Sorting Dicoms

AFNI Message Board
1

Hello AFNI Experts,

We have recently collected some data from the Martinos Center. They way it is collected all of the scans from the entire protocol (resting state, task, DWI) are in one folder. I would like to be able to sort the dicoms into their appropriate run…so that I have a folder with the task data, folder with DWI data, etc. These were collected via a Siemens scanner I believe. At this point, I do not want to convert them to AFNI or NIFTI files, I would just like to sort the dicoms.

I have been looking into the Dimon data set.

As a first pass, I simply entered the following command for one subject:

Dimon Biograph_mMR-51006-20160907-103311-000700/MR* -dicom_org

I get the following error: Argument list too long.

Any thoughts? Can I use Dimon for this type of issue?

Thanks,

Emily

2

Hi Emily,

Dimon really likes each run to be separated into separate folders. Fortunate, there’s a script for that - @move.to.series.dirs. On data I have from Martinos it has worked quite well. You can then run Dimon to later convert each series on each resulting folder separately.

Best,
Peter

3

Thanks Peter! So I am getting an error: /Users/emilybelleau/abin/@move.to.series.dirs: Argument list too long.

I used the following command: @move.to.eries.dirs Biograph_mMR-51006-20160907-103311-000700/MR*

I also have files that begin with PT (pet scan), which I plan to do in a separate script.

Any thoughts?

Thanks so much!

Emily

4

Hi Peter,

I think what is happening is that these are 3D DICOM files, such that a whole volume is contained in a single file. Would this script be able to handle something like this?

Thanks,
Emily

5

Hi Emily,

The script is not even starting due to the shell
error, so the 3D format is not yet relevant. I am
adding a little update so that you can ask the
AFNI programs to do the globbing. Give me a
moment…

  • rick
6

Hi Emily,

There is now a -glob option in @move.to.series.dirs,
so you should be able to call it like this, adding -glob
and putting the wildcard in quotes:

@move.to.series.dirs -glob 'Biograph_mMR-51006-20160907-103311-000700/MR*'

If you want this immediately, I can send you 2 files
via email to put into your abin. If you want to wait
until tonight, I will do a build and it will be available
sometime between 5 and 6 pm, say.

Just let me know if you want that right away.

  • rick
7

Hi Emily,

This update was ready yesterday afternoon, so please
feel to give it a try if you wish to. You should be able to
update to the current version using:

@update.afni.binaires -d

After which “afni -ver” should show version AFNI_16.2.18 .

Please let me know how it goes.

Thanks,

  • rick
8

Thanks so much Rick! I appreciate it! What a big help!

Emily

9

Glad it worked for you!

  • rick