Dear. Freesurfer team. Thanks so much your help and advice.
Based on the comments, I'm trying freesurfer version 5.3.0 instead of 4.5.0 now. In our experiment, each participant is scanned twice on different days and the functional scan's brain volume are different (some scans have 33 number of slices, some have 32 number of slices). Since participants moved a bit between scans on the same day, and the head position is different between different days, my advisor advised me to do co-registration between different functional scans and then do co-registration between anatomical and functional scans. My question is this. If I do motion-correction such that we align all EPI data to the first EPI of the first functional scan, will it be enough for co-registration between different functional scans and different days? Or should I do coregistration-specific process such as mri_robust_register, mri_robust_template etc? Or I guess the method I choose should depend on how much the participant moved between scans and how much different the head position was between different days? For example, if the participant was very still between runs and the head position was not that too different, this motion correction is enough for coregistration between functional scans. However, if not, I should do coregistration-specific process such as mri_robust_register, mri_robust_template etc? I'd appreciate any of your advice. Please feel free to let me know your thoughts. Best, Ji Won 2016-02-08 22:31 GMT-05:00 Douglas Greve <gr...@nmr.mgh.harvard.edu>: > In 4.5 I don't think there is a way to run it when different runs have > different number of slices. Version 5+ will handle it properly. If you > really want to use 4.5, then you'll have to put it in a different > functional subdir (FSD, eg, bold), and create a new analysis for it, then > combine them together after analysis. A bit of a hassle. > > > On 2/8/16 5:58 PM, Ji Won Bang wrote: > > Dear. Freesurfer team. > > As another attempt, I run the motion correction without the argument > -targrun: > > mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino > > However, I get the same error message again. > > Why is that? > > Thanks so much for your effort and time. > > I appreciate it a lot. > > Best, > Ji Won > > > 2016-02-08 17:16 GMT-05:00 Ji Won Bang <kirsten...@gmail.com>: > >> Dear. Freesurfer team. >> >> I'd appreciate any advice from you. >> >> When doing the motion correction, I'd like to align all EPI >> data(bold_retino) to the first EPI of target run(bold_decode/003). However, >> the number of slices for target run(33) and the number of slices(32) for >> input run(bold_retino) are different. >> >> When I type: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino >> -targrun $DATA_DIR/$SUBJECT/bold_decode/003 >> >> Freesurfer says that: >> ** FATAL ERROR: perhaps you could make your datasets match? >> ERROR: 3dvolreg >> Invalid null command. >> >> These two kinds of run (bold_decode, bold_retino) were collected in one >> scan per subject, so the head position should not be too different... >> >> Do you have any suggestions for fixing this error? >> >> Should I do 3dWarp -deoblique? >> >> Thank you so much. >> >> Best, >> Ji Won >> >> 2016-02-08 16:30 GMT-05:00 Ji Won Bang < <kirsten...@gmail.com> >> kirsten...@gmail.com>: >> >>> Dear. Freesurfer team. >>> >>> Hi. >>> >>> I'm using freesurfer 4.5 version. >>> >>> While doing the motion correction, an error occurred. >>> >>> the command I used: >>> mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun >>> $DATA_DIR/$SUBJECT/bold_decode/003 >>> >>> the error I have: >>> /home/jbang/Projects/replay/epi/replay01/bold_retino >>> 3dvolreg -verbose -dfile 025/fmc.mcdat -base >>> 025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix >>> 025/tmp.mc-afni2.32291/outvol.nii.gz 025/tmp.mc-afni2.32291/invol.nii.gz >>> ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit] >>> ++ Authored by: RW Cox >>> *+ WARNING: If you are performing spatial transformations on an >>> oblique dset, >>> such as 025/tmp.mc-afni2.32291/tempvol.nii.gz, >>> or viewing/combining it with volumes of differing obliquity, >>> you should consider running: >>> 3dWarp -deoblique >>> on this and other oblique datasets in the same session. >>> See 3dWarp -help for details. >>> ++ Oblique dataset:025/tmp.mc-afni2.32291/tempvol.nii.gz is 3.263868 >>> degrees from plumb. >>> ++ Reading in base dataset 025/tmp.mc-afni2.32291/tempvol.nii.gz >>> ++ Oblique dataset:025/tmp.mc-afni2.32291/invol.nii.gz is 4.564286 >>> degrees from plumb. >>> ++ centers of base and input datasets are 9.09 mm apart >>> ** Input ./invol.nii.gz+orig.HEAD and base ./tempvol.nii.gz+orig.HEAD >>> don't have same dimensions! >>> Input: nx=74 ny=74 nz=32 >>> Base: nx=74 ny=74 nz=33 >>> ** FATAL ERROR: perhaps you could make your datasets match? >>> ERROR: 3dvolreg >>> Invalid null command. >>> >>> I think it's because the volume size is different. >>> >>> The volume size for bold_retino is: number of slices 32 >>> The volume size for bold_decode: number of slices 33 >>> >>> What should I do to correct this error? >>> >>> Thank you for taking your time. >>> >>> Best, >>> Ji Won >>> >> >> > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 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. > >
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