Hello,
I have a time series (.hdr/.img) that I want to overlay onto a surface, specifically the inflated surface from the anatomy. I suspect I have to use mri_vol2surf, which requires a source registration file. How do I get this file? Then once I have this file, will I be able to view step by step through the time series on the inflated volume?
Thanks for your help, Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Use bbregister. Run with --help to get docs (make sure to use --projfrac 0.5). Once you have it on the surface, you can step through each frame in freeview
On 04/05/2018 01:49 PM, Crawford, Anna wrote:
Hello,
I have a time series (.hdr/.img) that I want to overlay onto a surface, specifically the inflated surface from the anatomy. I suspect I have to use mri_vol2surf, which requires a source registration file. How do I get this file? Then once I have this file, will I be able to view step by step through the time series on the inflated volume?
Thanks for your help, Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello,
I used the following commands and then opened the surface as an overlay on the inflated volume, but I am not about to look at the time series. The view time course is grayed out so that I can not click on it. Did I miss a step or lose the actual time series somewhere?
bbregister --s S2sdt/subject/ --mov /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5
mri_vol2surf --src /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr --out /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz --srcreg /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat --hemi lh
Thank you, Anna
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Thursday, April 5, 2018 5:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Time Series to Surface
Use bbregister. Run with --help to get docs (make sure to use --projfrac 0.5). Once you have it on the surface, you can step through each frame in freeview
On 04/05/2018 01:49 PM, Crawford, Anna wrote:
Hello,
I have a time series (.hdr/.img) that I want to overlay onto a surface, specifically the inflated surface from the anatomy. I suspect I have to use mri_vol2surf, which requires a source registration file. How do I get this file? Then once I have this file, will I be able to view step by step through the time series on the inflated volume?
Thanks for your help, Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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
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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
No need to use --init-fsl (if using version 6). For mri_vol2surf add --projfrac 0.5 to sample in the middle of the ribbon (unless you specifically want to sample on the gray/white border)
On 4/6/18 10:11 AM, Crawford, Anna wrote:
Hello,
I used the following commands and then opened the surface as an overlay on the inflated volume, but I am not about to look at the time series. The view time course is grayed out so that I can not click on it. Did I miss a step or lose the actual time series somewhere?
bbregister --s S2sdt/subject/ --mov /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5
mri_vol2surf --src /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr --out /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz --srcreg /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat --hemi lh
Thank you, Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Thursday, April 5, 2018 5:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Time Series to Surface
Use bbregister. Run with --help to get docs (make sure to use --projfrac 0.5). Once you have it on the surface, you can step through each frame in freeview
On 04/05/2018 01:49 PM, Crawford, Anna wrote:
Hello,
I have a time series (.hdr/.img) that I want to overlay onto a surface, specifically the inflated surface from the anatomy. I suspect I have to use mri_vol2surf, which requires a source registration file. How do I get this file? Then once I have this file, will I be able to view step by step through the time series on the inflated volume?
Thanks for your help, Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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
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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I tried without --init-fsl and adding in the --projfrac 0.5 for mri_vol2surf, but I am still not able to view the time course.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu Sent: Friday, April 6, 2018 10:21 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Re: Time Series to Surface
No need to use --init-fsl (if using version 6). For mri_vol2surf add --projfrac 0.5 to sample in the middle of the ribbon (unless you specifically want to sample on the gray/white border)
On 4/6/18 10:11 AM, Crawford, Anna wrote:
Hello,
I used the following commands and then opened the surface as an overlay on the inflated volume, but I am not about to look at the time series. The view time course is grayed out so that I can not click on it. Did I miss a step or lose the actual time series somewhere?
bbregister --s S2sdt/subject/ --mov /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5
mri_vol2surf --src /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr --out /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz --srcreg /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat --hemi lh
Thank you, Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Thursday, April 5, 2018 5:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Time Series to Surface
Use bbregister. Run with --help to get docs (make sure to use --projfrac 0.5). Once you have it on the surface, you can step through each frame in freeview
On 04/05/2018 01:49 PM, Crawford, Anna wrote:
Hello,
I have a time series (.hdr/.img) that I want to overlay onto a surface, specifically the inflated surface from the anatomy. I suspect I have to use mri_vol2surf, which requires a source registration file. How do I get this file? Then once I have this file, will I be able to view step by step through the time series on the inflated volume?
