indi
indi > RE: Starting with this project
Jan 17, 2011 03:01 PM | Maarten Mennes
RE: Starting with this project
Hi Carolina,
There are two versions of the project: 1 that comes with the XNAT databasing system and 1 that comes without XNAT. The information and datasets included in both are exactly the same, it is the way things are stored and used that are different.
If you downloaded the XNAT version you can use the XNAT system to search trough the different datasets you downloaded and look at the various phenotypic information included. To start that you would double-click the INDI icon on the desktop of the VM. If you find datasets that you would like to analyze (e.g., all children between 7-18y), then you could select them and select 'download images' for those. That way you would download their scans to a new folder where you can start analyzing them. This could be done with the fcon_1000 scripts, yet those require nifti images.
The xml file you see in the folders you downloaded from the site are what gets added to XNAT if you run the uploadXML script. That actually adds all of that subject's information and imaging data to XNAT. From within XNAT you would have to 'download' them again (as explained above) to be able to process the images.
Alternatively you have the LITE release that do not require XNAT, nor the VM. They are just a collection of folders/images and a spreadsheet that contains the phenotypic information. Here, you are responsible yourself for storing them how you'd like and you would have to use e.g., excel to search through the spreadsheet. You can however immediately start processing the scans with the fcon_1000 scripts, provided you have the nifti version. We also provide the DICOM version for users how prefer DICOM over nifti and maybe already have their own processing path set up. With that said, you don't need to use the fcon_1000 scripts. If you already have a processing path in place, then by all means use that one. We made the scripts available for users who don't have a processing path in place, who would like to see what steps we applied, etc. They are free to use and modify in whatever way you want...
Maarten
There are two versions of the project: 1 that comes with the XNAT databasing system and 1 that comes without XNAT. The information and datasets included in both are exactly the same, it is the way things are stored and used that are different.
If you downloaded the XNAT version you can use the XNAT system to search trough the different datasets you downloaded and look at the various phenotypic information included. To start that you would double-click the INDI icon on the desktop of the VM. If you find datasets that you would like to analyze (e.g., all children between 7-18y), then you could select them and select 'download images' for those. That way you would download their scans to a new folder where you can start analyzing them. This could be done with the fcon_1000 scripts, yet those require nifti images.
The xml file you see in the folders you downloaded from the site are what gets added to XNAT if you run the uploadXML script. That actually adds all of that subject's information and imaging data to XNAT. From within XNAT you would have to 'download' them again (as explained above) to be able to process the images.
Alternatively you have the LITE release that do not require XNAT, nor the VM. They are just a collection of folders/images and a spreadsheet that contains the phenotypic information. Here, you are responsible yourself for storing them how you'd like and you would have to use e.g., excel to search through the spreadsheet. You can however immediately start processing the scans with the fcon_1000 scripts, provided you have the nifti version. We also provide the DICOM version for users how prefer DICOM over nifti and maybe already have their own processing path set up. With that said, you don't need to use the fcon_1000 scripts. If you already have a processing path in place, then by all means use that one. We made the scripts available for users who don't have a processing path in place, who would like to see what steps we applied, etc. They are free to use and modify in whatever way you want...
Maarten