From 45b53decb9b25e9c2fc42e1e25a71450028b7fb6 Mon Sep 17 00:00:00 2001 From: Hboni Date: Thu, 22 Nov 2018 11:45:42 +0100 Subject: [PATCH 1/4] Fixes misalignement and use of square bracket --- .../01-magnetic-resonance-imaging-data.md | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md index eb58ec1af9..e541154099 100644 --- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md +++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md @@ -272,17 +272,17 @@ combined image rather than an image from each coil. The following table recapitulates the different ways that specific fields have to be populated for functional sequences. | | RepetitionTime | SliceTiming | AcquisitionDuration | DelayTime | VolumeTiming | -|-------------------|:--------------:|:-------------:|:---------------------:|:-----------:|:--------------:| -| option 1 | [X] | | [ ] | | [ ] | -| option 2 | [ ] | [X] | | [ ] | [X] | -| option 3 | [ ] | | [X] | [ ] | [X] | -| sparse sequence 1 | [X] | [X] | [ ] | | [ ] | -| sparse sequence 1 | [X] | [X] | [ ] | [X] | [ ] | -| sparse sequence 1 | [X] | | [ ] | [X] | [ ] | +|-------------------|:--------------:|:-----------:|:-------------------:|:---------:|:------------:| +| option 1 | \[X] | | \[ ] | | \[ ] | +| option 2 | \[ ] | \[X] | | \[ ] | \[X] | +| option 3 | \[ ] | | \[X] | \[ ] | \[X] | +| sparse sequence 1 | \[X] | \[X] | \[ ] | | \[ ] | +| sparse sequence 1 | \[X] | \[X] | \[ ] | \[X] | \[ ] | +| sparse sequence 1 | \[X] | | \[ ] | \[X] | \[ ] | **Legend** -[X] --> has to be filled -[ ] --> has to be left empty +\[X] --> has to be filled +\[ ] --> has to be left empty empty cell --> can be specified but not required ##### fMRI task information From 2873d84fe9018529e7991783ac981b26ffd3ecb4 Mon Sep 17 00:00:00 2001 From: Hboni Date: Thu, 22 Nov 2018 12:00:37 +0100 Subject: [PATCH 2/4] Fixes misaligned table fence --- .../01-magnetic-resonance-imaging-data.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md index e541154099..a99a8802e2 100644 --- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md +++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md @@ -273,12 +273,12 @@ The following table recapitulates the different ways that specific fields have t | | RepetitionTime | SliceTiming | AcquisitionDuration | DelayTime | VolumeTiming | |-------------------|:--------------:|:-----------:|:-------------------:|:---------:|:------------:| -| option 1 | \[X] | | \[ ] | | \[ ] | -| option 2 | \[ ] | \[X] | | \[ ] | \[X] | -| option 3 | \[ ] | | \[X] | \[ ] | \[X] | -| sparse sequence 1 | \[X] | \[X] | \[ ] | | \[ ] | -| sparse sequence 1 | \[X] | \[X] | \[ ] | \[X] | \[ ] | -| sparse sequence 1 | \[X] | | \[ ] | \[X] | \[ ] | +| option 1 | \[X] | | \[ ] | | \[ ] | +| option 2 | \[ ] | \[X] | | \[ ] | \[X] | +| option 3 | \[ ] | | \[X] | \[ ] | \[X] | +| sparse sequence 1 | \[X] | \[X] | \[ ] | | \[ ] | +| sparse sequence 1 | \[X] | \[X] | \[ ] | \[X] | \[ ] | +| sparse sequence 1 | \[X] | | \[ ] | \[X] | \[ ] | **Legend** \[X] --> has to be filled From 3500e73f2a41b1779c81ec278f925169314dbece Mon Sep 17 00:00:00 2001 From: Hboni Date: Thu, 22 Nov 2018 12:10:13 +0100 Subject: [PATCH 3/4] Fixes misaligned table fence 2 --- .../01-magnetic-resonance-imaging-data.md | 20 +++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md index a99a8802e2..7fccfb34e2 100644 --- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md +++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md @@ -48,7 +48,7 @@ by Ben Inglis: | PartialFourier | RECOMMENDED. The fraction of partial Fourier information collected. Corresponds to DICOM Tag 0018, 9081 `Partial Fourier`. | | PartialFourierDirection | RECOMMENDED. The direction where only partial Fourier information was collected. Corresponds to DICOM Tag 0018, 9036 `Partial Fourier Direction`. | | PhaseEncodingDirection | RECOMMENDED. Possible values: `i`, `j`, `k`, `i-`, `j-`, `k-`. The letters `i`, `j`, `k` correspond to the first, second and third axis of the data in the NIFTI file. The polarity of the phase encoding is assumed to go from zero index to maximum index unless `-` sign is present (then the order is reversed - starting from the highest index instead of zero). `PhaseEncodingDirection` is defined as the direction along which phase is was modulated which may result in visible distortions. Note that this is not the same as the DICOM term `InPlanePhaseEncodingDirection` which can have `ROW` or `COL` values. This parameter is REQUIRED if corresponding fieldmap data is present or when using multiple runs with different phase