Re: [Freesurfer] long_mris_slopes
External Email - Use Caution That worked! *python2 /opt/softwarepackages/freesurfer/bin/long_mris_slopes --qdec qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time months --qcache fsaverage --sd $SUBJECTS_DIR* Thank you! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] long_mris_slopes
External Email - Use Caution This is a bit of a guess, but I think the issue is that the script requires python2, but your python interpreter (the 'python' command on your system) points to python3. You can check whether this is the case by running: python --version If that prints 'Python 3.x.y', the solution is to use a python2 interpreter to call mris_slopes_long. You will have to give it the full path to the script though. E.g., if your python2 interpreter is 'python2' and you have FreeSurfer setup correctly in your shell, then you could do: python2 $FREESURFER_HOME/bin/long_mris_slopes To run your command (where is all the arguments you posted). Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany > On 10/22/2021 3:05 AM Veena Nair wrote: > > > External Email - Use Caution > > Hello, I am trying to do some preliminary analysis of a > longitudinal dataset, following the tutorial. > > I am running FS on Ubuntu 20.04 and > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > > I have finished processing the dataset; to prepare the data for the > statistical analysis, I am running this command. > > long_mris_slopes --qdec long.qdec.table.dat --meas thickness --hemi lh > --do-avg --do-rate --do-pcl --do-spc --do-stack --do-label --time years > --qcache fsaverage --sd $SUBJECTS_DIR > > But I get the following error- > File "/opt/softwarepackages/freesurfer/bin/long_mris_slopes", line 448 > print '\nERROR: Specify --qdec (and other required arguments)\n' > ^ > SyntaxError: invalid syntax > I tried (as sudo) fixing the typo in the script, but that didn't help!! > I tried switching from python version 3 to 2 [a previous post on this issue > had recommended the solution], but that didn't help. > > I would appreciate any inputs on how to fix this issue. > > Thank you. > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1QUc7jiTjtKBNZvhJ-9T0nliU1sykrdVxolEUPmOWHZd8DB2GXZa-SedyUsDpuphvls7AAqX266yAoEOyvvIiqQHnnNxG50Bd4cb_yXvF0cZJq0VMP-cwuTkZb-Lehzw7XqqB1Ge4ph34dG_z3CEWUIe0VubkrWu4bCTBEXKLOBROLBLDGAm3EowXQ-Fupd1eQ5Rfs2Zz7DSDVfBlxgRof8eeJkxhsydYWf3p2_Zp_HsrRtxdaRBIK0InUQT1AZbN/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] long_mris_slopes
External Email - Use Caution Hello, I am trying to do some preliminary analysis of a longitudinal dataset, following the tutorial. I am running FS on Ubuntu 20.04 and freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c I have finished processing the dataset; to prepare the data for the statistical analysis, I am running this command. long_mris_slopes --qdec long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pcl --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR But I get the following error- File "/opt/softwarepackages/freesurfer/bin/long_mris_slopes", line 448 print '\nERROR: Specify --qdec (and other required arguments)\n' ^ SyntaxError: invalid syntax I tried (as sudo) fixing the typo in the script, but that didn't help!! I tried switching from python version 3 to 2 [a previous post on this issue had recommended the solution], but that didn't help. I would appreciate any inputs on how to fix this issue. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Re: [Freesurfer] long_mris_slopes error
Hi Carolina, probably you are not interested in the average thickness, so you can drop --do-avg . Also usually people decide between pc1 and spc. The stack is also not really necessary unless you want to look at it. Try to remove the trailing / at fsaverage and --sd $SUBJECTS_DIR that should fix your error. Best, Martin On 02/24/2015 01:54 PM, carolina.mr wrote: Hi FreeSurfer experts, I am trying to run Longitudinal Two Steps analysis. In the long_mris_slopes I run the following command: long_mris_slopes --qdec $SUBJECTS_DIR/qdec/longRRMSP01.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage/ --sd $SUBJECTS_DIR/ And, after some processing, it appears the error message: mv ./tmp-P01_TP_lh_thickness_C8c_pE/lh.tmp.mgh /analise//P01_TP/surf/lh.long.thickness-spc.fwhm0.fsaverage/.mgh mv: rename ./tmp-P01_TP_lh_thickness_C8c_pE/lh.tmp.mgh to /analise//P01_TP/surf/lh.long.thickness-spc.fwhm0.fsaverage/.mgh: No such file or directory ERROR 1 : mv ./tmp-P01_TP_lh_thickness_C8c_pE/lh.tmp.mgh /analise//P01_TP/surf/lh.long.thickness-spc.fwhm0.fsaverage/.mgh did not work? In the base folder, /surf, I can find many .mgh archives, for example: lh.long.thickness-spc.fwhm0.mgh (and others with other fwhm smoothing factors). But I can't find any lh.long.thicknessfsaverage files. I did all the previous processing as it appears in the Longitudinal FS Tutorials. I also tried to run qcache with the base file, but it says it is not necessary, since it is a base file. Should I run qcache first with each subject / time point before? Thank you, Carolina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ 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
Hi FreeSurfer experts, I am trying to run Longitudinal Two Steps analysis. In the long_mris_slopes I run the following command: long_mris_slopes --qdec $SUBJECTS_DIR/qdec/longRRMSP01.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage/ --sd $SUBJECTS_DIR/ And, after some processing, it appears the error message: mv ./tmp-P01_TP_lh_thickness_C8c_pE/lh.tmp.mgh /analise//P01_TP/surf/lh.long.thickness-spc.fwhm0.fsaverage/.mgh mv: rename ./tmp-P01_TP_lh_thickness_C8c_pE/lh.tmp.mgh to /analise//P01_TP/surf/lh.long.thickness-spc.fwhm0.fsaverage/.mgh: No such file or directory ERROR 1 : mv ./tmp-P01_TP_lh_thickness_C8c_pE/lh.tmp.mgh /analise//P01_TP/surf/lh.long.thickness-spc.fwhm0.fsaverage/.mgh did not work? In the base folder, /surf, I can find many .mgh archives, for example: lh.long.thickness-spc.fwhm0.mgh (and others with other fwhm smoothing factors). But I can't find any lh.long.thicknessfsaverage files. I did all the previous processing as it appears in the Longitudinal FS Tutorials. I also tried to run qcache with the base file, but it says it is not necessary, since it is a base file. Should I run qcache first with each subject / time point before? Thank you, Carolina ___ 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.
Re: [Freesurfer] long_mris_slopes bug
Hi Katherine, are you sure you downloaded the right executable for your operating system? It seems to be not able to run the command (exec format error). Did you replace mri_convert? what happens if you run the command yourself: mri_convert --frame 0 ./tmp-0001_base_lh_thickness_3f8Byr/glm/beta.mgh ./tmp-0001_base_lh_thickness_3f8Byr/beta0.mgh Best, Martin On 05/16/2014 04:45 PM, Katherine Reiter wrote: Hi Freesurfer experts, I'm working on analyzing longitudinal data using the longitudinal 2-stage model. When running the data through long_mris_slopes, I was getting the following error message: ERROR 1 : mris_calc compute sym. pct. change (spc) problem? I saw in previous messages that this is the result of a bug. I found the fix under the release notes, though after downloading it and placing the fix in the bin and makign these files executable, I keep receiving the following error messages. Does anyone have any insight into the problem and possible solutions? mri_convert --frame 0 ./tmp-0001_base_lh_thickness_3f8Byr/glm/beta.mgh ./tmp-0001_base_lh_thickness_3f8Byr/beta0.mgh Traceback (most recent call last): File /Applications/freesurfer//bin/long_mris_slopes, line 744, in module run_cmd(cmd,'mri_convert split frames 0 did not work?') File /Applications/freesurfer//bin/long_mris_slopes, line 422, in run_cmd retcode = subprocess.call(args) File /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py, line 486, in call return Popen(*popenargs, **kwargs).wait() File /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py, line 672, in __init__ errread, errwrite) File /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py, line 1202, in _execute_child raise child_exception OSError: [Errno 8] Exec format error Thank you, Katherine Reiter, M.S. Clinical Psychology Doctoral Student Marquette University Phone: (414) 288-3807 Email: katherine.rei...@marquette.edu mailto:katherine.rei...@marquette.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ 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 bug
Hi Freesurfer experts, I'm working on analyzing longitudinal data using the longitudinal 2-stage model. When running the data through long_mris_slopes, I was getting the following error message: ERROR 1 : mris_calc compute sym. pct. change (spc) problem? I saw in previous messages that this is the result of a bug. I found the fix under the release notes, though after downloading it and placing the fix in the bin and makign these files executable, I keep receiving the following error messages. Does anyone have any insight into the problem and possible solutions? mri_convert --frame 0 ./tmp-0001_base_lh_thickness_3f8Byr/glm/beta.mgh ./tmp-0001_base_lh_thickness_3f8Byr/beta0.mgh Traceback (most recent call last): File /Applications/freesurfer//bin/long_mris_slopes, line 744, in module run_cmd(cmd,'mri_convert split frames 0 did not work?') File /Applications/freesurfer//bin/long_mris_slopes, line 422, in run_cmd retcode = subprocess.call(args) File /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py, line 486, in call return Popen(*popenargs, **kwargs).wait() File /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py, line 672, in __init__ errread, errwrite) File /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py, line 1202, in _execute_child raise child_exception OSError: [Errno 8] Exec format error Thank you, Katherine Reiter, M.S. Clinical Psychology Doctoral Student Marquette University Phone: (414) 288-3807 Email: katherine.rei...@marquette.edu ___ 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.
