External Email - Use Caution
It might be easier to use the HCP’s TaskAnalysis Pipeline (of which there will
be a new version in the master development branch shortly that has improvements
for the HCP Lifespan projects), as that is designed to work directly with the
other outputs of the HCP Pipeline. It is correct that we recommend starting
from the cleaned and MSMAll aligned functional MRI data:
${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_MSMAll_hp0_clean.dtseries.nii
It would be nice to support fsfast also as it is a surface-based approach, but
I don’t personally have any experience with fsfast. Thus far, the FSL
developers have been most engaged in supporting CIFTI with their tools (and the
HCP’s task analysis pipeline is based on FSL’s FEAT), but I would be happy to
work with the FreeSurfer developers to figure out the best way for users to
process CIFTI data with fsfast if there is a mutual interest in this.
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 11:39 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Analysing HCP Data in freesurfer
External Email - Use Caution
I am trying to analyse the HCP-Aging vismotor task fMRI
data<https://secure-web.cisco.com/1Z30FmBulf3wPk8ZI1piszdCtNxfv_oM8hAju_21Q2rqxpYuGRsbRPC84dN3sp47oBdJLeOU7T9szqn8hcIkH4BhLhOBGhJvd5XLqntcuUFtPaWurM0LgbDUCjvps3yPQB_EvdAfv_Ao-NgAp8KZNUYyv4AybUV5-WXbC3PjGeQIaj7FgDLIVaKTIx1Snw558T4Vnz72IWqJurISu__OS0h5zc-uKdjgeB4bPhvloeUMkY57oe6VxBLQ93zhlWAyKpxdlrKxLcu1BnxApRJa6kA/https%3A%2F%2Fwww.humanconnectome.org%2Fstudy%2Fhcp-lifespan-aging%2Fproject-protocol%2Ftask-protocols-hcp-aging>
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
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
External Email - Use Caution
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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Poortata Shirish Lalwani
<poort...@umich.edu<mailto:poort...@umich.edu>>
Reply-To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, July 29, 2021 at 10:23 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto: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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