Hi Ivan,

1) it means that the voxel sizes across your images are different. Do mri_info on the images to see what's going on. Usually this is no problem if the differences are tiny. Just a warning.

2) yes, the longs are all in the same space as the base, you can map images to the rawavg from the cross runs with a single command:

cd $SUBJECTS_DIR/<tpid>.long.<baseid>/mri

mri_convert -ait transforms/<tpid>_to_<tpid>.long.<baseid>.lta \
-rl $SUBJCECTS_DIR/<tpid>/mri/rawavg.mgz \
-rt nearest aseg.mgz aseg-in-rawavg.mgz

for other images (not segmentations, e.g. brainmask, use '-rt cubic' instead of nearest neighbor).

Best, Martin

On 11/22/2013 09:22 PM, Kirov, Ivan wrote:

Dear FreeSurfer group/Dr. Reuter,

My questions are in regards to the LONG stream.

My version is: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

1) Error message
During the creation of the BASE, I get the following error in the beginning of the recon:
>>>WARNING: Image geometries differ across time, maybe due to aquisition changes?
This can potentially bias a longitudinal study! Will continue in 10s.<<<<
What should I be aware of in regards to this error?

The images were all acquired using the same MPRAGE protocol.
All timepoints were fed MPRAGEs reconstructed in the axial orientation, but some may have been reconstructed at an angle. I was assured that this is not an issue for FreeSurfer, but could this be the reason for the error?

2) Conversion of LONG run aseg.mgz segmentations to native anatomical space

Executing the commands for converting aseg.mgz to native space (as noted in the FsAnat-to-NativeAnat wiki entry) in the folder of a long run (me1.long.me_base) does not convert.

It seems to me that (unlike the cross runs) the long runs are all in the same space (in the template/ base space?) and their rawavg.mgz does not match that of the corresponding cross run. Some insight on this would be appreciated.

The question is how to convert an individual long run's aseg.mgz into native anatomical space. Perhaps using the rawavg.mgz from the corresponding cross run?

Thank you very much!
Ivan

--

Ivan Kirov, PhD
Postdoctoral fellow
New York University School of Medicine
Center for Biomedical Imaging
660 1st Ave, 4th floor, New York, NY 10016
Tel: 212-263-3337
Fax: 212-263-7541

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Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

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