encoding directions (which can be later used for field inhomogeneity correction). | -| EffectiveEchoSpacing | RECOMMENDED. The "effective" sampling interval, specified in seconds, between lines in the phase-encoding direction, defined based on the size of the reconstructed image in the phase direction. It is frequently, but incorrectly, referred to as "dwell time" (see `DwellTime` parameter below for actual dwell time). It is required for unwarping distortions using field maps. Note that beyond just in-plane acceleration, a variety of other manipulations to the phase encoding need to be accounted for properly, including partial fourier, phase oversampling, phase resolution, phase field-of-view and interpolation.2 This parameter is REQUIRED if corresponding fieldmap data is present. | +| EffectiveEchoSpacing | RECOMMENDED. The "effective" sampling interval, specified in seconds, between lines in the phase-encoding direction, defined based on the size of the reconstructed image in the phase direction. It is frequently, but incorrectly, referred to as "dwell time" (see `DwellTime` parameter below for actual dwell time). It is required for unwarping distortions using field maps. Note that beyond just in-plane acceleration, a variety of other manipulations to the phase encoding need to be accounted for properly, including partial fourier, phase oversampling, phase resolution, phase field-of-view and interpolation.2 This parameter is REQUIRED if corresponding fieldmap data is present. | | TotalReadoutTime | RECOMMENDED. This is actually the "effective" total readout time , defined as the readout duration, specified in seconds, that would have generated data with the given level of distortion. It is NOT the actual, physical duration of the readout train. If `EffectiveEchoSpacing` has been properly computed, it is just `EffectiveEchoSpacing * (ReconMatrixPE - 1)`.3 . This parameter is REQUIRED if corresponding "field/distortion" maps acquired with opposing phase encoding directions are present (see 8.9.4). | 2Conveniently, for Siemens’ data, this value is easily obtained as @@ -69,7 +69,7 @@ first "effective" echo and the center of the last "effective" echo. | EchoTime | RECOMMENDED. The echo time (TE) for the acquisition, specified in seconds. This parameter is REQUIRED if corresponding fieldmap data is present or the data comes from a multi echo sequence. Corresponds to DICOM Tag 0018, 0081 `Echo Time` (please note that the DICOM term is in milliseconds not seconds). | | InversionTime | RECOMMENDED. The inversion time (TI) for the acquisition, specified in seconds. Inversion time is the time after the middle of inverting RF pulse to middle of excitation pulse to detect the amount of longitudinal magnetization. Corresponds to DICOM Tag 0018, 0082 `Inversion Time` (please note that the DICOM term is in milliseconds not seconds). | | SliceTiming | RECOMMENDED. The time at which each slice was acquired within each volume (frame) of the acquisition. Slice timing is not slice order -- rather, it is a list of times (in JSON format) containing the time (in seconds) of each slice acquisition in relation to the beginning of volume acquisition. The list goes through the slices along the slice axis in the slice encoding dimension (see below). Note that to ensure the proper interpretation of the `SliceTiming` field, it is important to check if the (optional) `SliceEncodingDirection` exists. In particular, if `SliceEncodingDirection` is negative, the entries in `SliceTiming` are defined in reverse order with respect to the slice axis (i.e., the final entry in the `SliceTiming` list is the time of acquisition of slice 0). This parameter is REQUIRED for sparse sequences that do not have the `DelayTime` field set. In addition without this parameter slice time correction will not be possible. | -| SliceEncodingDirection | RECOMMENDED. Possible values: `i`, `j`, `k`, `i-`, `j-`, `k-` (the axis of the NIfTI data along which slices were acquired, and the direction in which `SliceTiming` is defined with respect to). `i`, `j`, `k` identifiers correspond to the first, second and third axis of the data in the NIfTI file. A `-` sign indicates that the contents of `SliceTiming` are defined in reverse order - that is, the first entry corresponds to the slice with the largest index, and the final entry corresponds to slice index zero. When present, the axis defined by `SliceEncodingDirection` needs to be consistent with the ‘slice_dim’ field in the NIfTI header. When absent, the entries in `SliceTiming` must be in the