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-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve > <dgr...@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 f
Re: [Freesurfer] Re: Time Series to Surface
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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@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
