Hi, Paul
I think I found the cause. The label of my mask is 10,11,20,21,30,…,8058, it isn’t 1:112. I think this explains why the timeseries I extracted is 420*8058 size and just the corresponding columns (10,11,20,21,30,…,8058) have values and other columns are all zeros.
Is there any command in FSL I can use to change the label into 1:112
Best
Zhen
> 在 2019年3月19日,下午3:11,Zhen Zhou <[log in to unmask]> 写道:
>
> Yes, each of the ROIS in the mask file have a unique integer label. I have used MATLAB to check it . The command I used is :
>
> fslmeants -i fMRIAfterDenoise.nii.gz - - labe=Harvard_warped.nii.gz -o meants.txt
>
> The output in meants.txt is still a 420*8058 size text file.
>
> Best
> Zhen
>
>> 在 2019年3月19日,上午9:56,paul mccarthy <[log in to unmask]> 写道:
>>
>> Do each of your ROIs have a unique integer label? This is required in
>> order to use the --label option.
>>
>> Cheers,
>>
>> Paul
>>
>> On 19/03/2019, Zhen Zhou <[log in to unmask]> wrote:
>>> Yeah, I have tried the - - label option. For example, the ROI mask has 112
>>> ROIs, in which about 80000 voxels is included.
>>>
>>> Using the - -label option give me a 420*80000 size matrix instead of a
>>> 420*112 size matrix. Is there any way to change the result?
>>>
>>> Best
>>> Zhen
>>>
>>>> 在 2019年3月19日,上午4:41,paul mccarthy <[log in to unmask]> 写道:
>>>>
>>>> Hi Zhen,
>>>>
>>>> The --label option should do what you want:
>>>>
>>>> --label input 3D label image (generate separate mean for each
>>>> integer label value - cannot be used with showall)
>>>>
>>>> Cheers,
>>>>
>>>> Paul
>>>>
>>>> On 18/03/2019, Zhen Zhou <[log in to unmask]> wrote:
>>>>> Dear FSL experts,
>>>>>
>>>>> I have a preprocessed 4D nii file (with 420 time points), and a ROI mask
>>>>> (with 112 ROIs).
>>>>> I want to use the ROI to extract time series. When I use fslmeants, I
>>>>> found
>>>>> the output is a text file with a 420*1 matrix. It seems like the time
>>>>> series
>>>>> has beed averaged over all ROIs.
>>>>> Is there any way not to average over the ROIs, i.e., to generate a
>>>>> 420*112
>>>>> size matrix. I didn’t find any options of fslmeants which can do this.
>>>>>
>>>>> Zhen
>>>>> Best
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