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The output from the cluster command is the file to feed to the --label argument of fslmeants.

You'll use your corrp image from the TBSS analysis as the input to that command.

Be warned - if the clusters are touching just a little bit then you'll still get one big cluster and it's quite hard to break up. You could consider masking with an atlas file from $FSLDIR/data/atlases.

Kx

Sent from my iPhone, please excuse any typos or excessive brevity

On 16 Jan 2014, at 01:08, Andrew Martin <[log in to unmask]> wrote:

Yeah I have run a group analysis and want to extract values for the 4 significant clusters. I have created a cluster image and entered that into fslmeants with the all_FA_skelotonised.nii.gz image but I can't seem to get the --label command to work. What file should follow the --label command?


Thanks so much for your help
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Kirstie Whitaker [[log in to unmask]]
Sent: Thursday, 16 January 2014 10:30 AM
To: [log in to unmask]
Subject: Re: [FSL] fslmeants with more than 1 cluster

I'm not quite sure what you're asking. There are two possibilities:

If you are using individual subject's original scans, and therefore a mask in subject space rather than MNI space (that maybe you've back projected using fnirt or flirt) then you can use fslstats with the -k and -M flags. You could still run fslmeants, you'll only get one subject's values that way, but at least you'll have your values from the cluster. You could write a little for loop to speed up the extraction.

If you have run a group analysis (eg: TBSS, VBM) and you want to extract values from a cluster that shows a significant results then you can run fslmeants on the (eg) all_FA.nii.gz or all_FA_skeletonised.nii.gz image. These are 4D files that have images for all participants and importantly they're all in the same space as the result file that you'll pass to the cluster command.

I hope this helps.

Kx




On 16 January 2014 00:19, Andrew Martin <[log in to unmask]> wrote:
Thanks Kristie
When using fslmeants, do I use the _FA.nii.gz files for each individual in the origdata folder as the input file?
Regards
Andrew
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Kirstie Whitaker [[log in to unmask]]
Sent: Thursday, 16 January 2014 9:43 AM
To: [log in to unmask]
Subject: Re: [FSL] fslmeants with more than 1 cluster

The --label option with fslmeants is what you want. You'll need to run the cluster tool (called cluster: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Cluster) on your FA results file first in order to make the cluster image that you need. Save it using the -o flag in cluster and pass that output file to fslmeants.

Kx


On 15 January 2014 23:34, Andrew Martin <[log in to unmask]> wrote:
Hi experts
I have a mask with 4 clusters in and I want to extract the individual participants FA values within each cluster. If I use fslmeants -i filtered_func_data -o meants.txt -m my_mask I'm assuming it will average over all 4 clusters and provide 1 value. Is there a way to extract 4 values or do I need to create 4 masks?
Regards
Andrew



--
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

Mailing Address
Douglas House
18b Trumpington Road
Cambridge, CB2 8AH

Phone: +44 7583 535 307
Website: www.kirstiewhitaker.com



--
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

Mailing Address
Douglas House
18b Trumpington Road
Cambridge, CB2 8AH

Phone: +44 7583 535 307
Website: www.kirstiewhitaker.com