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Practice Working with Data

In this exercise, you will take what you've learned from the course & tutorials so far and apply it to a new dataset.


Preparations

If You're at an Organized Course

If you are taking one of the formally organized courses, everything has been set up for you on the provided laptop. The only thing you will need to do is run the following commands in every new terminal window (aka shell) you open throughout this tutorial. Copy and paste the commands below to get started:

export SUBJECTS_DIR=$TUTORIAL_DATA/practice_with_data
cd $SUBJECTS_DIR


To copy: Highlight the command in the box above, right click and select copy (or use keyboard shortcut Ctrl+c), then use the middle button of your mouse to click inside the terminal window (this will paste the command). Press enter to run the command. These two commands set the SUBJECTS_DIR variable to the directory where the data is stored and then navigates into this directory. You can now skip ahead to the tutorial (below the gray line).

If You're not at an Organized Course

If you are NOT taking one of the formally organized courses, then to follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own data paths and subject names. These are the commands that you need to run before getting started:

<source_freesurfer>
export TUTORIAL_DATA=<path_to_your_tutorial_data>
export SUBJECTS_DIR=$TUTORIAL_DATA/practice_with_data
cd $SUBJECTS_DIR


Finding the correct input for the FreeSurfer pipeline

Let's pretend that you just finished scanning a research subject. You collected several different kinds of scans. You would like to get reconstructed surfaces off of this data. What do you do first?

Presumably, you have copied the dicoms for this subject off the scanner to somewhere else. Running the dcmunpack command on the directory in which the dicoms are located creates a text file showing the name of the scan (as you named it on the scanner) and the dicom series each scan corresponds with. From there, you can identify the T1-weighted image you want to use as input to FreeSurfer.

For the purposes of this tutorial, we have a directory of dicoms for you to work with here:

$TUTORIAL_DATA/practice_with_data/dicoms

Open a terminal window. It will be easiest to 'cd' into the directory above to work with the dataset.

Now, run the help flag to learn how to set up the dcmunpack command to create the text file mentioned above:

dcmunpack -help

Type your best guess at the correct command and corresponding flags into the terminal window and see if it works. If it's not working and you give up, scroll down past the arrows to see the correct command setup.

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dcmunpack -src . -scanonly scan.log

Some explanation on the command:

Depending on how many dicoms are in the directory, this command can take a few minutes to a half hour to run. If it is taking too long, feel free to hit Ctrl+c to cancel it and look at the files that were created when we ran this command previously (details below).

Running the dcmunpack command above creates the text file scan.log as well as unpack.log and dicomdir.sumfile. Feel free to use more or any text editor (gedit, emacs, pico, etc.) to view these files. Typically, it is only necessary to check the scan.log:

more scan.log

For the purposes of this tutorial, we have only put a few dicoms in this practice directory. When you look at your scan.log, you'll see:

 13      T1w_MPR_vNav_4e  ok  256 256 176   1 mri00001.dcm
 18        rfMRI_REST_AP  ok  104 104  72 600 mri00177.dcm

A typical scan.log may look something like this (make your browser window as wide as possible):