Thanks for your help, Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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
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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
what is your freeview command line? Do you see a "frame" slider bar?
On 4/6/18 10:46 AM, Crawford, Anna wrote:
I tried without --init-fsl and adding in the --projfrac 0.5 for mri_vol2surf, but I am still not able to view the time course.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu Sent: Friday, April 6, 2018 10:21 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Re: Time Series to Surface
No need to use --init-fsl (if using version 6). For mri_vol2surf add --projfrac 0.5 to sample in the middle of the ribbon (unless you specifically want to sample on the gray/white border)
On 4/6/18 10:11 AM, Crawford, Anna wrote:
Hello,
I used the following commands and then opened the surface as an overlay on the inflated volume, but I am not about to look at the time series. The view time course is grayed out so that I can not click on it. Did I miss a step or lose the actual time series somewhere?
bbregister --s S2sdt/subject/ --mov /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5
mri_vol2surf --src /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr --out /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz --srcreg /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat --hemi lh
Thank you, Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Thursday, April 5, 2018 5:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Time Series to Surface
Use bbregister. Run with --help to get docs (make sure to use --projfrac 0.5). Once you have it on the surface, you can step through each frame in freeview
On 04/05/2018 01:49 PM, Crawford, Anna wrote:
Hello,
I have a time series (.hdr/.img) that I want to overlay onto a surface, specifically the inflated surface from the anatomy. I suspect I have to use mri_vol2surf, which requires a source registration file. How do I get this file? Then once I have this file, will I be able to view step by step through the time series on the inflated volume?
Thanks for your help, Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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
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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I just opened freeview and loaded everything in the GUI. I did not use the command line to open it. I do not see a slider bar.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu Sent: Friday, April 6, 2018 11:54 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Re: Re: Time Series to Surface
what is your freeview command line? Do you see a "frame" slider bar?
On 4/6/18 10:46 AM, Crawford, Anna wrote:
I tried without --init-fsl and adding in the --projfrac 0.5 for mri_vol2surf, but I am still not able to view the time course.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu Sent: Friday, April 6, 2018 10:21 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Re: Time Series to Surface
No need to use --init-fsl (if using version 6). For mri_vol2surf add --projfrac 0.5 to sample in the middle of the ribbon (unless you specifically want to sample on the gray/white border)
On 4/6/18 10:11 AM, Crawford, Anna wrote:
Hello,
I used the following commands and then opened the surface as an overlay on the inflated volume, but I am not about to look at the time series. The view time course is grayed out so that I can not click on it. Did I miss a step or lose the actual time series somewhere?
bbregister --s S2sdt/subject/ --mov /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5
mri_vol2surf --src /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr --out /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz --srcreg /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat --hemi lh
Thank you, Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Thursday, April 5, 2018 5:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Time Series to Surface
Use bbregister. Run with --help to get docs (make sure to use --projfrac 0.5). Once you have it on the surface, you can step through each frame in freeview
On 04/05/2018 01:49 PM, Crawford, Anna wrote:
Hello,
I have a time series (.hdr/.img) that I want to overlay onto a surface, specifically the inflated surface from the anatomy. I suspect I have to use mri_vol2surf, which requires a source registration file. How do I get this file? Then once I have this file, will I be able to view step by step through the time series on the inflated volume?
Thanks for your help, Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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
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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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
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Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
How many frames are in your input file? Eg, if you run mri_info on it?
On 4/6/18 12:05 PM, Crawford, Anna wrote:
I just opened freeview and loaded everything in the GUI. I did not use the command line to open it. I do not see a slider bar.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu Sent: Friday, April 6, 2018 11:54 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Re: Re: Time Series to Surface
what is your freeview command line? Do you see a "frame" slider bar?
