Data Processing - Revision history

Huawu at 21:23, 11 February 2026

2026-02-11T21:23:12Z

← Older revision		Revision as of 21:23, 11 February 2026
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	Most data processing is done in individual laboratories and tailored to specific data sets. There are certain general processing methods that are provided by the CNI staff. These methods are intended to improve the quality of specific data acquired with certain protocols (EPI, Spiral, Diffusion) within the CNI facility. This [[Data Processing]] page first defines these CNI-specific methods. This is followed by links to external sites either at Stanford or elsewhere that offer software for processing MRI and EEG data.		Most data processing is done in individual laboratories and tailored to specific data sets. There are certain general processing methods that are provided by the CNI staff. These methods are intended to improve the quality of specific data acquired with certain protocols (EPI, Spiral, Diffusion) within the CNI facility. This [[Data Processing]] page first defines these CNI-specific methods. This is followed by links to external sites either at Stanford or elsewhere that offer software for processing MRI and EEG data.

	~~= CNI Data Information =~~

	~~== Gradient-echo EPI ==~~
	~~Many labs at CNI use a gradient-echo EPI sequence for BOLD fMRI imaging. This sequence is a modified version of the stock EPI sequence provided by GE. Some useful information about this sequence:~~
	* The name of the custom PSD is '''cni_epi'''.
	* Slice order: The slices are acquired interleaved by default, with odd slices first, then even slices. Be sure to take this into account when doing slice timing correction. You can use the "TriggerTime" field in the DICOM head to confirm the slice acquisition timing. Also note that the time points at which slices are acquired are equally spaced within the TR.
	* Triggering: There is a UserCV to control the acquisition trigger. You can have no special triggering (scan starts when you hit 'Scan'), external trigger to start the scan (see [[MR Hardware#Scan Triggers]] for details), or cardiac gating.
	* Image reconstruction size: By default, the images are reconstructed at the native image size instead of being zero-padded up to the next higher power of two. This results in faster recons, smaller files, and no image interpolation, so it is generally preferred. But, if you want power-of-two image sizes, you can change this UserCV to get that behavior.
	* Phase encoding gradient: To use FSL's TOPUP for EPI distortion correction, you need to acquire a pair of EPI scans with the same prescription except for the reversed phase encoding gradient polarity. There is a UserCV to control the PE polarity (called "pepolar" in GE's term). In most common cases, the phase encoding gradient is along AP/PA direction, and when pepolar = 0, the encoding goes from posterior to anterior ("j" in BIDS convension), and when pepolar = 1, the encoding goes from anterior to posterior ("j-" in BIDS convension).

	~~== Spiral ==~~

	~~== Arterial-Spin Labeling (ASL) ==~~
	Sequence: The newest ASL sequence from GE is a pseudo-continuous sequence called 3DASL. By default it is set to create a Cerebral Bloodflow (CBF) volume as a post-processing task (reported in ml/100gm/min). Separate from post-processing, the sequence produces 2 volumes, a perfusion-weighted (PW) volume and a PD volume. The PW volume is created from subtracting the tagged volume from the control volume during the scan sequence.

	~~'''ASL-specific considerations''':~~
	* ''Post-Label Delay (PLD)'': default is 2025ms
	** This should be edited to reflect population being studied. Populations with faster heart rates (such as children) should have a shorter post-label delay (e.g. healthy teens can be successfully scanned at 1525ms)
	** PLD is saved as inversion time (TI) in the dicom headers
	* ''Labeling time (LT)'': default is 1450ms
	* ''Slice thickness'': default is 4mm
	** minimum is 2mm
	* ''Spiral arms'': default is 8
	** This is most significant means of adjusting spatial resolution. More arms = better spatial resolution in each slice.
	* ''Prescription'': The inferior edge of the prescription box must align with the base of the cerebellum. This ensure the labeling plane (which is just inferior to the prescription box) is aligned to tag the blood passing through the carotid arteries in the neck before entering the brain.
	** It is very important that the subject's head is aligned straight in the scanner. Tilting can result in poor labeling or artifacts in the PW volume (and subsequently the CBF volume).

	~~'''Processing ASL Data''':~~
	Analyses can be conducted on the CBF volume or on the PW volume. The CBF volume already has CBF quantified (naturally) based on the below information. This volume can be spatially normalized and analyzed in a similar way as processed fMRI data.

