Greetings,
Thank you for the answer. We are currently collecting data so it seems MIST will be something to try out soon.
I could not find materials for running the vertex analysis. I would be grateful to have those instructions.
All the very best,
Jetro
From: Mark Jenkinson <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Wednesday, 15 August 2018 at 0.25
To: "[log in to unmask]" <[log in to unmask]>
Subject: Re: [FSL] Manual edits to FIRST output
Hi,
I'm afraid I don't quite understand what you want.
If you have already edited the images then there is nothing more to do to obtain a mask - you've just created it. So I would not run any FIRST boundary correction script afterwards, as you've already done a manual boundary correction.
Unfortunately it is very difficult to redo the training for FIRST and you would probably need hundreds of images to do a good job. However, you can use MIST and is something that you could try if you were interested. But if you only have a limited dataset and you've already done the manual editing, then there isn't anything to gain from running MIST or FIRST. If you have not manually edited all the images and you've got a lot left to do then it would be worth trying MIST.
If you want to do a vertex analysis on your manually edited data then you can't use the standard scripts but I did propose a method on the FSL email list a while ago that would do this if you are interested.
All the best,
Mark
On 25 Jul 2018, at 08:01, Jetro Tuulari <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Greetings,
I am currently working on a pediatric data set.
I used FSL FIRST tool to obtain the subcortical segmentation by using run_first_all command but would like to perform minor edits to some of the structures.´I manually edited the boundaries to fit the structures.
Questions
1. I would like to confirm that this would be the correct way of running the analysis on the edited images
a. first_boundary_corr with –b none to keep all the boundary voxels (that I have edited manually)
b. first_mult_bcorr
2. Should I preferably run the above steps to each of the structures separately?
3. Would it be possible to use my data to replace augment or alternatively replace the MGH templates that FIRST uses?
Thank you in advance for your help!
All the very best,
Jetro Tuulari
M.D. / PhD
University of Turku
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