Re: [Freesurfer] long_mris_slopes sign of do-rate
Hi Vincent, yes, it is tp2-tp1 / time_delta so thinning is negative, thickening positive. I'll correct the help text, the tutorial is right. It knows about the time point ordering because of the time column. Best, Martin On 08/02/2013 09:04 PM, vbrun...@nmr.mgh.harvard.edu wrote: Dear Freesurfer experts, I have followed the LongitudinalTutorial with two time points + two groups and now, after looking at the output of the qdec analysis, I just want to make sure I haven't made a sign error as for the control group the difference is as expected around 0 but for the experimental group I see negative values (= thinning?) all over the place which seems weird, just want to make sure I got this right: I set the time variable to 0 for the baseline scan and to 1 for the after-intervention-scan. Is it correct that for do-rate the calculation is then only thickness of tp2 - thickness of tp1 and not the other way around? I ask because in the long_mris_slopes -help it says that do-rate would yield the thinning in mm/time and if this means that a positive value stands for thinning then this would contradict what I understood from the Tutorial where it says for the rate thick2-thick1 is calculated, so a positive value should mean thickening. Also, how does long_mris_slopes know which one is tp1 and which one is tp2? I assume it takes the first entry in the fsid column of long.qdec.table.dat as tp1 and the second entry below as tp2? Hm, I see no other possibilities of making a sign error during the whole process, did anyone report a similar issue? Thanks for your help! Best, Vincent ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ 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 sign of do-rate
Dear Freesurfer experts, I have followed the LongitudinalTutorial with two time points + two groups and now, after looking at the output of the qdec analysis, I just want to make sure I haven't made a sign error as for the control group the difference is as expected around 0 but for the experimental group I see negative values (= thinning?) all over the place which seems weird, just want to make sure I got this right: I set the time variable to 0 for the baseline scan and to 1 for the after-intervention-scan. Is it correct that for do-rate the calculation is then only thickness of tp2 - thickness of tp1 and not the other way around? I ask because in the long_mris_slopes -help it says that do-rate would yield the thinning in mm/time and if this means that a positive value stands for thinning then this would contradict what I understood from the Tutorial where it says for the rate thick2-thick1 is calculated, so a positive value should mean thickening. Also, how does long_mris_slopes know which one is tp1 and which one is tp2? I assume it takes the first entry in the fsid column of long.qdec.table.dat as tp1 and the second entry below as tp2? Hm, I see no other possibilities of making a sign error during the whole process, did anyone report a similar issue? Thanks for your help! Best, Vincent ___ 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.
Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Dear Freesurfer experts, thanks to your help I was able to install the new version and run the „long_mris_slopes“ command. In the next step I shrank the longitudinal QDEC table into the cross sectional form by using “long_qdec_table” which also worked so far. Loading that table into QDEC and generating stats data table is no problem but afterwards, when I try to analyze the data in the “Design” section, I received an error message. It always says “couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file”. As an additional explanation for this example: 1CAGB is the base for the first time point CA and the second time point GB. Files with the wanted name exist in the surf directories of the two time points but not in the surf directory of the base. The closest thing in the base surf directory is called “lh.long.thikness.avg.fwhm10.mgh”. Could it be that there is a mistake in the “cross.qdec.table.dat”? Just like in the manual for creating the “long.qdec.table.dat”, I listed all the single time points under fsid and the base under fsid-base.and created the cross table afterwards. But when I open the “cross.qdec.table.dat”, the base names (1CAGB etc. in this example) are listed under “fsid”. Did I do something wrong during the creation of the long.qdec.table.dat or the cross.qdec.table.dat? Do you have any other explanation otherwise? Thank you very much for your help! Best regards Peter Bohn From: mreu...@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 06:57:16 -0700 To: bohn-pe...@gmx.de; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Not totally sure with 5.0, but I don't think it requires same voxel space for all time points (since 5.1), so it should work to run the analysis with 5.3 on that data. Cheers Martin Peter Bohn bohn-pe...@gmx.de wrote: Thanks a lot! Do I have to repeat creating the base and the longitudinal runs once I use the new version or are they compatible concerning this aspect? Thank you very much! Best regards Peter From: mreu...@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 02:46:05 -0700 To: bohn-pe...@gmx.de; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Yes, those scripts are available since 5.2. You need to update to a newer version. Best Martin Peter Bohn bohn-pe...@gmx.de wrote: Hi Martin, thanks a lot fort he quick reply! When I type freesurfer into the window it shows me v5.0.0 as the version. Sorry for my prior mistake concerning the version’s name. All other commands I use run perfectly fine. Thanks once again! Best regards Peter From: mreu...@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 05:21:39 -0400 To: bohn-pe...@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Hi Peter, can you run any free surfer command at all? Looks to me that you did not source free surfer. What happens if you typefreesurferinto the terminal window? It should print the version. Best, Martin On Jun 20, 2013, at 5:17 AM, Peter Bohn bohn-pe...@gmx.de wrote: Dear Freesurfer experts, I was trying to run some longitudinal analysis but whenever I want to use the commands “long_mris_slopes” or “long_qdec_table” I just get “command not found” as an answer. When I try to look up a package that might include the command, by typing “cnf long_mris_slopes”, I also just get “command not found” as an answer. We are currently using version v 1.313.2.6. Does anyone of you know if the two commands that I would like to run, are included in this version? Where would I have to look for the additional package if it exists? Or am I by any chance just typing the commands incorrect? Many thanks for the help! Sincerely yours Peter___Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -Dr. Martin ReuterAssistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email:mreu...@nmr.mgh.harvard.edu reuter@mit.eduWeb : http://reuter.mit.edu ___ 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
Re: [Freesurfer] long_mris_slopes/cross.qdec.table.dat
Dear Freesurfer experts, Or could it be that I made a mistake creating the “Qdecrc” file? I simply created a text file in the qdec directory and named it “$SUBJECTS_DIR/qdec/.Qdecrc” and put the four lines in it as advised. Should it just be named “.Qdecr” or is there supposed to be an empty line somewhere in the file? Thanks a lot! Best regards Peter From: bohn-pe...@gmx.de To: mreu...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Date: Mon, 1 Jul 2013 15:32:04 +0200 Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Dear Freesurfer experts, thanks to your help I was able to install the new version and run the „long_mris_slopes“ command. In the next step I shrank the longitudinal QDEC table into the cross sectional form by using “long_qdec_table” which also worked so far. Loading that table into QDEC and generating stats data table is no problem but afterwards, when I try to analyze the data in the “Design” section, I received an error message. It always says “couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file”. As an additional explanation for this example: 1CAGB is the base for the first time point CA and the second time point GB. Files with the wanted name exist in the surf directories of the two time points but not in the surf directory of the base. The closest thing in the base surf directory is called “lh.long.thikness.avg.fwhm10.mgh”. Could it be that there is a mistake in the “cross.qdec.table.dat”? Just like in the manual for creating the “long.qdec.table.dat”, I listed all the single time points under fsid and the base under fsid-base.and created the cross table afterwards. But when I open the “cross.qdec.table.dat”, the base names (1CAGB etc. in this example) are listed under “fsid”. Did I do something wrong during the creation of the long.qdec.table.dat or the cross.qdec.table.dat? Do you have any other explanation otherwise? Thank you very much for your help! Best regards Peter Bohn From: mreu...@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 06:57:16 -0700 To: bohn-pe...@gmx.de; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Not totally sure with 5.0, but I don't think it requires same voxel space for all time points (since 5.1), so it should work to run the analysis with 5.3 on that data. Cheers Martin Peter Bohn bohn-pe...@gmx.de wrote: Thanks a lot! Do I have to repeat creating the base and the longitudinal runs once I use the new version or are they compatible concerning this aspect? Thank you very much! Best regards Peter From: mreu...@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 02:46:05 -0700 To: bohn-pe...@gmx.de; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Yes, those scripts are available since 5.2. You need to update to a newer version. Best Martin Peter Bohn bohn-pe...@gmx.de wrote: Hi Martin, thanks a lot fort he quick reply! When I type freesurfer into the window it shows me v5.0.0 as the version. Sorry for my prior mistake concerning the version’s name. All other commands I use run perfectly fine. Thanks once again! Best regards Peter From: mreu...@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 05:21:39 -0400 To: bohn-pe...@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Hi Peter, can you run any free surfer command at all? Looks to me that you did not source free surfer. What happens if you typefreesurferinto the terminal window? It should print the version. Best, Martin On Jun 20, 2013, at 5:17 AM, Peter Bohn bohn-pe...@gmx.de wrote: Dear Freesurfer experts, I was trying to run some longitudinal analysis but whenever I want to use the commands “long_mris_slopes” or “long_qdec_table” I just get “command not found” as an answer. When I try to look up a package that might include the command, by typing “cnf long_mris_slopes”, I also just get “command not found” as an answer. We are currently using version v 1.313.2.6. Does anyone of you know if the two commands that I would like to run, are included in this version? Where would I have to look for the additional package if it exists? Or am I by any chance just typing the commands incorrect? Many thanks for the help! Sincerely yours Peter___Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -Dr. Martin ReuterAssistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email:mreu...@nmr.mgh.harvard.edu reuter@mit.eduWeb : http://reuter.mit.edu
Re: [Freesurfer] long_mris_slopes/cross.qdec.table.dat
