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:
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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:
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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" <mreuter@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.shatil@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://urldefense.proofpoint.com/v2/url?u=https-3A__mail.n mr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIDaQ&c=0hCx1u36- XAMUG1zdNEI2VR5Zeej6Q9MkDa5wSI1xHs&r=c8tCT8JoleOWQHKl- lalzjTpMaI7DRlUG6IrEQzbQkM&m=A1N4zBC63pmEhHrG2hvWgwxPxONtuqVj75vYRCCP c5Y&s=dJedOp_zbQ8lK_MlhZ0ytsq3vTXyy8_TjrmrzJVPdlA&e=
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