Re: [Freesurfer] Preprocessing functional MRI

I dont see an obvious way but I dont use this tool often. You may want to create a new post and ask others.

-Zeke

On 04/26/2016 06:01 PM, Martin Juneja wrote:

Hi Zeke,

Thank you so much ! It's working really well now. I have one more question- is there any way I can display labels (name of the areas) as well on the maps I see (using tksurfer command you suggested).

Thanks Zeke once again.

On Tue, Apr 26, 2016 at 4:44 PM, Z K <zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu> wrote:

The "freadFloat: fread failed" is a warning, not an error, and can be
ignored.

The ces.nii.gz, cesvar.nii.gz, sig.nii.gz files are surface overlays
stored in a "volume" format, so they have to be viewed on the surface.
You can do with this with something like:

    $> tksurferfv fsaverage lh inflated -ov sig.nii.gz -fminmax 2 3

-Zeke


On 04/26/2016 04:07 PM, Martin Juneja wrote:
> Hello again,
>
> Somehow I figured out the error I had related to *.config. Now I am able
> to run successfully all the 8 steps for 1 subject. I can see all the
> files generated in a new folder i.e. ces.nii.gz, cesvar.nii.gz,
> sig.nii.gz etc.
> But when I try to display any of these files using FreeView (after
> overlaying over inflated surface), it doesn't display anything and gives
> me error "freadFloat: fread failed".
>
> I would really appreciate any suggestions how can I display functional
> connectivity maps?
>
> Thanks,
> MJ
>
> On Tue, Apr 26, 2016 at 10:53 AM, Martin Juneja <mj70481@gmail.com <mailto:mj70481@gmail.com>
> <mailto:mj70481@gmail.com <mailto:mj70481@gmail.com>>> wrote:
>
>     Hello everyone,
>
>     I am following this page to process fMRI data:
>http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
>
>     I am able to run until step-3 but at step 4, I am not sure what
>     should be directory to run this command. If I run the command in
>     SUBJECTS_DIR directory, it runs for a second and creates a
>     mean*.config file. But next step 5 requires *.config file to run,
>     not the mean*.config
>
>     Just a quick background:
>     I preprocessed all subjects structural data using recon-all and the
>     processed folders are in my FreeSurfer SUBJECTS_DIR path and the
>     folder after preprocessing functional data (after running step-3) is
>     also in SUBJECTS_DIR path.
>
>     Any help would be greatly appreciated.
>
>     MJ
>
>
>
>
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