  1            Localizer  ok  256 256   3   1 mri00003.dcm
  2             AAHScout  ok  160 160 128   1 mri00004.dcm
  3             AAHScout  ok  162 162   5   1 mri00133.dcm
  4             AAHScout  ok  162 162   3   1 mri00139.dcm
  5             AAHScout  ok  162 162   3   1 mri00141.dcm
  6    Localizer_aligned  ok  256 256   9   1 mri00151.dcm
  7           T1w_setter  ok   32  32  32   1 mri00152.dcm
  8      T1w_MPR_vNav_4e err  192 192  23   1 mri00305.dcm
  9      T1w_MPR_vNav_4e  ok  256 256 176   4 mri00345.dcm
 10      T1w_MPR_vNav_4e  ok  256 256 176   4 mri00344.dcm
 11      T1w_MPR_vNav_4e  ok  256 256 176   4 mri00343.dcm
 12      T1w_MPR_vNav_4e  ok  256 256 176   1 mri00391.dcm
 13      T1w_MPR_vNav_4e  ok  256 256 176   1 mri00392.dcm
 14 gre_field_mapping_2mm  ok   64  64  72   1 mri02842.dcm
 15  SpinEchoFieldMap_AP  ok  936 936   1   3 mri02879.dcm
 16  SpinEchoFieldMap_PA  ok  936 936   1   3 mri02882.dcm
 17        rfMRI_REST_AP  ok  936 936   1   1 mri02885.dcm
 18        rfMRI_REST_AP  ok  936 936   1 600 mri02886.dcm
 19        rfMRI_REST_AP  ok    0   0   1   1 mri03485.dcm
 20 t1_mp2rage_sag_p3_iso_TI_0700-2500  ok  256 240 176   1 mri03489.dcm
 21 t1_mp2rage_sag_p3_iso_TI_0700-2500  ok  256 240 176   1 mri03487.dcm
 22 t1_mp2rage_sag_p3_iso_TI_0700-2500  ok  256 240 176   1 mri03498.dcm
 23 t1_mp2rage_sag_p3_iso_TI_0700-2500  ok  256 240 176   1 mri03495.dcm
 24 t1_mp2rage_sag_p3_iso_TI_0700-2500  ok  256 240 176   1 mri03519.dcm
 25 t1_mp2rage_sag_p3_iso_TI_0700-2500  ok  256 240 176   1 mri03520.dcm
 26 t1_mp2rage_sag_p3_iso_TI_1300-2700  ok  256 240 176   1 mri04572.dcm
 27 t1_mp2rage_sag_p3_iso_TI_1300-2700  ok  256 240 176   1 mri04567.dcm
 28 t1_mp2rage_sag_p3_iso_TI_1300-2700  ok  256 240 176   1 mri04586.dcm
 29 t1_mp2rage_sag_p3_iso_TI_1300-2700  ok  256 240 176   1 mri04588.dcm
 30 t1_mp2rage_sag_p3_iso_TI_1300-2700  ok  256 240 176   1 mri04544.dcm
 31 t1_mp2rage_sag_p3_iso_TI_1300-2700  ok  256 240 176   1 mri04543.dcm
 32        t2_tse_ax-2mm  ok  512 512  27   1 mri05614.dcm
 33           T2w_setter  ok   32  32  32   1 mri05626.dcm
 34         T2w_SPC_vNav err  192 192  17   1 mri05663.dcm
 35         T2w_SPC_vNav  ok  256 256 176   1 mri05758.dcm
 36         T2w_SPC_vNav  ok  256 256 176   1 mri05757.dcm
 37 gre3D_1iso_PAT2x2_12e  ok  256 256 176  12 mri06089.dcm
 38 gre3D_1iso_PAT2x2_12e  ok  256 256 176  12 mri06083.dcm
 39 gre3D_1iso_PAT2x2_12e  ok  256 256 176  12 mri06081.dcm
 40 gre3D_1iso_PAT2x2_12e  ok  256 256 176   1 mri06099.dcm
 41 dMRI_dir98_AP_Blue_Umbrella  ok  1400 1400   1   1 mri12593.dcm
 42 dMRI_dir98_AP_Blue_Umbrella  ok  1400 1400   1  99 mri12594.dcm
 43 dMRI_dir98_AP_Blue_Umbrella  ok    0   0   1   1 mri12693.dcm
 44 t1_mp2rage_sag_p3_iso_TI_1900-3210  ok  256 240 176   1 mri12713.dcm
 45 t1_mp2rage_sag_p3_iso_TI_1900-3210  ok  256 240 176   1 mri12712.dcm
 46 t1_mp2rage_sag_p3_iso_TI_1900-3210  ok  256 240 176   1 mri12717.dcm
 47 t1_mp2rage_sag_p3_iso_TI_1900-3210  ok  256 240 176   1 mri12716.dcm
 48 t1_mp2rage_sag_p3_iso_TI_1900-3210  ok  256 240 176   1 mri12731.dcm
 49 t1_mp2rage_sag_p3_iso_TI_1900-3210  ok  256 240 176   1 mri12737.dcm
 50              BIAS_BC  ok  128 128  88   1 mri13750.dcm
 51            BIAS_32ch  ok  128 128  88   1 mri13902.dcm
 52            BIAS_32ch  ok  128 128  88   1 mri13840.dcm
 53   T1w_MPR_ABCD_800um  ok  320 300 208   1 mri14015.dcm
 54              tfl_DBS  ok  320 260 160   1 mri14379.dcm
 55        t2_tse_ax-2mm  ok  512 512  27   1 mri14395.dcm
 56    T2w_SPC_HCP_700um  ok  320 320 256   1 mri14409.dcm
 57    T2w_SPC_HCP_700um  ok  320 320 256   1 mri14468.dcm
 58        t2_tse_ax-2mm  ok  512 512  27   1 mri14934.dcm

