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Hi FS experts,
I appreciate it if you help me with a question on your longitudinal processing pipeline. If I use FreeSurfer to generate an unbiased T1 image template from N time points (non-linear registration), then how can I apply the within subject transformation matrix (Jacobian matrix) to that subject's DTI maps. Does FreeSurfer save the transformation matrix from N.Time-Points toward Template image? and if so, in which folder directory it will be saved? Also, given that FS uses vertices, should I first convert that transformation matrix to voxel space (eg. using surf2voxels ?) and then multiply that into different time-points of one's DTI images. Hope my questions are clear and looking forward to hearing from you:-)
Best Suzan
Where is the non-linear registration coming from? Our long stream uses affine.
On 3/11/2021 2:59 PM, Suzan Maleki wrote:
External Email - Use Caution
Hi FS experts,
I appreciate it if you help me with a question on your longitudinal processing pipeline. If I use FreeSurfer to generate an unbiased T1 image template from N time points (non-linear registration), then how can I apply the within subject transformation matrix (Jacobian matrix) to that subject's DTI maps. Does FreeSurfer save the transformation matrix from N.Time-Points toward Template image? and if so, in which folder directory it will be saved? Also, given that FS uses vertices, should I first convert that transformation matrix to voxel space (eg. using surf2voxels ?) and then multiply that into different time-points of one's DTI images. Hope my questions are clear and looking forward to hearing from you:-)
Best Suzan --
*Suzan Maleki*
PhD Student
*Brain, Mind and Society Research Hub*
*Turner Institute for Brain and Mental Health*
School of Psychological Sciences
Monash University 770 Blackburn Road
Clayton VIC 3800 Australia
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Hi Suzan,
actually it uses rigid within-subject registration. The transformation files should be in ./mri/transforms (in long and in base).
Best, Martin
On 17. Mar 2021, at 23:05, Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> wrote:
Where is the non-linear registration coming from? Our long stream uses affine.
On 3/11/2021 2:59 PM, Suzan Maleki wrote: Hi FS experts,
I appreciate it if you help me with a question on your longitudinal processing pipeline. If I use FreeSurfer to generate an unbiased T1 image template from N time points (non-linear registration), then how can I apply the within subject transformation matrix (Jacobian matrix) to that subject's DTI maps. Does FreeSurfer save the transformation matrix from N.Time-Points toward Template image? and if so, in which folder directory it will be saved? Also, given that FS uses vertices, should I first convert that transformation matrix to voxel space (eg. using surf2voxels ?) and then multiply that into different time-points of one's DTI images. Hope my questions are clear and looking forward to hearing from you:-)
Best Suzan -- Suzan Maleki PhD Student
Brain, Mind and Society Research Hub Turner Institute for Brain and Mental Health School of Psychological Sciences Monash University 770 Blackburn Road Clayton VIC 3800 Australia
E: suzan.maleki@monash.edumailto:suzan.maleki@monash.edu W: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be www.brainmindsociety.comhttp://secure-web.cisco.com/1M6vSPYqb65gIKRIqlIXOxRCakYwAxILKD95WLgcR2yCqQ6FXOXYsUKLisZX_eo6DtPs_HkX41KUS-wdwR3-UUrSwZVKwj4QR-JQ-WtH-ekOi0o5q4S8eDq1e1GZ_7TXHnz3ZjThx0R4ZgLFYplk7EtY3q9xpN0zGJqMX4I9HV4IxesVFR3Dci-egNDSgM_I04pSUMo6AZVL8Fy67fo8c_xj2BeTO7a5esTW0rGywnZPFkaxAzEkybdos2U3PYqLud5SODh1HulyUS0nqlcmR0g/http%3A%2F%2Fwww.brainmindsociety.com%2F
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Thanks a lot Martin. Regards Suzan
On Thu, 18 Mar 2021 at 9:09 pm, Reuter, Martin,Ph.D. < MREUTER@mgh.harvard.edu> wrote:
Hi Suzan,
actually it uses rigid within-subject registration. The transformation files should be in ./mri/transforms (in long and in base).
Best, Martin
On 17. Mar 2021, at 23:05, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Where is the non-linear registration coming from? Our long stream uses affine.
