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Hello FreeSurfer experts,
It seems that all the subjects adopt a single same paradigm file in FsFast, am I correct? So how to handle it if each subject has different paradigm files, e.g., different onset time and duration? I could do the first-level analysis in each individual data, however, I cannot concatenate data with 'isxconcat-sess' due to that there is not an analysis folder generated from a same paradigm file. Any suggestions?
Thanks and best regards,
Lizhi
While the name of the paradigm file must be the same across runs and subjects, the contents paradigm file can be different. That should be able to handle what you are doing
On 2/22/19 3:42 PM, Zhi Li wrote:
External Email - Use Caution
Hello FreeSurfer experts,
It seems that all the subjects adopt a single same paradigm file in FsFast, am I correct? So how to handle it if each subject has different paradigm files, e.g., different onset time and duration? I could do the first-level analysis in each individual data, however, I cannot concatenate data with 'isxconcat-sess' due to that there is not an analysis folder generated from a same paradigm file. Any suggestions?
Thanks and best regards,
Lizhi
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thank you very much. You mean the generated paradigm folders (e.g., taskname.sm05.lh) and analysis.info, contrast.mat and contrast.config should be the same among all the subjects, even the onset and duration of each stimulus in each subject were different? Hence I could use the paradigm folders generated from the 1-st level modelling of any subjects in the 2-nd level modelling, is that correct?
On Fri, 22 Feb 2019 at 16:35, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
While the name of the paradigm file must be the same across runs and subjects, the contents paradigm file can be different. That should be able to handle what you are doing
On 2/22/19 3:42 PM, Zhi Li wrote:
External Email - Use CautionHello FreeSurfer experts,
It seems that all the subjects adopt a single same paradigm file in FsFast, am I correct? So how to handle it if each subject has different paradigm files, e.g., different onset time and duration? I could do the first-level analysis in each individual data, however, I cannot concatenate data with 'isxconcat-sess' due to that there is not an analysis folder generated from a same paradigm file. Any suggestions?
Thanks and best regards,
Lizhi
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 paradigm info is in a file, not a folder (eg, subject1/bold/003/taskname.par, subject1/bold/004/taskname.par, subject5/bold/001/taskname.par). When you make an analysis (mkanalysis-sess), you should then spcify the paradigm file with --par taskname.par. mkanlaysis-sess is run without reference to the subjects. Eg, the name of the analysis (--analysis analysisname) is independent of the subject. Maybe you are confusing the analysisname and the paradigm?
On 2/25/19 9:50 AM, Zhi Li wrote:
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Thank you very much. You mean the generated paradigm folders (e.g., taskname.sm05.lh) and analysis.info http://analysis.info, contrast.mat and contrast.config should be the same among all the subjects, even the onset and duration of each stimulus in each subject were different? Hence I could use the paradigm folders generated from the 1-st level modelling of any subjects in the 2-nd level modelling, is that correct?
On Fri, 22 Feb 2019 at 16:35, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
While the name of the paradigm file must be the same across runs and subjects, the contents paradigm file can be different. That should be able to handle what you are doing On 2/22/19 3:42 PM, Zhi Li wrote:External Email - Use Caution Hello FreeSurfer experts, It seems that all the subjects adopt a single same paradigm file in FsFast, am I correct? So how to handle it if each subject has different paradigm files, e.g., different onset time and duration? I could do the first-level analysis in each individual data, however, I cannot concatenate data with 'isxconcat-sess' due to that there is not an analysis folder generated from a same paradigm file. Any suggestions? Thanks and best regards, Lizhi _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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I see. So the mkanlaysis-sess just input the name of paradigm file into the analysis.info. Thank you very much.
On Mon, 25 Feb 2019 at 13:47, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
The paradigm info is in a file, not a folder (eg, subject1/bold/003/taskname.par, subject1/bold/004/taskname.par, subject5/bold/001/taskname.par). When you make an analysis (mkanalysis-sess), you should then spcify the paradigm file with --par taskname.par. mkanlaysis-sess is run without reference to the subjects. Eg, the name of the analysis (--analysis analysisname) is independent of the subject. Maybe you are confusing the analysisname and the paradigm?
On 2/25/19 9:50 AM, Zhi Li wrote:
External Email - Use CautionThank you very much. You mean the generated paradigm folders (e.g., taskname.sm05.lh) and analysis.info http://analysis.info, contrast.mat and contrast.config should be the same among all the subjects, even the onset and duration of each stimulus in each subject were different? Hence I could use the paradigm folders generated from the 1-st level modelling of any subjects in the 2-nd level modelling, is that correct?
On Fri, 22 Feb 2019 at 16:35, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
While the name of the paradigm file must be the same across runs and subjects, the contents paradigm file can be different. That should be able to handle what you are doing On 2/22/19 3:42 PM, Zhi Li wrote:External Email - Use Caution Hello FreeSurfer experts, It seems that all the subjects adopt a single same paradigm file in FsFast, am I correct? So how to handle it if each subject has different paradigm files, e.g., different onset time and duration? I could do the first-level analysis in each individual data, however, I cannot concatenate data with 'isxconcat-sess' due to that there is not an analysis folder generated from a same paradigm file. Any suggestions? Thanks and best regards, Lizhi _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
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Greve, Douglas N.,Ph.D. -
Zhi Li