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.
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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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" 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.nmr.mgh.harvard.ed...
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.
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@sunnybrook.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" 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.nmr.mgh.harvard.ed...
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.
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.
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" <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=
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.
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.
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Shatil, Anwar Shahadat