Re: [Freesurfer] Two Different T1 Acquisition Planes as recon-all Inputs

[Bruce Fischl]

Hi Doug

two aren't necessarily better than one. It depends on your coil/field 
strength and amount of motion. In particular, a coronal and a sagittal 
will have differential distortions that will blur the average. It might 
still help if your data is noisy - it's hard to say a priori, but something 
to watch out for. Sagittal is also usually better since ear-to-ear is the 
shortest distance


Bruce


On Mon, 25 
Apr 2016, Douglas Merkitch wrote:



Hello Freesurfer experts,
We currently acquire two sagittal T1s (136 slices) in our protocol so that
we can take advantage of freesurfer's motion correction algorithm; however,
we would like to add a coronal T1 (196 slices). In order to cut down on scan
time, we are also considering dropping one of the the sagittal T1s and using
one sagittal and one coronal T1 as inputs for freesurfer recon-all.

When I specified these sagittal and coronal inputs for the recon-all for our
test subject, we received the "ERROR: inputs have mismatched dimensions!" My
main questions are the following:

If we do cut one of the sagittal T1 scans, 
1) Would it be possible to use one sagittal and one coronal T1 as inputs?
The sequences are identical except for the acquisition plane and number of
slices.

2) If it is possible (perhaps by registering with mri_robust_register), what
would be the correct procedure for matching the dimensions of these two
scans?

3) Are there any other considerations or possible problems with this and
does this approach have merit (i.e. would it be advisable to just use one T1
input instead of two T1 inputs that have different acquisition planes)?

Any insight would be greatly appreciated!

Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: douglas_merki...@rush.edu






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[Freesurfer] Two Different T1 Acquisition Planes as recon-all Inputs

[Douglas Merkitch]

Hello Freesurfer experts,

We currently acquire two sagittal T1s (136 slices) in our protocol so that we 
can take advantage of freesurfer's motion correction algorithm; however, we 
would like to add a coronal T1 (196 slices). In order to cut down on scan time, 
we are also considering dropping one of the the sagittal T1s and using one 
sagittal and one coronal T1 as inputs for freesurfer recon-all.

When I specified these sagittal and coronal inputs for the recon-all for our 
test subject, we received the "ERROR: inputs have mismatched dimensions!" My 
main questions are the following:

If we do cut one of the sagittal T1 scans,
1) Would it be possible to use one sagittal and one coronal T1 as inputs? The 
sequences are identical except for the acquisition plane and number of slices.

2) If it is possible (perhaps by registering with mri_robust_register), what 
would be the correct procedure for matching the dimensions of these two scans?

3) Are there any other considerations or possible problems with this and does 
this approach have merit (i.e. would it be advisable to just use one T1 input 
instead of two T1 inputs that have different acquisition planes)?

Any insight would be greatly appreciated!

Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: douglas_merki...@rush.edu





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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.