I have used that before and it seems to work. What version are you/they using? I remember this kind of problem years ago when FSFAST was using SPM to initialize the registration; at some point SPM changed the interpretation of the coordinates which caused a left-right reversal.
On 5/4/2020 3:25 PM, Peled, Noam wrote:
They are using dcm2niix of MRIcroGL
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Douglas N. Greve *Sent:* Monday, May 4, 2020 2:11 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] recon-all and fMRI coordinates mismatch
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-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Douglas N. Greve *Sent:* Monday, May 4, 2020 1:48 PM *To:* freesurfer@nmr.mgh.harvard.edu <mailto: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-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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