.. include:: ../global.rst fMRI oriented scripts ===================== .. include:: ../notes/params-file-tip.rst .. _cross_bold_pp_161012: cross_bold_pp_161012.csh ------------------------ generic EPI (BOLD) pre-processing Usage: cross_bold_pp_161012.csh [instructions_file] Examples:: cross_bold_pp_161012.csh VB16168.params **Required parameters** .. list-table:: :widths: 15 15 60 :header-rows: 1 * - Variable - Values - Description * - patid - |patid_vals| - |patid_desc| * - irun - |irun_vals| - |irun_desc| * - fstd - |fstd_vals| - |fstd_desc| * - mprs - |mprs_vals| - |mprs_desc| * - inpath - |inpath_vals| - |inpath_desc| * - target - |target_vals| - |target_desc| * - go - |go_vals| - |go_desc| * - nx - |nx_vals| - |nx_desc| * - ny - |ny_vals| - |ny_desc| * - skip - |skip_vals| - |skip_desc| * - TR_vol - |TR_vol_vals| - |TR_vol_desc| * - TR_slc - |TR_slc_vals| - |TR_slc_desc| * - epidir - |epidir_vals| - |epidir_desc| * - economy - |economy_vals| - |economy_desc| * - epi2atl - |epi2atl_vals| - |epi2atl_desc| * - FDthresh - |FDthresh_vals| - |FDthresh_desc| * - normode - |normode_vals| - |normode_desc| * - dwell - |dwell_vals| - |dwell_desc| * - ped - |ped_vals| - |ped_desc| * - rsam_cmnd - |rsam_cmnd_vals| - |rsam_cmnd_desc| (recommended: :ref:`one_step_resample`) ============= =========================================================================================== Economy value Files to be removed ============= =========================================================================================== > 2 original bold run images > 3 frame-aligned images (_faln) > 4 cross-realigned avg images (_r3d_avg or xr3d_BC_avg if $BiasField) (only if $epi2atl == 0) ============= =========================================================================================== **Field map correction parameters (required)** ======== ============== ======================= Variable Values Description ======== ============== ======================= **Option 1** (:ref:`measured_fm` - gradient echo) --------------------------------------------------- gre |gre_vals| |gre_desc| delta |delta_vals| |delta_desc| TE_vol |TE_vol_vals| |TE_vol_desc| **Option 2** (:ref:`measured_fm` - spin echo) --------------------------------------------------- sefm |sefm_vals| |sefm_desc| TE_vol |TE_vol_vals| |TE_vol_desc| **Option 3** (:ref:`mean_fm`) --------------------------------------------------- FMmean |FMmean_vals| |FMmean_desc| **Option 4** (:ref:`basis_opt_fm`) --------------------------------------------------- FMmean |FMmean_vals| |FMmean_desc| FMBases |FMBases_vals| |FMBases_desc| ======== ============== ======================= **Optional parameters** .. include:: ../notes/cross-bold-optional-tip.rst .. list-table:: :widths: 15 5 5 75 :header-rows: 1 * - Variable - Values - Default - Description * - tse - |tse_vals| - - |tse_desc| * - pdt2 - |pdt2_vals| - - |pdt2_desc| * - day1_patid - |day1_patid_vals| - - |day1_patid_desc| * - day1_path - |day1_path_vals| - - |day1_path_desc| * - scrdir - |scrdir_vals| - - |scrdir_desc| * - sorted - |sorted_vals| - |sorted_default| - |sorted_desc| * - MB - |MB_skip_vals| - |MB_skip_default| - |MB_skip_desc| * - sx - |sx_vals| - |sx_default| - |sx_desc| * - sy - |sy_vals| - |sy_default| - |sy_desc| * - E4dfp - |E4dfp_vals| - |E4dfp_default| - |E4dfp_desc| * - use_anat_ave - |use_anat_ave_vals| - |use_anat_ave_default| - |use_anat_ave_desc| * - min_frames - |min_frames_vals| - |min_frames_crossbold_default| - |min_frames_desc| * - interleave - |interleave_vals| - - |interleave_desc| * - seqstr - |seqstr_vals| - - |seqstr_desc| * - MBfac - |MBfac_vals| - |MBfac_default| - |MBfac_desc| * - lomotil - |lomotil_vals| - - |lomotil_desc| * - BiasField - |BiasField_vals| - |BiasField_default| - |BiasField_desc| * - FDtype - |FDtype_vals| - |FDType_default| - |FDtype_desc| * - anat_aveb - |anat_aveb_vals| - - |anat_aveb_desc| * - anat_avet - |anat_avet_vals| - |anat_avet_default| - |anat_avet_desc| (set excessively high to skip DVARS censoring) * - cross_day_nostretch - |cross_day_nostretch_vals| - |cross_day_nostretch_default| - |cross_day_nostretch_desc| * - Gad - |Gad_vals| - |Gad_default| - |Gad_desc| **Additional optional parameters** .. include:: ../notes/any-value-warning.rst .. list-table:: :widths: 10 90 :header-rows: 1 * - Variable - Description * - goto_UNWARP - |goto_UNWARP_desc| * - epi_zflip - |epi_zflip_desc| * - Siemens_interleave - |Siemens_interleave_desc| * - nounpack - |nounpack_desc| **Processing steps** .. list-table:: :widths: 25 15 30 :class: wrap-rows :header-rows: 1 * - Step description - Function - Output * - Convert bold run DICOM data to 4dfp format - :ref:`dcm_to_4dfp` - * - Convert mosaic format to volume (if not $nounpack) - :ref:`unpack_4dfp` - **bold/** |br| _b.4dfp.img * - Correct slice timing and odd/even slice intensities (if not $MB) - :ref:`frame_align_4dfp`, :ref:`deband_4dfp` - **bold/** |br| _b_faln.4dfp.img |br| _b_faln_dbnd.4dfp.img * - Motion correction via rigid body transform of each volume to reference frame - :ref:`cross_realign3d_4dfp` - **bold/** |br| _b[_faln_dbnd]_xr3d.4dfp.img |br| _b[_faln_dbnd]_r3d_avg.4dfp.img |br| _b[_faln_dbnd]_xr3d.mat * - Bias field correction (if $BiasField) - FSL bet, FSL fast, :ref:`extend_fast_4dfp` - **bold/** |br| _b[_faln_dbnd]_xr3d_BC_avg.4dfp.img |br| **atlas/** |br| [_faln_dbnd]_xr3d_avg_brain.nii.gz |br| [_faln_dbnd]_xr3d_avg_brain_restore(.4dfp.img, .nii.gz) * - Compute and apply within-run mode 1000 normalization - :ref:`normalize_4dfp`, :ref:`scale_4dfp` - **bold/** |br| _b[_faln_dbnd]_xr3d[_BC]_norm.4dfp.img * - Extract/format movement data from cross-realign output - :ref:`mat2dat` - **movement/** |br| _b[_faln_dbnd]_xr3d(.dat, .ddat, .rdat) * - Extract EPI first frame (anatomy) image and create functional volume conc file - :ref:`paste_4dfp`, :ref:`conc_4dfp` - **atlas/** |br| _anat_ave.4dfp.img |br| _func_vols.conc * - Compute high movement frames using FD (if $FDthresh specified) and DVARS (stops here if $min_frames criteria not met) - FD.awk (using .ddat movement file), :ref:`run_dvar_4dfp` - **movement/** |br| [_faln_dbnd]_xr3d.FD |br| **atlas/** |br| [_faln_dbnd]_xr3d.FD.format (if $FDthresh) |br| _func_vols(.vals, .dat, .crit, .xmgr, .format) * - Make func_vols_ave image with high movement frames removed - :ref:`actmapf_4dfp` - **atlas/** |br| _func_vols_ave.4dfp.img * - Compute cross-session BOLD atlas transform if $day1_patid specified (then skips to applying EPI transform step) - :ref:`cross_day_imgreg_4dfp`, :ref:`t4_mul` - **atlas/** |br| _anat_ave_to__t4 |br| (and other intermediate t4 files) * - Convert MPRAGE DICOM data to 4dfp format (if not $E4dfp) - :ref:`dcm_to_4dfp` - **atlas/** |br| _mpr#.4dfp.img * - Convert MPRAGE images to tranverse orientation (if not already) - :ref:`c2t_4dfp` or :ref:`s2t_4dfp` - **atlas/** |br| _mpr#T.4dfp.img * - Compute MPRAGE average - :ref:`avgmpr_4dfp` - **atlas/** |br| _mpr_n#.4dfp.img * - Create transverse t2w image (if $tse or $pdt) - :ref:`collate_slice_4dfp` if $tse, :ref:`extract_frame_4dfp` (second frame) if $pdt, :ref:`c2t_4dfp` or :ref:`s2t_4dfp` - **atlas/** |br| _t2w[T].4dfp.img * - Compute EPI to atlas transform - :ref:`epi2mpr2atl2_4dfp` if neither $tse nor $pdt, otherwise :ref:`epi2t2w2mpr2atl2_4dfp` - **atlas/** |br| _anat_ave_to__t4 |br| (and other intermediate t4 files) * - Make atlas transformed EPI average image and t2w in 111, 222, and 333 atlas space - :ref:`t4img_4dfp` - **atlas/** |br| _(anat\|func_vols)_ave_on__111.4dfp.img |br| _(anat\|func_vols)_ave_on__222.4dfp.img |br| _(anat\|func_vols)_ave_on__333.4dfp.img * - Compute field mapping correction - :ref:`fmri_unwarp_170616` - **unwarp/** |br| _(anat|func_vols)_ave_uwrp.4dfp.img * - Compute and apply unwarped epi to atlas transform - :ref:`imgreg_4dfp`, :ref:`t4_mul`, :ref:`t4img_4dfp` - **unwarp/** |br| _(anat\|func_vols)_ave_uwrp_on__111.4dfp.img |br| _(anat\|func_vols)_ave_uwrp_on__222.4dfp.img |br| _(anat\|func_vols)_ave_uwrp_on__333.4dfp.img * - One-step resample unwarped images - $rsam_cmnd - **bold/** |br| _[_faln_dbnd]_xr3d_uwrp_atl.4dfp.img .. _fmri_unwarp_170616: fmri_unwarp_170616.tcsh ----------------------- distortion correction wrapper script for fMRI preprocessing .. _measured_fm: Measured field map ++++++++++++++++++ Usage: fmri_unwarp_170616.tcsh -map .. list-table:: :class: wrap-row :header-rows: 1 * - Variable - Values - Description * - patid - |patid_vals| - |patid_desc| * - epi - |epi_vals| - |epi_desc| * - mag - |mag_vals| - |mag_desc| * - phase - |phase_vals| - |phase_desc| * - dwell - |dwell_vals| - |dwell_desc| * - te - |TE_vol_vals| - |TE_vol_desc| * - ped - |ped_vals| - |ped_desc| * - delta - |delta_vals| - |delta_desc| (required only for gradient-echo field map) .. _mean_fm: Mean field map ++++++++++++++ Usage: fmri_unwarp_170616.tcsh -mean .. list-table:: :class: wrap-row :header-rows: 1 * - Variable - Values - Description * - epi - |epi_vals| - |epi_desc| * - FMmean - |FMmean_vals| - |FMmean_desc| * - epi_to_atl_t4 - |epi2atl_t4_vals| - |epi2atl_t4_desc| * - dwell - |dwell_vals| - |dwell_desc| * - ped - |ped_vals| - |ped_desc| .. _basis_opt_fm: basis_opt field map +++++++++++++++++++ Usage: fmri_unwarp_170616.tcsh -basis [t2w brain mask] .. list-table:: :class: wrap-row :header-rows: 1 * - Variable - Values - Description * - epi - |epi_vals| - |epi_desc| * - t2w - |t2w_vals| - |t2w_desc| * - FMmean - |FMmean_vals| - |FMmean_desc| * - epi_to_t2w_t4 - |epi2t2w_t4_vals| - |epi2t2w_t4_desc| * - epi_to_atl_t4 - |epi2atl_t4_vals| - |epi2atl_t4_desc| * - dwell - |dwell_vals| - |dwell_desc| * - ped - |ped_vals| - |ped_desc| * - nbasis - |nbasis_vals| - |nbasis_desc| N.B.: with option -basis, basis_opt optimizes the value (aka, echo spacing) by default |br| .. _sefm_pp_AZS: sefm_pp_AZS.csh --------------- merge AP/PA into one image and run topup to derive field map Usage: sefm_pp_AZS.csh [instructions file] Examples:: sefm_pp_AZS.csh PSQ0001_s1.params ../PSQ_study.params .. list-table:: :class: wrap-row :header-rows: 1 * - Variable - Values - Description * - patid - |patid_vals| - |patid_desc| * - sefm - |sefm_vals| - |sefm_desc| * - sorted - 1 - |sorted_desc| (must be sorted) .. _one_step_resample: one_step_resample.csh --------------------- one step resampling with support for bias field correction Usage: one_step_resample.csh [instructions] Examples:: one_step_resample.csh VB16168.params Params variables .. list-table:: :class: wrap-row :header-rows: 1 * - Variable - Values - Description * - patid - |patid_vals| - |patid_desc| * - day1_patid - |day1_patid_vals| - |day1_patid_desc| * - day1_path - |day1_path_vals| - |day1_path_desc| * - irun - |irun_vals| - |irun_desc| Instructions variables .. list-table:: :class: wrap-row :header-rows: 1 * - Variable - Values - Description * - use_anat_ave - |use_anat_ave_vals| - |use_anat_ave_desc| * - outres - |outres_vals| - |outres_desc| * - target - |target_vals| - |target_desc| * - MB - |MB_skip_vals| - |MB_skip_desc| * - BiasField - |BiasField_vals| - |BiasField_desc| epi2mpr2atlv_4dfp ----------------- EPI :math:`\rightarrow` T1W :math:`\rightarrow` atlas Usage: epi2mpr2atlv_4dfp [useold] [atlas target [711-2? OR -T] [-S] [noinit] Examples:: epi2mpr2atlv_4dfp stem9_anat_ave stem9_654-3 useold 711-2C epi2mpr2atlv_4dfp stem9_anat_ave stem9_654-3 useold -T/data/cninds01/atlas/NP765 -S711-2B Options ======= ============================================================================ useold inhibits re-computation of all t4 files noinit inhibits reinitialization of epi->mpr t4 files -T atlas target (specified string should include path) (default is 711-2B) -S specifies the atlas space (requires -T) (currently only 711-2B is supported) ======= ============================================================================ N.B.: Any image argument may include a path, e.g., /data/petmr1/data7/stem/96_06_14_stem9/stem9_654-3 N.B.: All named images must be in either ANALYZE or 4dfp format. ANALYZE will be converted to 4dfp epi2t2w2mpr2atlv_4dfp --------------------- EPI :math:`\rightarrow` T2W :math:`\rightarrow` T1W :math:`\rightarrow` atlas (8 parameter cross-modal; for “low” res fMRI) Usage: epi2t2w2mpr2atlv_4dfp [useold] [atlas_target] Examples:: epi2t2w2mpr2atlv_4dfp stem9_anat_ave stem9_643-2 stem9_654-3 useold 711-2Y .. list-table:: :widths: 15 15 25 10 :class: wrap-rows :header-rows: 1 * - Step description - Function - Inputs - Output * - Compute MPR to atlas transform - :ref:`mpr2atl_4dfp` - - ${mpr}_to_${target}_t4 * - Blur images - :ref:`gauss_4dfp` - t_half = 1.1 - ${mpr}_g11 |br| ${t2w}_g11 |br| ${epi}_g11 * - Compute MPR brain mask - :ref:`msktgen_4dfp` - - ${mpr}_mskt * - Compute (iteratively) T2w to MPR transform - :ref:`imgreg_4dfp`, using blurred (\*_g11) images as source/target - **w/ unmasked mpr** (source_mask = none) |br| modes[1] = 1024 + 3 |br| **w/ masked mpr** (source_mask = ${mpr}_mskt) |br| modes[2] = 1024 + 3 |br| modes[3] = 2048 + 3 + 8 + 64 |br| modes[4] = 8192 + 2048 + 3 + 8 + 64 - ${t2w}_to_${mpr}_t4 * - Compute EPI brain mask - :ref:`gauss_4dfp`, :ref:`imgmax_4dfp`, :ref:`img2msk_4dfp`, :ref:`maskimg_4dfp` - f_half = .3 |br| threshold = .2 * max(blurred epi) - ${epi}_msk * - Compute EPI (iteratively) to T2w transform - :ref:`imgreg_4dfp`, using blurred (\*_g11) images as source/target - **w/ original epi** (source_msk = none) |br| modes[1] = 1024 + 3 |br| **w/ masked epi** (source_msk=${epi}_msk) |br| modes[2] = 1024 + 3 |br| modes[3] = 3072 + 3 + 8 + 64 |br| modes[4] = 8192 + 2048 + 3 + 8 + 64 - ${epi}_to_${t2w}_t4 * - Combine transforms - :ref:`t4_mul` - ${t2w}_to_${mpr}_t4, ${mpr}_to_${target}_t4 |br| ${epi}_to_${t2w}_t4, ${t2w}_to_${target}_t4 |br| ${epi}_to_${t2w}_t4, ${t2w}_to_${mpr}_t4 - ${t2w}_to_${target}_t4 |br| ${epi}_to_${target}_t4 |br| ${epi}_to_${mpr}_t4 N.B.: Any argument may include a path, e.g., /data/petmr1/data7/stem/96_06_14_stem9/stem9_654-3 N.B.: All named images must be in either ANALYZE or 4dfp format. ANALYZE will be converted to 4dfp N.B.: 'useold' instructs epi2t2w2mpr2atlv_4dfp to use existing t4 files N.B.: The default atlas_target is 711-2B .. _epi2t2w2mpr2atl1_4dfp: epi2t2w2mpr2atl1_4dfp --------------------- EPI :math:`\rightarrow` T2W :math:`\rightarrow` T1W :math:`\rightarrow` atlas (9 parameter cross-modal; for “high” res fMRI) Usage: epi2t2w2mpr2atl1_4dfp [useold] [711-2? OR -T] [-S] Examples:: epi2t2w2mpr2atl1_4dfp stem9_anat_ave stem9_643-2 stem9_654-3 711-2B epi2t2w2mpr2atl1_4dfp stem9_anat_ave stem9_654-3 useold -T/data/cninds01/atlas/NP765 -S711-2B .. list-table:: :widths: 15 15 25 10 :class: wrap-rows :header-rows: 1 * - Step description - Function - Inputs - Output * - Compute MPR to atlas transform - :ref:`mpr2atl_4dfp` - - ${mpr}_to_${target}_t4 * - Compute MPR brain mask - :ref:`msktgen_4dfp` - - ${mpr}_mskt * - Compute (iteratively) T2w to MPR transform - :ref:`imgreg_4dfp` - **w/ original mpr** (source_mask = none) |br| modes[1] = 1024 + 3 |br| **w/ masked mpr** (source_mask = ${mpr}_mskt) |br| modes[2] = 1024 + 3 |br| modes[3] = 2048 + 3 + 8 + 64 |br| modes[4] = 8192 + 2048 + 3 + 8 - ${t2w}_to_${mpr}_t4 * - Compute EPI brain mask - :ref:`gauss_4dfp`, :ref:`imgmax_4dfp`, :ref:`img2msk_4dfp`, :ref:`maskimg_4dfp` - f_half = .3 |br| threshold = .2 * max(blurred epi) - ${epi}_msk * - Compute EPI (iteratively) to T2w transform - :ref:`imgreg_4dfp` - **w/ original epi** (source_msk = none) |br| modes[1] = 1024 + 3 |br| **w/ masked epi** (source_msk=${epi}_msk) |br| modes[2] = 1024 + 3 |br| modes[3] = 3072 + 3 + 8 |br| modes[4] = 8192 + 2048 + 3 + 8 - ${epi}_to_${t2w}_t4 * - Combine transforms - :ref:`t4_mul` - ${t2w}_to_${mpr}_t4, ${mpr}_to_${target}_t4 |br| ${epi}_to_${t2w}_t4, ${t2w}_to_${target}_t4 |br| ${epi}_to_${t2w}_t4, ${t2w}_to_${mpr}_t4 - ${t2w}_to_${target}_t4 |br| ${epi}_to_${target}_t4 |br| ${epi}_to_${mpr}_t4 N.B.: Any image argument may include a path, e.g., /data/petmr1/data7/stem/96_06_14_stem9/stem9_654-3 