On 3/11/2021 2:59 PM, Suzan Maleki wrote:
Hi FS experts,
I appreciate it if you help me with a question on your longitudinal processing pipeline. If I use FreeSurfer to generate an unbiased T1 image template from N time points (non-linear registration), then how can I apply the within subject transformation matrix (Jacobian matrix) to that subject's DTI maps. Does FreeSurfer save the transformation matrix from N.Time-Points toward Template image? and if so, in which folder directory it will be saved? Also, given that FS uses vertices, should I first convert that transformation matrix to voxel space (eg. using surf2voxels ?) and then multiply that into different time-points of one's DTI images. Hope my questions are clear and looking forward to hearing from you:-)
Best Suzan -- *Suzan Maleki* PhD Student
*Brain, Mind and Society Research Hub* *Turner Institute for Brain and Mental Health*
https://secure-web.cisco.com/1VYK3ECYsk4HG3cJB4v55sfUrC1kNxoXtT9D0AdKjGdnG8eWrLW-mA-XGpzlCi6UgPlHtalL6mrFdh5sGWvr_QbjXcuN33OnWCUavBMYGeZQcWqJSEVd1e-gycUNpie8xoL_s5ChiTl_36FRL7qnFjj_OhyTqxmGvP5xBA-GCvqoCM1ACEkVWZqN4hH1HI_GOk7PViEtGFYlpq_XDWXbQskgQ6EzINzxad3JIc3K_Y4uAP-6TXUJ3n6HeoC-kD_ZygxCo2uroGBjg92JiDurDSSBvGYBxkeas68yRCWY9E5E/https%3A%2F%2Fwww.google.com%2Fmaps%2Fsearch%2F770%2BBlackburn%2BRoad%2B%250D%250A%2B%250D%250A%2BClayton%2BVIC%2B3800%2BAustralia%3Fentry%3Dgmail%26source%3DgSchool of Psychological Sciences Monash University 770 Blackburn Road https://secure-web.cisco.com/1VYK3ECYsk4HG3cJB4v55sfUrC1kNxoXtT9D0AdKjGdnG8eWrLW-mA-XGpzlCi6UgPlHtalL6mrFdh5sGWvr_QbjXcuN33OnWCUavBMYGeZQcWqJSEVd1e-gycUNpie8xoL_s5ChiTl_36FRL7qnFjj_OhyTqxmGvP5xBA-GCvqoCM1ACEkVWZqN4hH1HI_GOk7PViEtGFYlpq_XDWXbQskgQ6EzINzxad3JIc3K_Y4uAP-6TXUJ3n6HeoC-kD_ZygxCo2uroGBjg92JiDurDSSBvGYBxkeas68yRCWY9E5E/https%3A%2F%2Fwww.google.com%2Fmaps%2Fsearch%2F770%2BBlackburn%2BRoad%2B%250D%250A%2B%250D%250A%2BClayton%2BVIC%2B3800%2BAustralia%3Fentry%3Dgmail%26source%3Dg Clayton VIC 3800 Australia https://secure-web.cisco.com/1VYK3ECYsk4HG3cJB4v55sfUrC1kNxoXtT9D0AdKjGdnG8eWrLW-mA-XGpzlCi6UgPlHtalL6mrFdh5sGWvr_QbjXcuN33OnWCUavBMYGeZQcWqJSEVd1e-gycUNpie8xoL_s5ChiTl_36FRL7qnFjj_OhyTqxmGvP5xBA-GCvqoCM1ACEkVWZqN4hH1HI_GOk7PViEtGFYlpq_XDWXbQskgQ6EzINzxad3JIc3K_Y4uAP-6TXUJ3n6HeoC-kD_ZygxCo2uroGBjg92JiDurDSSBvGYBxkeas68yRCWY9E5E/https%3A%2F%2Fwww.google.com%2Fmaps%2Fsearch%2F770%2BBlackburn%2BRoad%2B%250D%250A%2B%250D%250A%2BClayton%2BVIC%2B3800%2BAustralia%3Fentry%3Dgmail%26source%3Dg
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Douglas N. Greve -
Reuter, Martin,Ph.D. -
Suzan Maleki