Thank you Mark for clearing that up, so is it okay to use the GM mask or should I be generating a whole brain mask with fslmaths?
Many thanks
Reem
On 2/06/2011, at 19:28, "Mark Jenkinson" <[log in to unmask]> wrote:
> Hi Reem,
>
> The mask should be a mask of the non-zero probability voxels
> (so typically the brain mask).
>
> A threshold of 0 means that nothing passes FDR.
> It will hopefully change when you use the right mask.
>
> All the best,
> Mark
>
>
> On 2 Jun 2011, at 07:15, Reem Jan wrote:
>
>> Hi Steve, Gwenaelle and Hannah
>>
>> I’ve followed this thread and I had a similar question to Hannah which has been answered very well by Steve and Gwenaelle.
>>
>> As a consequence of this thread, I have applied FDR correction to my grot_vox_p_tstat images (after inverting them and obtaining the 1_minus_grot_vox_p_tstat images), and I had a simple question regarding the fdr command:
>>
>> Fdr –i 1_minus_grot_vox_p_tstat1 –m mask –q 0.05
>>
>> What kind of mask can we input here?
>> I tried running the fdr command without a mask and got the output “Probability threshold is 0”. What does this mean? Will this change if include a mask in the command?
>>
>> Your advice on this is much appreciated.
>>
>> Kind regards
>> Reem
>>
>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Stephen Smith
>> Sent: Wednesday, June 01, 2011 8:13 PM
>> To: [log in to unmask]
>> Subject: Re: [FSL] fsl VBM -clusters
>>
>> Hi
>>
>> On 31 May 2011, at 12:01, Hannah Bruehl wrote:
>>
>>
>> Hi to All,
>>
>> I ran an fsl VBM analysis in order to bolster my cortical thickness analysis. Uncorrected (tfce-p-tstat file), I see clusters in roughly the same area as in the CT analysis. I'd now like to extract all the relevant information about those clusters, which I understand I need to do using "cluster" and have 2 questions.
>> 1: is there a rule of thumb as to how many voxels one reports for an uncorrected p, say 300 and up or sth like this?
>>
>> We would not put it like this - in general you should use corrected p-values, whether you are doing voxelwise, clusterwise or TFCE-based thresholding - i.e. you should be using corrected p-values output by randomise, or else taking uncorrected p-values and feeding them into a further correction process such as FDR. Simply limiting the number of voxels in a cluster does not directly let you control what the corrected p-value is.
>>
>>
>> 2: apparently, the coordinates I get are in aligned anatomical space, since that is what it says when I open the relevant contrast in fslview. How to I get MNI or Talairach coordinates then?
>>
>> randomise works in the space of the data you feed into it. If you have used FSL-VBM then your group testing in randomise will almost certainly be in MNI152 space already.
>>
>>
>> and , related, how do i get a mean percentage about the structure the cluster is located in, since that is changing when clicking around in a given cluster within fslview?
>>
>> Do you mean wrt a particular atlas?
>>
>>
>>
>>
>>
>> Thanks,
>>
>> hannah
>>
>>
>>
>> ---------------------------------------------------------------------------
>> 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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