Hi Martin and all, I would like to ask you if by comparing tp1 thickness-spc with tp2 (and comparing tp2 with tp3) using the base brain between tp1,2 and 3 (altogether) I have messed up methodologically.
I was expecting a rise in cortical thickness in certain areas between tp1 and tp2 followed by a greater rise between tp2 and tp3. I did not expect however a host of other changes which were not seen when viewing spc of tp1, 2 and 3 together. Most of these effects seem to be basically mirror-effects e.g. if there is a rise between tp1 and tp2, there is a drop in thickness in the same area between tp2 and tp3 and vice versa. This happened in several subjects and in variable brain regions. I would like to know if this is because of some methodological flaw. For example, should I run the whole longitudinal stream 2 more times (once to compare tp1 and tp2, and the second time to compare tp2 to tp3)? Also, when viewing the spc of tp1, tp2 and tp3 together are we just looking at the change between timepoints 1 and 3? Many thanks for the help, All the best, Seán On 27 June 2011 11:50, Seán Froudist Walsh <froud...@tcd.ie> wrote: > Hi Martin, > > That worked! Thanks a lot, > > Seán > > > On 23 June 2011 18:22, Martin Reuter <mreu...@nmr.mgh.harvard.edu> wrote: > >> Hi Sean, >> >> I think the --out... names need to be without the ending (mgh) >> so for example --out-avg=long23.thickness-avg >> >> Maybe that'll fix it. >> >> Best, Martin >> >> On Thu, 2011-06-23 at 09:12 -0700, Seán Froudist Walsh wrote: >> > Dear FreeSurfers, >> > >> > I am looking for a little help comparing longitudinal data. I have >> > three timepoints on each patient and have been able to get individual >> > spc-thickness maps using the long_mris_slopes command where my table >> > included all three time points. I would however like to compare >> > different timepoints with each other: tp3-tp2 and tp2-tp1. >> > >> > I was hoping it would be as simple as specifying a new qdec table >> > including (for example) only tp3 and tp2, and giving new output names >> > using the following command >> > >> > long_mris_slopes --qdec ./qdec/long.qdec.tableTP23.dat --meas >> > thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack >> > --do-label --out-avg=long23.thickness-avg.mgh >> > --out-rate=long23.thickness-rate.mgh >> > --out-pc1=long23.thickness-pc1.mgh --out-spc=long23.thickness-spc.mgh >> > --out-stack=long23.thickness-stack.mgh --out-label=long23.cortex >> > --time scan --qcache fsaverage >> > >> > but I get the following error: >> > >> > mris_calc: >> > Sorry, but I seem to have encountered an error. >> > While making backup of internal data arrays, >> > it seems that some of the backups already exist. >> > >> > I'm not really sure what the internal data arrays are, and would >> > greatly appreciate any help. >> > >> > Many thanks in advance and all the best, >> > >> > Seán >> > >> > _______________________________________________ >> > 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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