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
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