Thanks, Martin for the info. We are studying the effect of drug usage on LGI over time Jon
----- Original Message ----- From: "Martin Reuter" mreuter@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, May 19, 2014 3:30:48 PM Subject: Re: [Freesurfer] Fwd: LGI qdec analysis on longitiudinal data
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