diff --git a/CHANGELOG.md b/CHANGELOG.md index e0e6bc3..d2e6ce3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,7 +27,7 @@ This document contains the Spec2nii release history in reverse chronological ord --------------------------------- - Added handling for the GE jpress sequence (for JH HURCULES sequence) - Added twix handling of the HYPER (smm_svs_herc_hyper) sequence (added by Aaron Gudmundson) -- Better handling of partial acqusitions of Siemens and Philips HYPER sequence. +- Better handling of partial acquisitions of Siemens and Philips HYPER sequence. 0.6.7 (Wednesday 15th March 2023) --------------------------------- @@ -63,7 +63,7 @@ This document contains the Spec2nii release history in reverse chronological ord - SPAR/SDAT pipeline now handles HYPER special case. - Data/list pipeline now handles HYPER special case. - Fixed issue with XA Twix PatientSex and TxOffset attributes. -- Reenable Bruker conversion. +- Re-enable Bruker conversion. 0.6.0 (Wednesday 11th January 2023) ----------------------------------- diff --git a/spec2nii/Philips/philips_data_list.py b/spec2nii/Philips/philips_data_list.py index 3b59927..03b8e00 100644 --- a/spec2nii/Philips/philips_data_list.py +++ b/spec2nii/Philips/philips_data_list.py @@ -117,7 +117,7 @@ def read_data_list_pair(data_file, list_file, aux_file, special_case=None): elif data_type == 'STD_1'\ and (special_case == 'hyper' or 'hyper' in meta['ProtocolName'].lower()): - # Handle the water ref acqusition of the HYPER sequence + # Handle the water ref acquisition of the HYPER sequence meta.set_dim_info( 0, diff --git a/spec2nii/Siemens/dicomfunctions.py b/spec2nii/Siemens/dicomfunctions.py index ce0b7fa..f211d04 100644 --- a/spec2nii/Siemens/dicomfunctions.py +++ b/spec2nii/Siemens/dicomfunctions.py @@ -48,7 +48,7 @@ def xa_or_vx(img): if img.dcm_data.SOPClassUID == '1.2.840.10008.5.1.4.1.1.4': raise IncompatibleSOPClassUID( f'spec2nii detected SOPClassUID {img.dcm_data.SOPClassUID}.' - ' This normaly contains MR imaging (not spectroscopy) data.' + ' This normally contains MR imaging (not spectroscopy) data.' ' This data was collected on a' f' {img.dcm_data.SoftwareVersions} baseline scanner.' ' spec2nii is tested on VA-VE, XA20, and XA30 DICOM files.') @@ -516,7 +516,7 @@ def set_standard_def(nifti_mrs_key, location, key, cast=None): pass # # 5.1 MRS specific Tags - # 'EchoTime' - requires substantial extraction from the full protocol incase there are multiple + # 'EchoTime' - requires substantial extraction from the full protocol in case there are multiple # sub-values, e.g. summing the three TEs of a sLAASER sequence together. fullcsa = csar.get_csa_header(dcmdata.dcm_data, csa_type='series') xprot = parse_buffer(fullcsa['tags']['MrPhoenixProtocol']['items'][0]) diff --git a/spec2nii/Siemens/rda.py b/spec2nii/Siemens/rda.py index 24f0ad0..a3cc25e 100644 --- a/spec2nii/Siemens/rda.py +++ b/spec2nii/Siemens/rda.py @@ -20,7 +20,7 @@ class MRSINotHandledError(Exception): def _locale_float(x): - """Handle locale specific flaoting point representations in header + """Handle locale specific floating point representations in header :param x: Header value as string with either . or , decimal separator :type x: str diff --git a/spec2nii/Siemens/twix_special_case.py b/spec2nii/Siemens/twix_special_case.py index 51f0c67..276bacf 100644 --- a/spec2nii/Siemens/twix_special_case.py +++ b/spec2nii/Siemens/twix_special_case.py @@ -15,8 +15,8 @@ def smm_svs_herc_hyper(twixObj, reord_data, meta_obj, dim_tags, subseq, subseq_n a water reference for each. Data is organized into 4 blocks: - 1. Short TE Reference : 35ms Unsupressed Water - 2. Long TE Reference : 80ms Unsupressed Water + 1. Short TE Reference : 35ms Unsuppressed Water + 2. Long TE Reference : 80ms Unsuppressed Water 3. Short TE Unedited : 35ms Water Suppressed PRESS 4. Long TE Edited : 80ms Water Suppressed HERCULES diff --git a/spec2nii/Siemens/twixfunctions.py b/spec2nii/Siemens/twixfunctions.py index 744ea85..f5c0198 100644 --- a/spec2nii/Siemens/twixfunctions.py +++ b/spec2nii/Siemens/twixfunctions.py @@ -825,7 +825,7 @@ def CSIOrientations(slice_normal, ip_rot, fov_pe, fov_ro, fov_sl, n_pe, n_ro, n_ base_pos -= slice_normal * (fov_sl / 2 - fov_sl / n_sl / 2) fov_sl /= n_sl - # Sagital + # Sagittal if mo_case == 0: print('Mirror along ROW/readout direction: VB = LIN, VE+ = SEG') dRowVec_vector *= -1.0 diff --git a/spec2nii/spec2nii.py b/spec2nii/spec2nii.py index e999032..ad8b6c5 100644 --- a/spec2nii/spec2nii.py +++ b/spec2nii/spec2nii.py @@ -412,7 +412,7 @@ def auto(self, args): setattr(args, 'special', None) self.philips(args) - # Philips DATA/LIST - Reject bcause of unknown aux file format. + # Philips DATA/LIST - Reject because of unknown aux file format. elif args.file.suffix.lower() in ('.data', '.list'): raise Spec2niiError( 'Automatic conversion not setup for data/list conversion. ' @@ -450,7 +450,7 @@ def auto(self, args): self.philips_dicom(args) else: raise Spec2niiError(f'Unknown DICOM manufacturer {manufacturer}.') - # No sucessful ID as DICOM - fail at automatic load. + # No successful ID as DICOM - fail at automatic load. except pdcm.errors.InvalidDicomError: raise Spec2niiError( 'Unable to automatically identify file type. '