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R!s* !XM: sK@Nn@Nk@Npp@N;p #\#`!hPPP<* p(:  7Zp@NHܠ !\^* !x: 咐p@Npp@N3#@ H* p: |R!s!< @M@N /V`/@M(   ` `@&/@M#\#` PP" @M&'D '@@MВ!\ @Mא@M@M,P@M* ɖ * ,ډ: @M@M0@!* #8 @M* p: !"!!!ؠ@M, [: WD@M@Ml@Mjh@Mh @M|А* ?: d@@Mc` 㿠@7??@@㿠@7l??@@sleep 1sleep 1x|%s%s%s%s %s%s%s%s %s.%s.proc%s version ...... %s ImgLib version ....... %s %cExecuted on .......... %s Command line: %s Waiting for file %s for %d more seconds Timed out waiting for %s. %sWaiting for data from %s: %d more seconds %sTimed out reading from list %snum_slices %d images_per_slice %d NEX %d xsize %d ysize %d part_phase %d part_read %d oversample %d interleave %d read_fov %d phase_fov %d xextra %d xover %d magnitude_image %d I_image %d Q_image %d phase_image %d time_data %d rotation 0 reflection_x 1 reflection_y 0.hdr%d %d %d %hd.hdr.irp.bfloat.bshort.buchar.img.MRnonemm0%m/%d/%y%H:%M:%S%s.hdr%d %d %d %d%s.buchar%s.bshort%s.bfloatScSthdr.img.irp.IMG.IRPIMGFUCLA Brain Mappinganonymous%hd%hd%hd%hd%s%hd%s%hd%s%s%s%hd%s%hd%s%s%s%s%s%s%s%s%s%f%s%frUC Read Image %d,%d r ***** ImbLib Error handler ***** ===> unix error: %sAn ImgLib function received an unrecognized data type as an argument.Divide by zero error.A function returned an invalid memory address.Array range error.An ImgLib function received a pointer to NIL.The image pointer is NIL.There is not enough memory to complete this operation.Memory error - usually allocation.This function accepts only positive inputs.Attempted to reallocated already assigned pointer.The overlay routine failed.The mdisplay routine failed.Auto range does not function properly with negative input data.The threshold cannot be negative.A scale factor of zero was found.This volume display is not available.The data exceeds the valid range for this function.This functions halted while waiting for data.There was a problem during data type conversion.The input data contained a limited range of values: auto detection of intensity range may be poor.To preserve image quality, your data were rescaled; the resolution of the output type was less than that of the original data.An unrecognized display mode was selected.There was a problem opening an image headerThe header could not be openedThe file does not containa valid genesis (Signa) headerThe header is the wrong size.The header contains invalid data.The image file does not have a corresponding header.The header requests interpolation in both X and Y. It is probably corrupted.The Image could not be opened.There is a problem with the image file.Having trouble with that paradigm file Premature end of file.A required file could not be found.The log file could not be opened.This image file type is not recognized.A file could not be written successfully.A file could not be read successfully.A file could not be opened successfully.A file could not be closed successfully.There is a problem with the selected fileThe data values exceed the range for the selected data type.The file name is not valid.The file could not be opened for reading.The file could not be opened for writing.The file could not be opened for appending.An unknown error occured. An internal program error occured in an ImgLib routine. The reported error was: ===> %s The error message was: ===> %s Sometimes, you can find the source of the error by examining the processing files created by the program you are running (they typically end in .proc ) If you cannot resolve the problem, contact Mark Cohen (mscohen@ucla.edu) **** %hd: %s **** truefalseShowError: %s(%d) on %s! ERROR: The file '%s' rcould not be read. wcould not be written. rwcould not be opened for read/write. acould not be opened for appending. could not be used. The file %s could not be opened ck_fwrite: Memory location: %ld Requested size: %ld %sck_fread: Memory location: %ld Requested size: %ld ck_fclose: error on file close Error allocating memory for: %s! ck_malloc: Error allocating memory for: %s! cpy_alloc: %s = %s (%08x = %08x) Undefined type in vsmul Undefined type in vsmul Undefined type in vadd Undefined type in vsub Undefined type in vmul vdiv -- Undefined type Undefined type in vminmax Undefined type in vsq Undefined type in vsq Undefined type in vssq Undefined type in vsum nonemm%-80.80sUCLA MRI0%m/%d/%Y%H:%M:%SmmE%0.3dS%0.2dI%0.2d%m/%d/%Y%H:%M:%S%sShow Header, ver 2.01 Dec 23, 1998. Name = %s hk.size_of_hdr: %d hk.data_type: "%-10s" hk.db_name: "%-8s" hk.extents: %d hk.session_error: %d hk.regular: '%c' hk.hkey_unused0: '%c' dime.dim: [%d] | %.4d | [hex] %04x | dime.vox_units: "%-4s" dime.cal_units: "%-8s" dime.flags: %04x dime.datatype: %d dime.bitpix: %d dime.dim_un0: %d dime.pixdim[%d]: %f dime.vox_offset: %f dime.funused1: %f dime.funused2: %f dime.funused3: %f dime.cal_max: %f dime.cal_min: %f dime.compressed: %ld dime.verified: %ld dime.glmax: %ld dime.glmin: %ld hist.descrip: "%-40.40s" "%-40.40s" hist.aux_file: "%-24s" hist.orient: "%c" hist.originator: "%-10s" hist.generated: "%-10s" hist.scannum: "%-10s" hist.patient_id: "%-10s" hist.exp_date: "%-10s" hist.exp_time: "%-10s" hist.hist_un0: "%-3s" hist.views: %ld hist.vols_added: %ld hist.start_field: %ld hist.field_skip: %ld hist.omax: %ld hist.omin: %ld hist.smax: %ld hist.smin: %ld --: illegal option -- %c: option requires an argument -- %co:i:W:Z:N:T:f:x:F:Vbh? o:i:W:Z:N:T:f:x:F:Vbh?Correction factor (f) must range between 0 and 1 Usage: %s -i input_file -o output_file [ -W smoothing width -Z smoothing width (Z) -N Noise Threshold -T output file type (default '5' = analyze, '1' = bshort, '2' = bfloat) -F Fill value - prior to smoothing, pad all pixels below this with this value -f correction factor (0 - 1.0) strength of correction to apply ] -b output a 'bias field' image Only the base name of the output file is needed (always outputs bfloat) The first two arguments are required. %s -h shows a longer help screen %s is designed as a simple and rapid tool for correcting slowly varying image intensity deviations in medical (esp. Magnetic Resonance) images. %s works by calculating a highly smoothed version of the input data, and then normalizing the input image by this smoothed data set. To prevent a variety of serious artifacts, including edge blooming and noise amplification, the program first calculates which locations are within the volume of interest. Before smoothing, all out of volume (i.e. noise) pixels, are first set equal to the average intensity within the data volume. After smoothing and normalization, these locations are given the arbitrary intensity of zero. Parameters: User MUST enter input (-i) and output (-o) file names. -W in-plane smoothing (in pixels) defaults to three-eighths of the image width. -Z through plane smoothing (in slices) defaults to three-eighths the number of slices. -N noise threshold amplitude below which pixels will be classified as non-image By default, this is determined by the program. -T output file type: 1 = bshort 2 = bfloat 5 = analyze (default) -f correction factor (0 - 1.0) strength of intensity correction. Defaults to 1. -b output a 'bias field' image -G input and output will be Signa genesis format. Output image name will have 'c' added -> E1041S2I001.MR becomes Ec1041S2I001.MR The image file name base must follow -G. ( -G E1041S2* ) --------- THIS MUST BE THE LAST COMMAND LINE ARGUMENT!!!