On Fri, Mar 21, 2014 at 4:44 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Is the time between tp1 and tp2 the same for all subjects? If not, are
you using that information?

On 03/21/2014 04:15 PM, Peggy Skelly wrote:
> The overall question is: did the cortical thickness of healthy
> hemispheres (of stroke subjects) change from tp1 to tp2, and does it
> correlate with the change in their functional measure? So I was using
> the long.thickness-rate measure and qdec.
>
> Peggy
>
>
> On Fri, Mar 21, 2014 at 1:38 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>
> mri_label2label needs to be called with --surfreg
> fsaverage_sym.sphere.reg
>
> Martin, can you modify long_mris_slopes to add this?
>
> But another question is exactly what you want to do in the end. What
> function of the slopes and hemisphere are you trying to compute?
>
> doug
>
>
> On 03/21/2014 01:20 PM, Peggy Skelly wrote:
> > I tried your suggestion (using subjTP/xhemi in place of subjTP)
> in the
> > qdec table. I doesn't work because long_mris_slopes uses subjTP and
> > subjBase to create "subjTP.long.subjBase", the directory of the
> actual
> > data. Extra slashes "/" in the name create an incorrect name (i.e.
> > subjTP/xhemi.long.subjBase/xhemi).
> >
> > So I tried copying the contents of the /xhemi subdirectories into a
> > different $SUBJECTS_DIR with timepoint and base names the way
> > long_mris_slopes expects them:
> > subjdir_xhemi/subjTP1.long.subjbase
> > subjdir_xhemi/subjTP2.long.subjbase
> > subjdir_xhemi/subjbase
> >
> > This works to create appropriate path/filenames for
> long_mris_slopes.
> > But ...
> >
> > The problem now is when long_mris_slopes calls mri_label2label
> > (mapping cortex labels to fsaverage_sym), the file
> surf/rh.sphere.reg
> > is not found. It's not in the /xhemi/surf directory. It is in the
> > original subject directory. xhemi/surf/ only
> > contains rh.fsaverage_sym.sphere.reg.
> >
> > Any suggestions? Am I approaching this problem (combining healthy
> > hemispheres in a longitudinal study) correctly?
> >
> > Peggy
> >
> >
> >
> > On Mon, Mar 17, 2014 at 3:35 PM, Douglas N Greve
> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
> >
> >
> > I'm not sure this will work but try entering the subjectids
> in the
> > qdec
> > table as subjectTP and subjectTP/xhemi and use subject as
> the base (TP
> > is just a shorthand for time point, use whatever you used)
> > doug
> >
> > On 03/17/2014 01:09 PM, Peggy Skelly wrote:
> > > The patch works! Thank you.
> > >
> > > Now, to compute the longitudinal measures: I don't see
> > 'long_mris_slopes
> > > --help' mentioning xhemi, so I suppose
> > > it won't be able to find the flipped subjects. Is there a
> way to
> > > copy/rename the <subj>/xhemi/ directory
> > > to $SUBJECTS_DIR so I could run long_mris_slopes?
> > >
> > > Peggy
> > >
> > > On 3/14/14, 7:13 PM, Peggy Skelly wrote:
> > >> Thanks -- (I thought I might not have understood the
> processing
> > >> pipeline properly.)
> > >>
> > >> I'm running 5.3, I'll try the patch and let you know how
> it works.
> > >>
> > >> Peggy
> > >>
> > >>
> > >> On 3/14/14, 16:07 , Douglas N Greve wrote:
> > >>> Actually, I don't think this will work. What version of
> FS are you
> > >>> running?
> > >>>
> > >>> I've created a patch of the 5.3 recon-all here
> > >>>
> > >>>
> >
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/recon-all.53.patch
> > >>>
> > >>>
> > >>> Copy this to $FREESURFER_HOME/bin/recon-all (after making a
> > backup!)
> > >>>
> > >>> then re-run
> > >>>
> > >>> doug
> > >>>
> > >>>
> > >>> On 03/14/2014 03:57 PM, Douglas N Greve wrote:
> > >>>> You have uncovered a bug. I don't think anyone has
> tried to run
> > >>>> xhemi on
> > >>>> a longitudinal data set before. There is a work-around.
> First run
> > >>>>
> > >>>> xhemireg --s subject --no-tal
> > >>>>
> > >>>> Then run
> > >>>>
> > >>>> surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym
> --rh
> > --xhemi
> > >>>>
> > >>>> I think this should work
> > >>>>
> > >>>> doug
> > >>>>
> > >>>>
> > >>>> On 03/14/2014 03:39 PM, Peggy Skelly wrote:
> > >>>>> Hi All,
> > >>>>>
> > >>>>> Although the question of flipping hemispheres has come up
> > before, I
> > >>>>> still struggling with it.
> > >>>>> I'm working on a longitudinal study with stroke subjects
> > (half with lh
> > >>>>> lesions, half with rh lesions). We want to compare
> only the
> > >>>>> non-lesioned, healthy, hemispheres at 2 timepoints
> (pre- and
> > >>>>> post-therapy).
> > >>>>>
> > >>>>> Using the tutorial
> > >>>>>
> >
> (http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial_freeview)
> > >>>>> as
> > >>>>> a guide, I've completed the longitudinal analysis
> > (cross-base-long
> > >>>>> steps) for both lh- and rh-lesioned subjects.
> > >>>>>
> > >>>>> I've done the thickness data qcache for the right/healthy
> > hemi for the
> > >>>>> lh-lesioned group:
> > >>>>> long_mris_slopes --qdec
> > long_qdec_lh_lesion_subjects_table.dat --meas
> > >>>>> thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc
> > --do-stack
> > >>>>> --do-label --time my_time_var --qcache fsaverage_sym --sd
> > >>>>> $SUBJECTS_DIR
> > >>>>>
> > >>>>> Convert the long_qdec_lh_lesion_subjects_table.dat into a
> > >>>>> cross.qdec.table.dat to use in qdec. This works
> well---I can
> > look for
> > >>>>> clusters where athe average thickness-rate is
> different from 0.
> > >>>>>
> > >>>>> How can I combine the rh-lesioned group with the first
> group?
> > >>>>>
> > >>>>> I thought I could flip hemispheres of the results at each
> > subject's
> > >>>>> longitudinal output timepoint with:
> > >>>>> surfreg --s subj1_Tp1.long.subj1_base --t
> fsaverage_sym --rh
> > --xhemi
> > >>>>>
> > >>>>> but this terminated with an error:
> > >>>>>> recon-all -sb s1311_15T_post.long.s1311_15T_base/xhemi
> > -talairach
> > >>>>>>
> > >>>>>> ERROR: Are you trying to run or re-run a longitudinal
> time
> > point?
> > >>>>>> If so, please specify the following parameters:
> > >>>>>>
> > >>>>>> \' -long <tpNid> <templateid> \'
> > >>>>>>
> > >>>>>> where <tpNid> is the time point id (SAME as
> cross
> > sectional
> > >>>>>> ID) and <templateid> is the ID created in the
> > -base run.
> > >>>>>> The directory <tpNid>.long.<templateid> will be
> > created
> > >>>>>> automatically or used for output, if it already
> > exists.
> > >>>>> I know it's recommended to flip hemispheres after
> processing
> > >>>>>
> >
> (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg34040.html).
> > >>>>>
> > >>>>> When (and how) is it best done?
> > >>>>>
> > >>>>> Thanks,
> > >>>>> Peggy
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>> _______________________________________________
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> > >
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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