Dear fs-fast wizards,
doing monkey fMRI in Bremen (block desing so far) I run into the problem that analysing the data from one session does not lead to well defined activation maps. Therefore I would like to pool over several sessions (always within one subject). Unfortunately I have did not manage to always position the slices at the same position, I recorded a different number of runs each session. Now my assumption is all I need to do is define according df and sf files and be done with. But at what stage (mc-sess, spatialsmooth-sess, mkanalysis-sess.new, selxavg-sess, mkcontrast-sess or stxgrinfer-sess)? Is it advisable to motion correct all session runs together, or combine the data after that step? So excuse me for my uneducated question, but I would be delighted to tap into this list's vast knowledge before debarking into computationally long experiments. One more question, is it necessary/helpful to record low-res anatomicals before functional runs to register separate sessions, or is this step avoidable.
Regards Sebastian
One way to do it is, as you suggest, just put all the runs into the same bold directory, then just use mc as registration. This works to some extent. The main problem with it is that you can get fairly different B0 distortion between sessions because of the different head/body position in the scanner, and this can cause the mc algorithm to moderately misalign the sessions. You can try it out and see how well it works using tkregister2 (can't fixed it with tkregister2 though).
The other thing you can do is to analyze each session separately, then combine them together in talairach space with a fixed effects analysis (isxavg-fe-sess), assuming you've done the first couple of freesurfer analysis steps.
is it necessary/helpful to record low-res anatomicals before
functional runs
I don't find it helpful for registration purposes, though you do need good anatomicals at some point.
doug
Sebastian Moeller wrote:
Dear fs-fast wizards,
doing monkey fMRI in Bremen (block desing so far) I run into the problem that analysing the data from one session does not lead to well defined activation maps. Therefore I would like to pool over several sessions (always within one subject). Unfortunately I have did not manage to always position the slices at the same position, I recorded a different number of runs each session. Now my assumption is all I need to do is define according df and sf files and be done with. But at what stage (mc-sess, spatialsmooth-sess, mkanalysis-sess.new, selxavg-sess, mkcontrast-sess or stxgrinfer-sess)? Is it advisable to motion correct all session runs together, or combine the data after that step? So excuse me for my uneducated question, but I would be delighted to tap into this list's vast knowledge before debarking into computationally long experiments. One more question, is it necessary/helpful to record low-res anatomicals before functional runs to register separate sessions, or is this step avoidable.
Regards Sebastian
Hi. I was handed some data analyzed with freesurfer, and I would like to know what is the exact resolution of the T1 mri, i.e. 1.25mm x 3mm x 2mm for example. Where can I look in the freesurfer folder to find out?
Thanks
Hi Daniel,
you need to look at your original data (e.g. dicom files). You can mri_info to tell you.
Bruce
On Tue, 20 Sep 2005, Daniel Goldenholz wrote:
Hi. I was handed some data analyzed with freesurfer, and I would like to know what is the exact resolution of the T1 mri, i.e. 1.25mm x 3mm x 2mm for example. Where can I look in the freesurfer folder to find out?
Thanks
Hi Bruce
I am not sure that I have the original dicom files. I did find a file called COR-.info in mri/orig/ This is the filedump... Perhaps this has the answer?
imnr0 1 imnr1 256 ptype 2 x 256 y 256 fov 0.256000 thick 0.001000 psiz 0.001000 locatn 0.000000 strtx -0.128000 endx 0.128000 strty -0.128000 endy 0.128000 strtz -0.128000 endz 0.128000 tr 0.000000 te 0.000000 ti 0.000000 xform /local_mount/space/linus/7/users/sms/MRI/ips015c/mri/transforms/talairach.xfm ras_good_flag 1 x_ras -1.000000 0.000000 0.000000 y_ras 0.000000 0.000000 -1.000000 z_ras 0.000000 1.000000 0.000000 c_ras -10.110786 29.012054 -11.469879
Bruce Fischl wrote:
Hi Daniel,
you need to look at your original data (e.g. dicom files). You can mri_info to tell you.
Bruce
On Tue, 20 Sep 2005, Daniel Goldenholz wrote:
Hi. I was handed some data analyzed with freesurfer, and I would like to know what is the exact resolution of the T1 mri, i.e. 1.25mm x 3mm x 2mm for example. Where can I look in the freesurfer folder to find out?
Thanks
the COR files will always be 1mm isotropic, since we resample the data to ensure it is
On Tue, 20 Sep 2005, Daniel Goldenholz wrote:
Hi Bruce
I am not sure that I have the original dicom files. I did find a file called COR-.info in mri/orig/ This is the filedump... Perhaps this has the answer?
imnr0 1 imnr1 256 ptype 2 x 256 y 256 fov 0.256000 thick 0.001000 psiz 0.001000 locatn 0.000000 strtx -0.128000 endx 0.128000 strty -0.128000 endy 0.128000 strtz -0.128000 endz 0.128000 tr 0.000000 te 0.000000 ti 0.000000 xform /local_mount/space/linus/7/users/sms/MRI/ips015c/mri/transforms/talairach.xfm ras_good_flag 1 x_ras -1.000000 0.000000 0.000000 y_ras 0.000000 0.000000 -1.000000 z_ras 0.000000 1.000000 0.000000 c_ras -10.110786 29.012054 -11.469879
Bruce Fischl wrote:
Hi Daniel,
you need to look at your original data (e.g. dicom files). You can mri_info to tell you.
Bruce
On Tue, 20 Sep 2005, Daniel Goldenholz wrote:
Hi. I was handed some data analyzed with freesurfer, and I would like to know what is the exact resolution of the T1 mri, i.e. 1.25mm x 3mm x 2mm for example. Where can I look in the freesurfer folder to find out?
Thanks
Hi Daniel,
Is it possible to get the original dicom data? You said the data were already processed by Freesurfer when they got to you, so maybe whoever gave them to you can point you to the whereabouts of the raw dicom files?
Ev
On Tue, 20 Sep 2005, Daniel Goldenholz wrote:
Hi Bruce
I am not sure that I have the original dicom files. I did find a file called COR-.info in mri/orig/ This is the filedump... Perhaps this has the answer?
imnr0 1 imnr1 256 ptype 2 x 256 y 256 fov 0.256000 thick 0.001000 psiz 0.001000 locatn 0.000000 strtx -0.128000 endx 0.128000 strty -0.128000 endy 0.128000 strtz -0.128000 endz 0.128000 tr 0.000000 te 0.000000 ti 0.000000 xform /local_mount/space/linus/7/users/sms/MRI/ips015c/mri/transforms/talairach.xfm ras_good_flag 1 x_ras -1.000000 0.000000 0.000000 y_ras 0.000000 0.000000 -1.000000 z_ras 0.000000 1.000000 0.000000 c_ras -10.110786 29.012054 -11.469879
Bruce Fischl wrote:
Hi Daniel,
you need to look at your original data (e.g. dicom files). You can mri_info to tell you.
Bruce
On Tue, 20 Sep 2005, Daniel Goldenholz wrote:
Hi. I was handed some data analyzed with freesurfer, and I would like to know what is the exact resolution of the T1 mri, i.e. 1.25mm x 3mm x 2mm for example. Where can I look in the freesurfer folder to find out?
Thanks
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Daniel Goldenholz -
Doug Greve -
Evelina Busa -
Sebastian Moeller