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Hi,
It's my first time using FreeSurfer and I'd like some guidance regarding some of my steps.
I'm attempting to perform myelin mapping as outlined in the paper by Righart (2017) Ann Neurol. Overall, I want to calculate myelin maps from each subject, sample them from the mid-cortical level to create cortical myelin surface maps, and perform vertexwise and ROI based analyses.
Here's what I've done so far:
1. recon-all for all the subjects 2. Used bbregister to register the native T2 scans to the conformed T1 scans using this command: bbregister --s C01 --mov C01_T2.nii --init-fsl --reg register.dat --t2 (my understanding here is that this generates the .dat file that has the transformation to register the T2 image to the conformed orig.mgz file from subject C01) 3. Applied the register.dat file to the native T2 using mri_vol2vol --mov C01_T2.nii --o T2_conformed.mgz --fstarg --reg register.dat (this registers the T2 to the orig.mgz file in the conformed space)
The next step for me is to perform mri_vol2surf. My question here is, which file should I select for the --srcreg flag and what should the --trgsubject input be? Secondly, am I on the right track to complete the analysis i.e., correct file types and my understanding of the steps? Clarifications regarding these questions and any suggestions for further directions will be very helpful!
Let me know. Thanks!
That all looks correct. For the registration, just use --regheader C01
On 4/24/18 11:12 AM, Abdullah Ishaque wrote:
Hi,
It's my first time using FreeSurfer and I'd like some guidance regarding some of my steps.
I'm attempting to perform myelin mapping as outlined in the paper by Righart (2017) Ann Neurol. Overall, I want to calculate myelin maps from each subject, sample them from the mid-cortical level to create cortical myelin surface maps, and perform vertexwise and ROI based analyses.
Here's what I've done so far:
- recon-all for all the subjects
- Used bbregister to register the native T2 scans to the conformed T1
scans using this command: bbregister --s C01 --mov C01_T2.nii --init-fsl --reg register.dat --t2 (my understanding here is that this generates the .dat file that has the transformation to register the T2 image to the conformed orig.mgz file from subject C01) 3. Applied the register.dat file to the native T2 using mri_vol2vol --mov C01_T2.nii --o T2_conformed.mgz --fstarg --reg register.dat (this registers the T2 to the orig.mgz file in the conformed space)
The next step for me is to perform mri_vol2surf. My question here is, which file should I select for the --srcreg flag and what should the --trgsubject input be? Secondly, am I on the right track to complete the analysis i.e., correct file types and my understanding of the steps? Clarifications regarding these questions and any suggestions for further directions will be very helpful!
Let me know. Thanks!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi,
Thank you for the prompt response.
I used the following command:
mri_vol2surf --src Myelin_conformed.mgz (T1/T2 image after mri_vol2vol from the previous step) --out C01 --regheader C01 --hemi lh --projfrac 0.5
This created two files called COR-.info and COR001. I tried loaded the COR001 file into freeview and tksurfer, but I keep the error "MRISalloc(8229512, 76): could allocated faces \ cannot allocate memory
Am I making a mistake somewhere?
Thanks,
On Tue, Apr 24, 2018 at 11:34 AM, Douglas Greve dgreve@mgh.harvard.edu wrote:
That all looks correct. For the registration, just use --regheader C01
On 4/24/18 11:12 AM, Abdullah Ishaque wrote:
Hi,
It's my first time using FreeSurfer and I'd like some guidance regarding some of my steps.
I'm attempting to perform myelin mapping as outlined in the paper by Righart (2017) Ann Neurol. Overall, I want to calculate myelin maps from each subject, sample them from the mid-cortical level to create cortical myelin surface maps, and perform vertexwise and ROI based analyses.
Here's what I've done so far:
- recon-all for all the subjects
- Used bbregister to register the native T2 scans to the conformed T1
scans using this command: bbregister --s C01 --mov C01_T2.nii --init-fsl --reg register.dat --t2 (my understanding here is that this generates the .dat file that has the transformation to register the T2 image to the conformed orig.mgz file from subject C01) 3. Applied the register.dat file to the native T2 using mri_vol2vol --mov C01_T2.nii --o T2_conformed.mgz --fstarg --reg register.dat (this registers the T2 to the orig.mgz file in the conformed space)
The next step for me is to perform mri_vol2surf. My question here is, which file should I select for the --srcreg flag and what should the --trgsubject input be? Secondly, am I on the right track to complete the analysis i.e., correct file types and my understanding of the steps? Clarifications regarding these questions and any suggestions for further directions will be very helpful!
