Matthew,
Thanks, you are correct. There was an error in my pre-processing of the files. Once I corrected that, randomise worked fine.
Thanks again,
Michael
On Fri, 13 Jan 2012 15:34:36 +0000, Matthew Webster <[log in to unmask]> wrote:
>Hello Michael,
> Your all_FA_skeletonised.nii.gz consists of the same image repeated 12 times - could there have been an error in merging the individual files? By default randomise 2.9 will detect and remove voxels with a constant timeseries from the data - which in this case is all the voxels! You can disable this behaviour with --norcmask, but I think you will want to check how the all_FA_skeletonised image was generated first.
>
>Hope this helps,
>
>Matthew
>
>> Matthew,
>>
>> Okay, great. I uploaded the data. The file name is:
>>
>> upload_michael_fsl.tar.gz
>>
>> The 6-digit reference number is: 294333
>>
>> Please let me know, if you need any additional information.
>>
>> Thanks,
>>
>> Michael
>>
>> On Mon, 9 Jan 2012 15:50:54 +0000, Matthew Webster <[log in to unmask]> wrote:
>>
>>> Hello Michael,
>>> If you want to upload your input files to:
>>>
>>> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
>>>
>>> and let me know the 6-digit reference number, I will check to see if this is a bug introduced into randomise 2.9.
>>>
>>> Many Regards
>>>
>>> Matthew
>>>> One more thing, regarding this issue,
>>>>
>>>> I'm currently running fsl 4.1 (build 419) and randomise v2.9. I installed my fsl package via Debian.
>>>>
>>>> This is where I am getting the error message.
>>>>
>>>> Just on a hunch, i ran the same command line on our old server that had FSL 4.1 (build 416) and randomise v2.6, and I received no error message. The analysis actually worked.
>>>>
>>>> So,I'm not so sure what is going on. Is there a bug in v2.9, possibly?
>>>>
>>>> My older version of randomise is installed on Redhat 2.6.9.
>>>>
>>>> I've installed build 419 of FSL via the Debian package where we are running Ubuntu. Could that be an issue?
>>>>
>>>> Michael
>>>>
>>>> On Mon, 9 Jan 2012 14:13:29 +0000, Michael Keaser <[log in to unmask]> wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> Yes, I double checked in FSLview (and also in AFNI viewer) that both sets of masks overlay the data.
>>>>>
>>>>> I tried gunzipping the nii files for both the masks and the all_skelentonized data see if that was the issue, and still the same error occurs.
>>>>>
>>>>> Michael
>>>>>
>>>>>
>>>>> On Mon, 9 Jan 2012 13:52:36 +0000, Matthew Webster <[log in to unmask]> wrote:
>>>>>
>>>>>> Hi,
>>>>>> Can you double check that the mask overlaps the data ( e.g. just quickly check them in FSLview? )
>>>>>>
>>>>>> Many Regards
>>>>>>
>>>>>> Matthew
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> Thanks for your response.
>>>>>>>
>>>>>>> Unfortunately, I've tried using both mask optoins mean_FA_mask and mean_FA_skeleton.nii.gz, and I still get the same error message.
>>>>>>>
>>>>>>> Anybody else having the same issue or is there another step that I am missing?
>>>>>>>
>>>>>>> Michael
>>>>>>> ________________________________________
>>>>>>> From: Haitao Ge
>>>>>>> Sent: Saturday, January 07, 2012 8:47 AM
>>>>>>> To: [log in to unmask]
>>>>>>> Subject: Re: [FSL] TBSS exception
>>>>>>>
>>>>>>> Hi Michael
>>>>>>>
>>>>>>> I think you have input the wrong mask. You have input the mean FA skeleton
>>>>>>> instead of mean FA mask.
>>>>>>>
>>>>>>> Haitao
>>>>>>>
>>>>>>> Center for Sectional and Imaging Anatomy
>>>>>>> Shandong University School of Medicine
>>>>>>> 44#, West Wenhua Rd.
>>>>>>> Jinan 250012, Shandong
>>>>>>> P.R.China
>>>>>>>
>>>>>>> -----原始邮件-----
>>>>>>> From: Michael Keaser
>>>>>>> Sent: Saturday, January 07, 2012 5:44 AM
>>>>>>> To: [log in to unmask]
>>>>>>> Subject: Re: [FSL] TBSS exception
>>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> I too have had the same problem with the error mask is blank.
>>>>>>>
>>>>>>> Here is my command and the output from it:
>>>>>>>
>>>>>>> randomise -i all_FA_skeletonised.nii.gz -o pairedT -d design-glm.mat -t
>>>>>>> design-glm.con -f design-glm.fts -m mean_FA_skeleton.nii.gz -e
>>>>>>> design-glm.grp -T
>>>>>>> randomise options: -i all_FA_skeletonised.nii.gz -o pairedT -d
>>>>>>> design-glm.mat -t design-glm.con -f design-glm.fts -m
>>>>>>> mean_FA_skeleton.nii.gz -e design-glm.grp -T
>>>>>>> Loading Data: ERROR: Program failed
>>>>>>>
>>>>>>> An exception has been thrown
>>>>>>> Data mask is blank.
>>>>>>>
>>>>>>>
>>>>>>> I'm not sure what is going on. Anyone have any ideas? Your help would
>>>>>>> greatly be appreciated.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Michael
>>>>>>>
>>>>
>>
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