order of increasing slice index as defined by the NIfTI header. | +| SliceEncodingDirection | RECOMMENDED. Possible values: `i`, `j`, `k`, `i-`, `j-`, `k-` (the axis of the NIfTI data along which slices were acquired, and the direction in which `SliceTiming` is defined with respect to). `i`, `j`, `k` identifiers correspond to the first, second and third axis of the data in the NIfTI file. A `-` sign indicates that the contents of `SliceTiming` are defined in reverse order - that is, the first entry corresponds to the slice with the largest index, and the final entry corresponds to slice index zero. When present, the axis defined by `SliceEncodingDirection` needs to be consistent with the ‘slice_dim’ field in the NIfTI header. When absent, the entries in `SliceTiming` must be in the order of increasing slice index as defined by the NIfTI header. | | DwellTime | RECOMMENDED. Actual dwell time (in seconds) of the receiver per point in the readout direction, including any oversampling. For Siemens, this corresponds to DICOM field (0019,1018) (in ns). This value is necessary for the (optional) readout distortion correction of anatomicals in the HCP Pipelines. It also usefully provides a handle on the readout bandwidth, which isn’t captured in the other metadata tags. Not to be confused with `EffectiveEchoSpacing`, and the frequent mislabeling of echo spacing (which is spacing in the phase encoding direction) as "dwell time" (which is spacing in the readout direction). | #### RF & Contrast @@ -249,7 +249,7 @@ JSON file. | Field name | Definition | | :------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | RepetitionTime | REQUIRED. The time in seconds between the beginning of an acquisition of one volume and the beginning of acquisition of the volume following it (TR). Please note that this definition includes time between scans (when no data has been acquired) in case of sparse acquisition schemes. This value needs to be consistent with the `pixdim[4]` field (after accounting for units stored in `xyzt_units` field) in the NIfTI header. This field is mutually exclusive with `VolumeTiming` and is derived from DICOM Tag 0018, 0080 and converted to seconds. | -| VolumeTiming | REQUIRED. The time at which each volume was acquired during the acquisition. It is described using a list of times (in JSON format) referring to the onset of each volume in the BOLD series. The list must have the same length as the BOLD series, and the values must be non-negative and monotonically increasing. This field is mutually exclusive with `RepetitionTime` and `DelayTime`. If defined, this requires acquisition time (TA) be defined via either `SliceTiming` or `AcquisitionDuration` be defined. | +| VolumeTiming | REQUIRED. The time at which each volume was acquired during the acquisition. It is described using a list of times (in JSON format) referring to the onset of each volume in the BOLD series. The list must have the same length as the BOLD series, and the values must be non-negative and monotonically increasing. This field is mutually exclusive with `RepetitionTime` and `DelayTime`. If defined, this requires acquisition time (TA) be defined via either `SliceTiming` or `AcquisitionDuration` be defined. | | TaskName | REQUIRED. Name of the task. No two tasks should have the same name. Task label (`task-`) included in the file name is derived from this field by removing all non alphanumeric (`[a-zA-Z0-9]`) characters. For example task name `faces n-back` will corresponds to task label `facesnback`. An optional but RECOMMENDED convention is to name resting state task using labels beginning with `rest`. | For the fields described above and in the following section, the term "Volume" @@ -265,7 +265,7 @@ combined image rather than an image from each coil. | :-------------------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | NumberOfVolumesDiscardedByScanner | RECOMMENDED. Number of volumes ("dummy scans") discarded by the scanner (as opposed to those discarded by the user post hoc) before saving the imaging file. For example, a sequence that automatically discards the first 4 volumes before saving would have this field as 4. A sequence that doesn't discard dummy scans would have this set to 0. Please note that the onsets recorded in the \_event.tsv file should always refer to the beginning of the acquisition of the first volume in the corresponding imaging file - independent of the value of `NumberOfVolumesDiscardedByScanner` field. | | NumberOfVolumesDiscardedByUser | RECOMMENDED. Number of volumes ("dummy