Hi Jon,
The commands look OK. The files
lh.pial_lgi.fwhm10.fsaverage.mgz
are the individual smoothed lgi files (one for each time point) and
should not be in the base, only in the .long. directories, so everything
is OK.
When running qdec, you can analyze the change or the average of this
across subjects. You should have those files in the base, e.g.
lh.long.pial_lgi-pc1.fwhm15.fsaverage.mgh
for the percent change. This is what you can compare cross sectionally.
For that you have to edit the $SUBJECTS_DIR/qdec/.Qdecrc file and add
these lines:
MEASURE1 = long.pial_lgi-pc1
MEASURE2 = long.pial_lgi-spc
MEASURE3 = long.pial_lgi-rate
MEASURE4 = long.pial_lgi-avg
(you only need to add the ones you actually want to use in qdec).
You can then run qdec and do all kinds of analysis on any of those files
and other variables from the qdec table:
qdec --table ./qdec/cross.qdec.table.dat
You will see in the /Design/ tab, that you can now select e.g.
long.thickness-rate under /Measure/ as the dependent variable.
See also:
http://freesurfer.net/fswiki/LongitudinalTwoStageModel
The two stage model
1. runs an analysis on a subject level to compute e.g. percent change of
some measure, usually thickness
2. runs a group analysis as a second stage, using the change measures
from step 1.
You finished stage 1. Good luck with stage 2 :-).
Martin
Best, Martin
On 05/19/2014 03:53 PM, Jon Wieser wrote:
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
--
Martin Reuter, Ph.D.
Instructor in Neurology
Harvard Medical School
Assistant in Neuroscience
Dept. of Radiology, Massachusetts General Hospital
Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
Computer Science and Artificial Intelligence Lab,
Dept. of Electrical Engineering and Computer Science,
Massachusetts Institute of Technology
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web : http://reuter.mit.edu
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