Yes, I am currently giving freesurfer an atlas (711-2B / TRIO_Y_NDC to be specific) transformed 111 MP-RAGE file. The concern is that if I use mri_convert, I want to specifically return to the same 111 volume size and space and I provided as accurately as possible (hopefully using the inverse of the total transform applied to the image during processing). I know Matt Glasser has worked out a way to convert (and apparently re-register?) surfaces to caret, and I will talk with him later this week to walk through this procedure, but I was hoping that freesurfer could directly output the surfaces in the original space.
-Alex ~)-------------
---------------------------------------------------------------------- Alexander Li Cohen alexc@npg.wustl.edu (WORK Email) alexcohen@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine ----------------------------------------------------------------------
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On Aug 25, 2009, at 11:57 AM, Donna Dierker wrote:
Alan: Alex is detecting areal boundaries with functional connectivity on lots of subjects:
Cohen, A.L., Fair, D.A., Dosenbach, N.U.F., Miezin, F.M., Dierker, D., Van Essen, D.C., Schlaggar, B.L., and Petersen, S.E. (2008) Defining functional areas in individual human brains using resting functional connectivity MRI. http://dx.doi.org/10.1016/j.neuroimage.2008.01.066
Alex: Freesurfer can write surfaces (and possibly volumes) out in multiple ways. See output of mri_convert and mris_convert for helpful details. I have also found this web site very helpful:
http://www.wideman-one.com/gw/brain/fs/coords/fscoords.htm
Just double-checking: So you are giving Freesurfer a T1 that has already been put through Avi's imgreg (i.e., in 711-2* space)?
Donna
On 08/25/2009 11:40 AM, Alan Anticevic wrote:
Alex,
We ran into the same problem a while ago for some of our studies. We did the following:
- Convert an Avi preprocessed T1 MPRAGE into a FreeSurfer-native
format and provided it the appropriate orientation and image center. 2. Next, we simply ran recon-all on this file (single MPRAGE). Then we take the the final segmentation output (at least the aseg file) and convert it back to a 4dfp file, which is perfectly aligned with the original T1 image.
It is my understanding that FreeSurfer completes the segmentation on the orignal image in it's native space, hence the alignment.
However, the FreeSurfer surfaces we get are misaligned with the T1 and I am assuming this is what you need for your work. Donna Dierker and I have a script that may make your life a lot easier by converting surfaces from FreeSurfer into Caret including creating a mid-thickness surface. However, I would need to know a bit more about what you are trying to accomplish and I can help you use the tools we have. Best, Alan
On Aug 25, 2009, at 11:23 AM, Alexander Li Cohen wrote:
Hi all, Just starting using Freesurfer, and while I did search the mailing list archive, I didn't see a ready answer for this question:
I would like to use Freesurfer to generate surfaces for my subjects (currently using Caret's SureFit routine), however I need to maintain a specific atlas space for my subjects (in this case, the WU 711-2B, T88-derived space). I can imagine two possibilities, but not how to do them, nor which is more accurate/appropriate:
- Input the raw T1 for my subject in scanner space (1x1x1
isovolumetric) and then convert the Freesurfer surface and volume outputs to my atlas space using a previously defined linear affine transform (using local scripts written by Avi). This requires Freesurfer to back-convert all results to the original supplied space, then for me to additionally learn how to transform the surfaces.
- Input the T1 for my subject already in my atlas space, and have
Freesurfer output all results in the original supplied space. This, however, will be providing Freesurfer with data that has undergone an additional transform, but is obviously simpler....
in either case, the methodological question becomes simply: how can I tell recon-all to output all files in the original space provided. Given that it must perform the necessary transforms to get into the internal MNI305 space (I'm assuming), I'm simply wanting to undo all of the applied transforms. For obvious reasons, I want to use the same affine transform and transform routine consistently across this and my other datatypes.
As a side note, there appears to be a switch for recon-all: -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol yet there is no documentation as to what this determines, nor whether the raw, or locally atlas-aligned data should be provided. (Avi didn't know either...)
Many Thanks!
-Alex Li Cohen ~)-----------------
Alexander Li Cohen alexc@npg.wustl.edu (WORK Email) alexcohen@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine
This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately.
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Alan Anticevic
Department of Psychology - CCP Lab Washington University in St. Louis One Brookings Dr., Campus Box 1125 St. Louis, MO 63110 Phone: 314-935-8547
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Alex,
My code converts the FreeSurfer surfaces into caret format and applies the appropriate transformations when Freesurfer is given data that is already in Wash U standard space. It is based on things that Donna originally figured out. Shortly, I will extend this to the volume parcellations output by FreeSurfer (Bruce told me how to do it; I just need to implement it in my script).
