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-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 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-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.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
