I'd like to create some summary images (.tiff, .png ) so that I can quickly inspect subcortical structure segmentation quality on a large number of subjects.
I know I can open tkmedit and extract a series of tiff images, I've also been playing with Slicer3 but again I have to load the data for each subject.
I'd also like to hone in on particular structures, for example, to extract images only showing the hippocampus (whole segmentation or outline) on the T1 3D backdrop, does anything exist in Freesurfer to do this from the command line?
Essentially I'm looking for something similar to the first_roi_slicerdir command in FSL as I found this a really quick way of visually checking segmented data.
Any advice around this would be a great help,
Thanks John
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Hi John
we do have some scripts around that will create webpages of snapshots, and in the upcoming release freeview will also support the syntax:
freeview -v vol.mgz:structure=17 ...
to automatically compute the slice that contains the most of label 17 (left hippocampus in this case). You can also specify the slice orientation and that it should take a snapshot and exit. The nmovie utility is then handy for zipping through a bunch of snapshots.
Note that putting together a pipeline for easy reviewing of large numbers of datasets is something we are going to be working on. Also, you might check with JB Poline (ccd), as I know it's something he has thought about seriously.
cheers Bruce
On Thu, 14 Apr 2011, McLean John (NHS Greater Glasgow & Clyde) wrote:
I'd like to create some summary images (.tiff, .png ) so that I can quickly inspect subcortical structure segmentation quality on a large number of subjects.
I know I can open tkmedit and extract a series of tiff images, I've also been playing with Slicer3 but again I have to load the data for each subject.
I'd also like to hone in on particular structures, for example, to extract images only showing the hippocampus (whole segmentation or outline) on the T1 3D backdrop, does anything exist in Freesurfer to do this from the command line?
Essentially I'm looking for something similar to the first_roi_slicerdir command in FSL as I found this a really quick way of visually checking segmented data.
Any advice around this would be a great help,
Thanks John
This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful.
Thank you for your co-operation.
NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere For more information and to find out how you can switch, visit www.connectingforhealth.nhs.uk/nhsmail
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Bruce Fischl -
McLean John (NHS Greater Glasgow & Clyde)