Just saw that you already found those settings.
these measures are the vertex wise results from the first level analysis on the (smoothed) LGI data. avg: average lgi at that location across time (within each subject). rate: the change of lgi per time unit (years). pc1: the percent change with respect to the first time point spc: symmetrized percent change (rate with respect to the average)
if any of this is meaningful for LGI, I don't know, you were the one trying to do this analysis ;-).
Best, Martin
On 05/19/2014 04:20 PM, Jon Wieser wrote:
I added the following lines to the .Qdecrc file in my home directory
MEASURE1 = long.pial_lgi-avg MEASURE2 = long.pial_lgi-rate MEASURE3 = long.pial_lgi-pc1 MEASURE4 = long.pial_lgi-spc
qdec's Analyze is working now.
what specifically do :( long.pial_lgi-avg, long.pial_lgi-rate, long.pial_lgi-pc1, long.pial_lgi-spc ) measure regarding the LGI ?
Jon
----- Forwarded Message ----- From: "Jon Wieser" wieser@uwm.edu To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Monday, May 19, 2014 2:53:43 PM Subject: [Freesurfer] LGI qdec analysis on longitiudinal data
Hi freesurfer experts
I am trying to analyze the longitudinal effects on LGI. I've run all my subject's through the longitudinal processing stream.
I set-up my qdec dat file:
fsid fsid-base years 100674-0107 100674_base 1.6 100674-0408 100674_base 2.8 100674-0605 100674_base 0 100712-0505 100712_base 0 100712-0708 100712_base 3.2 100712-1006 100712_base 1.4 100724-0605 100724_base 0 100724-0808 100724_base 3.2 100724-1206 100724_base 1.5 100733-0106 100733_base 0 100733-0507 100733_base 1.3 100733-1008 100733_base 2.8
I ran long_mris_slopse for both hemispheres:
long_mris_slopes --qdec ./UCSD_subj_NIDA_LGI.qdec.dat --meas pial_lgi --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd /Studies/UCSDsubjects-NIDA/Cluster_Proc
long_mris_slopes --qdec ./UCSD_subj_NIDA_LGI.qdec.dat --meas pial_lgi --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd /Studies/UCSDsubjects-NIDA/Cluster_Proc
i also ran long_qdec_table
long_qdec_table --qdec ./UCSD_subj_NIDA_LGI.qdec.dat --cross --out ./qdec/cross.qdec.table.dat
then I ran qdec:
qdec --table ./qdec/cross.qdec.table.dat
I specified pial_lgi as the Measure, and selected years as the covariate when I press Analyze, I get the following error: Error in Analyze: Couldn't open 100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgz or mgh file
when looking in the directories, I have lh.pial_lgi.fwhm10.fsaverage.mgh files in the 100674-0107.long.100674_base directories:
\100674-0107.long.100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100724-0605.long.100724_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100674-0107.long.100674_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100724-0605.long.100724_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100674-0408.long.100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100724-0808.long.100724_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100674-0408.long.100674_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100724-0808.long.100724_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100674-0605.long.100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100724-1206.long.100724_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100674-0605.long.100674_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100724-1206.long.100724_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100712-0505.long.100712_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100733-0106.long.100733_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100712-0505.long.100712_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100733-0106.long.100733_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100712-0708.long.100712_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100733-0507.long.100733_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100712-0708.long.100712_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100733-0507.long.100733_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100712-1006.long.100712_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100733-1008.long.100733_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100712-1006.long.100712_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100733-1008.long.100733_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh
but not in the following directories 100674_base/surf 100712_base/surf 100724_base/surf 100733_base/surf
How can I fix this?
Jon