MNI's Medical Imaging NetCDF format (output may not work) Legal values for -in_type (-it) and -out_type (-ot) are: Specifying the Input and Output File Types Use this number of slices when converting DICOM mosaics Output is embedded in a volume like name, or in stats-table like name (measure, columns, rows) If they do not, use tkregister2 to fix it.Īpply inverse transform given by xfm or m3z files. The main and aux volumes should overlap very closely. To evaluate the result, run: tkmedit -f $SUBJECTS_DIR/talairach/mri/orig.mgz -aux. This properly accounts for the case where the input volume does not have it's coordinate center at 0. To convert a subject's orig volume to talairach space, execute the following lines: cd subjectid/mri, mkdir talairach, mri_convert orig.mgz -apply_transform transforms/talairach.xfm -oc 0 0 0. An example of a transform file is talairach.xfm as found in subjectid/mri/transforms.
This reads the transform file and applies the transform (when -apply_inverse_transform is used, the transform is inverted an then applied). The volume can be resampled into another space by supplying a transform using the -apply_transform flag. Set the values outside of the image that may rotate in if a transform is applied to valĪpply transform given by xfm or m3z files. Output data is a stats table (use -like to pass template table for measure, columns, and rows heads)ĭon't change type of input to that of template Input data is a stats table as produced by asegstats2table or aparcstats2table Write out bshort/bfloat files in little endian Reduce voxel size by a factor of N in all dimensions Note: you can use tkregister2 to help determine the correct orientation string. Invalid combinations are detected immediately, an error printed, and the program exits. Some invalid ones are DPS (D is not a valid letter), RRS (can't specify R twice), RAP (A and P refer to the same axis). There are 48 valid combinations (eg, RAS LPI, SRI). Eg, if the volume is axial starting inferior and going superior the slice is oriented such that nose is pointing up and the right side of the subject is on the left side of the image, then this would correspond to LPS, ie, as the column increases, you move to the patients left as the row increases, you move posteriorly, and as the slice increases, you move superiorly. The third character of ostring determines the direction of increasing slice. The second character of ostring determines the direction of increasing row. The first character of ostring determines the direction of increasing column. You'll have to determine the correct ostring for your data. This is usually described by the direction cosine information as originally derived from the dicom but might not be available in all data sets. The ostring is three letters that roughly describe how the volume is oriented. (2) specify an orientation string with -in_orientation ostring and -out_orientation ostring Supply the orientation information in the form of an orientation string (ostring). If you don't know what a direction cosine is, don't use this method. (1) explicitly specify the direction cosines with -iid, -ijd, -ikd. OK, there are two ways to specify this information on the command-line. Finally, you risk incorporating a left-right flip in your data if you do it incorrectly. Second, don't think you are going to learn all you need to know from this documentation. Don't fool yourself into thinking otherwise. First of all, determining and setting the orientation is hard. For NIFTI, it is stored as the qform matrix. For analyze files, it will be stored in the output.mat file. However, if you have some way of knowing which direction is which, you can use these options to incorporate this information into the header of the output format. It is generally pretty easyto determine which direction Anterior/Posterior or Inferior/Superior are. Ideally, the orientation information is derived from a DICOM file so that you have some confidence that it is correct. If it is correct, this will make it wrong! If you are having problems with fslview displaying your data, consult the FSL website for methods to reorient. This is only to be used when the orientation information in the input file is *wrong*. Legal values for -in_tye (-it) and -out_type (-ot) are listed under optional flagged arguments.ĭo not use this to try to change the orientation for FSL. Second, the user can explicity set the type of file using -in_type and/or -out_type. img are assumed to be in spm analyze format). First, mri_convert will try to figure it out on its own from the format of the file name (eg, files that end in. The file type can be specified in two ways. Mri_convert is a general purpose utility for converting between different file formats. Specifying the Input and Output File Types.
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