N.B.: All named images must be in 4dfp format N.B.: -S specifies the atlas space. The only currently supported atlas space is 711-2B .. _epi2t2w2mpr2atl2_4dfp: epi2t2w2mpr2atl2_4dfp --------------------- EPI :math:`\rightarrow` T2W :math:`\rightarrow` T1W :math:`\rightarrow` atlas (6 parameter cross-modal; best for distorted fMRI) Usage: epi2t2w2mpr2atl2_4dfp [useold] [711-2? OR -T] [-S] Examples:: epi2t2w2mpr2atl2_4dfp stem9_anat_ave stem9_643-2 stem9_654-3 711-2B epi2t2w2mpr2atl2_4dfp stem9_anat_ave stem9_654-3 useold -T/data/cninds01/atlas/NP765 -S711-2B **Processing steps** .. list-table:: :widths: 15 15 25 10 :class: wrap-rows :header-rows: 1 * - Step description - Function - Inputs - Output * - Compute MPR to atlas transform - :ref:`mpr2atl_4dfp` - - ${mpr}_to_${target}_t4 * - Compute T2w to MPR transform - :ref:`imgreg_4dfp` - modes[1] = 4096 + 3 |br| modes[2] = 1024 + 3 |br| modes[3] = 2048 + 3 |br| modes[4] = 2048 + 3 [+ 8 + 64 if thin t2w] |br| modes[5] = modes[4] + 8192 - ${t2w}_to_${mpr}_t4 * - Compute EPI brain mask - :ref:`gauss_4dfp`, :ref:`imgmax_4dfp`, :ref:`img2msk_4dfp`, :ref:`maskimg_4dfp` - f_half = .3 |br| threshold = .2 * max(blurred epi) - ${epi}_msk * - Compute (iteratively) EPI to T2w transform - :ref:`imgreg_4dfp` - **w/ original epi** (source_msk = none) |br| modes[1] = 4096 + 3 |br| modes[2] = 1024 + 3 |br| **w/ masked epi** (source_msk = ${epi}_msk) |br| modes[3] = 1024 + 3 |br| modes[4] = 3072 + 3 |br| modes[5] = 8192 + 2048 + 3 - ${epi}_to_${t2w}_t4 * - Combine transforms - :ref:`t4_mul` - ${t2w}_to_${mpr}_t4, ${mpr}_to_${target}_t4 |br| ${epi}_to_${t2w}_t4, ${t2w}_to_${target}_t4 |br| ${epi}_to_${t2w}_t4, ${t2w}_to_${mpr}_t4 - ${t2w}_to_${target}_t4 |br| ${epi}_to_${target}_t4 |br| ${epi}_to_${mpr}_t4 N.B.: Any image argument may include a path, e.g., /data/petmr1/data7/stem/96_06_14_stem9/stem9_654-3 N.B.: All named images must be in 4dfp format N.B.: -S specifies the atlas space. The only currently supported atlas space is 711-2B .. _cross_day_imgreg_4dfp: cross_day_imgreg_4dfp --------------------- link first session atlas transform to subsequent sessions via EPI “anat_ave” Usage: cross_day_imgreg_4dfp [options] Examples:: cross_day_imgreg_4dfp tpj0202 /data/petsun24/data1/tpj0201/atlas tpj0201 711-2Y cross_day_imgreg_4dfp tpj0202 /data/petsun24/data1/tpj0201/atlas tpj0201 -T/data/cninds01/data2/ATLAS/ALLEGRA_Y_111 Options ========== ===================================================== -a specify image filename trailer (default = "anat_ave") -nostretch disable stretch in transform -setecho set echo -S specify atlas space (default=711-2B) ========== ===================================================== N.B.: cross_day_imgreg_4dfp must be run in the current atlas directory N.B.: may be of form 711-2? OR -T/path/image compute_run_sd1.csh ------------------- run var_4dfp -sn4 on all bold directories (\*xr3d_norm and \*xr3d_atl) and makes movies Usage: compute_run_sd1.csh Examples:: compute_run_sd1.csh VB15792 cross_day_imgreg_4dfp --------------------- compute cross-session BOLD atlas transform Usage: cross_day_imgreg_4dfp [options] Examples:: cross_day_imgreg_4dfp tpj0202 /data/petsun24/data1/tpj0201/atlas