Let me know. Thanks!
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
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.
Specify a file format for the output (eg, C01.mgz)
On 4/24/18 3:17 PM, Abdullah Ishaque wrote:
External Email - Use Caution
Hi,
Thank you for the prompt response.
I used the following command:
mri_vol2surf --src Myelin_conformed.mgz (T1/T2 image after mri_vol2vol from the previous step) --out C01 --regheader C01 --hemi lh --projfrac 0.5
This created two files called COR-.info and COR001. I tried loaded the COR001 file into freeview and tksurfer, but I keep the error "MRISalloc(8229512, 76): could allocated faces \ cannot allocate memory
Am I making a mistake somewhere?
Thanks,
On Tue, Apr 24, 2018 at 11:34 AM, Douglas Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
That all looks correct. For the registration, just use --regheader C01 On 4/24/18 11:12 AM, Abdullah Ishaque wrote:Hi, It's my first time using FreeSurfer and I'd like some guidance regarding some of my steps. I'm attempting to perform myelin mapping as outlined in the paper by Righart (2017) Ann Neurol. Overall, I want to calculate myelin maps from each subject, sample them from the mid-cortical level to create cortical myelin surface maps, and perform vertexwise and ROI based analyses. Here's what I've done so far: 1. recon-all for all the subjects 2. Used bbregister to register the native T2 scans to the conformed T1 scans using this command: bbregister --s C01 --mov C01_T2.nii --init-fsl --reg register.dat --t2 (my understanding here is that this generates the .dat file that has the transformation to register the T2 image to the conformed orig.mgz file from subject C01) 3. Applied the register.dat file to the native T2 using mri_vol2vol --mov C01_T2.nii --o T2_conformed.mgz --fstarg --reg register.dat (this registers the T2 to the orig.mgz file in the conformed space) The next step for me is to perform mri_vol2surf. My question here is, which file should I select for the --srcreg flag and what should the --trgsubject input be? Secondly, am I on the right track to complete the analysis i.e., correct file types and my understanding of the steps? Clarifications regarding these questions and any suggestions for further directions will be very helpful! Let me know. Thanks! _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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 <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.-- *Abdullah Ishaque, BSc.* MD/PhD Student, Neuroscience and Mental Health Institute Faculty of Medicine and Dentistry, University of Alberta aishaque@ualberta.ca mailto:aishaque@ualberta.ca
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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I did: mri_vol2surf --src Myelin_conformed.mgz --out C01_myelin.mgz --regheader C01 --hemi lh --projfrac 0.5
Now I'm just getting the error "freadFloat: fread failed" a whole bunch of times and the terminal gets stuck. Any suggestions?
I checked Myelin_conformed.mgz and loaded it with orig.mgz in freeview and they look fine with great overlap and registration
Thanks!
On Tue, Apr 24, 2018 at 1:23 PM, Douglas Greve dgreve@mgh.harvard.edu wrote:
Specify a file format for the output (eg, C01.mgz)
On 4/24/18 3:17 PM, Abdullah Ishaque wrote:
External Email - Use CautionHi,
Thank you for the prompt response.
I used the following command:
mri_vol2surf --src Myelin_conformed.mgz (T1/T2 image after mri_vol2vol from the previous step) --out C01 --regheader C01 --hemi lh --projfrac 0.5
This created two files called COR-.info and COR001. I tried loaded the COR001 file into freeview and tksurfer, but I keep the error "MRISalloc(8229512, 76): could allocated faces \ cannot allocate memory
Am I making a mistake somewhere?
Thanks,
On Tue, Apr 24, 2018 at 11:34 AM, Douglas Greve dgreve@mgh.harvard.edu wrote:
That all looks correct. For the registration, just use --regheader C01
On 4/24/18 11:12 AM, Abdullah Ishaque wrote:
Hi,
It's my first time using FreeSurfer and I'd like some guidance regarding some of my steps.
I'm attempting to perform myelin mapping as outlined in the paper by Righart (2017) Ann Neurol. Overall, I want to calculate myelin maps from each subject, sample them from the mid-cortical level to create cortical myelin surface maps, and perform vertexwise and ROI based analyses.
