Hi,
On 21 May 2008, at 13:01, Eva Kenny wrote:
> Dear FSL,
>
> Please could you tell me if it is possible to find the peak
> coordinates
> from the Melodic IC results. Ideally I would like an output which
> tells me
> the peak activation areas for IC 1, IC 2 and so on. Is this possible?
Yes, you can extract the relevant timepoint from melodic_IC using
fslroi and then use the -x option in fslstats.
If you want more than one maximum (ie local maxima) then you can use
the cluster command.
Cheers, Steve.
>
>
> I read the email discussion below but was unsure what I enter as the
> threshold. Should it be 2.3, or is there somewhere I can find the
> threshold
> for each IC. I had a look in the Melodic stats folder the first 2
> columns
> are the variance, but I was unable to work out what the next 2
> columns are.
>
> Many thanks in advance for your help on this,
> Eva
>
>
> On Tue, 30 Jan 2007 16:15:09 +0000, Steve Smith <[log in to unmask]>
> wrote:
>
>> 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
>> ------------------------------------------------------------------------
>> ---
>> =
>> =
>> =
>> =
>> =====================================================================
>
---------------------------------------------------------------------------
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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