scans") discarded by the user before including the file in the dataset. If possible, including all of the volumes is strongly recommended. Please note that the onsets recorded in the \_event.tsv file should always refer to the beginning of the acquisition of the first volume in the corresponding imaging file - independent of the value of `NumberOfVolumesDiscardedByUser` field. | -| DelayTime | RECOMMENDED. User specified time (in seconds) to delay the acquisition of data for the following volume. If the field is not present it is assumed to be set to zero. Corresponds to Siemens CSA header field `lDelayTimeInTR`. This field is REQUIRED for sparse sequences using the `RepetitionTime` field that do not have the `SliceTiming` field set to allowed for accurate calculation of "acquisition time". This field is mutually exclusive with `VolumeTiming`. | +| DelayTime | RECOMMENDED. User specified time (in seconds) to delay the acquisition of data for the following volume. If the field is not present it is assumed to be set to zero. Corresponds to Siemens CSA header field `lDelayTimeInTR`. This field is REQUIRED for sparse sequences using the `RepetitionTime` field that do not have the `SliceTiming` field set to allowed for accurate calculation of "acquisition time". This field is mutually exclusive with `VolumeTiming`. | | AcquisitionDuration | RECOMMENDED. Duration (in seconds) of volume acquisition. Corresponds to DICOM Tag 0018,9073 `Acquisition Duration`. This field is REQUIRED for sequences that are described with the `VolumeTiming` field and that not have the `SliceTiming` field set to allowed for accurate calculation of "acquisition time". This field is mutually exclusive with `RepetitionTime`. | | DelayAfterTrigger | RECOMMENDED. Duration (in seconds) from trigger delivery to scan onset. This delay is commonly caused by adjustments and loading times. This specification is entirely independent of `NumberOfVolumesDiscardedByScanner` or `NumberOfVolumesDiscardedByUser`, as the delay precedes the acquisition. | @@ -273,12 +273,12 @@ The following table recapitulates the different ways that specific fields have t | | RepetitionTime | SliceTiming | AcquisitionDuration | DelayTime | VolumeTiming | |-------------------|:--------------:|:-----------:|:-------------------:|:---------:|:------------:| -| option 1 | \[X] | | \[ ] | | \[ ] | -| option 2 | \[ ] | \[X] | | \[ ] | \[X] | -| option 3 | \[ ] | | \[X] | \[ ] | \[X] | -| sparse sequence 1 | \[X] | \[X] | \[ ] | | \[ ] | -| sparse sequence 1 | \[X] | \[X] | \[ ] | \[X] | \[ ] | -| sparse sequence 1 | \[X] | | \[ ] | \[X] | \[ ] | +| option 1 | \[X] | | \[ ] | | \[ ] | +| option 2 | \[ ] | \[X] | | \[ ] | \[X] | +| option 3 | \[ ] | | \[X] | \[ ] | \[X] | +| sparse sequence 1 | \[X] | \[X] | \[ ] | | \[ ] | +| sparse sequence 1 | \[X] | \[X] | \[ ] | \[X] | \[ ] | +| sparse sequence 1 | \[X] | | \[ ] | \[X] | \[ ] | **Legend** \[X] --> has to be filled From d67b8c3d0aac319bf45b508ae368f6d9f85e6e84 Mon Sep 17 00:00:00 2001 From: Hboni Date: Thu, 22 Nov 2018 12:15:46 +0100 Subject: [PATCH 4/4] Fixes long line --- .../01-magnetic-resonance-imaging-data.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md index 7fccfb34e2..ad806968a8 100644 --- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md +++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md @@ -269,7 +269,8 @@ combined image rather than an image from each coil. | AcquisitionDuration | RECOMMENDED. Duration (in seconds) of volume acquisition. Corresponds to DICOM Tag 0018,9073 `Acquisition Duration`. This field is REQUIRED for sequences that are described with the `VolumeTiming` field and that not have the `SliceTiming` field set to allowed for accurate calculation of "acquisition time". This field is mutually exclusive with `RepetitionTime`. | | DelayAfterTrigger | RECOMMENDED. Duration (in seconds) from trigger delivery to scan onset. This delay is commonly caused by adjustments and loading times. This specification is entirely independent of `NumberOfVolumesDiscardedByScanner` or `NumberOfVolumesDiscardedByUser`, as the delay precedes the acquisition. | -The following table recapitulates the different ways that specific fields have to be populated for functional sequences. +The following table recapitulates the different ways that specific fields have +to be populated for functional sequences. | | RepetitionTime | SliceTiming | AcquisitionDuration | DelayTime | VolumeTiming | |-------------------|:--------------:|:-----------:|:-------------------:|:---------:|:------------:|