We are having an issue with scripts we used in freesurfer 4.5.0 but no longer work in 5.0.0. It is the mc-sess step, and we receive:
ERROR: Flag -toff unrecognized. -sf sf -df df -fsd bold -rlf ./tmp_run_list -toff 0 Done...
On the wiki, that flag is still recognized. When we delete it, we then receive a "by run" or "by session" error. I suspect this has something to do with the freesurfer or AFNI update, but we do not know what the new mc-sess takes as tags since the wiki has not changed. Does anybody know how mc-sess has changed?
Thank you, Luis L.S.
Hi Luis,
On Nov 28, 2010, at 16:48 , Luis Lafer-Sousa wrote:
We are having an issue with scripts we used in freesurfer 4.5.0 but no longer work in 5.0.0. It is the mc-sess step, and we receive:
ERROR: Flag -toff unrecognized. -sf sf -df df -fsd bold -rlf ./tmp_run_list -toff 0
judging from ./tmp_run_list you might be using scripts similar to the ones I use... (then again I might be wrong), but my scripts will definitely cause the same problems for me,,,
Done...
On the wiki, that flag is still recognized. When we delete it, we then receive a "by run" or "by session" error. I suspect this has something to do with the freesurfer or AFNI update, but we do not know what the new mc-sess takes as tags since the wiki has not changed. Does anybody know how mc-sess has changed?
Have a look at $FREESURFER_HOME/fsfast/bin/mc-sess thgis is the script that gets called. It looks like the target offset is not "wired" inside this script anymore. I seem to recall that Doug recommends to moco each run to its middle frame now. I do think it would be great if we still had the option to specify one frame from a single run as target for motion correction for non-human primates. The reason being the following: Occasionally (more often than one would like) some frames in monkey scans are really distorted due to the monkey displacing the field lines during a TR; in the past it was an improvement for the moco to pick a frame that was not affected by these artifacts. (Even using EPI unwarping with a fieldmap and fancy phased array coils does not remove this problem fully). This is going to be tricky if mc-sess insist on the middle frame for each run (as some of those might be really rotten). Doug, do you think it would be possible to resurrect the possibility to specify toff and run (I think a number of monkey researchers would be happy).
Best Sebastian
Thank you, Luis L.S. _______________________________________________ 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 the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Luis and Sebastian, you are right that -toff is not accepted anymore. The way that the motion correction (and func-anat reg) work now is that a functional template is created, and this template is used as the reference for MC and reg. This prevents the user from using a different template for each. The template is created with mktemplate-sess. By default, this will use the middle time point, but you can spec any time point that you want with the -frame option. Run with -help to get more info.
doug
Sebastian Moeller wrote:
Hi Luis,
On Nov 28, 2010, at 16:48 , Luis Lafer-Sousa wrote:
We are having an issue with scripts we used in freesurfer 4.5.0 but no longer work in 5.0.0. It is the mc-sess step, and we receive:
ERROR: Flag -toff unrecognized. -sf sf -df df -fsd bold -rlf ./tmp_run_list -toff 0
judging from ./tmp_run_list you might be using scripts similar to the ones I use... (then again I might be wrong), but my scripts will definitely cause the same problems for me,,,
Done...
On the wiki, that flag is still recognized. When we delete it, we then receive a "by run" or "by session" error. I suspect this has something to do with the freesurfer or AFNI update, but we do not know what the new mc-sess takes as tags since the wiki has not changed. Does anybody know how mc-sess has changed?
Have a look at $FREESURFER_HOME/fsfast/bin/mc-sess thgis is the script that gets called. It looks like the target offset is not "wired" inside this script anymore. I seem to recall that Doug recommends to moco each run to its middle frame now. I do think it would be great if we still had the option to specify one frame from a single run as target for motion correction for non-human primates. The reason being the following: Occasionally (more often than one would like) some frames in monkey scans are really distorted due to the monkey displacing the field lines during a TR; in the past it was an improvement for the moco to pick a frame that was not affected by these artifacts. (Even using EPI unwarping with a fieldmap and fancy phased array coils does not remove this problem fully). This is going to be tricky if mc-sess insist on the middle frame for each run (as some of those might be really rotten). Doug, do you think it would be possible to resurrect the possibility to specify toff and run (I think a number of monkey researchers would be happy).
Best Sebastian
Thank you, Luis L.S. _______________________________________________ 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 the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Doug,
On Nov 29, 2010, at 7:51 , Douglas N Greve wrote:
Luis and Sebastian, you are right that -toff is not accepted anymore. The way that the motion correction (and func-anat reg) work now is that a functional template is created, and this template is used as the reference for MC and reg. This prevents the user from using a different template for each.
Ah, that sounds like an improvement then.
The template is created with mktemplate-sess. By default, this will use the middle time point, but you can spec any time point that you want with the -frame option. Run with -help to get more info.
Ah, super that is a rather simple change to include in my processing stream... (I hope this is all that will be required for v5 :))
Best Sebastian
doug
Sebastian Moeller wrote:
Hi Luis,
On Nov 28, 2010, at 16:48 , Luis Lafer-Sousa wrote:
We are having an issue with scripts we used in freesurfer 4.5.0 but no longer work in 5.0.0. It is the mc-sess step, and we receive:
ERROR: Flag -toff unrecognized. -sf sf -df df -fsd bold -rlf ./tmp_run_list -toff 0
judging from ./tmp_run_list you might be using scripts similar to the ones I use... (then again I might be wrong), but my scripts will definitely cause the same problems for me,,,
Done...
On the wiki, that flag is still recognized. When we delete it, we then receive a "by run" or "by session" error. I suspect this has something to do with the freesurfer or AFNI update, but we do not know what the new mc-sess takes as tags since the wiki has not changed. Does anybody know how mc-sess has changed?
Have a look at $FREESURFER_HOME/fsfast/bin/mc-sess thgis is the script that gets called. It looks like the target offset is not "wired" inside this script anymore. I seem to recall that Doug recommends to moco each run to its middle frame now. I do think it would be great if we still had the option to specify one frame from a single run as target for motion correction for non-human primates. The reason being the following: Occasionally (more often than one would like) some frames in monkey scans are really distorted due to the monkey displacing the field lines during a TR; in the past it was an improvement for the moco to pick a frame that was not affected by these artifacts. (Even using EPI unwarping with a fieldmap and fancy phased array coils does not remove this problem fully). This is going to be tricky if mc-sess insist on the middle frame for each run (as some of those might be really rotten). Doug, do you think it would be possible to resurrect the possibility to specify toff and run (I think a number of monkey researchers would be happy).
Best Sebastian
Thank you, Luis L.S. _______________________________________________ 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 the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Luis Lafer-Sousa -
Sebastian Moeller