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?
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
>------------------------------------------------------------------------
>---
>=========================================================================
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