tpj0201 711-2Y cross_day_imgreg_4dfp tpj0202 /data/petsun24/data1/tpj0201/atlas tpj0201 -T/data/cninds01/data2/ATLAS/ALLEGRA_Y_111 Options ========== ===================================================== -a specify image filename trailer (default = "anat_ave") -nostretch disable stretch in transform -setecho set echo -S specify atlas space (default=711-2B) ========== ===================================================== N.B.: cross_day_imgreg_4dfp must be run in the current atlas directory N.B.: may be of form 711-2? OR -T/path/image .. _run_dvar_4dfp: run_dvar_4dfp ------------- compute format (identify frames with too much motion) (:ref:`dvar_4dfp` wrapper) Usage: run_dvar_4dfp <(conc) concfile> [options] Options ======= ========================================================================================= -d debug mode -v verbose mode -p specify printer on which to plot generated .dat.ps file -P print previously generated results on specified printer (run on SunOS) -x set frame rejection threshold (default = mode + 2.5*(left s.d.) over non-skipped frames) ======= ========================================================================================= N.B.: run_dvar_4dfp is a wrapper for dvar_4dfp N.B.: options -b -m -n -t are passed to dvar_4dfp N.B.: option -s is always passed to dvar_4dfp .. _conc_4dfp: conc_4dfp --------- create conc file Usage: conc_4dfp <(conc) outroot> <(4dfp) 1> <(4dfp) 2> ... Examples:: conc_4dfp vb13157_faln_dbnd_xr3d_atl vb13157_b?_faln_dbnd_xr3d_atl.4dfp.img Options ======= ================================================================== -w supress inclusion of current working directory in listed file path -l read input 4dfp list ======= ================================================================== N.B.: output conc file always has extension "conc" N.B.: only files in or below the current working directory can be correctly addressed conc_mv ------- update conc file 4dfp image pointers Usage: conc_mv Examples:: conc_mv TC26851_rmsp_faln_dbnd_xr3d_atl.conc /data/nil-bluearc/raichle/gusnard/np751 auto_evolve/AVI_TEST Options == ======================================= -v verbose mode -t practice mode ( not changed) == ======================================= conc2format ----------- compute conc-specific format using a fixed number of pre-steady state frames Examples:: conc2format vb13157_faln_dbnd_xr3d_atl.conc 4 Options == ================================= -v verbose mode -X label first frame of each run 'X' == ================================= RFX2.csh -------- random effects analysis (1 or 2 groups) Usage: RFX2.csh [ ] Options == ===================================================== -d debug mode -R suppress creation of large rec files (bootstrap mode) == ===================================================== N.B.: name 4dfp images on which to run the t-test N.B.: are 4dfp 'n' images (number of subjects for which each voxel is defined) N.B.: If one group is entered a t-test will be run on this group against the null hypothesis of 0 N.B.: If two groups are entered a t-test will be run comparing the two groups and the computed statistic is Welch's approximate t' (Eqn. 8.11, p. 129 in Zar.)