Peace,
Matt.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Alexander Li Cohen Sent: Tuesday, August 25, 2009 12:15 PM To: Donna Dierker Cc: Alan Anticevic; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Input/Output to specific atlas space/dimensions?
Yes, I am currently giving freesurfer an atlas (711-2B / TRIO_Y_NDC to be specific) transformed 111 MP-RAGE file. The concern is that if I use mri_convert, I want to specifically return to the same 111 volume size and space and I provided as accurately as possible (hopefully using the inverse of the total transform applied to the image during processing). I know Matt Glasser has worked out a way to convert (and apparently re-register?) surfaces to caret, and I will talk with him later this week to walk through this procedure, but I was hoping that freesurfer could directly output the surfaces in the original space.
-Alex ~)-------------
---------------------------------------------------------------------- Alexander Li Cohen alexc@npg.wustl.edu (WORK Email) alexcohen@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine ----------------------------------------------------------------------
This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately.
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
On Aug 25, 2009, at 11:57 AM, Donna Dierker wrote:
Alan: Alex is detecting areal boundaries with functional connectivity on lots of subjects:
Cohen, A.L., Fair, D.A., Dosenbach, N.U.F., Miezin, F.M., Dierker, D., Van Essen, D.C., Schlaggar, B.L., and Petersen, S.E. (2008) Defining functional areas in individual human brains using resting functional connectivity MRI.
http://dx.doi.org/10.1016/j.neuroimage.2008.01.066
Alex: Freesurfer can write surfaces (and possibly volumes) out in multiple ways. See output of mri_convert and mris_convert for helpful details. I have also found this web site very helpful:
http://www.wideman-one.com/gw/brain/fs/coords/fscoords.htm
Just double-checking: So you are giving Freesurfer a T1 that has already been put through Avi's imgreg (i.e., in 711-2* space)?
Donna
On 08/25/2009 11:40 AM, Alan Anticevic wrote:
Alex,
We ran into the same problem a while ago for some of our studies. We did the following:
- Convert an Avi preprocessed T1 MPRAGE into a FreeSurfer-native
format and provided it the appropriate orientation and image center. 2. Next, we simply ran recon-all on this file (single MPRAGE). Then we take the the final segmentation output (at least the aseg file) and convert it back to a 4dfp file, which is perfectly aligned with the original T1 image.
It is my understanding that FreeSurfer completes the segmentation on the orignal image in it's native space, hence the alignment.
However, the FreeSurfer surfaces we get are misaligned with the T1 and I am assuming this is what you need for your work. Donna Dierker and I have a script that may make your life a lot easier by converting surfaces from FreeSurfer into Caret including creating a mid-thickness surface. However, I would need to know a bit more about what you are trying to accomplish and I can help you use the tools we have. Best, Alan
On Aug 25, 2009, at 11:23 AM, Alexander Li Cohen wrote:
Hi all, Just starting using Freesurfer, and while I did search the mailing list archive, I didn't see a ready answer for this question:
I would like to use Freesurfer to generate surfaces for my subjects (currently using Caret's SureFit routine), however I need to maintain a specific atlas space for my subjects (in this case, the WU 711-2B, T88-derived space). I can imagine two possibilities, but not how to do them, nor which is more accurate/appropriate:
- Input the raw T1 for my subject in scanner space (1x1x1
isovolumetric) and then convert the Freesurfer surface and volume outputs to my atlas space using a previously defined linear affine transform (using local scripts written by Avi). This requires Freesurfer to back-convert all results to the original supplied space, then for me to additionally learn how to transform the surfaces.
- Input the T1 for my subject already in my atlas space, and have
Freesurfer output all results in the original supplied space. This, however, will be providing Freesurfer with data that has undergone an additional transform, but is obviously simpler....
in either case, the methodological question becomes simply: how can I tell recon-all to output all files in the original space provided. Given that it must perform the necessary transforms to get into the internal MNI305 space (I'm assuming), I'm simply wanting to undo all of the applied transforms. For obvious reasons, I want to use the same affine transform and transform routine consistently across this and my other datatypes.
As a side note, there appears to be a switch for recon-all: -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol yet there is no documentation as to what this determines, nor whether the raw, or locally atlas-aligned data should be provided. (Avi didn't know either...)
Many Thanks!
-Alex Li Cohen ~)-----------------
Alexander Li Cohen alexc@npg.wustl.edu (WORK Email) alexcohen@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine
This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately.
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Alan Anticevic
Department of Psychology - CCP Lab Washington University in St. Louis One Brookings Dr., Campus Box 1125 St. Louis, MO 63110 Phone: 314-935-8547
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Alexander Li Cohen -
Matt Glasser