Hi Peter, it needs to be .Qdecrc and have these lines: MEASURE1 = long.thickness-avg MEASURE2 = long.thickness-rate MEASURE3 = long.thickness-pc1 MEASURE4 = long.thickness-spc You will then see in the /Design/ tab in Qdec, that you can now select e.g. long.thickness-rate under /Measure/ as the dependent variable. You wrote below that you get this error: couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file note that thickness is spelled with 'ck'. Check your .Qdecrc if there's a typo. Best, Martin On 07/01/2013 09:45 AM, Peter Bohn wrote: Dear Freesurfer experts, Or could it be that I made a mistake creating the “Qdecrc” file? I simply created a text file in the qdec directory and named it “$SUBJECTS_DIR/qdec/.Qdecrc” and put the four lines in it as advised. Should it just be named “.Qdecr” or is there supposed to be an empty line somewhere in the file? Thanks a lot! Best regards Peter From: bohn-pe...@gmx.de To: mreu...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Date: Mon, 1 Jul 2013 15:32:04 +0200 Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Dear Freesurfer experts, thanks to your help I was able to install the new version and run the „long_mris_slopes“ command. In the next step I shrank the longitudinal QDEC table into the cross sectional form by using “long_qdec_table” which also worked so far. Loading that table into QDEC and generating stats data table is no problem but afterwards, when I try to analyze the data in the “Design” section, I received an error message. It always says “couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file”. As an additional explanation for this example: 1CAGB is the base for the first time point CA and the second time point GB. Files with the wanted name exist in the surf directories of the two time points but not in the surf directory of the base. The closest thing in the base surf directory is called “lh.long.thikness.avg.fwhm10.mgh”. Could it be that there is a mistake in the “cross.qdec.table.dat”? Just like in the manual for creating the “long.qdec.table.dat”, I listed all the single time points under fsid and the base under fsid-base.and created the cross table afterwards. But when I open the “cross.qdec.table.dat”, the base names (1CAGB etc. in this example) are listed under “fsid”. Did I do something wrong during the creation of the long.qdec.table.dat or the cross.qdec.table.dat? Do you have any other explanation otherwise? Thank you very much for your help! Best regards Peter Bohn From: mreu...@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 06:57:16 -0700 To: bohn-pe...@gmx.de; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Not totally sure with 5.0, but I don't think it requires same voxel space for all time points (since 5.1), so it should work to run the analysis with 5.3 on that data. Cheers Martin Peter Bohn bohn-pe...@gmx.de wrote: Thanks a lot! Do I have to repeat creating the base and the longitudinal runs once I use the new version or are they compatible concerning this aspect? Thank you very much! Best regards Peter From: mreu...@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 02:46:05 -0700 To: bohn-pe...@gmx.de; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Yes, those scripts are available since 5.2. You need to update to a newer version. Best Martin Peter Bohn bohn-pe...@gmx.de wrote: Hi Martin, thanks a lot fort he quick reply! When I type freesurfer into the window it shows me v5.0.0 as the version. Sorry for my prior mistake concerning the version’s name. All other commands I use run perfectly fine. Thanks once again! Best regards Peter From: mreu...@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 05:21:39 -0400 To: bohn-pe...@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Hi Peter, can you run any free surfer command at all? Looks to me that you did not source free surfer. What happens if you type freesurfer into the terminal window? It should print the version. Best, Martin On Jun 20, 2013, at 5:17 AM, Peter Bohn bohn-pe...@gmx.de mailto:bohn-pe...@gmx.de wrote: Dear Freesurfer experts, I was trying to run some longitudinal analysis but whenever I want
Re: [Freesurfer] long_mris_slopes/cross.qdec.table.dat
Dear Martin, ”thickness” was a typo. Can you maybe check my attached file? I suppose that I put the four lines in it correctly. I only named it “.Qdecrc”. When I save the file in the qdec folder of my Subject directory, the file isn´t visible anymore. Is it supposed to be like that? It is there but not visible. Furthermore I can´t chose e.g. long.thickness-rate in the Design Tab. Thank you very much and I am sorry for bothering you so much. Best regards Peter Date: Mon, 1 Jul 2013 11:33:39 -0400 From: mreu...@nmr.mgh.harvard.edu To: bohn-pe...@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/cross.qdec.table.dat Hi Peter, it needs to be .Qdecrc and have these lines: MEASURE1 = long.thickness-avg MEASURE2 = long.thickness-rate MEASURE3 = long.thickness-pc1 MEASURE4 = long.thickness-spc You will then see in the Design tab in Qdec, that you can now select e.g. long.thickness-rate under Measure as the dependent variable. You wrote below that you get this error: couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file note that thickness is spelled with 'ck'. Check your .Qdecrc if there's a typo. Best, Martin On 07/01/2013 09:45 AM, Peter Bohn wrote: Dear Freesurfer experts, Or could it be that I made a mistake creating the “Qdecrc” file? I simply created a text file in the qdec directory and named it “$SUBJECTS_DIR/qdec/.Qdecrc” and put the four lines in it as advised. Should it just be named “.Qdecr” or is there supposed to be an empty line somewhere in the file? Thanks a lot! Best regards Peter From: bohn-pe...@gmx.de To: mreu...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Date: Mon, 1 Jul 2013 15:32:04 +0200 Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Dear Freesurfer experts, thanks to your help I was able to install the new version and run the „long_mris_slopes“ command. In the next step I shrank the longitudinal QDEC table into the cross sectional form by using “long_qdec_table” which also worked so far. Loading that table into QDEC and generating stats data table is no problem but afterwards, when I try to analyze the data in the “Design” section, I received an error message. It always says “couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file”. As an additional explanation for this example: 1CAGB is the base for the first time point CA and the second time point GB. Files with the wanted name exist in the surf directories of the two time points but not in the surf directory of the base. The closest thing in the base surf directory is called “lh.long.thikness.avg.fwhm10.mgh”. Could it be that there is a mistake in the “cross.qdec.table.dat”? Just like in the manual for creating the “long.qdec.table.dat”, I listed all the single time points under fsid and the base under fsid-base.and created the cross table afterwards. But when I open the “cross.qdec.table.dat”, the base names (1CAGB etc. in this example) are listed under “fsid”. Did I do something wrong during the creation of the long.qdec.table.dat or the cross.qdec.table.dat? Do you have any other explanation otherwise? Thank you very much for your help! Best regards Peter Bohn From: mreu...@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 06:57:16 -0700 To: bohn-pe...@gmx.de; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Not totally sure with 5.0, but I don't think it requires same voxel space for all time points (since 5.1), so it should work to run
Re: [Freesurfer] long_mris_slopes/cross.qdec.table.dat
Hi Peter, file looks good, you could try adding a newline at the end. The file should be hidden (all files starting with a . are hidden). Not sure why you cannot select the rate as the measure. Is your environment variable ($SUBJECTS_DIR) setup correctly? Best, Martin On 07/01/2013 12:00 PM, Peter Bohn wrote: Dear Martin, ”thickness” was a typo. Can you maybe check my attached file? I suppose that I put the four lines in it correctly. I only named it “.Qdecrc”. When I save the file in the qdec folder of my Subject directory, the file isn´t visible anymore. Is it supposed to be like that? It is there but not visible. Furthermore I can´t chose e.g. long.thickness-rate in the Design Tab. Thank you very much and I am sorry for bothering you so much. Best regards Peter Date: Mon, 1 Jul 2013 11:33:39 -0400 From: mreu...@nmr.mgh.harvard.edu To: bohn-pe...@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/cross.qdec.table.dat Hi Peter, it needs to be .Qdecrc and have these lines: MEASURE1 = long.thickness-avg MEASURE2 = long.thickness-rate MEASURE3 = long.thickness-pc1 MEASURE4 = long.thickness-spc You will then see in the /Design/ tab in Qdec, that you can now select e.g. long.thickness-rate under /Measure/ as the dependent variable. You wrote below that you get this error: couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file note that thickness is spelled with 'ck'. Check your .Qdecrc if there's a typo. Best, Martin On 07/01/2013 09:45 AM, Peter Bohn wrote: Dear Freesurfer experts, Or could it be that I made a mistake creating the “Qdecrc” file? I simply created a text file in the qdec directory and named it “$SUBJECTS_DIR/qdec/.Qdecrc” and put the four lines in it as advised. Should it just be named “.Qdecr” or is there supposed to be an empty line somewhere in the file? Thanks a lot! Best regards Peter From: bohn-pe...@gmx.de mailto:bohn-pe...@gmx.de To: mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Date: Mon, 1 Jul 2013 15:32:04 +0200 Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Dear Freesurfer experts, thanks to your help I was able to install the new version and run the „long_mris_slopes“ command. In the next step I shrank the longitudinal QDEC table into the cross sectional form by using “long_qdec_table” which also worked so far. Loading that table into QDEC and generating stats data table is no problem but afterwards, when I try to analyze the data in the “Design” section, I received an error message. It always says “couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file”. As an additional explanation for this example: 1CAGB is the base for the first time point CA and the second time point GB. Files with the wanted name exist in the surf directories of the two time points but not in the surf directory of the base. The closest thing in the base surf directory is called “lh.long.thikness.avg.fwhm10.mgh”. Could it be that there is a mistake in the “cross.qdec.table.dat”? Just like in the manual for creating the “long.qdec.table.dat”, I listed all the single time points under fsid and the base under fsid-base.and created the cross table afterwards. But when I open the “cross.qdec.table.dat”, the base names (1CAGB etc. in this example) are listed under “fsid”. Did I do something wrong during the creation of the long.qdec.table.dat or the cross.qdec.table.dat? Do you have any other explanation otherwise? Thank you very much for your help! Best regards Peter Bohn From: mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 06:57:16 -0700 To: bohn-pe...@gmx.de mailto:bohn-pe...@gmx.de; freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Not totally sure with 5.0, but I don't think it requires same voxel space for all time points (since 5.1), so it should work to run the analysis with 5.3 on that data. Cheers Martin Peter Bohn bohn-pe...@gmx.de mailto:bohn-pe...@gmx.de wrote: Thanks a lot! Do I have to repeat creating the base and the longitudinal runs once I use the new version or are they compatible concerning this aspect? Thank you very much! Best regards Peter From
[Freesurfer] long_mris_slopes/long_qdec_table command not found
Dear Freesurfer experts, I was trying to run some longitudinal analysis but whenever I want to use the commands “long_mris_slopes” or “long_qdec_table” I just get “command not found” as an answer. When I try to look up a package that might include the command, by typing “cnf long_mris_slopes”, I also just get “command not found” as an answer. We are currently using version v 1.313.2.6. Does anyone of you know if the two commands that I would like to run, are included in this version? Where would I have to look for the additional package if it exists? Or am I by any chance just typing the commands incorrect? Many thanks for the help! Sincerely yours Peter ___ 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.
Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Hi Peter, can you run any free surfer command at all? Looks to me that you did not source free surfer. What happens if you type freesurfer into the terminal window? It should print the version. Best, Martin On Jun 20, 2013, at 5:17 AM, Peter Bohn bohn-pe...@gmx.de wrote: Dear Freesurfer experts, I was trying to run some longitudinal analysis but whenever I want to use the commands “long_mris_slopes” or “long_qdec_table” I just get “command not found” as an answer. When I try to look up a package that might include the command, by typing “cnf long_mris_slopes”, I also just get “command not found” as an answer. We are currently using version v 1.313.2.6. Does anyone of you know if the two commands that I would like to run, are included in this version? Where would I have to look for the additional package if it exists? Or am I by any chance just typing the commands incorrect? Many thanks for the help! Sincerely yours Peter ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ 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.
Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Yes, those scripts are available since 5.2. You need to update to a newer version. Best Martin Peter Bohn bohn-pe...@gmx.de wrote: Hi Martin, thanks a lot fort he quick reply! When I type freesurfer into the window it shows me v5.0.0 as the version. Sorry for my prior mistake concerning the version’s name. All other commands I use run perfectly fine. Thanks once again! Best regards Peter From: mreu...@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 05:21:39 -0400 To: bohn-pe...@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Hi Peter, can you run any free surfer command at all? Looks to me that you did not source free surfer. What happens if you typefreesurferinto the terminal window? It should print the version. Best, Martin On Jun 20, 2013, at 5:17 AM, Peter Bohn bohn-pe...@gmx.de wrote: Dear Freesurfer experts, I was trying to run some longitudinal analysis but whenever I want to use the commands “long_mris_slopes” or “long_qdec_table” I just get “command not found” as an answer. When I try to look up a package that might include the command, by typing “cnf long_mris_slopes”, I also just get “command not found” as an answer. We are currently using version v 1.313.2.6. Does anyone of you know if the two commands that I would like to run, are included in this version? Where would I have to look for the additional package if it exists? Or am I by any chance just typing the commands incorrect? Many thanks for the help! Sincerely yours Peter___Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -Dr. Martin ReuterAssistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email:mreu...@nmr.mgh.harvard.edu reuter@mit.eduWeb : http://reuter.mit.edu ___ 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. -- Sent from my phone, please excuse brevity.___ 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.
Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Hi Peter we use semething similar, although we've extended it and made it significantly more accurate. If you want to contact the CMA you can try: Dave Kennedy kenn...@nmr.mgh.harvard.edu cheers Bruce On Thu, 20 Jun 2013, Peter Bohn wrote: Dear Freesurfer experts, I was trying to run some longitudinal analysis but whenever I want to use th e commands “long_mris_slopes” or “long_qdec_table” I just get “command not found” as an answer. When I try to look up a package that might include the command, by typing “cnf long_mris_slopes”, I also just get “command not found” as an answer. We are currently using ver sion v 1.313.2.6. Does anyone of you know if the two commands that I would like to run, are in cluded in this version? Where would I have to look for the additional package if it exists? Or am I by any chance just typing the comma nds incorrect? Many thanks for the help! Sincerely yours Peter ___ 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.
Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Not totally sure with 5.0, but I don't think it requires same voxel space for all time points (since 5.1), so it should work to run the analysis with 5.3 on that data. Cheers Martin Peter Bohn bohn-pe...@gmx.de wrote: Thanks a lot! Do I have to repeat creating the base and the longitudinal runs once I use the new version or are they compatible concerning this aspect? Thank you very much! Best regards Peter From: mreu...@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 02:46:05 -0700 To: bohn-pe...@gmx.de; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Yes, those scripts are available since 5.2. You need to update to a newer version. Best Martin Peter Bohn bohn-pe...@gmx.de wrote: Hi Martin, thanks a lot fort he quick reply! When I type freesurfer into the window it shows me v5.0.0 as the version. Sorry for my prior mistake concerning the version’s name. All other commands I use run perfectly fine. Thanks once again! Best regards Peter From: mreu...@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 05:21:39 -0400 To: bohn-pe...@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Hi Peter, can you run any free surfer command at all? Looks to me that you did not source free surfer. What happens if you typefreesurferinto the terminal window? It should print the version. Best, Martin On Jun 20, 2013, at 5:17 AM, Peter Bohn bohn-pe...@gmx.de wrote: Dear Freesurfer experts, I was trying to run some longitudinal analysis but whenever I want to use the commands “long_mris_slopes” or “long_qdec_table” I just get “command not found” as an answer. When I try to look up a package that might include the command, by typing “cnf long_mris_slopes”, I also just get “command not found” as an answer. We are currently using version v 1.313.2.6. Does anyone of you know if the two commands that I would like to run, are included in this version? Where would I have to look for the additional package if it exists? Or am I by any chance just typing the commands incorrect? Many thanks for the help! Sincerely yours Peter___Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -Dr. Martin ReuterAssistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email:mreu...@nmr.mgh.harvard.edu reuter@mit.eduWeb : http://reuter.mit.edu ___ 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. -- Sent from my phone, please excuse brevity. ___ 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. -- Sent from my phone, please excuse brevity.___ 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.
Re: [Freesurfer] long_mris_slopes / mris_calc problem
I was able to solve my problem in my earlier email included below. I downloaded a new verison of mris_calc made it executable with chmod +x FILE and then replaced it in the bin folder. I included this response in case anyone else runs into the same problem and does a search. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-intel/ Hello Freesurfer experts, I am working on a study that wants to compare pre/post cortical thickness on an intervention group and a control group. I am using FS 5.1 on a Mac. I have processed all the recons through the longitudinal stream as described in the wiki/tutorial. However when I go to prepare the data using this command: long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage It seems to run fine at first but after a minute or so it hits this command and crashes: mris_calc -o /Applications/freesurfer/subjects/SPIN073/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-SPIN073_lh_thickness_igG3e9/beta1.mgh div ./tmp-SPIN073_lh_thickness_igG3e9/beta0.mgh It prints: ERROR 1 : mris_calc compute sym. pct. change (spc) problem? And then returns to my command prompt. I searched online and found someone last year asked the same question here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-September/020311.html However the response links to an updated version of mris_calc but when I click the link it says I do not have permission the access. Thanks for any help in advance. -Andrew ___ 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 / mris_calc problem
Hello Freesurfer experts, I am working on a study that wants to compare pre/post cortical thickness on an intervention group and a control group. I am using FS 5.1 on a Mac. I have processed all the recons through the longitudinal stream as described in the wiki/tutorial. However when I go to prepare the data using this command: long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage It seems to run fine at first but after a minute or so it hits this command and crashes: mris_calc -o /Applications/freesurfer/subjects/SPIN073/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-SPIN073_lh_thickness_igG3e9/beta1.mgh div ./tmp-SPIN073_lh_thickness_igG3e9/beta0.mgh It prints: ERROR 1 : mris_calc compute sym. pct. change (spc) problem? And then returns to my command prompt. I searched online and found someone last year asked the same question here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-September/020311.html However the response links to an updated version of mris_calc but when I click the link it says I do not have permission the access. Thanks for any help in advance. -Andrew ___ 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.
