External Email - Use Caution
Like I said before, the HCP has a task analysis pipeline written specifically
for CIFTI (and FSL also has CIFTI enabled tools).
https://secure-web.cisco.com/16-PqNZ69sCQhtOyBAv6e4grcj8m_fit1m4rcGKVXpOrLNVugaZo3icg0pLBSV4wtun0b4kmIikMHHHnTTJ7vO1EHem-hIoujNWBxSlJ30hgliCDTAjse7ynaaSJ0_zENeFeTnpx1U5M0vk6Vm5vHlw-UWhHaveKjv14mj99lDc67AKfXabxEuoywh3rH3XnOo8WQm_7IHtXEEeGL8raiZ76ZsLZUfbL_j1-ulO04Mzaqf3cqMwu-W8VswfCB7FzwP3a9VSoY0ToeI_pWG6_m6g/https%3A%2F%2Fgithub.com%2FWashington-University%2FHCPpipelines%2Ftree%2Fmaster%2FTaskfMRIAnalysis
We will be merging in a new version in the next few days.
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: Friday, July 30, 2021 at 7:43 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Analysing HCP Data in freesurfer
External Email - Use Caution
I wanted to perform event related analysis of the task fmri data but create my
own design file for the analysis. Also I do prefer to do it in surface space.
I have been able to use FSL for task fmri analysis on the unprocessed raw
volume file and run event related analysis on the HCP young dataset by
modifying the HCP pipeline. But wasn't able to find a straight forward way to
do so with HCP lifespan dataset using the recommended aligned files. FSL can't
open the dtseries.nii file so I am guessing it needs something else? If you can
share the code that can do glm fitting and cope estimation in surface space for
the lifespan data (assuming I just didn't locate it right), that would be
immensely helpful.
Relatedly, my understanding is that this should be straightforward even in
freesurfer since it is simple glm fitting. I figured all the necessary files
are already created for the HCP data and it is just a matter of renaming files
and modifying the directory structure in a way Freesurfer prefers. But maybe
not? I am not sure what files the smoothing function is looking for. I do think
it would be really useful for many other users to be able to work with HCP data
in freesurfer. Thanks for your help in doing this.
Best,
Pia
On Thu, Jul 29, 2021, 11:48 AM Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
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<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 11:39 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto: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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