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I am trying to analyse the HCP-Aging vismotor task fMRI data with an event-based design. The provided file is dtseries.nii format and is the recommended starting point for tfMRI analyses by HCP-Aging. The cleaned file is precisely aligned across subjects using the MSMAll multimodal surface registration and is created applying GenericfMRIVolumeProcessingPipeline, GenericfMRISurfaceProcessingPipeline, hcp_fix_multi_run, and MSMAllPipeline. I was hoping to simply run GLM analysis on this file in fsfast but I am not sure which files the smoothing function is searching for since it is surface-based analysis.

On Thu, Jul 29, 2021 at 10:29 AM Glasser, Matthew <glasserm@wustl.edu> wrote:

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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-bounces@nmr.mgh.harvard.edu> on behalf of Poortata Shirish Lalwani <poortata@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

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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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