Here's what I've done so far:
- recon-all for all the subjects
- Used bbregister to register the native T2 scans to the conformed T1
scans using this command: bbregister --s C01 --mov C01_T2.nii --init-fsl --reg register.dat --t2 (my understanding here is that this generates the .dat file that has the transformation to register the T2 image to the conformed orig.mgz file from subject C01) 3. Applied the register.dat file to the native T2 using mri_vol2vol --mov C01_T2.nii --o T2_conformed.mgz --fstarg --reg register.dat (this registers the T2 to the orig.mgz file in the conformed space)
The next step for me is to perform mri_vol2surf. My question here is, which file should I select for the --srcreg flag and what should the --trgsubject input be? Secondly, am I on the right track to complete the analysis i.e., correct file types and my understanding of the steps? Clarifications regarding these questions and any suggestions for further directions will be very helpful!
Let me know. Thanks!
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
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.
-- *Abdullah Ishaque, BSc.* MD/PhD Student, Neuroscience and Mental Health Institute Faculty of Medicine and Dentistry, University of Alberta aishaque@ualberta.ca
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
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.
External Email - Use Caution
Hi,
I figured that part out: I can't load surfaces as volumes in freeview, but rather i need to load them as an overlay to the subject white, or pial surfaces.
I have another question for which I can't find an answer to. After registering myelin maps to the individual subjects, how do I register/transform them into the subjects' longitudinal T1s (obtained after the recon-all long command)?
The broad goal that I am trying to achieve is longitudinal myelin analysis. Any feedback is appreciated. Thanks!
On Tue, Apr 24, 2018 at 1:30 PM, Abdullah Ishaque aishaque@ualberta.ca wrote:
I did: mri_vol2surf --src Myelin_conformed.mgz --out C01_myelin.mgz --regheader C01 --hemi lh --projfrac 0.5
Now I'm just getting the error "freadFloat: fread failed" a whole bunch of times and the terminal gets stuck. Any suggestions?
I checked Myelin_conformed.mgz and loaded it with orig.mgz in freeview and they look fine with great overlap and registration
Thanks!
On Tue, Apr 24, 2018 at 1:23 PM, Douglas Greve dgreve@mgh.harvard.edu wrote:
Specify a file format for the output (eg, C01.mgz)
On 4/24/18 3:17 PM, Abdullah Ishaque wrote:
External Email - Use CautionHi,
Thank you for the prompt response.
I used the following command:
mri_vol2surf --src Myelin_conformed.mgz (T1/T2 image after mri_vol2vol from the previous step) --out C01 --regheader C01 --hemi lh --projfrac 0.5
This created two files called COR-.info and COR001. I tried loaded the COR001 file into freeview and tksurfer, but I keep the error "MRISalloc(8229512, 76): could allocated faces \ cannot allocate memory
Am I making a mistake somewhere?
Thanks,
On Tue, Apr 24, 2018 at 11:34 AM, Douglas Greve dgreve@mgh.harvard.edu wrote:
That all looks correct. For the registration, just use --regheader C01
On 4/24/18 11:12 AM, Abdullah Ishaque wrote:
Hi,
It's my first time using FreeSurfer and I'd like some guidance regarding some of my steps.
I'm attempting to perform myelin mapping as outlined in the paper by Righart (2017) Ann Neurol. Overall, I want to calculate myelin maps from each subject, sample them from the mid-cortical level to create cortical myelin surface maps, and perform vertexwise and ROI based analyses.
Here's what I've done so far:
- recon-all for all the subjects
- Used bbregister to register the native T2 scans to the conformed T1
scans using this command: bbregister --s C01 --mov C01_T2.nii --init-fsl --reg register.dat --t2 (my understanding here is that this generates the .dat file that has the transformation to register the T2 image to the conformed orig.mgz file from subject C01) 3. Applied the register.dat file to the native T2 using mri_vol2vol --mov C01_T2.nii --o T2_conformed.mgz --fstarg --reg register.dat (this registers the T2 to the orig.mgz file in the conformed space)
The next step for me is to perform mri_vol2surf. My question here is, which file should I select for the --srcreg flag and what should the --trgsubject input be? Secondly, am I on the right track to complete the analysis i.e., correct file types and my understanding of the steps? Clarifications regarding these questions and any suggestions for further directions will be very helpful!
Let me know. Thanks!
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
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.
-- *Abdullah Ishaque, BSc.* MD/PhD Student, Neuroscience and Mental Health Institute Faculty of Medicine and Dentistry, University of Alberta aishaque@ualberta.ca
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
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.
