.. include:: ../global.rst Registration scripts =============================== mpr2atl_4dfp ------------ single T1W :math:`\rightarrow` atlas Usage: mpr2atl_4dfp [options] Examples:: mpr2atl_4dfp vc1234_654-3[.4dfp.img] mpr2atl_4dfp vc1234_654-3[.4dfp.img] -T/data/petsun23/data1/atlas/NP345_111[.4dfp.img] -S711-2B Options =========================== ======================================================= 711-2 specify 711-2? series atlas representative target image -T specify arbitrary atlas representative target image -S* specify atlas space (default=711-2B space) crossmodal use cross-modal mpr->target registration useold suppress recomputation of existing t4 file redo suppress initialization of existing t4 file setecho set echo =========================== ======================================================= N.B.: may include a path, e.g., /data/petmr1/data7/stem9/scout/654-3 |br| N.B.: must be in either ANALYZE short int or 4dfp format; ANALYZE will be converted to 4dfp |br| .. _mpr2atl1_4dfp: mpr2atl1_4dfp ------------- T1W :math:`\rightarrow` atlas Usage: mpr2atl1_4dfp [options] Examples:: mpr2atl1_4dfp vc1234_654-3[.4dfp.img] mpr2atl1_4dfp vc1234_654-3[.4dfp.img] -T/data/petsun23/data1/atlas/NP345[.4dfp.img] Options ========================= =================================================== -T specify arbitrary atlas representative target image crossmodal use cross-modal mpr->target registration useold suppress recomputation of existing t4 file redo suppress t4 file initialization setecho set echo ========================= =================================================== .. _avgmpr_4dfp: avgmpr_4dfp ----------- multiple T1W :math:`\rightarrow` atlas Usage: avgmpr_4dfp ... [useold] [711-2 OR -T] Examples:: avgmpr_4dfp va2345_mpr1 va2345_mpr2 va2345_mpr3 va2345_mpr4 va2345_mpr_n4 avgmpr_4dfp va2345_mpr1 va2345_mpr2 va2345_mpr3 va2345_mpr4 none Options ====== ======================================================================================= useold suppresses unnecessary recomputation of atlas transformation, e.g., _to_711-2B_t4 ====== ======================================================================================= N.B.: Each named image must be in 4dfp format and acquired in the same subject. Mixed orientations are allowed. Any component image filename may include a unix path. N.B.: If = "none", t4 and lst files will be generated but averaged images will not. t2w2mpr_4dfp ---------------------- T2W :math:`\rightarrow` T1W :math:`\rightarrow` atlas [1]_ Usage: t2w2mpr_4dfp <4dfp mprage> <4dfp t2w> [options] Examples:: t2w2mpr_4dfp vc6383_130-4 vc6383_130-5 Options ========== ========================================================= -T specify atlas target ( may include absolute path) nostretch disable stretch setecho set echo debug debug mode ========== ========================================================= N.B.: t2w2mpr_4dfp assumes that <4dfp mprage> is in the current working directory and that its atlas transform, e.g., vc6383_130-4_to_711-2V_t4 exists and is in the current working directory epi2t1w_4dfp ---------------------- EPI :math:`\rightarrow` T1W [1]_ Usage: epi2t1w_4dfp <4dfp epi> <4dfp t1w> Examples:: epi2t1w_4dfp 070630_4TT00280_t1w 070630_4TT00280_anat_ave -T/data/cninds01/data2/atlas/TRIO_Y_NDC N.B.: epi2t1w_4dfp assumes that the <4dfp t1w> atlas transform, e.g.,070630_4TT00280_t1w_to_TRIO_Y_NDC_t4 exists and is in the current working directory N.B.: is either '711-2?' or '-T/targetpath/target' make_mprage_avg_4dfp ------------------------------ compute T1W anatomical average for group (list directed) [1]_ Usage: make_mprage_avg_4dfp Examples:: make_mprage_avg_4dfp NP659_all NP659_mpr_t4.lst N.B.: the output average will be named _mpr_avg N.B.: make_mprage_avg_4dfp assumes that the MP-RAGE 4dfp image files are in the same directories together their atlas transform t4files N.B.: should list the t4files including path (e.g.: vc12605c/PROCESSED/vc12605c_949-3_to_711-2Y_t4) Inputs t4file_list ls vc?????c/PROCESSED/\*t4 | awk '$1 !~/anat/' >! msktgen_4dfp ---------------------- create tailored mask (by inversion of atlas transform) [1]_ Usage: msktgen_4dfp <(4dfp) image> [threshold] -T -S Examples:: msktgen_4dfp 4859-5_mpr msktgen_4dfp 4859-5_mpr -T/data/petsun29/data1/atlas/NP345_111[.4dfp.img] -S711-2B Options =============== ====================================================================================================== threshold specify threshold for mask (default is 200) - use a higher threshold for a tighter mask and vice versa -S specify atlas space (default=711-2B space) -T specify atlas target =============== ====================================================================================================== N.B.: msktgen_4dfp uses the first legitimate atlas transform t4 file it sees in the current working directory, i.e., one of _to_711-2*_t4 or one of _to__t4 cross_mpr_imgreg_4dfp ------------------------------- compute cross-session T1W atlas transform [1]_ Usage: cross_mpr_imgreg_4dfp Examples:: cross_mpr_imgreg_4dfp /data/disk1/P44W_16800_L1 /data/disk2/P44W_16800_L2 711-2L cross_mpr_imgreg_4dfp /data/disk1/P44W_16800_L1 /data/disk2/P44W_16800_L2 /bmr01/01/nmrgrp/avi/P44W_C_111 N.B.: may be of the form '711-2[B-Z]' OR '-T[mypath/]mytarget' N.B.: cross_mpr_imgreg_4dfp assumes that each session patid is :t newatl_init_4dfp -------------------------- initialize creation of a cohort-specific atlas-representative target image [1]_ .. Attention:: After successful execution, execute newatl_refine_4dfp Usage: newatl_init_4dfp Examples:: newatl_init_4dfp symph-mpr_to_711-2B_t4.lst 711-2S Options == ================================================================================================= -m mask all input images (each input image must be paired with a 4dfp mask named _mask) == ================================================================================================= N.B.: is a text file listing the absolute addresses of extant atlas transform t4files corresponding to a set of structural images N.B.: specifies the name of the new atlas representative target image N.B.: itself and the t4files named in it may exist in other directories N.B.: all images (\*.4dfp.img and \*.4dfp.ifh) referred to in must exist either in their original directory or in the current working directory - newatl_init_4dfp will copy these images into the cwd as necessary newatl_refine_4dfp ---------------------------- refine cohort-specific atlas-representative target image [1]_ .. Attention:: Execute after successful completion of newatl_init_4dfp Usage: newatl_refine_4dfp Examples:: newatl_refine_4dfp 711-2S Options ======= ================================================================================================== -b suppress gauss 1.1 pre-blur of component images -m mask all input images ((each input image must be paired with a 4dfp mask named _mask) -T set reference target to specified image (default = /data/petsun43/data1/atlas/711-2B) ======= ================================================================================================== N.B.: specifies the name of the new atlas representative target image N.B.: all images (\*.4dfp.img and \*.4dfp.ifh) referred to in .lst must exist in the working directory .. [1] Assumes pre-existing atlas-transform t4 file