Hi Bruce,

Thank you for your reply.

Initially a PAR/REC file was used to obtain an anat.nii file. This is used to create the [CROSS]. Two timepoints ([CROSS-1] and [CROSS-2]) was used to create the [BASE]. 

• Is it because there is too many file formats, and if so, how should this be managed? Is it possible to run freesurfer directly from the PAR/REC file?
  
• Is the “Image geometries differ across time” related to the difference in acquisition parameters mentioned in the warning?

Best regards 

Kasper Jessen

2015-10-10 16:12 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:

Hi Kasper

what was your input volume? The .02sec change in TR won't mean anything,
although it is a bit surprising to see, as is the fact that the other
parameters (flip angle, TE, etc...) don't seem to be preserved. We usually
read those right out of the dicom files if that is what you used as input.
Not sure why we would preserve the TR but not the other parameters.

cheers
Bruce

On Sat, 10 Oct 2015, Kasper Jessen wrote:

>
> Dear Freesurfer group,
>
> When looking through the log after running recon-all, i have noticed two
> different errors in the logs. The one being about 'volumes differ in
> acquisition parameters' and the other 'Image geometries differ across time,
> maybe due to aquisition changes?'.
>
> Volumes differ in acquisition parameters
> v1acq fa=0.000000 tr=10.032000 te=0.000000 ti=0.000000
> v2acq fa=0.000000 tr=10.012000 te=0.000000 ti=0.000000
> WARNING: Image geometries differ across time, maybe due to aquisition
> changes?
> This can potentially bias a longitudinal study! Will continue in 10s.
>
> What do the above errors mean and is it something we should be worried
> about?
>
> Best regards,
> Kasper Jessen
> MD, PhD Student
>
>
>

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