# CSI - Crime Scene Investigation v1.0 # adaptation of TATORT3 script to obtain t-maps, b-maps, and error variance map # TATORT3 (c) 2002 RENE MANDL # this script (c) 2002 MATTHIJS VINK # # You can perform 1 or 2 analyses on the same data set. Simply remove the first character from the relevant lines in the second # analysis section. If you want to perform only one analysis, then simply ignore the questions for the second analysis. # # To return to the current directory (or any other directory) change the relevant section in the bottom of the script # # This script can be edited so that it automatically runs for multiple subjects (ask Matthijs Vink for more info) # echo echo echo echo ' *******************************************' echo ' -*- -*-' echo ' -*- CSI -*-' echo ' -*- -*-' echo ' -*- Crime Scene Investigation for fMRI -*-' echo ' -*- -*-' echo ' -*- v1.0 -*-' echo ' *******************************************' echo echo ' program to obtain t-maps, b-maps, and error variance maps ' echo echo '(c) MATTHIJS VINK and RENE MANDL' echo echo echo echo -n 'SUBJECTNAME: ' read PREFIX echo echo -n 'COMPLETE PATH NAME FOR THE DATA (if NOT same directory as current directory) (eg '/data/v22/matthijs/mit/subject1212/' ): ' read LOCATIE echo echo -n 'MATRIXNAME: ' read MATRIXNAME echo echo -n 'NUMBER OF FACTORS FOR MATRIX (+ 1 !!): ' read AANTAL echo echo echo -n 'NUMBER OF SCANS: ' read SCANNUM echo echo 'SECOND ANALYSIS' echo echo -n 'SECOND ANALYSIS - MATRIXNAME (optional): ' read MATRIXNAME2 echo echo -n 'SECOND ANALYSIS - NUMBER OF FACTORS FOR MATRIX (+ 1 !!): ' read AANTAL echo echo echo -n 'SECOND ANALYSIS - NUMBER OF SCANS: ' read SCANNUM2 echo cd ${LOCATIE} echo echo 'Location of the data:... ' pwd echo echo #************ RENAMING OLD t-MAPS FILES ************** cp ${PREFIX}_tMaps.mnc.gz ${PREFIX}_old_tMaps.mnc.gz rm ${PREFIX}_tMaps.mnc.gz cp ${PREFIX}_tMaps_montreal_305.mnc.gz ${PREFIX}_old_tMaps_montreal_305.mnc.gz rm ${PREFIX}_tMaps_montreal_305.mnc.gz echo echo #************ RM=/bin/rm MV=/bin/mv GZIP=/bin/gzip GUNZIP=/bin/gunzip ECHO=/bin/echo BYTESWAP=/usr/local/bin/byteswap CAT=/bin/cat RAWTOMINC=/home/mandl/UMCU_tools_1.0/bin/rawtominc MINCRESHAPE=/home/mandl/UMCU_tools_1.0/bin/mincreshape MINCMODIFYHEADER=/home/mandl/UMCU_tools_1.0/bin/minc_modify_header MINCSHIFT=/home/mandl/UMCU_tools_1.0/bin/mincshift MRITOSELF=/home/mandl/UMCU_tools_1.0/bin/mritoself FMRITOTAL=/home/mandl/UMCU_tools_1.0/bin/fmritotal.tcl MINCINFO=/home/mandl/UMCU_tools_1.0/bin/mincinfo MINCCONCAT=/home/mandl/UMCU_tools_1.0/bin/mincconcat MINCMATH=/home/mandl/UMCU_tools_1.0/bin/mincmath MINCMASK=/home/mandl/UMCU_tools_1.0/bin/mincmask MINCMATHMORPH=/home/mandl/UMCU_tools_1.0/bin/mincmathmorph MINCRESAMPLE=/home/mandl/UMCU_tools_1.0/bin/mincresample MINCEXTRACT=/home/mandl/UMCU_tools_1.0/bin/mincextract XFMCONCAT=/home/mandl/UMCU_tools_1.0/bin/xfmconcat XFMINVERT=/home/mandl/UMCU_tools_1.0/bin/xfminvert PARAM2XFM=/home/mandl/UMCU_tools_1.0/bin/param2xfm CONVERTXFMTOFLIPS=/home/mandl/UMCU_tools_1.0/bin/convert_xfm_to_flips.tcl MINCFLIPS=/home/mandl/UMCU_tools_1.0/bin/mincflips NORMALIZEAVGSPLITCOLUMNS=/home/mandl/UMCU_tools_1.0/bin/normalize_avg_splitcolumns.tcl CONCATCOLUMNS=/home/mandl/UMCU_tools_1.0/bin/concatcolumns.tcl MINCMULTIREG=/home/mandl/UMCU_tools_1.0/bin/mincmultireg export VOLUME_CACHE_THRESHOLD=-1 BOUNDINGBOXTHRESHOLD=100 #************ UNZIP RELEVANT FILES ************** echo echo echo 'Decompressing relevant files:...' echo $GUNZIP ${PREFIX}_func_ext_tal.mnc.gz $GUNZIP ${PREFIX}_lastfunctvol_mask_ext_tal.mnc.gz #************ FIRST ANALYSIS ************** $NORMALIZEAVGSPLITCOLUMNS 920 ${PREFIX}_func_avgs.txt ${PREFIX}_avgs_normalized_cols.txt $CONCATCOLUMNS ${LOCATIE}${MATRIXNAME} ${PREFIX}_avgs_normalized_cols.txt " " ${PREFIX}_regression_matrix.txt export VOLUME_CACHE_THRESHOLD=-1 # t-maps $MINCMULTIREG -regressorfile ${PREFIX}_regression_matrix.txt -nsamples ${SCANNUM} -nregressors ${AANTAL} -maskfile ${PREFIX}_lastfunctvol_mask_ext_tal.mnc ${PREFIX}_func_ext_tal.mnc ${PREFIX}_tMaps.mnc $MINCRESAMPLE -transformation ${PREFIX}_tMap_to_montreal_305.xfm -like ${PREFIX}_tMaps.mnc -znelements 50 -tricubic ${PREFIX}_tMaps.mnc ${PREFIX}_tMaps_montreal_305.mnc # b-maps $MINCMULTIREG -statistic "bmap" -regressorfile ${PREFIX}_regression_matrix.txt -nsamples ${SCANNUM} -nregressors ${AANTAL} -maskfile ${PREFIX}_lastfunctvol_mask_ext_tal.mnc ${PREFIX}_func_ext_tal.mnc ${PREFIX}_bMaps.mnc $MINCRESAMPLE -transformation ${PREFIX}_tMap_to_montreal_305.xfm -like ${PREFIX}_bMaps.mnc -znelements 50 -tricubic ${PREFIX}_bMaps.mnc ${PREFIX}_bMaps_montreal_305.mnc # variance-maps $MINCMULTIREG -statistic "variance" -regressorfile ${PREFIX}_regression_matrix.txt -nsamples ${SCANNUM} -nregressors ${AANTAL} -maskfile ${PREFIX}_lastfunctvol_mask_ext_tal.mnc ${PREFIX}_func_ext_tal.mnc ${PREFIX}_varianceMaps.mnc $MINCRESAMPLE -transformation ${PREFIX}_tMap_to_montreal_305.xfm -like ${PREFIX}_varianceMaps.mnc -znelements 50 -tricubic ${PREFIX}_varianceMaps.mnc ${PREFIX}_varianceMaps_montreal_305.mnc #XXXXXXXXXXXXXXXX OPTIONAL SECOND ANALYSIS XXXXXXXXXXXXXXXXXXXXXXXXXXX #************ SECOND ANALYSIS ************** #$NORMALIZEAVGSPLITCOLUMNS 920 ${PREFIX}_func_avgs.txt ${PREFIX}_avgs_normalized_cols.txt #$CONCATCOLUMNS ${LOCATIE}${MATRIXNAME2} ${PREFIX}_avgs_normalized_cols.txt " " ${PREFIX}_regression_matrix2.txt #export VOLUME_CACHE_THRESHOLD=-1 # t-maps #$MINCMULTIREG -regressorfile ${PREFIX}_regression_matrix2.txt -nsamples ${SCANNUM2} -nregressors ${AANTAL2} -maskfile ${PREFIX}_lastfunctvol_mask_ext_tal.mnc ${PREFIX}_func_ext_tal.mnc ${PREFIX}_tMaps_2.mnc #$MINCRESAMPLE -transformation ${PREFIX}_tMap_to_montreal_305.xfm -like ${PREFIX}_tMaps_2.mnc -znelements 50 -tricubic ${PREFIX}_tMaps_2.mnc ${PREFIX}_tMaps_montreal_305_2.mnc # b-maps #$MINCMULTIREG -statistic "bmap" -regressorfile ${PREFIX}_regression_matrix2.txt -nsamples ${SCANNUM2} -nregressors ${AANTAL2} -maskfile ${PREFIX}_lastfunctvol_mask_ext_tal.mnc ${PREFIX}_func_ext_tal.mnc ${PREFIX}_bMaps_2.mnc #$MINCRESAMPLE -transformation ${PREFIX}_tMap_to_montreal_305.xfm -like ${PREFIX}_bMaps_2.mnc -znelements 50 -tricubic ${PREFIX}_bMaps_2.mnc ${PREFIX}_bMaps_montreal_305_2.mnc # variance-maps #$MINCMULTIREG -statistic "variance" -regressorfile ${PREFIX}_regression_matrix2.txt -nsamples ${SCANNUM2} -nregressors ${AANTAL2} -maskfile ${PREFIX}_lastfunctvol_mask_ext_tal.mnc ${PREFIX}_func_ext_tal.mnc ${PREFIX}_varianceMaps_2.mnc #$MINCRESAMPLE -transformation ${PREFIX}_tMap_to_montreal_305.xfm -like ${PREFIX}_varianceMaps_2.mnc -znelements 50 -tricubic ${PREFIX}_varianceMaps_2.mnc ${PREFIX}_varianceMaps_montreal_305_2.mnc #XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX #************ ZIP RELEVANT FILES ************** echo echo 'Compressing files:...' echo $GZIP *.mnc #****** #XXXXXXXXXXXXXXXXXX RETURN TO DIRECTORY XXXXXXXXXXXXXXXXXXXXXXXXXXXX #cd/ #XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX EOF