	* Homogeneous blood/brain partition coefficient for water is 0.9 ml/g
	* Labeling inversion efficiency is 80% for a 3T scanner
	* T1 of blood is 1.6s at a 3T scanner
	* Saturation time is 2s
	* Overall efficiency is 0.6
	* The PD volume is used as a reference image

	~~Alternatively, you can quantify CBF yourself from the PW volume if you'd like to use different parameters or would like to perform additional spatial/intensity corrections before CBF quantification.~~

	~~== Diffusion Imaging ==~~

	= CNI Data processing =		= CNI Data processing =

Huawu: /* Gradient-echo EPI */

2026-02-11T20:33:46Z

Gradient-echo EPI

← Older revision		Revision as of 20:33, 11 February 2026
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	== Gradient-echo EPI ==		== Gradient-echo EPI ==
	Many labs at CNI use a gradient-echo EPI sequence for BOLD fMRI imaging. This sequence is a modified version of the stock EPI sequence provided by GE. Some useful information about ~~his~~ sequence:		Many labs at CNI use a gradient-echo EPI sequence for BOLD fMRI imaging. This sequence is a modified version of the stock EPI sequence provided by GE. Some useful information about this sequence:
	* The name of the custom PSD is '''cni_epi'''.		* The name of the custom PSD is '''cni_epi'''.
	* Slice order: The slices are acquired interleaved by default, with odd slices first, then even slices. Be sure to take this into account when doing slice timing correction. You can use the "TriggerTime" field in the DICOM head to confirm the slice acquisition timing. Also note that the time points at which slices are acquired are equally spaced within the TR.		* Slice order: The slices are acquired interleaved by default, with odd slices first, then even slices. Be sure to take this into account when doing slice timing correction. You can use the "TriggerTime" field in the DICOM head to confirm the slice acquisition timing. Also note that the time points at which slices are acquired are equally spaced within the TR.
	* Triggering: There is a UserCV to control the acquisition trigger. You can have no special triggering (scan starts when you hit '~~scan~~'), external trigger to start the scan (see [[MR Hardware#Scan Triggers]] for details), or cardiac gating.		* Triggering: There is a UserCV to control the acquisition trigger. You can have no special triggering (scan starts when you hit 'Scan'), external trigger to start the scan (see [[MR Hardware#Scan Triggers]] for details), or cardiac gating.
	* Image reconstruction size: By default, the images are reconstructed at the native image size instead of being zero-padded up to the next higher power of two. This results in faster recons, smaller files, and no image interpolation, so it is generally preferred. But, if you want -power-of-two image sizes, you can change this UserCV to get that behavior.		* Image reconstruction size: By default, the images are reconstructed at the native image size instead of being zero-padded up to the next higher power of two. This results in faster recons, smaller files, and no image interpolation, so it is generally preferred. But, if you want power-of-two image sizes, you can change this UserCV to get that behavior.
			* Phase encoding gradient: To use FSL's TOPUP for EPI distortion correction, you need to acquire a pair of EPI scans with the same prescription except for the reversed phase encoding gradient polarity. There is a UserCV to control the PE polarity (called "pepolar" in GE's term). In most common cases, the phase encoding gradient is along AP/PA direction, and when pepolar = 0, the encoding goes from posterior to anterior ("j" in BIDS convension), and when pepolar = 1, the encoding goes from anterior to posterior ("j-" in BIDS convension).

