Hi Anwar, I see, you want to convert the mgh file back to some text table. Not sure how that worked, but I think mri_convert could do it (but maybe only for a single subject with several structures, not sure about multiple subjects - this is a stacked file). Another way is to open the mgh in matlab or python and then you get a vector and output it to a text file.
Best, Martin On Tue, 2018-09-04 at 20:05 +0000, Shatil, Anwar Shahadat wrote: > External Email - Use Caution > > Hi Martin/Doug: > > Still looking for an answer. Could not find a way to list the > percentage change values for each subject in a tabular form. > > Thanks, > > Anwar > > On 2018-08-30, 12:15 PM, "Shatil, Anwar Shahadat" <anwar.shatil@sunn > ybrook.ca> wrote: > > External Email - Use Caution > > Hello Martin: > > I am using freesurfer 6.0.0 and the long_mris_slopes version 1.42 > (that came with it by default). > > If I omit --out-pc1 but keep --do-pc1 still do not get any output > as a .dat or .stats file. I only get .mgh file in surf folder. > > I need percentage change values of tp2 from tp1 for each subject > in a tabular form. > > Best, > > Anwar > > On 2018-08-30, 3:22 AM, "Martin Reuter" <mreu...@nmr.mgh.harvard > .edu> wrote: > > 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. 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