Hi - it is for the cluster-forming threshold (as opposed to the final
p-value thresholding). In your case you have already thresholded so
you can set this to e.g. 0.00001
Cheers.
On 26 Dec 2007, at 08:29, Naama Barnea-Goraly wrote:
>
> Thank you so much for your reply. One more question - then what
> would the threshold be in "cluster" ( -t --thresh). Does it refer to
> the p-value?
>
> Thanks,
>
> Naama
>
> On Dec 24, 2007, at 12:16 PM, Steve Smith wrote:
>
>> Hi,
>>
>> On 21 Dec 2007, at 22:06, Naama Barnea-Goraly wrote:
>>
>>>
>>> Dear FSL list,
>>>
>>> Questions about extracting values from clusters of significant FA
>>> differences generated in TBSS:
>>>
>>> 1. How can I get a list of clusters by size with coordinates of
>>> peak differences ect (kind of like the table in SPM?). I tried to
>>> use cluster on my tbss_maxc_tstat image but I get only one cluster
>>> and it looks like there should be more. Plus I don't get the
>>> values of peak differences within the cluster.
>>
>> If you mask the tstat image with the maxc, something like
>> fslmaths grot_maxc_tstat1 -thr 0.95 -bin -mul grot_tstat1
>> clusters_grot_tstat1
>> then you can feed this output into cluster and tell it to output
>> local maxima etc. This should give you everything you want; it just
>> won't ive you p-values for the clusters, but you already know that
>> all clusters are p<0.05 corrected.
>>
>>> 2. How to separate the clusters to extract values from each
>>> cluster separately?
>>
>> The above should do that, in the same way that FEAT does. Also, if
>> you use the -o option to cluster, you can get an image of cluster-
>> index-number output as well.
>>
>>> Once I have the peak coordinates with the cluster I can generate
>>> the list of values using fslmeants - but what radius does it use?
>>> If I want to get values of the voxel only within the limits of my
>>> significant cluster do I use:
>>>
>>> fslmeants -i all_FA_skeletonised -c x, y, z -m my_mask ?
>>
>> Yes - you can select individual clusters by running the cluster-
>> index-number output image through fslmaths first.
>>
>> Cheers.
>>
>>>
>>>
>>> Is there a manual for these operations? If so I am sorry for
>>> missing it..
>>>
>>> Thank you so much for your help,
>>>
>>> Naama
>>>
>>>
>>> Naama Barnea-Goraly M.D.
>>> Research Associate
>>> Center for Interdisciplinary Brain Sciences Research
>>> Stanford University Division of Child and Adolescent Psychiatry
>>> 401 Quarry Rd. MC 5795
>>> Stanford University School of Medicine
>>> Stanford, CA 94305-5795
>>> fax: (650) 724-4794
>>> Phone: (650) 724-3779
>>>
>>>
>>> CONFIDENTIALITY NOTICE: This e-mail communication and any
>>> attachments may contain confidential information for the use of
>>> the designated recipients named above. If you are not the
>>> intended recipient, you are hereby notified that you have received
>>> this communication in error and that any review, disclosure,
>>> dissemination, distribution or copying of it or its contents is
>>> prohibited. If you have received this communication in error,
>>> please notify Stanford Medical Center immediately by telephone at
>>> (650) 725-5722 and destroy all copies of this communication and
>>> any attachments. Thank you.
>>>
>>>
>>
>>
>> ---------------------------------------------------------------------------
>> Stephen M. Smith, Professor of Biomedical Engineering
>> Associate Director, Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>> +44 (0) 1865 222726 (fax 222717)
>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>> ---------------------------------------------------------------------------
>
>
> Naama Barnea-Goraly M.D.
> Research Associate
> Center for Interdisciplinary Brain Sciences Research
> Stanford University Division of Child and Adolescent Psychiatry
> 401 Quarry Rd. MC 5795
> Stanford University School of Medicine
> Stanford, CA 94305-5795
> fax: (650) 724-4794
> Phone: (650) 724-3779
>
>
> CONFIDENTIALITY NOTICE: This e-mail communication and any
> attachments may contain confidential information for the use of the
> designated recipients named above. If you are not the intended
> recipient, you are hereby notified that you have received this
> communication in error and that any review, disclosure,
> dissemination, distribution or copying of it or its contents is
> prohibited. If you have received this communication in error,
> please notify Stanford Medical Center immediately by telephone at
> (650) 725-5722 and destroy all copies of this communication and any
> attachments. Thank you.
>
>
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------
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