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 $m end
But still I get errors like “Error: input frame = 2, input volume only has 1 frames”. (when I used frame = 2.4. Hence, it seems that we cannot use non-integral inputs) So, my question is: (1) How should I specify frames when I use multi-band data? (2) Regarding (1), what temporal resolution do I get when I use TR = 0.8? (for example, TER = 0.8/20 = 0.04 or anything like that) (3) Or, is there anything wrong with my commands other than frames?
Thank you, Keishi
Hi Keishi,
the frame parameter is the frame in the contrast file. Most of the time this file will only have one frame (-frame 0) unless you have specified a multivariate contrast. This does not have anything to do with multiband. What is your intention when looping through from 0 to 19?
doug
On 1/28/18 11:41 PM, Keishi NOMURA wrote:
Hi all,
I’m using : freesurfer-Darwin-lion-stable-pub-v5.3.0
I’d like to plot HRF for each condition for each subject, using data acquired by multi-band EPI. Here are the commands I used:
funcroi-config -roi rh.V1.roicfg -label rh.V1.label -analysis RH_fwhm8 -force funcroi-sess -s ORI01 -roi rh.V1.roicfg -df sessdirfile
# m: frames
foreach m ( 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 ) funcroi-table-sess -s ORI01 -df sessdirfile -roi rh.V1.roicfg -analysis RH_fwhm8 -c ASonlineRH -map cespct -o ./ROI/V1/ASonlineRH/ORI01.f$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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Douglas Greve -
Keishi NOMURA