	== Spiral ==		== Spiral ==

Huawu: /* Gradient-echo EPI */

2026-01-26T21:10:06Z

Gradient-echo EPI

← Older revision		Revision as of 21:10, 26 January 2026
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	== Gradient-echo EPI ==		== Gradient-echo EPI ==
	Many labs at CNI use a gradient-echo EPI sequence for BOLD fMRI imaging. This sequence is a modified version of the stock EPI sequence provided by GE. Some useful information about his sequence:		Many labs at CNI use a gradient-echo EPI sequence for BOLD fMRI imaging. This sequence is a modified version of the stock EPI sequence provided by GE. Some useful information about his sequence:
	* The ~~latest version~~ is '''~~cni_epi_2201~~'''~~. Be sure that your PSD field shows this~~.		* The name of the custom PSD is '''cni_epi'''.
	* Slice order: The slices are acquired interleaved by default, with odd slices first, then even slices. ~~(Kendrick Kay from the Wandell lab has confirmed this [[GE_Processing#Interleave\|empirically]].)~~ Be sure to take this into account when doing slice timing correction. You can use the "TriggerTime" field in the DICOM head to confirm the slice acquisition timing. Also note that the time points at which slices are acquired are equally spaced within the TR.		* Slice order: The slices are acquired interleaved by default, with odd slices first, then even slices. Be sure to take this into account when doing slice timing correction. You can use the "TriggerTime" field in the DICOM head to confirm the slice acquisition timing. Also note that the time points at which slices are acquired are equally spaced within the TR.
	* Triggering: There is a UserCV to control the acquisition trigger. You can have no special triggering (scan starts when you hit 'scan'), external trigger to start the scan (see [[MR Hardware#Scan Triggers]] for details), or cardiac gating.		* Triggering: There is a UserCV to control the acquisition trigger. You can have no special triggering (scan starts when you hit 'scan'), external trigger to start the scan (see [[MR Hardware#Scan Triggers]] for details), or cardiac gating.
	* Image reconstruction size: By default, the images are reconstructed at the native image size instead of being zero-padded up to the next higher power of two. This results in faster recons, smaller files, and no image interpolation, so it is generally preferred. But, if you want -power-of-two image sizes, you can change this UserCV to get that behavior.		* Image reconstruction size: By default, the images are reconstructed at the native image size instead of being zero-padded up to the next higher power of two. This results in faster recons, smaller files, and no image interpolation, so it is generally preferred. But, if you want -power-of-two image sizes, you can change this UserCV to get that behavior.

imported>Huawu: /* Gradient-reversal Unwarping ('pepolar') */

2023-04-26T18:21:10Z

Gradient-reversal Unwarping ('pepolar')

← Older revision		Revision as of 18:21, 26 April 2023
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	Some of the CNI pulse sequences support reversing the gradient read-out direction (GE calls this 'pepolar' for 'phase-encode polarity'). If you acquire fMRI or diffusion data with one pepolar direction (e.g., pepolar=0, the default readout direction) and another dataset with the reversed direction (e.g., pepolar=1), then you can use the two sets of images to estimate the fieldmap and unwarp the data. For our multiband ('mux', aka SMS-EPI) pulse sequences, the gradient read-out direction can be set as a user CV.		Some of the CNI pulse sequences support reversing the gradient read-out direction (GE calls this 'pepolar' for 'phase-encode polarity'). If you acquire fMRI or diffusion data with one pepolar direction (e.g., pepolar=0, the default readout direction) and another dataset with the reversed direction (e.g., pepolar=1), then you can use the two sets of images to estimate the fieldmap and unwarp the data. For our multiband ('mux', aka SMS-EPI) pulse sequences, the gradient read-out direction can be set as a user CV.

	To unwarp the data, we suggest that you use the FSL [http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup topup] tools. For fMRI data, you ~~will~~ do something like this:		To unwarp the data, we suggest that you use the FSL [http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup topup] tools. The echo train length (etl) needed in the acquisition parameter text file can be calculated using the echo spacing multiplied by the phase encoding matrix size. Both parameters can be found in the image metadata (for example, EffectiveEchoSpacing and AcquisitionMatrixPE in the json file produced by dcm2niix). For fMRI data, you can then do something like this:

	echo '0 1 0 [etl]' > acq_params.txt		echo '0 1 0 [etl]' > acq_params.txt
	echo '0 -1 0 [etl]' >> acq_params.txt		echo '0 -1 0 [etl]' >> acq_params.txt
	~~# To compute the etl (echo train length), run:~~
	~~# fslhd rs_pe0.nii.gz \| grep desc~~
	~~# and compute acq[0]*ec/1000~~
	fsl5.0-fslroi rs_pe0.nii.gz bu 1 1		fsl5.0-fslroi rs_pe0.nii.gz bu 1 1
	fsl5.0-fslroi rs_pe1.nii.gz bd 1 1		fsl5.0-fslroi rs_pe1.nii.gz bd 1 1

imported>Huawu: /* Gradient-reversal Unwarping ('pepolar') */

2023-04-26T17:58:38Z

Gradient-reversal Unwarping ('pepolar')