--------- -V verbose mode -h print this note. More (y/n): %s This is part of a set of utilities to pre-process signa files for intensity correction, and to post-process the resulting files to convert them to a valid Signa format. ============== The tool Genesis2Analyze takes a series of ExxxxSxxxIxxx.MR files and makes them into a single 4-D analyze file. It also saves a record of the original names, and the complete header for each Typing Genesis2Analyze (my way of providing simple help) gives: Usage: Genesis2Analyze basename*.MR Renumber all files ending in '*.MR' with 3 digit numbers Create an analyze 4D file with these contents Note that you must keep a copy of the NameFile (which ends in .NAME_FILE) and the headers file, which ends in: .GenesisHeaders, in order to successfully reconstruct the genesis headers using Analyze2Genesis =============== Analyze2Genesis does the reverse operation, extracting each slice in an analyze file, and giving it a name and header from the output derived from Genesis2Analyze. Typing Analyze2Genesis gives: Usage: Analyze2Genesis -i AnalyzeInputFile -n NameFile Analyze2Genesis will convert a (4D) analyze file to a series of genesis files having names corresponding to the contents of the NameFile Note that you must keep a copy of the NameFile (which ends in .NAME_FILE) and the headers file, which ends in: .GenesisHeaders, in order to successfully reconstruct the genesis headers using Analyze2Genesis The user is responsible for ensuring that the name file has a separate entry for each slice location in the analyze file ================ A complete session transcript follows for RF correction. Note that the warning messages for mv and differing byte order are expected. Genesis2Analyze E*.MR Renaming files mv: E2123S2I124.MR and E2123S2I124.MR are identical. ... etc ... mv: E2123S2I100.MR and E2123S2I100.MR are identical. WARNING: Computer and data differ in byte order Patience for a moment Created Analyze (4D) file: E2123S2.img Save these files!: E2123S2.NAME_FILE and E2123S2.GenesisHdrs To create corresponding genesis images from an analyze file named XXX.img, use: Analyze2Genesis -n E2123S2.NAME_FILE -i XXX.img All done -------------------- > EQ -i E2123S2.img -o eqTst EQ $Revision: 1.22 $$Date: 2001/11/21 06:21:08 $ Working Done. Thank you for using EQ. mscohen@ucla.edu -- http://www.brainmapping.org -------------------- Analyze2Genesis -n E2123S2.NAME_FILE -i eqTst.img Using E2123S2.GenesisHdrs for genesis headers ...................................................................... > ls Ec* Ec2123S2I001.MR Ec2123S2I026.MR Ec2123S2I051.MR Ec2123S2I076.MR Ec2123S2I101.MR ... etc ... Ec2123S2I025.MR Ec2123S2I050.MR Ec2123S2I075.MR Ec2123S2I100.MR Mark S. Cohen, Ph.D. UCLA Brain Mapping Division 660 Charles Young Dr. S. Los Angeles, CA 90095 office: 310/897-1690 lab: 310/825-9142 http://www.brainmapping.org/ The data are being processed as %d slices Invalid header data The input file %s has dimensions %d(x) x %d(y) x %d(z) x %d(time) Processing in volume mode The smoothing width is %0.3f pixels in x %0.3f in y, and %0.3f pixels in z Image Dimensions ...... %hd (X) x %hd (Y) x %hd (Z ) x %hd (time ) Smoothing width ....... %0.3f pixels in x %0.3f pixels in y %0.3f pixels in z Current average: %0.3f Your threshold is probably too low. The threshold is currently %0.2f Suggestion: increase threshold to %0.2f Set new threshold? [y]/n: NnNew threshold level [%0.2f]: recalculating with threshold of %0.2f Valid points........... %ld Average image signal .. %0.3f Threshold used ........ %0.3f Fill used ............. %f Fill used ............. %f FTscale: %f .%s.Raw.hdrw%s.Raw.imgw%s.Smooth.hdrw%s.Smooth.imgw%s.mask.hdrw%d %d %d %dImage %hd was extracted Image %hd was extracted as %s.Raw.img, %s.Smooth.img and %s.mask.buchar %s.hdrw%d %d %d %d%s %s imgbfloatbshortUnrecognized output file type: %d BSHORTBFLOATANALYZESaving data as type: %s Unable to open %s . AbortingWorking Creating smoothing kernel %s.%s%s.%0.3d%s%s.%sUnable to open %s . Abortingtime point:%d Reading... * * The input data range is small. * Is it okay to multiply the values by %0.0f? *Yy Forming average... Average intensity is: %f Threshold -- %0.4f %d valid pts Populating background before smoothing... %s.Fill.hdrw%s.Fill.imgw First FFT... k-space smoothing... Second FFT... Reading (again) Saving a bias field image. Please enter a name (no extension): %s%s.hdrw%s.imgw%s.mask.bucharw%s.Corrected.hdrw%s.Corrected.imgw writing... Done. Thank you for using %s. mscohen@ucla.edu -- http://www.brainmapping.org ,00<0H0T0`0l0x00000000000000 0,080D0P0\0h0t0000000000000~0{0x(0u40r@0oL0lX0id0fp0c|0`0]  Y, Y|o. o  0 od..` ,@$Revision: 2.59 $$Date: 2002/01/08 16:52:16 $?$Revision: 1.22 $$Date: 2001/11/21 06:21:08 $wAnalyzeAPD2Signa GenesisMGH bfloatMGH bshortMGH bucharunrecognized file typeyinterp: ftmpyinterp: ftmpyinterp: stmpyinterp: stmpyinterp: ustmpyinterp: ustmpyinterp: ctmpyinterp: ctmpyinterp: uctmpyinterp: uctmpyinterp: itmpyinterp: itmpyinterp: dtmpyinterp: dtmpxinterp: ftmpxinterp: ftmpxinterp: uctmpxinterp: uctmpxinterp: ctmpxinterp: ctmpxinterp: ustmpxinterp: ustmpxinterp: stmpxinterp: stmpxinterp: itmpxinterp: itmpxinterp: dtmpxinterp: dtmpinterp2D: uiptrinterp2D: uiptrinterp2D: ucptrinterp2D: ucptrinterp2D: fptrinterp2D: fptrScaleImageSize: interpBuffScaleImageSize: interpBuffImageFlipY: scratch spacegaussian kernelsmoothed vectorconvolution vectorkernelsmoothlocal_inhistogramSmooth histsmoothed histogramhistogramrget_para_file_sizerirpStringwCreating Analyze Headerwwwwb.bshort.bfloat.buchar.img.img.mrBuffer for Signa HeaderReadheader - temp data storageUC_Readheader: headerDataRealLocalFile: headerDataReadheader: headerDataimageIdentOffsetHistOffsetSuiteOffsetExamOffsetSeriesOffsetImageOffsetUC_Readheader: Header DataUCReadimage--data bufferRead image bufferReadLocalFile contentsfloatshortunsigned shortcharunsigned charintdoublecomplexlongUnrecognized data typerwarwwrrNoYesFirstFT - vsmulcfft2d-FirstFTcfft3d-FirstFTQuadrant exchangeExtract image is out of rangeRaw ImageSaving smoothed fileSmoothed ImageSaving smoothed fileEqualized imageReading input fileimDatapadding data vector with little numbersgaussKernelrCouldn't create gaussian kernelwwReading image volumeIntensity scalingImageDataRangeExtract image is out of rangeFill ImageSaving smoothed fileFirstFTk-space smoothingReverse 2D Fourier transformReverse 3D Fourier transformMagnitude calculationReading image volume - second timeIntensity scalingExtractImageCorrected imageWriting bias field headerCorrected imageSaving corrected file 0. .`..1 Y, Y| Y Y ZH,H" Y (1 29$GS\jt^|HHHHHH@ (8@ @@@@ @@@$ , 4;IR]dpY {Y, `x  -H  [\D 1 xl 8h@ D8%h0 2 =x L<T\Z@@ eT o {   @8T T "8, !  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