Re: [Freesurfer] long_mris_slopes error
Hello Martin, everything works fine with the newer versions of files. Thanks for the help! Have a wonderful day ! Alex. Le 04/10/2012 8:04 PM, Martin Reuter a écrit : You need a newer version of glmfit. This is not the 5.1 I think. Best Martin Alex Hanganu al.hang...@yahoo.ca wrote: Hello Martin, thanks for the help, I changed all the scripts from that page, but the problem still persisted, so one of our colleagues found that the mri_glmfit from the ReleaseNotes (15.8MB) is for Linux, and we are using mac, so we changed back the mri_glmfit to the old version (6MB), and now we have another error: - SUBJECT pls_pd_base00 Running Within-Subject GLM Writing ./tmp-pls_pd_base00_lh_thickness_CMeqOW/X-long.mat ... mri_glmfit --y ./pls_pd_base00/surf/lh.long.thickness-stack.mgh --X ./tmp-pls_pd_base00_lh_thickness_CMeqOW/X-long.mat --allow-zero-dof --no-contrasts-ok --surf pls_pd_base00 lh --label ./pls_pd_base00/label/lh.long.cortex.label --glmdir ./tmp-pls_pd_base00_lh_thickness_CMeqOW/glm ERROR: Option --allow-zero-dof unknown ERROR 255 : mri_glmfit did not work? - Any ideas ? Thanks for the help, Best regards, Alex. *De :* Martin Reuter mreu...@nmr.mgh.harvard.edu *À :* Alexandru Hanganu al.hang...@yahoo.ca; FS Mailing List Freesurfer@nmr.mgh.harvard.edu *Envoyé le :* mercredi 3 octobre 2012 17h30 *Objet :* Re: [Freesurfer] long_mris_slopes error Not sure. Maybe try the updated scripts From http://martinos.org/~mreuter/long http://martinos.org/%7Emreuter/long/ Best Martin Alex Hanganu al.hang...@yahoo.ca wrote: Dear Freesurfer Experts, While performing the long_mris_slopes cmd, we receive an error: SUBJECT pls_pd_base00 Running Within-Subject GLM Writing ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/X-long.mat ... mri_glmfit --y /Applications/freesurfer/subjects/pls_pd_base00/surf/lh.long.thickness-stack.mgh --X ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/X-long.mat --allow-zero-dof --no-contrasts-ok --surf pls_pd_base00 lh --label /Applications/freesurfer/subjects/pls_pd_base00/label/lh.long.cortex.label --glmdir ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/glm Traceback (most recent call last): File /Applications/freesurfer/bin/long_mris_slopes, line 732, in module run_cmd(cmd,'mri_glmfit did not work?') File /Applications/freesurfer/bin/long_mris_slopes, line 422, in run_cmd retcode = subprocess.call(args) File /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py http://subprocess.py/, line 443, in call return Popen(*popenargs, **kwargs).wait() File /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py http://subprocess.py/, line 593, in __init__ errread, errwrite) File /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py http://subprocess.py/, line 1079, in _execute_child raise child_exception OSError: [Errno 8] Exec format error we changed the mris_calc and mri_glmfit files with the new ones (8.2MB / 15.8MB). Can you please help with this ? Thank you in advance, Sincerely, Alex. Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sent from my phone, please excuse brevity. ___ 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 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
Re: [Freesurfer] long_mris_slopes error
Hello Martin, thanks for the help, I changed all the scripts from that page, but the problem still persisted, so one of our colleagues found that the mri_glmfit from the ReleaseNotes (15.8MB) is for Linux, and we are using mac, so we changed back the mri_glmfit to the old version (6MB), and now we have another error: - SUBJECT pls_pd_base00 Running Within-Subject GLM Writing ./tmp-pls_pd_base00_lh_thickness_CMeqOW/X-long.mat ... mri_glmfit --y ./pls_pd_base00/surf/lh.long.thickness-stack.mgh --X ./tmp-pls_pd_base00_lh_thickness_CMeqOW/X-long.mat --allow-zero-dof --no-contrasts-ok --surf pls_pd_base00 lh --label ./pls_pd_base00/label/lh.long.cortex.label --glmdir ./tmp-pls_pd_base00_lh_thickness_CMeqOW/glm ERROR: Option --allow-zero-dof unknown ERROR 255 : mri_glmfit did not work? - Any ideas ? Thanks for the help, Best regards, Alex. De : Martin Reuter mreu...@nmr.mgh.harvard.edu À : Alexandru Hanganu al.hang...@yahoo.ca; FS Mailing List Freesurfer@nmr.mgh.harvard.edu Envoyé le : mercredi 3 octobre 2012 17h30 Objet : Re: [Freesurfer] long_mris_slopes error Not sure. Maybe try the updated scripts From http://martinos.org/~mreuter/long/ Best Martin Alex Hanganu al.hang...@yahoo.ca wrote: Dear Freesurfer Experts, While performing the long_mris_slopes cmd, we receive an error: SUBJECT pls_pd_base00 Running Within-Subject GLM Writing ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/X-long.mat ... mri_glmfit --y /Applications/freesurfer/subjects/pls_pd_base00/surf/lh.long.thickness-stack.mgh --X ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/X-long.mat --allow-zero-dof --no-contrasts-ok --surf pls_pd_base00 lh --label /Applications/freesurfer/subjects/pls_pd_base00/label/lh.long.cortex.label --glmdir ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/glm Traceback (most recent call last): File /Applications/freesurfer/bin/long_mris_slopes, line 732, in module run_cmd(cmd,'mri_glmfit did not work?') File /Applications/freesurfer/bin/long_mris_slopes, line 422, in run_cmd retcode = subprocess.call(args) File /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py, line 443, in call return Popen(*popenargs, **kwargs).wait() File /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py, line 593, in __init__ errread, errwrite) File /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py, line 1079, in _execute_child raise child_exception OSError: [Errno 8] Exec format error we changed the mris_calc and mri_glmfit files with the new ones (8.2MB / 15.8MB). Can you please help with this ? Thank you in advance, Sincerely, Alex. Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sent from my phone, please excuse brevity. 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 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.
Re: [Freesurfer] long_mris_slopes error
You need a newer version of glmfit. This is not the 5.1 I think. Best Martin Alex Hanganu al.hang...@yahoo.ca wrote: Hello Martin, thanks for the help, I changed all the scripts from that page, but the problem still persisted, so one of our colleagues found that the mri_glmfit from the ReleaseNotes (15.8MB) is for Linux, and we are using mac, so we changed back the mri_glmfit to the old version (6MB), and now we have another error: - SUBJECT pls_pd_base00 Running Within-Subject GLM Writing ./tmp-pls_pd_base00_lh_thickness_CMeqOW/X-long.mat ... mri_glmfit --y ./pls_pd_base00/surf/lh.long.thickness-stack.mgh --X ./tmp-pls_pd_base00_lh_thickness_CMeqOW/X-long.mat --allow-zero-dof --no-contrasts-ok --surf pls_pd_base00 lh --label ./pls_pd_base00/label/lh.long.cortex.label --glmdir ./tmp-pls_pd_base00_lh_thickness_CMeqOW/glm ERROR: Option --allow-zero-dof unknown ERROR 255 : mri_glmfit did not work? - Any ideas ? Thanks for the help, Best regards, Alex. De : Martin Reuter mreu...@nmr.mgh.harvard.edu À : Alexandru Hanganu al.hang...@yahoo.ca; FS Mailing List Freesurfer@nmr.mgh.harvard.edu Envoyé le : mercredi 3 octobre 2012 17h30 Objet : Re: [Freesurfer] long_mris_slopes error Not sure. Maybe try the updated scripts From http://martinos.org/~mreuter/long/ Best Martin Alex Hanganu al.hang...@yahoo.ca wrote: Dear Freesurfer Experts, While performing the long_mris_slopes cmd, we receive an error: SUBJECT pls_pd_base00 Running Within-Subject GLM Writing ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/X-long.mat ... mri_glmfit --y /Applications/freesurfer/subjects/pls_pd_base00/surf/lh.long.thickness-stack.mgh --X ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/X-long.mat --allow-zero-dof --no-contrasts-ok --surf pls_pd_base00 lh --label /Applications/freesurfer/subjects/pls_pd_base00/label/lh.long.cortex.label --glmdir ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/glm Traceback (most recent call last): File /Applications/freesurfer/bin/long_mris_slopes, line 732, in module run_cmd(cmd,'mri_glmfit did not work?') File /Applications/freesurfer/bin/long_mris_slopes, line 422, in run_cmd retcode = subprocess.call(args) File /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py, line 443, in call return Popen(*popenargs, **kwargs).wait() File /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py, line 593, in __init__ errread, errwrite) File /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py, line 1079, in _execute_child raise child_exception OSError: [Errno 8] Exec format error we changed the mris_calc and mri_glmfit files with the new ones (8.2MB / 15.8MB). Can you please help with this ? Thank you in advance, Sincerely, Alex. Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sent from my phone, please excuse brevity. 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. -- Sent from my phone, please excuse brevity.___ 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
Dear Freesurfer Experts, While performing the long_mris_slopes cmd, we receive an error: --- SUBJECT pls_pd_base00 Running Within-Subject GLM Writing ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/X-long.mat ... mri_glmfit --y /Applications/freesurfer/subjects/pls_pd_base00/surf/lh.long.thickness-stack.mgh --X ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/X-long.mat --allow-zero-dof --no-contrasts-ok --surf pls_pd_base00 lh --label /Applications/freesurfer/subjects/pls_pd_base00/label/lh.long.cortex.label --glmdir ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/glm Traceback (most recent call last): File /Applications/freesurfer/bin/long_mris_slopes, line 732, in module run_cmd(cmd,'mri_glmfit did not work?') File /Applications/freesurfer/bin/long_mris_slopes, line 422, in run_cmd retcode = subprocess.call(args) File /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py, line 443, in call return Popen(*popenargs, **kwargs).wait() File /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py, line 593, in __init__ errread, errwrite) File /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py, line 1079, in _execute_child raise child_exception OSError: [Errno 8] Exec format error --- we changed the mris_calc and mri_glmfit files with the new ones (8.2MB / 15.8MB). Can you please help with this ? Thank you in advance, Sincerely, Alex. ___ 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.
Re: [Freesurfer] long_mris_slopes error
Not sure. Maybe try the updated scripts From http://martinos.org/~mreuter/long/ Best Martin Alexandru Hanganu al.hang...@yahoo.ca wrote: Dear Freesurfer Experts, While performing the long_mris_slopes cmd, we receive an error: --- SUBJECT pls_pd_base00 Running Within-Subject GLM Writing ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/X-long.mat ... mri_glmfit --y /Applications/freesurfer/subjects/pls_pd_base00/surf/lh.long.thickness-stack.mgh --X ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/X-long.mat --allow-zero-dof --no-contrasts-ok --surf pls_pd_base00 lh --label /Applications/freesurfer/subjects/pls_pd_base00/label/lh.long.cortex.label --glmdir ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/glm Traceback (most recent call last): File /Applications/freesurfer/bin/long_mris_slopes, line 732, in module run_cmd(cmd,'mri_glmfit did not work?') File /Applications/freesurfer/bin/long_mris_slopes, line 422, in run_cmd retcode = subprocess.call(args) File /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py, line 443, in call return Popen(*popenargs, **kwargs).wait() File /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py, line 593, in __init__ errread, errwrite) File /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py, line 1079, in _execute_child raise child_exception OSError: [Errno 8] Exec format error --- we changed the mris_calc and mri_glmfit files with the new ones (8.2MB / 15.8MB). Can you please help with this ? Thank you in advance, Sincerely, Alex. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sent from my phone, please excuse brevity.___ 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.
Re: [Freesurfer] long_mris_slopes command: temporal average calculation
Hi Martin, I am a little confused about these mapped files in the base directories you are referring to. How would I check them? -Shannon K. On Fri, Sep 28, 2012 at 4:08 PM, Martin Reuter mreu...@nmr.mgh.harvard.eduwrote: I see, Usually people look at thickness maps and volume on an ROI basis. Volume on the surface I think is simply area times thickness. Not sure how meaningful that is as area of a vertex depends on the triangle mesh. Anyway, you look at smoothed maps on fsaverage. The average volume for each vertex should be somewhere in the middle of the individual values across time after they have been resampled to fsaverage. You can find the mapped files in the base directories. Can you double check that the average is in the middle of the time points? Best Martin Shannon Kogachi skoga...@gmail.com wrote: Hi Martin, I am running FS version 5.1. This is the command line I ran: long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas volume --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage These are the outputs I get, which are located in the subjects' base template surf folders: lh.long.volume-rate.fwhm10.mgh lh.long.volume-pc1.fwhm10.mgh lh.long.volume-avg.fwhm10.mgh lh.long.volume-spc.fwhm10.mgh I also get the files that end in fsaverage.mgh. I'm a little confused about this volume issue. In a previous post you said that long_mris_slopes works for surface maps (both thickness and volume should work). Therefore I used the long_mris_slopes for the volumes for a VBM analysis. Please let me know if this would not work. Thank you! -Shannon On Fri, Sep 28, 2012 at 4:02 AM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Shannon, that cannot be. It either indicates a serious bug (which we have not yet encountered in our data) or a problem with your processing. Can you send me: - the version you use - the command line you run - the output you get Also long_mris_slopes is designed for analyzing surface maps (analysis on a vertex by vertex basis). This is usually thickness. So I don't understand what 'volumes' you mean? For an ROI analysis based on stats files you need to use long_stats_slopes. Best, Martin On Thu, 2012-09-27 at 11:37 -1000, Shannon Kogachi wrote: Hi Martin, Each subject has 3-6 timepoints. They are all about one year apart. Here's an example of the discrepancy: one subject with 5 timepoints had volumes that ranged from 2.2-2.4. However, from the long_mris_slopes command, the temporal average volume was calculated to be 1.67. Thanks for your help! -Shannon K. On Thu, Sep 27, 2012 at 6:21 AM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Shannon, long_mris_slopes works for surface maps (both thickness and volume should work). In both cases it should compute the temporal average. I have another scripts that works for stats files (long_stats_slopes) in the same way. How many time points do you have, how far apart (equally spaced?). Best, Martin On Wed, 2012-09-26 at 14:59 -1000, Shannon Kogachi wrote: Hi Martin, When I used the long_mris_slopes command for the thickness, the average thickness calculated in FreeSurfer was pretty similar to averaging the values in FreeSurfer. Does this command only work thickness measures and not for volume or area? Thanks! -Shannon On Wed, Sep 26, 2012 at 2:49 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Shannon You probably mean average thickness. My scripts compute the temporal average from the linear fit (at mid time), which can be differed from simply averaging values. Best Martin Shannon Kogachi skoga...@gmail.com wrote: Hi, I had a question about how the temporal average is calculated for subjects with multiple timepoints. I used the long_mris_slopes command on a longitudinal set of data. However, when I compared the average volumes calculated through this command to the average volumes calculated in excel after extracting the same vertices at the individual timepoints, these values did not match up. The average volumes calculated through long_mris_slopes were smaller. Please let me
Re: [Freesurfer] long_mris_slopes command: temporal average calculation
Hi Shannon, that cannot be. It either indicates a serious bug (which we have not yet encountered in our data) or a problem with your processing. Can you send me: - the version you use - the command line you run - the output you get Also long_mris_slopes is designed for analyzing surface maps (analysis on a vertex by vertex basis). This is usually thickness. So I don't understand what 'volumes' you mean? For an ROI analysis based on stats files you need to use long_stats_slopes. Best, Martin On Thu, 2012-09-27 at 11:37 -1000, Shannon Kogachi wrote: Hi Martin, Each subject has 3-6 timepoints. They are all about one year apart. Here's an example of the discrepancy: one subject with 5 timepoints had volumes that ranged from 2.2-2.4. However, from the long_mris_slopes command, the temporal average volume was calculated to be 1.67. Thanks for your help! -Shannon K. On Thu, Sep 27, 2012 at 6:21 AM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Shannon, long_mris_slopes works for surface maps (both thickness and volume should work). In both cases it should compute the temporal average. I have another scripts that works for stats files (long_stats_slopes) in the same way. How many time points do you have, how far apart (equally spaced?). Best, Martin On Wed, 2012-09-26 at 14:59 -1000, Shannon Kogachi wrote: Hi Martin, When I used the long_mris_slopes command for the thickness, the average thickness calculated in FreeSurfer was pretty similar to averaging the values in FreeSurfer. Does this command only work thickness measures and not for volume or area? Thanks! -Shannon On Wed, Sep 26, 2012 at 2:49 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Shannon You probably mean average thickness. My scripts compute the temporal average from the linear fit (at mid time), which can be differed from simply averaging values. Best Martin Shannon Kogachi skoga...@gmail.com wrote: Hi, I had a question about how the temporal average is calculated for subjects with multiple timepoints. I used the long_mris_slopes command on a longitudinal set of data. However, when I compared the average volumes calculated through this command to the average volumes calculated in excel after extracting the same vertices at the individual timepoints, these values did not match up. The average volumes calculated through long_mris_slopes were smaller. Please let me know if there is a way to explain this discrepancy. Thank you! -Shannon K. __ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sent from my phone, please excuse brevity. 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] long_mris_slopes command: temporal average calculation
Hi Martin, I am running FS version 5.1. This is the command line I ran: long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas volume --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage These are the outputs I get, which are located in the subjects' base template surf folders: lh.long.volume-rate.fwhm10.mgh lh.long.volume-pc1.fwhm10.mgh lh.long.volume-avg.fwhm10.mgh lh.long.volume-spc.fwhm10.mgh I also get the files that end in fsaverage.mgh. I'm a little confused about this volume issue. In a previous post you said that long_mris_slopes works for surface maps (both thickness and volume should work). Therefore I used the long_mris_slopes for the volumes for a VBM analysis. Please let me know if this would not work. Thank you! -Shannon On Fri, Sep 28, 2012 at 4:02 AM, Martin Reuter mreu...@nmr.mgh.harvard.eduwrote: Hi Shannon, that cannot be. It either indicates a serious bug (which we have not yet encountered in our data) or a problem with your processing. Can you send me: - the version you use - the command line you run - the output you get Also long_mris_slopes is designed for analyzing surface maps (analysis on a vertex by vertex basis). This is usually thickness. So I don't understand what 'volumes' you mean? For an ROI analysis based on stats files you need to use long_stats_slopes. Best, Martin On Thu, 2012-09-27 at 11:37 -1000, Shannon Kogachi wrote: Hi Martin, Each subject has 3-6 timepoints. They are all about one year apart. Here's an example of the discrepancy: one subject with 5 timepoints had volumes that ranged from 2.2-2.4. However, from the long_mris_slopes command, the temporal average volume was calculated to be 1.67. Thanks for your help! -Shannon K. On Thu, Sep 27, 2012 at 6:21 AM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Shannon, long_mris_slopes works for surface maps (both thickness and volume should work). In both cases it should compute the temporal average. I have another scripts that works for stats files (long_stats_slopes) in the same way. How many time points do you have, how far apart (equally spaced?). Best, Martin On Wed, 2012-09-26 at 14:59 -1000, Shannon Kogachi wrote: Hi Martin, When I used the long_mris_slopes command for the thickness, the average thickness calculated in FreeSurfer was pretty similar to averaging the values in FreeSurfer. Does this command only work thickness measures and not for volume or area? Thanks! -Shannon On Wed, Sep 26, 2012 at 2:49 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Shannon You probably mean average thickness. My scripts compute the temporal average from the linear fit (at mid time), which can be differed from simply averaging values. Best Martin Shannon Kogachi skoga...@gmail.com wrote: Hi, I had a question about how the temporal average is calculated for subjects with multiple timepoints. I used the long_mris_slopes command on a longitudinal set of data. However, when I compared the average volumes calculated through this command to the average volumes calculated in excel after extracting the same vertices at the individual timepoints, these values did not match up. The average volumes calculated through long_mris_slopes were smaller. Please let me know if there is a way to explain this discrepancy. Thank you! -Shannon K. __ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sent from my phone, please excuse brevity. 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
Re: [Freesurfer] long_mris_slopes command: temporal average calculation
I see, Usually people look at thickness maps and volume on an ROI basis. Volume on the surface I think is simply area times thickness. Not sure how meaningful that is as area of a vertex depends on the triangle mesh. Anyway, you look at smoothed maps on fsaverage. The average volume for each vertex should be somewhere in the middle of the individual values across time after they have been resampled to fsaverage. You can find the mapped files in the base directories. Can you double check that the average is in the middle of the time points? Best Martin Shannon Kogachi skoga...@gmail.com wrote: Hi Martin, I am running FS version 5.1. This is the command line I ran: long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas volume --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage These are the outputs I get, which are located in the subjects' base template surf folders: lh.long.volume-rate.fwhm10.mgh lh.long.volume-pc1.fwhm10.mgh lh.long.volume-avg.fwhm10.mgh lh.long.volume-spc.fwhm10.mgh I also get the files that end in fsaverage.mgh. I'm a little confused about this volume issue. In a previous post you said that long_mris_slopes works for surface maps (both thickness and volume should work). Therefore I used the long_mris_slopes for the volumes for a VBM analysis. Please let me know if this would not work. Thank you! -Shannon On Fri, Sep 28, 2012 at 4:02 AM, Martin Reuter mreu...@nmr.mgh.harvard.eduwrote: Hi Shannon, that cannot be. It either indicates a serious bug (which we have not yet encountered in our data) or a problem with your processing. Can you send me: - the version you use - the command line you run - the output you get Also long_mris_slopes is designed for analyzing surface maps (analysis on a vertex by vertex basis). This is usually thickness. So I don't understand what 'volumes' you mean? For an ROI analysis based on stats files you need to use long_stats_slopes. Best, Martin On Thu, 2012-09-27 at 11:37 -1000, Shannon Kogachi wrote: Hi Martin, Each subject has 3-6 timepoints. They are all about one year apart. Here's an example of the discrepancy: one subject with 5 timepoints had volumes that ranged from 2.2-2.4. However, from the long_mris_slopes command, the temporal average volume was calculated to be 1.67. Thanks for your help! -Shannon K. On Thu, Sep 27, 2012 at 6:21 AM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Shannon, long_mris_slopes works for surface maps (both thickness and volume should work). In both cases it should compute the temporal average. I have another scripts that works for stats files (long_stats_slopes) in the same way. How many time points do you have, how far apart (equally spaced?). Best, Martin On Wed, 2012-09-26 at 14:59 -1000, Shannon Kogachi wrote: Hi Martin, When I used the long_mris_slopes command for the thickness, the average thickness calculated in FreeSurfer was pretty similar to averaging the values in FreeSurfer. Does this command only work thickness measures and not for volume or area? Thanks! -Shannon On Wed, Sep 26, 2012 at 2:49 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Shannon You probably mean average thickness. My scripts compute the temporal average from the linear fit (at mid time), which can be differed from simply averaging values. Best Martin Shannon Kogachi skoga...@gmail.com wrote: Hi, I had a question about how the temporal average is calculated for subjects with multiple timepoints. I used the long_mris_slopes command on a longitudinal set of data. However, when I compared the average volumes calculated through this command to the average volumes calculated in excel after extracting the same vertices at the individual timepoints, these values did not match up. The average volumes calculated through long_mris_slopes were smaller. Please let me know if there is a way to explain this discrepancy. Thank you! -Shannon K.
Re: [Freesurfer] long_mris_slopes command: temporal average calculation
Hi Shannon, long_mris_slopes works for surface maps (both thickness and volume should work). In both cases it should compute the temporal average. I have another scripts that works for stats files (long_stats_slopes) in the same way. How many time points do you have, how far apart (equally spaced?). Best, Martin On Wed, 2012-09-26 at 14:59 -1000, Shannon Kogachi wrote: Hi Martin, When I used the long_mris_slopes command for the thickness, the average thickness calculated in FreeSurfer was pretty similar to averaging the values in FreeSurfer. Does this command only work thickness measures and not for volume or area? Thanks! -Shannon On Wed, Sep 26, 2012 at 2:49 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Shannon You probably mean average thickness. My scripts compute the temporal average from the linear fit (at mid time), which can be differed from simply averaging values. Best Martin Shannon Kogachi skoga...@gmail.com wrote: Hi, I had a question about how the temporal average is calculated for subjects with multiple timepoints. I used the long_mris_slopes command on a longitudinal set of data. However, when I compared the average volumes calculated through this command to the average volumes calculated in excel after extracting the same vertices at the individual timepoints, these values did not match up. The average volumes calculated through long_mris_slopes were smaller. Please let me know if there is a way to explain this discrepancy. Thank you! -Shannon K. __ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sent from my phone, please excuse brevity. 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. -- Shannon Kogachi Clinical Research Coordinator Neuroscience and MRI Research Program Department of Medicine JABSOM, University of Hawaii 1356 Lusitana Street, 7th Floor Honolulu, HI 96813 (808) 691 - 8763 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] long_mris_slopes command: temporal average calculation
Hi, I had a question about how the temporal average is calculated for subjects with multiple timepoints. I used the long_mris_slopes command on a longitudinal set of data. However, when I compared the average volumes calculated through this command to the average volumes calculated in excel after extracting the same vertices at the individual timepoints, these values did not match up. The average volumes calculated through long_mris_slopes were smaller. Please let me know if there is a way to explain this discrepancy. Thank you! -Shannon K. ___ 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.
Re: [Freesurfer] long_mris_slopes command: temporal average calculation
Hi Shannon You probably mean average thickness. My scripts compute the temporal average from the linear fit (at mid time), which can be differed from simply averaging values. Best Martin Shannon Kogachi skoga...@gmail.com wrote: Hi, I had a question about how the temporal average is calculated for subjects with multiple timepoints. I used the long_mris_slopes command on a longitudinal set of data. However, when I compared the average volumes calculated through this command to the average volumes calculated in excel after extracting the same vertices at the individual timepoints, these values did not match up. The average volumes calculated through long_mris_slopes were smaller. Please let me know if there is a way to explain this discrepancy. Thank you! -Shannon K. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sent from my phone, please excuse brevity.___ 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.
Re: [Freesurfer] long_mris_slopes command: temporal average calculation
Hi Martin, When I used the long_mris_slopes command for the thickness, the average thickness calculated in FreeSurfer was pretty similar to averaging the values in FreeSurfer. Does this command only work thickness measures and not for volume or area? Thanks! -Shannon On Wed, Sep 26, 2012 at 2:49 PM, Martin Reuter mreu...@nmr.mgh.harvard.eduwrote: Hi Shannon You probably mean average thickness. My scripts compute the temporal average from the linear fit (at mid time), which can be differed from simply averaging values. Best Martin Shannon Kogachi skoga...@gmail.com wrote: Hi, I had a question about how the temporal average is calculated for subjects with multiple timepoints. I used the long_mris_slopes command on a longitudinal set of data. However, when I compared the average volumes calculated through this command to the average volumes calculated in excel after extracting the same vertices at the individual timepoints, these values did not match up. The average volumes calculated through long_mris_slopes were smaller. Please let me know if there is a way to explain this discrepancy. Thank you! -Shannon K. -- Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sent from my phone, please excuse brevity. 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. -- Shannon Kogachi Clinical Research Coordinator Neuroscience and MRI Research Program Department of Medicine JABSOM, University of Hawaii 1356 Lusitana Street, 7th Floor Honolulu, HI 96813 (808) 691 - 8763 ___ 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.
Re: [Freesurfer] long_mris_slopes error
Hi Hyojeong, on the wiki release notes is a fixed mris_calc binary. Best, Martin On Aug 11, 2011, at 8:00 AM, Administrator wrote: Dear Martin, I've received the same error as below which discussed previously. Would you tell me if you managed build a fixed file, please? Hyojeong Lee Hallym University College of Medicine, Anyang, Korea long_mris_slopes --qdec ./qdec/long.qdec.tem_VNL01_KCY.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time weeks --qcache fsaverage .. === SUBJECT VN1 fwhm 0 computing SPC mris_calc -o /Volumes/data/freesurfer_analysis/VN_longitudinal/VN1/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-VN1_lh_thickness_OLudiD/beta1.mgh div ./tmp-VN1_lh_thickness_OLudiD/beta0.mgh ERROR -10 : mris_calc compute sym. pct. change (spc) problem? ___ 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.
Re: [Freesurfer] long_mris_slopes error
Hi Derin, there is a know and fixed bug in mris_calc in the 5.1 release. It has difficulties with very long file names and returns a non zero exit code, which stops my script in some situations. I'll ask Nick if he can put up a fixed version of mris_calc for download. Best, Martin On Thu, 2011-07-21 at 15:18 -0500, Derin Cobia wrote: I received the follow error while running a set of subjects under 'long_mris_slopes,' and wasn't able to decipher the problem. It appears that mris_calc is not able to do the division for these files (dividing by 0 perhaps?). Any help appreciated, here's the command and tail end of output/error, thanks. -Derin long_mris_slopes --qdec ./qdec/CH_prog.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time scan_interval --qcache fsaverage === SUBJECT CH1840 fwhm 0 computing SPC mris_calc -o /disk/NIACAL_01/Trio/NMorph/PROCESSED_DATA/FREESURFER-v5.1.0/CH1840/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-CH1840_lh_thickness_FFrRIR/beta1.mgh div ./tmp-CH1840_lh_thickness_FFrRIR/beta0.mgh ERROR 1 : mris_calc compute sym. pct. change (spc) problem? ___ 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
I received the follow error while running a set of subjects under 'long_mris_slopes,' and wasn't able to decipher the problem. It appears that mris_calc is not able to do the division for these files (dividing by 0 perhaps?). Any help appreciated, here's the command and tail end of output/error, thanks. -Derin long_mris_slopes --qdec ./qdec/CH_prog.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time scan_interval --qcache fsaverage === SUBJECT CH1840 fwhm 0 computing SPC mris_calc -o /disk/NIACAL_01/Trio/NMorph/PROCESSED_DATA/FREESURFER-v5.1.0/CH1840/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-CH1840_lh_thickness_FFrRIR/beta1.mgh div ./tmp-CH1840_lh_thickness_FFrRIR/beta0.mgh ERROR 1 : mris_calc compute sym. pct. change (spc) problem? ___ 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.
Re: [Freesurfer] long_mris_slopes
Hi Sean, symmetrized percent change is a measure across time. for two time points it is just 100*(tp2-tp1)/(0.5*(tp1+tp2)) (if they are a time unit (usually year) apart, else we divide by time difference) You are basically fine. We need to distinguish between processing and post-processing. For processing it makes sense to have 3 time points in the base. You will get a subject template that initializes all time points. This enables you to to a 3time point analysis. It also reduces variability etc. If you run the stream with only two time points in the base for each interval independently you will basically only increase variability of your measures. Of course in post-processing you can look at each interval independently. So looking at the difference in the first interval and in the second separately and then comparing them is totally fine. Also SPC is fine, but: as noted above in SPC we divide by the average . That average of course will change between the intervals and it might be better to divide by the average of all three time points instead (there is no script for that). I don't think it'll make a big difference, though. Alternatively you could look at the difference per time (rate). On the cortex there is so much other variability (noise, non-linear registraton etc). You need to check if what you see is noise or significant. Of course it will go up and down in many regions, but that can all be noise. You should also take a look at the rate, because there you don't divide by the average. And your final question: when looking at spc of all three time points it is NOT the same as viewing only tp1 to tp3. SPC of all three time points is: 100*slope/(temporal average) we fit a line into each subject data and compute the slope (this is the change per time: rate) and divide by the temporal average which is the measure at the mid time. This is assuming there is a linear change Hope that helps. Best, Martin On Jun 28, 2011, at 9:34 AM, Seán Froudist Walsh wrote: Hi Martin and all, I would like to ask you if by comparing tp1 thickness-spc with tp2 (and comparing tp2 with tp3) using the base brain between tp1,2 and 3 (altogether) I have messed up methodologically. I was expecting a rise in cortical thickness in certain areas between tp1 and tp2 followed by a greater rise between tp2 and tp3. I did not expect however a host of other changes which were not seen when viewing spc of tp1, 2 and 3 together. Most of these effects seem to be basically mirror-effects e.g. if there is a rise between tp1 and tp2, there is a drop in thickness in the same area between tp2 and tp3 and vice versa. This happened in several subjects and in variable brain regions. I would like to know if this is because of some methodological flaw. For example, should I run the whole longitudinal stream 2 more times (once to compare tp1 and tp2, and the second time to compare tp2 to tp3)? Also, when viewing the spc of tp1, tp2 and tp3 together are we just looking at the change between timepoints 1 and 3? Many thanks for the help, All the best, Seán On 27 June 2011 11:50, Seán Froudist Walsh froud...@tcd.ie wrote: Hi Martin, That worked! Thanks a lot, Seán On 23 June 2011 18:22, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Sean, I think the --out... names need to be without the ending (mgh) so for example --out-avg=long23.thickness-avg Maybe that'll fix it. Best, Martin On Thu, 2011-06-23 at 09:12 -0700, Seán Froudist Walsh wrote: Dear FreeSurfers, I am looking for a little help comparing longitudinal data. I have three timepoints on each patient and have been able to get individual spc-thickness maps using the long_mris_slopes command where my table included all three time points. I would however like to compare different timepoints with each other: tp3-tp2 and tp2-tp1. I was hoping it would be as simple as specifying a new qdec table including (for example) only tp3 and tp2, and giving new output names using the following command long_mris_slopes --qdec ./qdec/long.qdec.tableTP23.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --out-avg=long23.thickness-avg.mgh --out-rate=long23.thickness-rate.mgh --out-pc1=long23.thickness-pc1.mgh --out-spc=long23.thickness-spc.mgh --out-stack=long23.thickness-stack.mgh --out-label=long23.cortex --time scan --qcache fsaverage but I get the following error: mris_calc: Sorry, but I seem to have encountered an error. While making backup of internal data arrays, it seems that some of the backups already exist. I'm not really sure what the internal data arrays are, and would greatly appreciate any help. Many thanks in advance and all the best, Seán ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] long_mris_slopes
Hi Martin and all, I would like to ask you if by comparing tp1 thickness-spc with tp2 (and comparing tp2 with tp3) using the base brain between tp1,2 and 3 (altogether) I have messed up methodologically. I was expecting a rise in cortical thickness in certain areas between tp1 and tp2 followed by a greater rise between tp2 and tp3. I did not expect however a host of other changes which were not seen when viewing spc of tp1, 2 and 3 together. Most of these effects seem to be basically mirror-effects e.g. if there is a rise between tp1 and tp2, there is a drop in thickness in the same area between tp2 and tp3 and vice versa. This happened in several subjects and in variable brain regions. I would like to know if this is because of some methodological flaw. For example, should I run the whole longitudinal stream 2 more times (once to compare tp1 and tp2, and the second time to compare tp2 to tp3)? Also, when viewing the spc of tp1, tp2 and tp3 together are we just looking at the change between timepoints 1 and 3? Many thanks for the help, All the best, Seán On 27 June 2011 11:50, Seán Froudist Walsh froud...@tcd.ie wrote: Hi Martin, That worked! Thanks a lot, Seán On 23 June 2011 18:22, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Sean, I think the --out... names need to be without the ending (mgh) so for example --out-avg=long23.thickness-avg Maybe that'll fix it. Best, Martin On Thu, 2011-06-23 at 09:12 -0700, Seán Froudist Walsh wrote: Dear FreeSurfers, I am looking for a little help comparing longitudinal data. I have three timepoints on each patient and have been able to get individual spc-thickness maps using the long_mris_slopes command where my table included all three time points. I would however like to compare different timepoints with each other: tp3-tp2 and tp2-tp1. I was hoping it would be as simple as specifying a new qdec table including (for example) only tp3 and tp2, and giving new output names using the following command long_mris_slopes --qdec ./qdec/long.qdec.tableTP23.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --out-avg=long23.thickness-avg.mgh --out-rate=long23.thickness-rate.mgh --out-pc1=long23.thickness-pc1.mgh --out-spc=long23.thickness-spc.mgh --out-stack=long23.thickness-stack.mgh --out-label=long23.cortex --time scan --qcache fsaverage but I get the following error: mris_calc: Sorry, but I seem to have encountered an error. While making backup of internal data arrays, it seems that some of the backups already exist. I'm not really sure what the internal data arrays are, and would greatly appreciate any help. Many thanks in advance and all the best, Seán ___ 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 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.
Re: [Freesurfer] long_mris_slopes
Hi Martin, That worked! Thanks a lot, Seán On 23 June 2011 18:22, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Sean, I think the --out... names need to be without the ending (mgh) so for example --out-avg=long23.thickness-avg Maybe that'll fix it. Best, Martin On Thu, 2011-06-23 at 09:12 -0700, Seán Froudist Walsh wrote: Dear FreeSurfers, I am looking for a little help comparing longitudinal data. I have three timepoints on each patient and have been able to get individual spc-thickness maps using the long_mris_slopes command where my table included all three time points. I would however like to compare different timepoints with each other: tp3-tp2 and tp2-tp1. I was hoping it would be as simple as specifying a new qdec table including (for example) only tp3 and tp2, and giving new output names using the following command long_mris_slopes --qdec ./qdec/long.qdec.tableTP23.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --out-avg=long23.thickness-avg.mgh --out-rate=long23.thickness-rate.mgh --out-pc1=long23.thickness-pc1.mgh --out-spc=long23.thickness-spc.mgh --out-stack=long23.thickness-stack.mgh --out-label=long23.cortex --time scan --qcache fsaverage but I get the following error: mris_calc: Sorry, but I seem to have encountered an error. While making backup of internal data arrays, it seems that some of the backups already exist. I'm not really sure what the internal data arrays are, and would greatly appreciate any help. Many thanks in advance and all the best, Seán ___ 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 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
Dear FreeSurfers, I am looking for a little help comparing longitudinal data. I have three timepoints on each patient and have been able to get individual spc-thickness maps using the long_mris_slopes command where my table included all three time points. I would however like to compare different timepoints with each other: tp3-tp2 and tp2-tp1. I was hoping it would be as simple as specifying a new qdec table including (for example) only tp3 and tp2, and giving new output names using the following command long_mris_slopes --qdec ./qdec/long.qdec.tableTP23.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --out-avg=long23.thickness-avg.mgh --out-rate=long23.thickness-rate.mgh --out-pc1=long23.thickness-pc1.mgh --out-spc=long23.thickness-spc.mgh --out-stack=long23.thickness-stack.mgh --out-label=long23.cortex --time scan --qcache fsaverage but I get the following error: mris_calc: Sorry, but I seem to have encountered an error. While making backup of internal data arrays, it seems that some of the backups already exist. I'm not really sure what the internal data arrays are, and would greatly appreciate any help. Many thanks in advance and all the best, Seán ___ 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.
Re: [Freesurfer] long_mris_slopes
Hi Sean, I think the --out... names need to be without the ending (mgh) so for example --out-avg=long23.thickness-avg Maybe that'll fix it. Best, Martin On Thu, 2011-06-23 at 09:12 -0700, Seán Froudist Walsh wrote: Dear FreeSurfers, I am looking for a little help comparing longitudinal data. I have three timepoints on each patient and have been able to get individual spc-thickness maps using the long_mris_slopes command where my table included all three time points. I would however like to compare different timepoints with each other: tp3-tp2 and tp2-tp1. I was hoping it would be as simple as specifying a new qdec table including (for example) only tp3 and tp2, and giving new output names using the following command long_mris_slopes --qdec ./qdec/long.qdec.tableTP23.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --out-avg=long23.thickness-avg.mgh --out-rate=long23.thickness-rate.mgh --out-pc1=long23.thickness-pc1.mgh --out-spc=long23.thickness-spc.mgh --out-stack=long23.thickness-stack.mgh --out-label=long23.cortex --time scan --qcache fsaverage but I get the following error: mris_calc: Sorry, but I seem to have encountered an error. While making backup of internal data arrays, it seems that some of the backups already exist. I'm not really sure what the internal data arrays are, and would greatly appreciate any help. Many thanks in advance and all the best, Seán ___ 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.