← Older revision		Revision as of 17:58, 26 April 2023
Line 51:		Line 51:
	Some of the CNI pulse sequences support reversing the gradient read-out direction (GE calls this 'pepolar' for 'phase-encode polarity'). If you acquire fMRI or diffusion data with one pepolar direction (e.g., pepolar=0, the default readout direction) and another dataset with the reversed direction (e.g., pepolar=1), then you can use the two sets of images to estimate the fieldmap and unwarp the data. For our multiband ('mux', aka SMS-EPI) pulse sequences, the gradient read-out direction can be set as a user CV.		Some of the CNI pulse sequences support reversing the gradient read-out direction (GE calls this 'pepolar' for 'phase-encode polarity'). If you acquire fMRI or diffusion data with one pepolar direction (e.g., pepolar=0, the default readout direction) and another dataset with the reversed direction (e.g., pepolar=1), then you can use the two sets of images to estimate the fieldmap and unwarp the data. For our multiband ('mux', aka SMS-EPI) pulse sequences, the gradient read-out direction can be set as a user CV.

	To unwarp the data, we suggest that you use the FSL [http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/~~TOPUP~~ topup] tools. For fMRI data, you will do something like this:		To unwarp the data, we suggest that you use the FSL [http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup topup] tools. For fMRI data, you will do something like this:

	echo '0 1 0 [etl]' > acq_params.txt		echo '0 1 0 [etl]' > acq_params.txt

imported>Catcam1: /* Arterial-Spin Labeling (ASL) */

2017-02-25T02:12:34Z

Arterial-Spin Labeling (ASL)

← Older revision		Revision as of 02:12, 25 February 2017
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	* ''Spiral arms'': default is 8		* ''Spiral arms'': default is 8
	** This is most significant means of adjusting spatial resolution. More arms = better spatial resolution in each slice.		** This is most significant means of adjusting spatial resolution. More arms = better spatial resolution in each slice.
	* ''Prescription'': The inferior edge of the prescription box must align with the cerebellum. This ensure the labeling plane (which is just inferior to the prescription box) is aligned to tag the blood passing through the carotid arteries in the neck before entering the brain.		* ''Prescription'': The inferior edge of the prescription box must align with the base of the cerebellum. This ensure the labeling plane (which is just inferior to the prescription box) is aligned to tag the blood passing through the carotid arteries in the neck before entering the brain.
	** It is very important that the subject's head is aligned straight in the scanner. Tilting can result in poor labeling or artifacts in the PW volume (and subsequently the CBF volume).		** It is very important that the subject's head is aligned straight in the scanner. Tilting can result in poor labeling or artifacts in the PW volume (and subsequently the CBF volume).

imported>Catcam1: /* Arterial-Spin Labeling (ASL) */

2017-02-25T01:56:55Z

Arterial-Spin Labeling (ASL)

← Older revision		Revision as of 01:56, 25 February 2017
Line 27:		Line 27:
	** It is very important that the subject's head is aligned straight in the scanner. Tilting can result in poor labeling or artifacts in the PW volume (and subsequently the CBF volume).		** It is very important that the subject's head is aligned straight in the scanner. Tilting can result in poor labeling or artifacts in the PW volume (and subsequently the CBF volume).

	'''Processing ASL Data'''		'''Processing ASL Data''':
	Analyses can be conducted on the CBF volume or on the PW volume. The CBF volume already has CBF quantified (naturally) based on the below information. This volume can be spatially normalized and analyzed in a similar way as processed fMRI data.		Analyses can be conducted on the CBF volume or on the PW volume. The CBF volume already has CBF quantified (naturally) based on the below information. This volume can be spatially normalized and analyzed in a similar way as processed fMRI data.

imported>Catcam1: /* Arterial-Spin Labeling (ASL) */

2017-02-25T01:56:25Z

Arterial-Spin Labeling (ASL)

← Older revision		Revision as of 01:56, 25 February 2017
Line 13:		Line 13:

	== Arterial-Spin Labeling (ASL) ==		== Arterial-Spin Labeling (ASL) ==
	Sequence: The newest ASL sequence from GE is a pseudo-continuous sequence called 3DASL. By default it is set to create a Cerebral Bloodflow (CBF) volume as a post-processing task. Separate from post-processing, the sequence produces 2 volumes, a perfusion-weighted (PW) volume and a PD volume. The PW volume is created from subtracting the tagged volume from the control volume during the scan sequence.		Sequence: The newest ASL sequence from GE is a pseudo-continuous sequence called 3DASL. By default it is set to create a Cerebral Bloodflow (CBF) volume as a post-processing task (reported in ml/100gm/min). Separate from post-processing, the sequence produces 2 volumes, a perfusion-weighted (PW) volume and a PD volume. The PW volume is created from subtracting the tagged volume from the control volume during the scan sequence.

