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. 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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
