Hi Anwar, what FS version are you using?
Also what happens if you omit the --out-pc1 but keep the --do-pc1 ? Also no output with that ending? It should write it to the default location. Best, Martin On Wed, 2018-08-29 at 16:45 +0000, Shatil, Anwar Shahadat wrote: > External Email - Use Caution > Dear Doug: > > I am trying to get a table containing pc1 values for each subject in > a longitudinal study and failed to extract this. I use the code > below: > > long_mris_slopes --qdec ./qdec/long.qdec.table.2.dat --meas thickness > --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label > --time years --qcache fsaverage --sd > /Users/richardaviv/Desktop/Longitudinal_FS --out-pc1 out-pc1.dat > > It says > long_mris_slopes: error: no such option: --out-pc1 > > > However in the --help file it says: > > Within-Subject Output: > Pass these to overwrite the default names: > > --out-avg=OUT_AVG filename to store temporal average in > <template>/stats/<OUT_AVG> (default: > long.<stats>.<meas>-avg.dat) > --out-rate=OUT_RATE > filename to store rate in > <template>/stats/<OUT_RATE> > (default: long.<stats>.<meas>-rate.dat) > --out-pc1fit=OUT_PC1FIT > filename to store pct. change (to tp1fit) in > <template>/stats/<OUT_PC1FIT> (default: > long.<stats>.<meas>-pc1fit.dat) > --out-pc1=OUT_PC1 filename to store pct. change (to tp1) in > <template>/stats/<OUT_PC1> (default: > long.<stats>.<meas>-pc1.dat) > --out-spc=OUT_SPC filename to store sym. pct. change in > <template>/stats/<OUT_SPC> (default: > long.<stats>.<meas>-spc.dat) > --out-resid=OUT_RESID > filename to store residual in > <template>/stats/<OUT_RESID> (default: > long.<stats>.<meas>-resid<resid>.dat), > requires > --resid <int> > --out-stack=OUT_STACK > filename to store stacked measure file > <template>/stats/<OUT_STACK> (default: > long.<stats>.<meas>-stack.dat) > > Stacked Tables: > To output tables with results from all subjects > > --stack-avg=STACK_AVG > full filename to stack temporal average > tables > (default no stacking) > --stack-rate=STACK_RATE > full filename to stack rate tables (default > no > stacking) > --stack-pc1fit=STACK_PC1FIT > full filename to stack pct. change to tp1fit > tables > (default no stacking) > --stack-pc1=STACK_PC1 > full filename to stack pct. change to tp1 > tables > (default no stacking) > --stack-spc=STACK_SPC > full filename to stack sym. pct. tables > (default no > stacking) > --stack-resid=STACK_RESID > full filename to stack residual tables > (default no > stacking) > > > Am I writing the code wrong?? I never got any long.<stats>.<meas>- > pc1.dat file in <template>/stats/ folder except bunch of mgh files > in <template>/surf/ folder. > > Thanks, > > Anwar > -- > > Anwar S. Shatil > > Research Assistant > Department of Medical Imaging > Sunnybrook Health Sciences Centre > Room AB204, 2075 Bayview Avenue > Toronto, ON M4N 3M5 > Tel: 416.480.6100 ext. 89617 > Email: anwar.sha...@sunnybrook.ca > This e-mail is intended only for the named recipient(s) and may > contain confidential, personal and/or health information (information > which may be subject to legal restrictions on use, retention and/or > disclosure). No waiver of confidence is intended by virtue of > communication via the internet. Any review or distribution by anyone > other than the person(s) for whom it was originally intended is > strictly prohibited. If you have received this e-mail in error, > please contact the sender and destroy all copies. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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.