	'''ASL-specific considerations''':		'''ASL-specific considerations''':
Line 26:		Line 26:
	* ''Prescription'': The inferior edge of the prescription box must align with the cerebellum. This ensure the labeling plane (which is just inferior to the prescription box) is aligned to tag the blood passing through the carotid arteries in the neck before entering the brain.		* ''Prescription'': The inferior edge of the prescription box must align with the cerebellum. This ensure the labeling plane (which is just inferior to the prescription box) is aligned to tag the blood passing through the carotid arteries in the neck before entering the brain.
	** It is very important that the subject's head is aligned straight in the scanner. Tilting can result in poor labeling or artifacts in the PW volume (and subsequently the CBF volume).		** It is very important that the subject's head is aligned straight in the scanner. Tilting can result in poor labeling or artifacts in the PW volume (and subsequently the CBF volume).

			'''Processing ASL Data'''
			Analyses can be conducted on the CBF volume or on the PW volume. The CBF volume already has CBF quantified (naturally) based on the below information. This volume can be spatially normalized and analyzed in a similar way as processed fMRI data.

			* Homogeneous blood/brain partition coefficient for water is 0.9 ml/g
			* Labeling inversion efficiency is 80% for a 3T scanner
			* T1 of blood is 1.6s at a 3T scanner
			* Saturation time is 2s
			* Overall efficiency is 0.6
			* The PD volume is used as a reference image

			Alternatively, you can quantify CBF yourself from the PW volume if you'd like to use different parameters or would like to perform additional spatial/intensity corrections before CBF quantification.

	== Diffusion Imaging ==		== Diffusion Imaging ==

imported>Catcam1: /* Arterial-Spin Labeling (ASL) */

2017-02-25T01:36:16Z

Arterial-Spin Labeling (ASL)

← Older revision		Revision as of 01:36, 25 February 2017
Line 13:		Line 13:

	== Arterial-Spin Labeling (ASL) ==		== Arterial-Spin Labeling (ASL) ==
			Sequence: The newest ASL sequence from GE is a pseudo-continuous sequence called 3DASL. By default it is set to create a Cerebral Bloodflow (CBF) volume as a post-processing task. Separate from post-processing, the sequence produces 2 volumes, a perfusion-weighted (PW) volume and a PD volume. The PW volume is created from subtracting the tagged volume from the control volume during the scan sequence.

			'''ASL-specific considerations''':
			* ''Post-Label Delay (PLD)'': default is 2025ms
			** This should be edited to reflect population being studied. Populations with faster heart rates (such as children) should have a shorter post-label delay (e.g. healthy teens can be successfully scanned at 1525ms)
			** PLD is saved as inversion time (TI) in the dicom headers
			* ''Labeling time (LT)'': default is 1450ms
			* ''Slice thickness'': default is 4mm
			** minimum is 2mm
			* ''Spiral arms'': default is 8
			** This is most significant means of adjusting spatial resolution. More arms = better spatial resolution in each slice.
			* ''Prescription'': The inferior edge of the prescription box must align with the cerebellum. This ensure the labeling plane (which is just inferior to the prescription box) is aligned to tag the blood passing through the carotid arteries in the neck before entering the brain.
			** It is very important that the subject's head is aligned straight in the scanner. Tilting can result in poor labeling or artifacts in the PW volume (and subsequently the CBF volume).

	== Diffusion Imaging ==		== Diffusion Imaging ==

imported>Bobd: /* CNI Data processing */

2016-01-23T19:40:28Z

CNI Data processing

← Older revision		Revision as of 19:40, 23 January 2016
Line 18:		Line 18:
	= CNI Data processing =		= CNI Data processing =

	See [[Linux notes]] for random notes on using the linux machines at the CNI.		See [[Linux notes]] for random notes on using the linux machines at the CNI. For a nice description of the various parameters involved in field map unwarping, see [http://support.brainvoyager.com/functional-analysis-preparation/27-pre-processing/459-epi-distortion-correction-echo-spacing.html this page].

	== Field map estimation ==		== Field map estimation ==