On 4/6/18 10:46 AM, Crawford, Anna wrote:
I tried without --init-fsl and adding in the --projfrac 0.5 for mri_vol2surf, but I am still not able to view the time course.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu Sent: Friday, April 6, 2018 10:21 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Re: Time Series to Surface
No need to use --init-fsl (if using version 6). For mri_vol2surf add --projfrac 0.5 to sample in the middle of the ribbon (unless you specifically want to sample on the gray/white border)
On 4/6/18 10:11 AM, Crawford, Anna wrote:
Hello,
I used the following commands and then opened the surface as an overlay on the inflated volume, but I am not about to look at the time series. The view time course is grayed out so that I can not click on it. Did I miss a step or lose the actual time series somewhere?
bbregister --s S2sdt/subject/ --mov /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5
mri_vol2surf --src /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr --out /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz --srcreg /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat --hemi lh
Thank you, Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Thursday, April 5, 2018 5:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Time Series to Surface
Use bbregister. Run with --help to get docs (make sure to use --projfrac 0.5). Once you have it on the surface, you can step through each frame in freeview
On 04/05/2018 01:49 PM, Crawford, Anna wrote:
Hello,
I have a time series (.hdr/.img) that I want to overlay onto a surface, specifically the inflated surface from the anatomy. I suspect I have to use mri_vol2surf, which requires a source registration file. How do I get this file? Then once I have this file, will I be able to view step by step through the time series on the inflated volume?
Thanks for your help, Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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
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.
===================================
Please consider the environment before printing this e-mailCleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
1227 frames
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu Sent: Friday, April 6, 2018 12:14 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Re: Re: Re: Time Series to Surface
How many frames are in your input file? Eg, if you run mri_info on it?
On 4/6/18 12:05 PM, Crawford, Anna wrote:
I just opened freeview and loaded everything in the GUI. I did not use the command line to open it. I do not see a slider bar.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu Sent: Friday, April 6, 2018 11:54 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Re: Re: Time Series to Surface
what is your freeview command line? Do you see a "frame" slider bar?
On 4/6/18 10:46 AM, Crawford, Anna wrote:
I tried without --init-fsl and adding in the --projfrac 0.5 for mri_vol2surf, but I am still not able to view the time course.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu Sent: Friday, April 6, 2018 10:21 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Re: Time Series to Surface
No need to use --init-fsl (if using version 6). For mri_vol2surf add --projfrac 0.5 to sample in the middle of the ribbon (unless you specifically want to sample on the gray/white border)
On 4/6/18 10:11 AM, Crawford, Anna wrote:
Hello,
I used the following commands and then opened the surface as an overlay on the inflated volume, but I am not about to look at the time series. The view time course is grayed out so that I can not click on it. Did I miss a step or lose the actual time series somewhere?
bbregister --s S2sdt/subject/ --mov /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5
mri_vol2surf --src /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr --out /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz --srcreg /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat --hemi lh
Thank you, Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Thursday, April 5, 2018 5:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Time Series to Surface
Use bbregister. Run with --help to get docs (make sure to use --projfrac 0.5). Once you have it on the surface, you can step through each frame in freeview
On 04/05/2018 01:49 PM, Crawford, Anna wrote:
Hello,
I have a time series (.hdr/.img) that I want to overlay onto a surface, specifically the inflated surface from the anatomy. I suspect I have to use mri_vol2surf, which requires a source registration file. How do I get this file? Then once I have this file, will I be able to view step by step through the time series on the inflated volume?
Thanks for your help, Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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
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.
===================================
Please consider the environment before printing this e-mailCleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Can you upload the volume (img and hdr) here: https://gate.nmr.mgh.harvard.edu/filedrop2
On 4/6/18 12:24 PM, Crawford, Anna wrote:
1227 frames
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu Sent: Friday, April 6, 2018 12:14 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Re: Re: Re: Time Series to Surface
How many frames are in your input file? Eg, if you run mri_info on it?
On 4/6/18 12:05 PM, Crawford, Anna wrote:
I just opened freeview and loaded everything in the GUI. I did not use the command line to open it. I do not see a slider bar.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu Sent: Friday, April 6, 2018 11:54 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Re: Re: Time Series to Surface
what is your freeview command line? Do you see a "frame" slider bar?
