This is the right way to do it, but it may be over kill. I doubt the fMRI results are going to change much whether you use the anatomical from first day only, the 2nd day only, or a combination of the two.
On 02/10/2016 01:25 PM, Martin Reuter wrote: > Hi, > > you should co register your structural scans with robust-register or > robust-template (if you have more than 2). This can be done into the > midspace to make sure both time points are mapped to avoid processing > bias. > > You can then register the functional scans to their corresponding > structurals and concat the transforms to get everything into the same > midspace. > > Best, Martin > > > On 02/10/2016 12:48 PM, Ji Won Bang wrote: >> 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 >> <mailto: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>: >>> >>> 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 list >>> Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto: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. >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Martin Reuter, PhD > Assistant Professor of Radiology, Harvard Medical School > Assistant Professor of Neurology, Harvard Medical School > A.A.Martinos Center for Biomedical Imaging > Massachusetts General Hospital > Research Affiliate, CSAIL, MIT > Phone: +1-617-724-5652 > Web :http://reuter.mit.edu > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
