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I’m not sure anyone has tried this yet. Which data are you trying to analyze?
I cannot tell from the below what type of data this is.
Matt.
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Poortata Shirish
Lalwani <poort...@umich.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, July 29, 2021 at 10:23 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Analysing HCP Data in freesurfer
External Email - Use Caution
Hello,
I am trying to use fsfast to perform 1st level GLM analysis on preprocessed
data from the HCP-Aging dataset which happens to be in a different space than
fsaverage. I followed the following steps:
First I smoothed the data which was in dtseries format
wb_command -cifti-smoothing *dtseries.nii 1.27 1.27 COLUMN f.sm3.dtseries.nii
-left-surface *L.midthickness_MSMAll.32k_fs_LR.surf.gii -right-surface
*R.midthickness_MSMAll.32k_fs_LR.surf.gii
Then extracted the left/right surface and volume
wb_command -cifti-separate f.sm3.dtseries.nii COLUMN -metric CORTEX_LEFT
f.L.func.gii -metric CORTEX_RIGHT f.R.func.gii -volume-all f.mni152.nii
Followed by creating a mask for the subcortical analysis
mri_binarize --i Atlas_ROIs.2.nii.gz --match 8 10 11 12 13 16
17 18 26 28 47 49 50 51 52 53 54 58 60 --o
subcortmask.nii.gz;
and creating a global mean .dat file.
wb_command -cifti-stats f.sm3.dtseries.nii -reduce MEAN > global.waveform.dat
Then I tried to run GLM analysis using FSFast. The subcortical analysis
completes without errors, but I am having trouble with the surfaces.
Surprisingly, the error seems to be at the Smoothing ACF step because it is
trying to perform it on volume even though I have specified that the analysis
should be in surface space. Attached are the selx3 log file and analysis info
file. Is there something with the analysis specification or in earlier
conversion steps? I would appreciate any help with this.
Thank you
Best,
Pia
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