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.

--log (str, default 'keep'):

Whether to keep ('keep') or remove ('remove') the temporary logs once jobs are completed. When a comma or pipe ('|') separated list is given, the log will be created at the first provided location and then linked or copied to other locations. The valid locations are:

'study' (for the default: <study>/processing/logs/comlogs location)
'session' (for <sessionid>/logs/comlogs)
'hcp' (for <hcp_folder>/logs/comlogs)
'<path>' (for an arbitrary directory).

--hcp_icafix_bolds (str, default detailed below):

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 [same default as for hcp_icafix and hcp_msmall].

--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 'compiled'):

Specifies the Matlab version, can be: - 'interpreted' - 'compiled' or - 'octave'.

--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

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"

QuNex documentation

hcp_dedrift_and_resample

hcp_dedrift_and_resample#