Hi - if you just type "cluster" you get the full usage - this
explains how to get the cluster index image which should give you
what you want.
Cheers.
On 30 Jan 2007, at 15:52, Wen-Ching Liu wrote:
> Hi Steve:
>
> Thanks for replying.
>
> Is there any other simple way to generate the "cluster_mask_zstats"
> using the output of Melodic ? The results from "cluster" are
> good, however,
> I won't be able to pin point which point belongs to which cluster.
> If there is a simple way to generate the "cluster_mask_zstats", it
> would be great.
>
> Thanks for sharing this great tool (FSL).
>
> best regards,
>
> Wen
>
>
> On Jan 30, 2007, at 3:39 AM, Steve Smith wrote:
>
>> Hi, these features come from running a FEAT analysis, not just by
>> running the cluster command, so this is as expected.
>> Cheers, Steve.
>>
>>
>> On 29 Jan 2007, at 23:20, Wen-Ching Liu wrote:
>>
>>> Hi Christian:
>>>
>>> After using the "cluster" command, I am able to display a list of
>>> the clusters with
>>> the threshold of 2.3. The output file is able to display the
>>> clusters using fslviewer.
>>> However, I was not able to generate the "cluster_mask_zstats"
>>> and the option of "cluster browser" in fslviewer was not able to
>>> be activated.
>>> I think probably I did not use the correct "options" or I did
>>> something wrong.
>>>
>>> Please advise. Thanks a lot.
>>>
>>>
>>> Wen
>>>
>>>
>>> On Jan 27, 2007, at 12:07 PM, Wen-Ching Liu wrote:
>>>
>>>> Hi Christian :
>>>>
>>>> Thanks, I will give it a try.
>>>>
>>>>
>>>> Wen
>>>>
>>>> ----- Original Message -----
>>>> From: Christian Beckmann <[log in to unmask]>
>>>> Date: Friday, January 26, 2007 5:19 pm
>>>> Subject: Re: [FSL] cluster for Melodic
>>>>
>>>>> Hi
>>>>>
>>>>> creating output similar to feat output is easy, just run 'cluster'
>>>>> on
>>>>> any of the melodic components - you'd just have to pick a
>>>>> threshold
>>>>> level. This you can get from the melodic thresholded maps (in
>>>>> blah.ica/stats when you click the 'Output full stats folder'
>>>>> option
>>>>> or when selecting --Ostats or --Oall at the command line). You can
>>>>>
>>>>> check for the lowest non-zero value in the thresholded maps (with
>>>>> avwmaths and avwstats) and then use this on the an unthresholded
>>>>> melodic map. You can extract separate maps from the 4D file
>>>>> melodic_IC using 'avwroi' or you can use avwsplit to split the 4D
>>>>> file into a sequence of 3d files).
>>>>> Using this to identify subclusters and location of local maxima is
>>>>>
>>>>> fine, though you should be careful not to confuse the Z maps
>>>>> generated by melodic with FEAT z maps generated under the null
>>>>> hypothesis when regressing against a design matrix.
>>>>> hope this helps
>>>>> christian
>>>>>
>>>>>
>>>>> On 26 Jan 2007, at 21:27, Wen-Ching Liu wrote:
>>>>>
>>>>>> Dear FSL users:
>>>>>>
>>>>>> I had posted a question yesterday to see if there is an easy way
>>>>>> to get the cluster information from Melodic program. Since
>>>>> there was
>>>>>> no answer, I assume there is no easy way to do it. I wonder how
>>>>>> difficult would this be. Can someone comment on this?
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>>
>>>>>>
>>>>>> Wen-Ching Liu, Ph.D.
>>>>>>
>>>>>> Assistant Professor
>>>>>> Functional Imaging Laboratory
>>>>>> Department of Radiology
>>>>>> University of Medicine and Dentistry
>>>>>> of New Jersey-New Jersey Medical School
>>>>>>
>>>>>> 973-972-2281/fax: 973-972-0836
>>>>>> http://njms.umdnj.edu/departments/radiology/fmri/index.cfm
>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> Christian F. Beckmann
>>>>> Oxford University Centre for Functional
>>>>> Magnetic Resonance Imaging of the Brain,
>>>>> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
>>>>> Email: [log in to unmask] -
>>>>> http://www.fmrib.ox.ac.uk/~beckmann/ Phone: +44(0)1865 222551
>>>>> Fax: +44(0)1865 222717
>>>>>
>>>
>>> Wen-Ching Liu, Ph.D.
>>>
>>> Assistant Professor
>>> Functional Imaging Laboratory
>>> Department of Radiology
>>> University of Medicine and Dentistry
>>> of New Jersey-New Jersey Medical School
>>>
>>> 973-972-2281/fax: 973-972-0836
>>> http://njms.umdnj.edu/departments/radiology/fmri/index.cfm
>>>
>>>
>>
>>
>> ---------------------------------------------------------------------
>> ------
>> 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
>> ---------------------------------------------------------------------
>> ------
>
> Wen-Ching Liu, Ph.D.
>
> Assistant Professor
> Functional Imaging Laboratory
> Department of Radiology
> University of Medicine and Dentistry
> of New Jersey-New Jersey Medical School
>
> 973-972-2281/fax: 973-972-0836
> http://njms.umdnj.edu/departments/radiology/fmri/index.cfm
>
>
------------------------------------------------------------------------
---
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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