Here, we made you work with fslroi to practice your command line skills, but using Python to do this is completely fine too. (You might wonder: well, why use fslroi while I could simply use Python to cut off the last two volumes? That’s a good point. T, origin = 'lower', cmap = 'gray' ) plt. figure ( figsize = ( 15, 5 )) for i in range ( func_fixed. isfile ( '' ): raise ValueError ( "Cannot find the file '' - did you name it correctly?" ) func_fixed = nib. Here, you can check if your fslroi command worked! It should show 10 volumes (vol 0-9), and the noise-volumes should be removed.''' if par_dir != 'solutions' : if not os. We’ll plot an axial slice for all 12 volumes below: Below, we loaded functional data from a very short run (only 12 volumes usually, runs are of course often much longer). For example, you can use it to remove the upper 20 slices in the X direction or remove several volumes (i.e., slicing in the “Time” direction, the fourth dimension of functional data). This command allows you to slice your file in several dimensions. get_fdata () print ( "Well done!" ) plot_ortho_slices ( t1 ) Īlright, let’s practice your CMD skills with one more nifty (pun intended) FSL command called fslroi. get_fdata () else : # admin account t1 = nib. isfile ( 't1w_' ): raise ValueError ( "Cannot find the file 't1w_' - did you name it correctly?" ) t1 = nib. ''' if par_dir != 'solutions' : # must be student account if not os. The slices should not be upside down anymore. Here, we test whether the reorientation process worked. To list the contents of your current directory, you can simply type ls. refers to the “parent directory”).Īnother useful command is ls, which stands for “list” and lists the contents of a directory. If you call the command pwd again, you should see that your current directory updated to /home/), you use the command: cd. ![]() Keep this tip in mind, as it will save you a lot of time when you need to execute long commands (e.g., cd /home/some/very/deeply/nested/directory/with/many/subdirectories). It won't complete your command all the way to cd week_5, because there are also other directories starting with week_ (i.e., week_1, week_2, etc.). ![]() ![]() For example, from your home directory, you can type cd w and then press the "tab" key, which will autocomplete the command to cd week_. I would be clear where the configuration of the threads has been defined, and the 1D, 2D and 3D access pattern depends on how you are interpreting your data and also how you are accessing them by 1D, 2D and 3D blocks of threads.Tip! In most terminals, you can use the tab key to "autocomplete" your commands. To sumup, it does it matter if you use a dim3 structure. Int y = blockIdx.y * blockDim.y + threadIdx.y īecause blockIdx.y and threadIdx.y will be zero. So, in both cases: dim3 blockDims(512) and myKernel>(.) you will always have access to threadIdx.y and threadIdx.z.Īs the thread ids start at zero, you can calculate a memory position as a row major order using also the ydimension: int x = blockIdx.x * blockDim.x + threadIdx.x The same happens for the blocks and the grid. When defining a variable of type dim3, any component left unspecified is initialized to 1. However, the access pattern depends on how you are interpreting your data and also how you are accessing them by 1D, 2D and 3D blocks of threads.ĭim3 is an integer vector type based on uint3 that is used to specify dimensions. The memory is always a 1D continuous space of bytes. The way you arrange the data in memory is independently on how you would configure the threads of your kernel.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |