Just to add one quick comment, I've always found that cluster outputs
a maximum of 3 decimal places and thus explains the value of 1 due to
rounding. Looking at the actual coordinates (e.g. fslview, or matlab),
will give the precise value.
On Mon, Dec 1, 2014 at 5:21 AM, Alshikho, Mohamad J.
<[log in to unmask]> wrote:
> Dear Anderson,
> I highly appreciate your interest in my issue!
> Sure! I checked all the images. For the subjects one, by one then I checked
> the (slicesdir) from the output of tbss_1_preproc *.nii.gz.
> The images looks fine.
> After Randomise I checked the *_Corrp_* images, Also they look fine.
>
> I ran fslstats _R for all the images as the following:
>
> fslstats tbss_tfce_corrp_tstat1.nii.gz -R
> 0.000000 0.821300
> fslstats tbss_tfce_corrp_tstat2.nii.gz -R
> 0.000000 0.049900
> slstats tbss_MD_tfce_corrp_tstat1.nii.gz -R
> 0.000000 0.022100
> slstats tbss_MD_tfce_corrp_tstat2.nii.gz -R
> 0.000000 0.998800
> fslstats tbss_AD_tfce_corrp_tstat1.nii.gz -R
> 0.000000 0.066900
> slstats tbss_AD_tfce_corrp_tstat2.nii.gz -R
> 0.000000 0.965600
> fslstats tbss_RD_tfce_corrp_tstat1.nii.gz -R
> 0.000000 0.021600
> fslstats tbss_RD_tfce_corrp_tstat2.nii.gz -R
> 0.000000 0.999800
>
> Anderson! Kindly, would you mind if I send you some images to your personal
> email, I can't send anything in JISCNAIL.
>
>
> Looking forward to learn from you and again thank you
>
> Mohamad
> ________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of
> Anderson M. Winkler [[log in to unmask]]
> Sent: Sunday, November 30, 2014 1:20 PM
>
> To: [log in to unmask]
> Subject: Re: [FSL] cluster & atlasquery
>
> Hi Mohamad,
>
> Did you open the images to see how do they look like? Do the images seem
> sensible before running randomise? Did you inspect visually the *_corrp_*
> images? And did you do so for both contrasts? In the outputs from "cluster",
> is the MAX always 1 for all contrasts, or do you see other values?
>
> The command fslstats tells exactly what are the range of values on each of
> the outputs (option -R) and, in addition to visual inspection, it can help
> to diagnose potential issues.
>
> All the best,
>
> Anderson
>
>
> On 30 November 2014 at 06:17, Alshikho, Mohamad J.
> <[log in to unmask]> wrote:
>>
>> Dear Anderson,
>> I ran the TBSS analysis for two groups 23 patients and 27 controls. I
>> collected the raw FA images for all the subjects in one folder then I
>> organized the data in this order (controls then patients).
>> I did the following:
>> Tbss_1_ preproc *.nii.gz
>> Tbss_2_reg -T
>> Tbss_3_postreg -S (I designed template from the best 24 FA images that I
>> have )
>> Tbss_4_prestats 0.2
>> design_ttest2 design 27 23
>> randomise -i all_RD_skeletonised -o tbss_RD -m mean_FA_skeleton_mask -d
>> design.mat -t design.con -n 10000 --T2 -V (I used 1000 permutations)
>>
>> Then I ran the analysis again for the non_FA maps.
>> At the end I ran the cluster command line as the following:
>>
>> cluster -i tbss_tfce_corrp_tstat2.nii.gz -t 0.95 -o cluster_index --mm
>> --osize=cluster_size > cluster_info.txt
>> cluster -i tbss_MD_tfce_corrp_tstat2.nii.gz -t 0.95 -o cluster_index --mm
>> --osize=cluster_size > cluster_info_MD.txt
>> cluster -i tbss_AD_tfce_corrp_tstat2.nii.gz -t 0.95 -o cluster_index --mm
>> --osize=cluster_size > cluster_info_AD.txt
>> cluster -i tbss_RD_tfce_corrp_tstat2.nii.gz -t 0.95 -o cluster_index --mm
>> --osize=cluster_size > cluster_info_RD.txt
>>
>> For all the previous commands (cluster ) I got one big cluster.
>>
>> The previous steps are exactly what I did. Looking forward for your
>> support!
