24 Mar
2014
24 Mar
'14
noon
In that case, you can just do a paired analysis. Do a search for that on the wiki and you'll find examples doug
On 3/21/14 5:50 PM, Peggy Skelly wrote:
The actual time between tp1 & tp2 varies for subjects, *but* every subject received the same "dose" of treatment between timepoints. To ask if the treatment changed a subject's cortical thickness, I'm not using the actual time difference, I'm using a constant 1 for the time difference. (i.e. in long.qdec.table tp1's time = 0, and tp2's time = 1 for all subjects.)
On Fri, Mar 21, 2014 at 4:44 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto: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> <mailto: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>> > <mailto: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 > > >>>>> > > >>>>> > > >>>>> > > >>>>> _______________________________________________ > > >>>>> Freesurfer mailing list > > >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > > 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>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > 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>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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