Hi,
I would advise you to not worry about it and move on with the pre-processing, along as you don't have volumes of all zeros in your original data. If I understand your email correctly, you only see all-zero volumes after saving the volume from FSLView and not in the original data. Is that right? If so, just move onto preprocessing and analysis. If you do have all-zero volumes then this is indicative of a problem in the acquisition or converting to nifti and you should investigate that further.
All the best,
Mark
On 19 Sep 2014, at 21:49, "Craig, Michael" <[log in to unmask]>
wrote:
> Hi Mark,
>
> Thanks for your email. I did try that and it appeared to have worked. When I save it after changing the min/max and reopen it in fslview, the first few volumes look good, but after that all the volumes are blank (they say intensity=0).
>
> Also, if this information isn't used in the analysis, would it be best for me to just not worry about displaying it and move on with the preprocessing?
>
> Thanks again for your help.
>
> best wishes,
> Mike
> On Sep 19, 2014, at 4:42 PM, Mark Jenkinson <[log in to unmask]>
> wrote:
>
>> Hi,
>>
>> Try changing the min/max display range values in FSLView.
>> The current max value is only 2.9, whereas the intensity is over 50 at the voxel your cursor is on.
>> There may or may not be information about the display range in the header of the image, but this information is not used in the analysis, only when viewing the image in FSLView, so you don't need to modify the image, just changed the max display value in FSLView.
>>
>> All the best,
>> Mark
>>
>>
>>
>> On 19 Sep 2014, at 21:05, "Craig, Michael" <[log in to unmask]> wrote:
>>
>>> Hi All,
>>>
>>> I have some EPI rat pup images I am trying to preprocess. When I convert the dicom files to nifti and open them in fslview they all come out mostly white. This is the case for all 600 volumes in the scan. I feel like there is a simple solution to this, probably something wrong in the image header, I'm just not sure what to change. I've attached a screen shot of what I'm seeing. Any suggestions on how to fix this? Thanks very much for your help.
>>>
>>> best wishes,
>>> Mike
>>>
>>> <Screen Shot 2014-09-19 at 4.04.15 PM.png>
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