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Hello FreeSurfer Experts,
Now I have a custom annotation file (only the cortical surface). May I ask how could I use it to extract the mean time series from the fsfast-preprocessed fMRI data? I have tried to transform this annotation file into anatomical volume first:
mri_aparc2aseg --s fsaverage --annot test --o test.mgz
It seems I cannot do it to the left and right surface respectively, right? How should use this .mgz file next? Any suggestions would be appreciated.
Best wishes,
Zhi Li
On 12/03/2018 03:14 PM, Zhi Li wrote:
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Hello FreeSurfer Experts,
Now I have a custom annotation file (only the cortical surface). May I ask how could I use it to extract the mean time series from the fsfast-preprocessed fMRI data? I have tried to transform this annotation file into anatomical volume first:
mri_aparc2aseg --s fsaverage --annot test --o test.mgz
It seems I cannot do it to the left and right surface respectively, right?
I'm not sure what you mean. It should do both left and right to create a single output file with both hemis.
How should use this .mgz file next? Any suggestions would be appreciated.
When running fcseed-config, specify --seg test.mgz and then select the segmentation id (--segid) that you want to use
Best wishes,
Zhi Li
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thank you for your kind reply. Sorry for the confusing question. Now I have an annotation file in fsaverage space. And I want to extracted mean time series from each roi in this annotation file from preprocessed fMRI data, e.g. fmc.odd.sm5.fsaverage.lh.nii.gz. I think the fcseed-config and fcseed-sess works when I input the volume data such as fmc.odd.nii.gz, namely in the individual space. I have tried transform this annotation file to the individual segmentation file, however, the segmentation was wrong for each roi. May I ask if it is available to extract time series from the surface data with the custom annotation file in the fsaverage space? I am not clear if I could use mri_segstats to achieve this, I found a example of this command in individual space "mri_segstats --seg aseg-in-func.img --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --excludeid 0 --i func.img --mask spmT.img --maskthresh 2.3 --sum bert.aseg-in-func.sum --avgwf bert.avgwf.dat --avgwfvol bert.avgwf.img". How could I apply it into the surface data? Any suggestions would be appreciated.
Best wishes,
Zhi
The easiest thing would be to run mri_segstats --annot subject lh yourannot --excludeid 0 --i fmc.odd.sm5.fsaverage.lh.nii.gz --avgwf avgwf.dat
avgwf.dat will have a row for each fmri time point and a column for each parcellation
On 12/06/2018 01:45 PM, Zhi Li wrote:
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Thank you for your kind reply. Sorry for the confusing question. Now I have an annotation file in fsaverage space. And I want to extracted mean time series from each roi in this annotation file from preprocessed fMRI data, e.g. fmc.odd.sm5.fsaverage.lh.nii.gz. I think the fcseed-config and fcseed-sess works when I input the volume data such as fmc.odd.nii.gz, namely in the individual space. I have tried transform this annotation file to the individual segmentation file, however, the segmentation was wrong for each roi. May I ask if it is available to extract time series from the surface data with the custom annotation file in the fsaverage space? I am not clear if I could use mri_segstats to achieve this, I found a example of this command in individual space "mri_segstats --seg aseg-in-func.img --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --excludeid 0 --i func.img --mask spmT.img --maskthresh 2.3 --sum bert.aseg-in-func.sum --avgwf bert.avgwf.dat --avgwfvol bert.avgwf.img". How could I apply it into the surface data? Any suggestions would be appreciated.
Best wishes,
Zhi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thank you very much, Douglas. It works now. How could I know the ROI index of each column in the .dat file? And if it is available to use pca during extracting time series as fcseed-config?
Best,
Zhi
On 12/06/2018 02:07 PM, Zhi Li wrote:
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Thank you very much, Douglas. It works now. How could I know the ROI index of each column in the .dat file?
If you add --sum sum.dat, the sum file will tell you the order
And if it is available to use pca during extracting time series as fcseed-config?
Not from mri_segstats. If that is the route you really want to go, then you will have to either program it yourself, or transfer the annot to each subject (mris_apply_reg), then transfer it to the volume (mri_aparc2aseg), then run fcseed-config specifying that output and the segmentation number you want
Best,
Zhi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Greve, Douglas N.,Ph.D. -
Zhi Li