Re: [Freesurfer] long_mris_slopes: error: cannot create a table with longitudinal pc1
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 +, 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" 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" .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 +, 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 > > /stats/ > (default: > > long..-avg.dat) > > --out-rate=OUT_RATE > > filename to store rate in > > /stats/ > > (default: long..- > rate.dat) > > --out-pc1fit=OUT_PC1FIT > > filename to store pct. change (to > tp1fit) in > > /stats/ > (default: > > long..-pc1fit.dat) > > --out-pc1=OUT_PC1 filename to store pct. change (to > tp1) in > > /stats/ > (default: > > long..-pc1.dat) > > --out-spc=OUT_SPC filename to store sym. pct. change > in > > /stats/ > (default: > > long..-spc.dat) > > --out-resid=OUT_RESID > > filename to store residual in > > /stats/ > (default: > > long..- > resid.dat), > > requires > > --resid > > --out-stack=OUT_STACK > > filename to store stacked measure > file > > /stats/ > (default: > > long..-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 >
Re: [Freesurfer] long_mris_slopes: error: cannot create a table with longitudinal pc1
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" 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" 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 +, 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 > /stats/ (default: > long..-avg.dat) > --out-rate=OUT_RATE > filename to store rate in > /stats/ > (default: long..-rate.dat) > --out-pc1fit=OUT_PC1FIT > filename to store pct. change (to tp1fit) in > /stats/ (default: > long..-pc1fit.dat) > --out-pc1=OUT_PC1 filename to store pct. change (to tp1) in > /stats/ (default: > long..-pc1.dat) > --out-spc=OUT_SPC filename to store sym. pct. change in > /stats/ (default: > long..-spc.dat) > --out-resid=OUT_RESID > filename to store residual in > /stats/ (default: > long..-resid.dat), > requires > --resid > --out-stack=OUT_STACK > filename to store stacked measure file > /stats/ (default: > long..-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..- > pc1.dat file in /stats/ folder except bunch of mgh files > in /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:
Re: [Freesurfer] long_mris_slopes: error: cannot create a table with longitudinal pc1
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" 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 +, 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 > /stats/ (default: > long..-avg.dat) > --out-rate=OUT_RATE > filename to store rate in > /stats/ > (default: long..-rate.dat) > --out-pc1fit=OUT_PC1FIT > filename to store pct. change (to tp1fit) in > /stats/ (default: > long..-pc1fit.dat) > --out-pc1=OUT_PC1 filename to store pct. change (to tp1) in > /stats/ (default: > long..-pc1.dat) > --out-spc=OUT_SPC filename to store sym. pct. change in > /stats/ (default: > long..-spc.dat) > --out-resid=OUT_RESID > filename to store residual in > /stats/ (default: > long..-resid.dat), > requires > --resid > --out-stack=OUT_STACK > filename to store stacked measure file > /stats/ (default: > long..-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..- > pc1.dat file in /stats/ folder except bunch of mgh files > in /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 >
Re: [Freesurfer] long_mris_slopes: error: cannot create a table with longitudinal pc1
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 +, 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 > /stats/ (default: > long..-avg.dat) > --out-rate=OUT_RATE > filename to store rate in > /stats/ > (default: long..-rate.dat) > --out-pc1fit=OUT_PC1FIT > filename to store pct. change (to tp1fit) in > /stats/ (default: > long..-pc1fit.dat) > --out-pc1=OUT_PC1 filename to store pct. change (to tp1) in > /stats/ (default: > long..-pc1.dat) > --out-spc=OUT_SPC filename to store sym. pct. change in > /stats/ (default: > long..-spc.dat) > --out-resid=OUT_RESID > filename to store residual in > /stats/ (default: > long..-resid.dat), > requires > --resid > --out-stack=OUT_STACK > filename to store stacked measure file > /stats/ (default: > long..-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..- > pc1.dat file in /stats/ folder except bunch of mgh files > in /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.
