Hi Keishi,
the frame parameter is the frame in the contrast file. Most of the time this file will only have one frame (-frame 0) unless you have specified a multivariate contrast. This does not have anything to do with multiband. What is your intention when looping through from 0 to 19?
doug
On 1/28/18 11:41 PM, Keishi NOMURA wrote:
Hi all,
I’m using : freesurfer-Darwin-lion-stable-pub-v5.3.0
I’d like to plot HRF for each condition for each subject, using data acquired by multi-band EPI. Here are the commands I used:
funcroi-config -roi rh.V1.roicfg -label rh.V1.label -analysis RH_fwhm8 -force funcroi-sess -s ORI01 -roi rh.V1.roicfg -df sessdirfile
# m: frames
foreach m ( 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 ) funcroi-table-sess -s ORI01 -df sessdirfile -roi rh.V1.roicfg -analysis RH_fwhm8 -c ASonlineRH -map cespct -o ./ROI/V1/ASonlineRH/ORI01.f$m.txt -frame $m end
Then I got an error like “Error: input frame = 2, input volume only has 1 frames”.
I referred to the related questions: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15883.html https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017958.htm... It seems that there is nothing wrong with these commands, except for specifying the frames. One possibility is that using multi-band data is somehow causing trouble. I’m now using multi-band factor = 8 and TR = 0.8 sec, so then I set the frames to multiple number of TR = 0.8, and ran the commands again:
foreach m ( 0.8 1.6 2.4 3.2 4.0 4.8 5.6 6.4 7.2 8.0 8.8 9.6 10.4 11.2 12.0 12.8 13.6 14.4 15.2 16 ) funcroi-table-sess -s ORI01 -df sessdirfile -roi rh.V1.roicfg -analysis RH_fwhm8 -c ASonlineRH -map cespct -o ./ROI/V1/ASonlineRH/ORI01.f$m.txt -frame $m end
But still I get errors like “Error: input frame = 2, input volume only has 1 frames”. (when I used frame = 2.4. Hence, it seems that we cannot use non-integral inputs) So, my question is: (1) How should I specify frames when I use multi-band data? (2) Regarding (1), what temporal resolution do I get when I use TR = 0.8? (for example, TER = 0.8/20 = 0.04 or anything like that) (3) Or, is there anything wrong with my commands other than frames?
Thank you, Keishi
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