Freesurfer] Quality of fMRI registration

There is no way to give a hard-and-fast threshold on the quality. 0.5-0.6 is not considered bad. If the registrations look good to you visually then it is fine On 4/5/18 5:43 PM, Arsenije Subotic wrote: Dear experts, When it comes to assessing the quality of fMRI integration in

Re: [Freesurfer] Re: Time Series to Surface

No need to use --init-fsl (if using version 6). For mri_vol2surf add --projfrac 0.5 to sample in the middle of the ribbon  (unless you specifically want to sample on the gray/white border) On 4/6/18 10:11 AM, Crawford, Anna wrote: > Hello, > > I used the following commands and then opened the

Re: [Freesurfer] Re: Time Series to Surface

Hello, I used the following commands and then opened the surface as an overlay on the inflated volume, but I am not about to look at the time series. The view time course is grayed out so that I can not click on it. Did I miss a step or lose the actual time series somewhere? bbregister --s

Re: [Freesurfer] Tracula - Could not find satisfactory control point fit

Hi Desiree - It looks like this is happening for the corticospinal tract. Is there anything going on with that scan in the area of that tract, let's say slices cut off from the top of the motor cortex or from the brainstem? Best, a.y From:

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

Hi Bruce, hi Srishti, I have exactly the same problem with several subjects rerunning recon-all and there was sufficient memory available. I also tried out the last command directly which resulted in the same error log. mri_normalize -f /home/anna/FREESURFER/00_DATA_MABT1T2/02a_MABT1T2_cross_

[Freesurfer] FSGD design for multi-centre study

Dear Freesurfer Developers, I'd like to do a standard CT analysis (patients vs. controls, covaried for age and sex) on data from a multi-centre study and I'm wondering how I should construct my FSGD file to code centre as a dummy variable. Currently, my FSGD looks something like this: