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.
[Freesurfer] long_mris_slopes: error: cannot create a table with longitudinal pc1
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 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.
