open-discussion
open-discussion > RE: Installation help
Nov 22, 2016 07:11 AM | Allen Waggoner
RE: Installation help
Originally posted by Rebecca Aaron:
Yes, that is correct. There is no reason for you to analyze the data on the host computer of the scanner. The data as you get it from the scanner will be in DICOM format. Most common fMRI analysis packages use the NIFTI format internally, but many of them can read and convert the Siemens DICOM files. If the package you choose can not read the Siemens DICOM files, then you can use the dcm2nii routine Juan mentioned (which is part of MRICron) to convert the data to NIFTI format. As Angela sort of pointed out, none of the typical packages for analyzing fMRI data have FDA approval, but since you said you are wanting to do this for research purposes that should not be a problem.
If your original question was really about what protocol to use on the scanner, look for a manual that came with your scanner entitled Operation Manual Neuro or maybe Operation Manual Neuro 3D. That manual will show you how to setup ep2d_bold sequence, which should already be on your scanner, to do fMRI experiments. Siemens service engineers may not be familiar with this protocol, but Siemens applications people should be, if they hesitate, show them the manual.
I and the others that have replied to you so far have assumed that you are either talking about protocols or fMRI analysis software, but it occurred to me that if you intend to do task based fMRI(as opposed to resting state), you might also be referring to stimulus presentation software. Stimulus presentation software also needs to be run on a separate computer from the scanner host computer. The ep2d_bold pulse sequence is setup to send a trigger pulse on a fiber-optic port from your console (or maybe a TTL port for older scanners) once per TR. You need to get that signal into the computer controlling the stimulus some way and use that trigger signal to change the states in your stimulus program. I know that at least NordicNeuroLab and Current Designs, there are probably other companies as well, sell devices that can take the scanner triggers and convert them into USB signals that look like keyboard presses. Keyboard presses should be easily accessible for any stimulus program that you write. There are lots of software packages available for doing stimulus presentations (https://en.wikipedia.org/wiki/Comparison...). You stimulus computer will of course need to be connected to a projector, or goggles, or headphones, or whatever type of device that you need to deliver the stimulus you want. There are a number of companies that sell MRI compatible, fMRI stimulation devices.
To summarize, to do fMRI you should not need to install any additional software on your scanner, but you do need to setup other computers for both stimulus presentation and data analysis. Setting up those computers is your responsibility, not Siemens.
Good luck,
Allen
So if I understand you correctly...you are
saying that we download the software on a separate device and then
put the images on that for analyzing then with the functional MRI
software?
Yes, that is correct. There is no reason for you to analyze the data on the host computer of the scanner. The data as you get it from the scanner will be in DICOM format. Most common fMRI analysis packages use the NIFTI format internally, but many of them can read and convert the Siemens DICOM files. If the package you choose can not read the Siemens DICOM files, then you can use the dcm2nii routine Juan mentioned (which is part of MRICron) to convert the data to NIFTI format. As Angela sort of pointed out, none of the typical packages for analyzing fMRI data have FDA approval, but since you said you are wanting to do this for research purposes that should not be a problem.
If your original question was really about what protocol to use on the scanner, look for a manual that came with your scanner entitled Operation Manual Neuro or maybe Operation Manual Neuro 3D. That manual will show you how to setup ep2d_bold sequence, which should already be on your scanner, to do fMRI experiments. Siemens service engineers may not be familiar with this protocol, but Siemens applications people should be, if they hesitate, show them the manual.
I and the others that have replied to you so far have assumed that you are either talking about protocols or fMRI analysis software, but it occurred to me that if you intend to do task based fMRI(as opposed to resting state), you might also be referring to stimulus presentation software. Stimulus presentation software also needs to be run on a separate computer from the scanner host computer. The ep2d_bold pulse sequence is setup to send a trigger pulse on a fiber-optic port from your console (or maybe a TTL port for older scanners) once per TR. You need to get that signal into the computer controlling the stimulus some way and use that trigger signal to change the states in your stimulus program. I know that at least NordicNeuroLab and Current Designs, there are probably other companies as well, sell devices that can take the scanner triggers and convert them into USB signals that look like keyboard presses. Keyboard presses should be easily accessible for any stimulus program that you write. There are lots of software packages available for doing stimulus presentations (https://en.wikipedia.org/wiki/Comparison...). You stimulus computer will of course need to be connected to a projector, or goggles, or headphones, or whatever type of device that you need to deliver the stimulus you want. There are a number of companies that sell MRI compatible, fMRI stimulation devices.
To summarize, to do fMRI you should not need to install any additional software on your scanner, but you do need to setup other computers for both stimulus presentation and data analysis. Setting up those computers is your responsibility, not Siemens.
Good luck,
Allen
Threaded View
| Title | Author | Date |
|---|---|---|
| Rebecca Aaron | Nov 18, 2016 | |
| Alex Dresner | Nov 20, 2016 | |
| Rebecca Aaron | Nov 21, 2016 | |
| Allen Waggoner | Nov 21, 2016 | |
| Angela Bernabeu | Nov 21, 2016 | |
| Rebecca Aaron | Nov 21, 2016 | |
| Allen Waggoner | Nov 22, 2016 | |
| Rebecca Aaron | Nov 28, 2016 | |
| Rebecca Aaron | Nov 28, 2016 | |
| Juan Felipe Orejuela | Nov 21, 2016 | |
| Scott Hoge | Nov 21, 2016 | |