hcp_dedrift_and_resample

qx_utilities.hcp.process_hcp.hcp_dedrift_and_resample(sinfo, options, overwrite=True, thread=0)

hcp_dedrift_and_resample [... processing options]

Runs the DeDriftAndResample step of the HCP Pipeline.

Warning

The code expects the input images to be named and present in the QuNex folder structure. The function will look into folder:

<session id>/hcp/<session id>

for files:

MNINonLinear/Results/<boldname>/
<boldname>_<hcp_cifti_tail>_hp<hcp_highpass>_clean.dtseries.nii

Parameters

--batchfile (str, default ''):

The batch.txt file with all the sessions information.

--sessionsfolder (str, default '.'):

The path to the study/sessions folder, where the imaging data is supposed to go.

--parsessions (int, default 1):

How many sessions to run in parallel.

--hcp_suffix (str, default ''):

Specifies a suffix to the session id if multiple variants are run, empty otherwise.

--logfolder (str, default ''):

The path to the folder where runlogs and comlogs are to be stored, if other than default.

--hcp_icafix_bolds (str, default ''):

List of bolds on which ICAFix was applied, with the same format as for ICAFix. Typically, this should be identical to the list used in the ICAFix run. If multi-run ICAFix was run with two or more groups then HCP MSMAll will be executed over the first specified group (and the scans listed for hcp_msmall_bolds must be limited to scans in the first concatenation group as well). If not provided MSMAll will assume multi-run ICAFix was executed with all bolds bundled together in a single concatenation called fMRI_CONCAT_ALL (i.e., same default behavior as in ICAFix).

--hcp_resample_concatregname (str, default 'MSMAll'):

Output name of the dedrifted registration.

--hcp_resample_regname (str, default '<hcp_msmall_outregname>_2_d40_WRN'):

Registration sphere name.

--hcp_icafix_highpass (int, default detailed below):

Value for the highpass filter, [0] for multi-run HCP ICAFix and [2000] for single-run HCP ICAFix. Should be identical to the value used for ICAFix.

--hcp_hiresmesh (int, default 164):

High resolution mesh node count.

--hcp_lowresmeshes (str, default 32):

Low resolution meshes node count. To provide more values separate them with commas.

--hcp_resample_reg_files (str, default detailed below):

Comma separated paths to the spheres output from the MSMRemoveGroupDrift pipeline [<HCPPIPEDIR>/global/templates/MSMAll/<file1>, <HCPPIPEDIR>/global/templates/MSMAll/<file2>]. Where <file1> is equal to: DeDriftingGroup.L.sphere.DeDriftMSMAll. 164k_fs_LR.surf.gii and <file2> is equal to DeDriftingGroup.R.sphere.DeDriftMSMAll. 164k_fs_LR.surf.gii

--hcp_resample_maps (str, default 'sulc,curvature,corrThickness,thickness'):

Comma separated paths to maps that will have the MSMAll registration applied that are not myelin maps.

--hcp_resample_myelinmaps (str, default 'MyelinMap,SmoothedMyelinMap'):

Comma separated paths to myelin maps.

--hcp_bold_smoothFWHM (int, default 2):

Smoothing FWHM that matches what was used in the fMRISurface pipeline.

--hcp_matlab_mode (str, default default detailed below):

Specifies the Matlab version, can be 'interpreted', 'compiled' or 'octave'. Inside the container 'octave' will be used, outside 'interpreted' is the default.

--hcp_icafix_domotionreg (bool, default detailed below):

Whether to regress motion parameters as part of the cleaning. The default value after a single-run HCP ICAFix is [TRUE], while the default after a multi-run HCP ICAFix is [FALSE].

--hcp_resample_dontfixnames (str, default 'NONE'):

A list of comma separated bolds that will not have HCP ICAFix reapplied to them. Only applicable if single-run ICAFix was used. Generally not recommended.

--hcp_resample_inregname (str, default 'NONE'):

A string to enable multiple fMRI resolutions (e.g._1.6mm).

--hcp_resample_use_ind_mean (str, default 'YES'):

Whether to use the mean of the individual myelin map as the group reference map's mean.

--hcp_resample_extractnames (str, default 'NONE'):

List of bolds and concat names provided in the same format as the hcp_icafix_bolds parameter. Defines which bolds to extract. Exists to enable extraction of a subset of the runs in a multi-run HCP ICAFix group into a new concatenated series.

--hcp_resample_extractextraregnames (str, default 'NONE'):

Extract multi-run HCP ICAFix runs for additional surface registrations, often MSMSulc

--hcp_resample_extractvolume (str, default 'NONE'):

Whether to also extract the specified multi-run HCP ICAFix from the volume data, requires hcp_resample_extractnames to work.

--hcp_msmall_templates (str, default <HCPPIPEDIR>/global/templates/MSMAll):

Path to directory containing MSMAll template files.

--hcp_msmall_myelin_target (str, default 'Q1-Q6_RelatedParcellation210.MyelinMap_BC_MSMAll_2_d41_WRN_DeDrift.32k_fs_LR.dscalar.nii'):

Myelin map target, will use Q1-Q6_RelatedParcellation210.MyelinMap_BC_MSMAll_2_d41_WRN_DeDrift.32k_fs_LR.dscalar.nii by default.

Output files

The results of this step will be populated in the MNINonLinear folder inside the same session's root hcp folder.

Notes

Mapping of QuNex parameters onto HCP Pipelines parameters:

Below is a detailed specification about how QuNex parameters are mapped onto the HCP Pipelines parameters.

hcp_dedrift_and_resample parameter mapping:

QuNex parameter	HCPpipelines parameter
hcp_resample_concatregname	concat-reg-name
hcp_resample_regname	registration-name
hcp_icafix_highpass	high-pass
hcp_hiresmesh	high-res-mesh
hcp_lowresmeshes	low-res-meshes
hcp_resample_reg_files	dedrift-reg-files
hcp_resample_maps	maps
hcp_resample_myelinmaps	myelin-maps
hcp_bold_smoothFWHM	smoothing-fwhm
hcp_matlab_mode	matlab-run-mode
hcp_icafix_domotionreg	motion-regression
hcp_msmall_myelin_target	myelin-target-file
hcp_resample_dontfixnames	dont-fix-names
hcp_resample_inregname	input-reg-name
hcp_resample_extractnames	multirun-fix-extract-names
hcp_resample_extractnames	multirun-fix-extract-concat-names
hcp_resample_extractextraregnames	multirun-fix-extract-extra-regnames
hcp_resample_extractvolume	multirun-fix-extract-volume
hcp_resample_use_ind_mean	use-ind-mean

Examples

HCP DeDriftAndResample after application of single-run ICAFix:

qunex hcp_dedrift_and_resample \
    --batchfile=processing/batch.txt \
    --sessionsfolder=sessions \
    --hcp_icafix_bolds="REST_1,REST_2,TASK_1,TASK_2" \
    --hcp_matlab_mode="interpreted"

HCP DeDriftAndResample after application of multi-run ICAFix:

qunex hcp_dedrift_and_resample \
    --batchfile=processing/batch.txt \
    --sessionsfolder=sessions \
    --hcp_icafix_bolds="GROUP_1:REST_1,REST_2,TASK_1|GROUP_2:REST_3,TASK_2" \
    --hcp_matlab_mode="interpreted"