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
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