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 <fis...@nmr.mgh.harvard.edu
<mailto:fis...@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: kaspe...@cnsr.dk <mailto:kaspe...@cnsr.dk> eller
kasper.jes...@regionh.dk <mailto:kasper.jes...@regionh.dk>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web : http://reuter.mit.edu
_______________________________________________
Freesurfer mailing list
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.