-- *Abdullah Ishaque, BSc.* MD/PhD Student, Neuroscience and Mental Health Institute Faculty of Medicine and Dentistry, University of Alberta aishaque@ualberta.ca
There is a registration file that gets created by the longitudinal processing that can be used with mri_vol2vol. I don't know where the LTA file is, but maybe Martin can weigh in.
On 05/08/2018 12:31 PM, Abdullah Ishaque wrote:
Hi,
I figured that part out: I can't load surfaces as volumes in freeview, but rather i need to load them as an overlay to the subject white, or pial surfaces.
I have another question for which I can't find an answer to. After registering myelin maps to the individual subjects, how do I register/transform them into the subjects' longitudinal T1s (obtained after the recon-all long command)?
The broad goal that I am trying to achieve is longitudinal myelin analysis. Any feedback is appreciated. Thanks!
On Tue, Apr 24, 2018 at 1:30 PM, Abdullah Ishaque <aishaque@ualberta.ca mailto:aishaque@ualberta.ca> wrote:
I did: mri_vol2surf --src Myelin_conformed.mgz --out C01_myelin.mgz --regheader C01 --hemi lh --projfrac 0.5 Now I'm just getting the error "freadFloat: fread failed" a whole bunch of times and the terminal gets stuck. Any suggestions? I checked Myelin_conformed.mgz and loaded it with orig.mgz in freeview and they look fine with great overlap and registration Thanks! On Tue, Apr 24, 2018 at 1:23 PM, Douglas Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: Specify a file format for the output (eg, C01.mgz) On 4/24/18 3:17 PM, Abdullah Ishaque wrote:Hi, Thank you for the prompt response. I used the following command: mri_vol2surf --src Myelin_conformed.mgz (T1/T2 image after mri_vol2vol from the previous step) --out C01 --regheader C01 --hemi lh --projfrac 0.5 This created two files called COR-.info and COR001. I tried loaded the COR001 file into freeview and tksurfer, but I keep the error "MRISalloc(8229512, 76): could allocated faces \ cannot allocate memory Am I making a mistake somewhere? Thanks, On Tue, Apr 24, 2018 at 11:34 AM, Douglas Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: That all looks correct. For the registration, just use --regheader C01 On 4/24/18 11:12 AM, Abdullah Ishaque wrote:Hi, It's my first time using FreeSurfer and I'd like some guidance regarding some of my steps. I'm attempting to perform myelin mapping as outlined in the paper by Righart (2017) Ann Neurol. Overall, I want to calculate myelin maps from each subject, sample them from the mid-cortical level to create cortical myelin surface maps, and perform vertexwise and ROI based analyses. Here's what I've done so far: 1. recon-all for all the subjects 2. Used bbregister to register the native T2 scans to the conformed T1 scans using this command: bbregister --s C01 --mov C01_T2.nii --init-fsl --reg register.dat --t2 (my understanding here is that this generates the .dat file that has the transformation to register the T2 image to the conformed orig.mgz file from subject C01) 3. Applied the register.dat file to the native T2 using mri_vol2vol --mov C01_T2.nii --o T2_conformed.mgz --fstarg --reg register.dat (this registers the T2 to the orig.mgz file in the conformed space) The next step for me is to perform mri_vol2surf. My question here is, which file should I select for the --srcreg flag and what should the --trgsubject input be? Secondly, am I on the right track to complete the analysis i.e., correct file types and my understanding of the steps? Clarifications regarding these questions and any suggestions for further directions will be very helpful! Let me know. Thanks! _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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 <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. -- *Abdullah Ishaque, BSc.* MD/PhD Student, Neuroscience and Mental Health Institute Faculty of Medicine and Dentistry, University of Alberta aishaque@ualberta.ca <mailto:aishaque@ualberta.ca> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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 <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. -- *Abdullah Ishaque, BSc.* MD/PhD Student, Neuroscience and Mental Health Institute Faculty of Medicine and Dentistry, University of Alberta aishaque@ualberta.ca <mailto:aishaque@ualberta.ca>-- *Abdullah Ishaque, BSc.* MD/PhD Student, Neuroscience and Mental Health Institute Faculty of Medicine and Dentistry, University of Alberta aishaque@ualberta.ca mailto:aishaque@ualberta.ca
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Douglas N. Greve
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Martin Reuter