If you were there at the scan, you probably know which scan above was intended to be the T1-weighted input to FreeSurfer. If you don't, you're typically looking for something called MPRAGE, MEMPRAGE, or SPGR with dimensions 256 x 256 x 176. In the above example, the scan we're interested in is called T1w_MPR_vNav_4e ("vNav" indicates navigators were used for motion correction and "4e" indicates 4 echoes were collected).

Some additional information about the above scan.log: Although T1w_MPR_vNav_4e is listed 6 times, this does not mean 6 of these scans were collected. Notice "err" for error after the first instance of T1w_MPR_vNav_4e as well as the incorrect dimensions. Notice that for some of the scans, there are 4 images in the series (indicated by the 4 following the numbers 256 256 176) and for some there is only 1 image in the series. The difference here is that dicom series with 4 images will provide the 4 echoes uncombined (as separate image files) while the other has combined the echoes by taking the RMS (root mean square) or "average" of the echoes.

We plan to use the RMS as input for FreeSurfer, therefore we will use this T1-weighted dicom series, as seen in the scan.log you produced:

 13      T1w_MPR_vNav_4e  ok  256 256 176   1 mri00001.dcm

Now that you've identified the scan you want to use as input to FreeSurfer, what command do you need to use to create surfaces on it?

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The correct answer is recon-all. But wait! Before we run that command, there are a few other matters to take care of...

First, before processing a subject with FreeSurfer, you always want to make sure you have:

  1. Sourced FreeSurfer (already done for you if you're at an organized course).

  2. Set the SUBJECTS_DIR variable to the location where the FreeSurfer output should go (make sure there is enough space [around ~300MB])!

For this exercise, let's put the FreeSurfer output directory for this subject just above the dicoms directory you have been working in. You can check where the SUBJECTS_DIR variable is currently set to by doing:

echo $SUBJECTS_DIR

If the output you get from the above command is not the directory above the dicoms directory, how would you change it to set it correctly?
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export SUBJECTS_DIR=$TUTORIAL_DATA/practice_with_data

Or, if you're not at an organized course and you're using a tcsh shell instead of bash, you would use setenv instead of export. (More info on this command and the different shells is here.)

Once your SUBJECTS_DIR is set, you can type up the recon-all command needed to process a subject using dicoms as the input. Try it out before looking at the answer. If things go horribly wrong, you can always do Ctrl+c to stop it :).

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Hint:

recon-all \
  -all \
  -i  <one slice in the anatomical dicom series> \
  -s  <subject id that you make up> \

Some explanation on the command:

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The answer (assumes you are still inside the dicoms directory):

recon-all -all -i mri00001.dcm  -s  Subj001

Feel free to run the command. You can let it run overnight or stop it at any point using Ctrl+c.

The command will create a new directory, called Subj001, in the directory above the dicoms directory. You can cd to that directory to see what has been created so far but you will have to open a new terminal window to do this if recon-all is still running.

The process is complete when the last line printed to the screen (and in the recon-all.log found in the subject's scripts directory) says "recon-all exited without errors". If you do let recon-all complete, you can use the freeview commands you learned in the other tutorials to open and inspect the data.

Batch Processing

Say you have DICOM files for hundreds of subjects and you want to process them using FreeSurfer. You can submit them to recon-all with just a couple of commands. For a sample script, look here. This information is linked to the course homepage at the bottom under "Additional Useful Information."


Summary

By the end of this exercise, you should know how to:

FsTutorial/Practice (last edited 2018-08-08 16:11:47 by EmmaBoyd)