On 4/6/18 10:46 AM, Crawford, Anna wrote:
I tried without --init-fsl and adding in the --projfrac 0.5 for mri_vol2surf, but I am still not able to view the time course.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu Sent: Friday, April 6, 2018 10:21 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Re: Time Series to Surface
No need to use --init-fsl (if using version 6). For mri_vol2surf add --projfrac 0.5 to sample in the middle of the ribbon (unless you specifically want to sample on the gray/white border)
On 4/6/18 10:11 AM, Crawford, Anna wrote:
Hello,
I used the following commands and then opened the surface as an overlay on the inflated volume, but I am not about to look at the time series. The view time course is grayed out so that I can not click on it. Did I miss a step or lose the actual time series somewhere?
bbregister --s S2sdt/subject/ --mov /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5
mri_vol2surf --src /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr --out /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz --srcreg /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat --hemi lh
Thank you, Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Thursday, April 5, 2018 5:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Time Series to Surface
Use bbregister. Run with --help to get docs (make sure to use --projfrac 0.5). Once you have it on the surface, you can step through each frame in freeview
On 04/05/2018 01:49 PM, Crawford, Anna wrote:
Hello,
I have a time series (.hdr/.img) that I want to overlay onto a surface, specifically the inflated surface from the anatomy. I suspect I have to use mri_vol2surf, which requires a source registration file. How do I get this file? Then once I have this file, will I be able to view step by step through the time series on the inflated volume?
Thanks for your help, Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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
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.
===================================
Please consider the environment before printing this e-mailCleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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
===================================
Please consider the environment before printing this e-mailCleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
What do I put for the email to send to? freesurfer@nmr.mgh.harvard.edu and freesurfer-bounces@nmr.mgh.harvard.edu said it was not a valid account
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu Sent: Friday, April 6, 2018 12:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Re: Re: Re: Re: Time Series to Surface
Can you upload the volume (img and hdr) here: https://gate.nmr.mgh.harvard.edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2
On 4/6/18 12:24 PM, Crawford, Anna wrote:
1227 frames
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Friday, April 6, 2018 12:14 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Re: Re: Re: Time Series to Surface
How many frames are in your input file? Eg, if you run mri_info on it?
On 4/6/18 12:05 PM, Crawford, Anna wrote:
I just opened freeview and loaded everything in the GUI. I did not use the command line to open it. I do not see a slider bar.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Friday, April 6, 2018 11:54 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Re: Re: Time Series to Surface
what is your freeview command line? Do you see a "frame" slider bar?
On 4/6/18 10:46 AM, Crawford, Anna wrote:
I tried without --init-fsl and adding in the --projfrac 0.5 for mri_vol2surf, but I am still not able to view the time course.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Friday, April 6, 2018 10:21 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Re: Time Series to Surface
No need to use --init-fsl (if using version 6). For mri_vol2surf add --projfrac 0.5 to sample in the middle of the ribbon (unless you specifically want to sample on the gray/white border)
On 4/6/18 10:11 AM, Crawford, Anna wrote:
Hello,
I used the following commands and then opened the surface as an overlay on the inflated volume, but I am not about to look at the time series. The view time course is grayed out so that I can not click on it. Did I miss a step or lose the actual time series somewhere?
bbregister --s S2sdt/subject/ --mov /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5
mri_vol2surf --src /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr --out /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz --srcreg /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat --hemi lh
Thank you, Anna
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Thursday, April 5, 2018 5:29 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Time Series to Surface
Use bbregister. Run with --help to get docs (make sure to use --projfrac 0.5). Once you have it on the surface, you can step through each frame in freeview
On 04/05/2018 01:49 PM, Crawford, Anna wrote:
Hello,
I have a time series (.hdr/.img) that I want to overlay onto a surface, specifically the inflated surface from the anatomy. I suspect I have to use mri_vol2surf, which requires a source registration file. How do I get this file? Then once I have this file, will I be able to view step by step through the time series on the inflated volume?
Thanks for your help, Anna
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freesurfer@nmr.mgh.harvard.edu
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Crawford, Anna -
Douglas Greve -
Douglas N. Greve