Hi Kasper,
if you use the same file formats and conversion tools across both time points, the images should be identical. Even after conversion to nii. Not sure why they are not.
Yes, both warnings are related to the acquisition parameters. The second should better say that header information is different or something like that. I see if I can improve that error message to be more specific in a future release.
Best, Martin
On 10/17/2015 08:59 AM, Kasper Jessen wrote:
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 mailto: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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.-- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper_j@cnsr.dk mailto:kasper_j@cnsr.dk eller kasper.jessen@regionh.dk mailto:kasper.jessen@regionh.dk
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