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