>>
>> Thanks a lot
>> Mohamad
>>
>>
>>
>>
>>
>>
>> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of
>> Anderson M. Winkler [[log in to unmask]]
>> Sent: Saturday, November 29, 2014 2:03 PM
>>
>> To: [log in to unmask]
>> Subject: Re: [FSL] cluster & atlasquery
>>
>> Hi Mohamad,
>>
>> It's not possible to tell only with the information you provided, but
>> assuming that everything went fine, and that design and contrasts are fine,
>> it can be that there is a global effect.
>>
>> However, the output of "cluster" shows that your maximum in the image is
>> 1, but this isn't in the outputs fromn randomise, because this max
>> represents a 1-p, and the minimum p is limited by the number of
>> permutations. In other words, if you run 5000 permutations, the max should
>> be, at best, 0.9998, not 1. Please, check if you didn't do other processing
>> in these outputs that shouldn't have been done.
>>
>> All the best,
>>
>> Anderson
>>
>>
>> On 28 November 2014 at 15:55, Alshikho, Mohamad J.
>> <[log in to unmask]> wrote:
>>>
>>> Dear Anderson,
>>> thank you very much for your answer.
>>> Kindly what is/ are the reasons for this result (1 big cluster with many
>>> tracts). Is it because of a technical issue or it is related to the data
>>> itself.
>>> Regarding the coordinate : I tried to find the coordinates manually using
>>> Fslview then I used
>>> fslmeants -i all_FA_skeletonized -c x y z
>>> to extract FA value for every subject tract
>>>
>>> Is this correct or do you suggest me better Idea.
>>>
>>> I highly appreciate your help in this
>>> Thanks
>>> ________________________________
>>> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of
>>> Anderson M. Winkler [[log in to unmask]]
>>> Sent: Friday, November 28, 2014 10:12 AM
>>> To: [log in to unmask]
>>> Subject: Re: [FSL] cluster & atlasquery
>>>
>>> Hi,
>>> You have just 1 big cluster with many tracts inside it. I don't think
>>> finding coordinates will be helpful, sorry...
>>> All the best,
>>> Anderson
>>>
>>>
>>>
>>> On 27 November 2014 at 14:54, M. alshikho <[log in to unmask]>
>>> wrote:
>>>>
>>>> Dear FSL experts,
>>>> In order to report the results of TBSS analysis, I did the following:
>>>>
>>>> cluster -i tbss_RD_tfce_corrp_tstat2.nii.gz -t 0.95 -o cluster_index
>>>> --mm --osize=cluster_size > cluster_info.txt
>>>>
>>>> The content of cluster_info is
>>>> Cluster Index Voxels MAX MAX X (mm) MAX Y (mm) MAX Z
>>>> (mm) COG X (mm) COG Y (mm) COG Z (mm)
>>>> 1 41305 1 11 -20 -1 0.979 -26.5 2.56
>>>>
>>>> Then I used fslmaths -dt int cluster_index.nii.gz -thr 1 -uthr 1 -bin
>>>> cluster_mask1 to create mask for this cluster.
>>>> Finaly I used atlas query as the following:
>>>> atlasquery -a "JHU White-Matter Tractography Atlas" -m
>>>> cluster_mask1.nii.gz
>>>>
>>>> the results are as the following:
>>>> Anterior thalamic radiation L:1.77475
>>>> Anterior thalamic radiation R:1.53817
>>>> Corticospinal tract L:1.3281
>>>> Corticospinal tract R:1.41649
>>>> Cingulum (cingulate gyrus) L:0.240552
>>>> Cingulum (cingulate gyrus) R:0.00225154
>>>> Cingulum (hippocampus) L:0.297494
>>>> Cingulum (hippocampus) R:0.00769883
>>>> Forceps major:0.383101
>>>> Forceps minor:0.0229028
>>>> Inferior fronto-occipital fasciculus L:1.04522
>>>> Inferior fronto-occipital fasciculus R:1.22639
>>>> Inferior longitudinal fasciculus L:1.68708
>>>> Inferior longitudinal fasciculus R:1.10311
>>>> Superior longitudinal fasciculus L:1.63842
>>>> Superior longitudinal fasciculus R:2.11788
>>>> Uncinate fasciculus L:0.236122
>>>> Uncinate fasciculus R:0.013945
>>>> Superior longitudinal fasciculus (temporal part) L:0.725336
>>>> Superior longitudinal fasciculus (temporal part) R:0.91892
>>>>
>>>> Now I have one cluster and the probability for many tracts in the same
>>>> cluster. How can I define the coordinate for every tracts from the output of
>>>> atalsquery?
>>>>
>>>> Thanks
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it
>>> is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
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>>
>>
>
--
Niels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
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