.. include:: ../global.rst Interconvert image formats ========================== .. _dcm_to_4dfp: dcm_to_4dfp ----------- DICOM :math:`\rightarrow` 4dfp Usage: dcm_to_4dfp [-b base] [-d gggg eeee] [-f] [-g] [-u] file(s) Slice Spacing Options: [-c] [-t or S or T] Slice Position Options: [-X] [-Y] [-Z] Examples:: dcm_to_4dfp * dcm_to_4dfp -b ID101 -f -g -u *IMA dcm_to_4dfp -d 0008 0030 -t 4.98 -g *.dcm dcm_to_4dfp -b P0089 -t T -g mydir/* Options ============== =============================================================================== [-b base] Output base filename follows the -b [-c] Slice Spacing: By Image Position (0020 0032) [-d gggg eeee] Divide series by group and element number (Default: ID series time (0008 0031)) [-f] Directories will be created, and dicom files will be moved [-g] Add image name, XYZ relative position, and number to rec file [-q] Slice Spacing: Do not compute by Image Position [-r] Rescale: Use the rescale slope and intercept fields [-t ] Slice Spacing: Use input value.[-t ] [-t T] Slice Spacing: Use Slice Thickness 0018 0050.[-t T] [-t S] Slice Spacing: Use Slice Spacing 0018 0088 [-t S] [-u] Output files named using sequence tag 0018 0024 plus number ============== =============================================================================== 4dfp Coordinant System is determined by Image Position (0020 0032). Multivolume and BOLD images are ordered by REL Image Number (0020 0013). [-X] Sagittal: image positions will be ordered low to high [-Y] Coronal: image positions will be high to low [-Z] Transverse: image positions will be high to low [-@ ] output big or little endian (default CPU endian) N.B.: -t S is the default slice spacing |br| N.B.: Default slice position is transverse ordered by REL Image Number (0020 0013) endian_4dfp ----------- report status and interconvert big :math:`\leftrightarrow` little endian Usage: endian_4dfp <(4dfp) image> Options ========= ============================================= -@ make <(4dfp) image> big, little or CPU endian -t perform var(log(fabs(.))) test ========= ============================================= N.B.: <(4dfp) image> may be overwritten |br| N.B.: absent option -@ endian_4dfp only reports state of <(4dfp) image> 4dfptoanalyze ------------- 4dfp :math:`\rightarrow` analyze 7.5 Usage: 4dfptoanalyze <(4dfp) filename> Options ======= =================================================================================== -c scale output values by specified factor -8 output 8 bit unsigned char -SPM99 include origin and scale in hdr (http:/wideman-one.com/gw/brain/analyze/format.doc) -@ output big or little endian (default CPU endian) ======= =================================================================================== analyzeto4dfp ------------- analyze 7.5 (int or char) :math:`\rightarrow` 4dfp Usage: analyzeto4dfp Options ======= ================================================= -s apply SPM2 ROIScaleFactor -x flip first axis -y flip second axis -z flip third axis -@ toutput big or little endian (default CPU endian) -O supply orientation code (in range [0-5]) ======= ================================================= N.B.: to convert SPM2 use options -x and -s ifh2hdr ------- create analyze 7.5 header Usage: ifh2hdr <(4dfp) file> examples:: ifh2hdr vc654_mpr_atl -r-500to1500 Options ================ ========= -r[to] set range ================ ========= hdr2txt ------- dump analyze 7.5 header info Usage: hdr2txt Examples:: hdr2txt brain_asig[.hdr] index2atl --------- convert atlas indices (ASCII text) to mm (e.g. atlas coordinates) Usage: index2atl <(4dfp) ifhroot> Examples:: index2atl -af time_BOXzstat_333_t88.4dfp.ifh time_BOXzstat_333_t88_index.lst Options ======= ============================================================================ -f input indices use FORTRAN convention (first index=1) (default first index=0) -a indices were read under orientation-specific 4dfp<->analyze flips -o output coordinates to specified file ======= ============================================================================ N.B.: <(4dfp) ifhroot> corresponds to the 4dfp image from which the indices were read asciito4dfp ----------- convert text columns to 4dfp format timeseries Usage: asciito4dfp <(4dfp) out> Options ======= ================================================ -@ output big or little endian (default CPU endian) ======= ================================================ N.B.: columns in map to voxels in <(4dfp) out> |br| N.B.: '#' in introduce comments |br| N.B.: lines beginning with '#' are included in <(4dfp) out>.img.rec mpetto4dfp ---------- convert microPET images  4dfp Usage: mpetto4dfp Examples:: mpetto4dfp m1042-cft1_v1 Options ======= =============================================================== -x flip x -y flip y -z flip z -w create frame duration listing for use with actmapf_4dfp -w -c scale all voxel values by specified factor -o name 4dfp output using specified string (default same as input) -@ output big or little endian (default input endian) ======= =============================================================== vto4dfp ------- Varian fid/procpar :math:`\rightarrow` 4dfp Usage: vto4dfp Examples:: vto4dfp /home/usr/shimonyj/vto4dfp/hard_010703 -odwi_010703 Options ======= ==================================================================== -v verbose mode -D suppress subtraction of k-space DC offset -I perform Fourier interpolation; output voxel count will be quadrupled -F phase reverse odd echos in multi-echo data -o specify 4dfp outroot (default="fid") -c intensity scale output (mag) image by specified constant -m scale voxel dimensions by specified constant -@ output big or little endian (default CPU endian) ======= ==================================================================== N.B.: vto4dfp expects to contain files "fid" and "procpar" .. _nifti_4dfp: nifti_4dfp ---------- interconvert nii :math:`\leftrightarrow` 4dfp Usage: nifti_4dfp -<4|n> [options] Examples:: nifti_4dfp -n time_BOXzstat_333_t88.4dfp.ifh time_BOXzstat_333_t88.nii Options ============ ================================================================ -T specify a t4 file to use converting TO NIfTI from 4dfp -n convert TO NIfTI from 4dfp -4 convert TO 4dfp from NIfTI -N suppress saving of mmppix and center fields in output ifh -@ specify endianness for output, b or B for big, l or L for little ============ ================================================================ N.B.: exactly one of -4 or -n must be specified |br| N.B.: ".4dfp.ifh" or ".nii" are appended to filenames specified without extension |br| N.B.: option -N has effect only on converting nii->4dfp |br| N.B.: option -T has effect only on converting 4dfp->nii niftigz_4dfp ------------ interconvert nii.gz :math:`\leftrightarrow` 4dfp (:ref:`nifti_4dfp` wrapper) Usage: niftigz_4dfp -<4|n> [options] Examples:: niftigz_4dfp -4 VB18896_mpr_n1_333_t88.nii.gz VB18896_mpr_n1_333_t88 Options (for more options, see :ref:`nifti_4dfp`) ======= ===================================================================== -v verbose mode -s skip specified number of frames at run start on 4dfp->NIfTI coversion ======= ===================================================================== N.B.: niftigz_4dfp always gzips NIfTI output but unzipped NIfTI input is left unchanged |br|