How was the nii created? Ie, how did it go from dicom to nii?
On 5/4/2020 1:56 PM, Peled, Noam wrote:
We are running a pilot, to try to analyze their epileptic monitoring
unit datasets using the Martinos tools (FreeSurfer and MNE)
The analysis was on an fMRI nii file, which I checked before running
fsFast, and it was LSA.
I wouldn’t suspect anything is wrong unless I knew how the results
should look like
Thanks,
Noam
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Douglas N. Greve
*Sent:* Monday, May 4, 2020 1:48 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] recon-all and fMRI coordinates mismatch
I'd need a lot more details. Where they using FreeSurfer? Sometimes
the data will go through several conversions and formats before
analysis. If the orientation info was lost or changed, then that could
explain it
On 5/4/2020 1:22 PM, Peled, Noam wrote:
Thanks Doug!
Good to know that.
I realized I had a problem when I got activation on the wrong side
(right finger tapping shows activation on the right hemisphere)
The analysis was done in another hospital when I just helped them
remotely. They told me that their analysis software shows the
activation is in the other hemisphere.
Any idea why something like that can happen?
Thanks,
Noam
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of
*Douglas N. Greve
*Sent:* Monday, May 4, 2020 1:03 PM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] recon-all and fMRI coordinates mismatch
The actual orientation of the input should not matter as long as
the nominal orientation matches the true orientation -- FS
automatically handles the orientation correctly. When you ask
whether the output will be "in RAS", are you asking whether the
left side is truly the left (and right is right)? If so, the
answer is yes.
On 5/4/2020 12:50 PM, Peled, Noam wrote:
Hello,
After running recon-all on a patient, the resulting T1.mgz
coordinates system turned to be LIA. Can I guarantee the
recon-all output will be in RAS?
I also would like to run FS-FAST on this patient’s fMRI task
dataset, which is in LSA.
Any recommendation what should I do to make sure both are in
the same coordinates system (I preferred RAS)?
Thanks,
Noam
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