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:
GroupDesc
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_
ed
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: freesurfer-boun...@n
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 S2s
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 s
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
Freesurfer
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 data
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
Sent: Friday, April 6, 2018 10:21 AM
To:
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
> _
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
Sent: Friday, April 6, 2018 11:54 AM
To:
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
> ___
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: [Freesurfer] Re: Re: Re: Time Series to Surface
How many frames
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 behalf of Douglas Greve
Sent: Friday, April 6
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
Sent: Friday, April 6, 2018 12:44 PM
To: f
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