The fwhm.dat file was in the right place. You passed the wrong folder to mri_glmfit-sim. You should pass it
cope7ACroi_rh.osgm.rfx doug On 11/03/2015 02:40 PM, s...@u.washington.edu wrote: > It's: > > mri_glmfit --y > /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/lh.cope$cope.mgh > --osgm --glmdir > /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope$cope\ACroi_lh.osgm.rfx > --surf fsaverage lh --label > /Applications/freesurfer/subjects/fsaverage/label/lh.AC.label > > fwhm.dat is actually in [MyData]/cope7ACroi_rh.osgm.rfx rather than > [MyData]/cope7ACroi_rh.osgm.rfx/osgm. I think that actually also happened for > some other files needed and I moved them. Is the problem something in my > mri_glmfit command? > > Susan > > On Tue, 3 Nov 2015, Douglas N Greve wrote: > >> it cannot find this file >> >> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm/fwhm.dat >> >> which should have been created by mri_glmfit. What is your mri_glmfit >> command line? >> >> Also, don't use --grf, that is for volumes only >> >> >> On 11/03/2015 02:27 PM, s...@u.washington.edu wrote: >>> Hi DOug, >>> >>> doug.log is attached >>> >>> the bash equivalent for |& is 2>&1 | >>> >>> thanks, >>> Susan >>> >>> On Tue, 3 Nov 2015, Douglas N Greve wrote: >>> >>>> I meant &. The & works for tcsh (or csh). Are you using bash? I'm not >>>> sure what the bash equivalent is. Maybe |2 instead of |& >>>> perhaps some bash experts can weigh in >>>> >>>> On 11/03/2015 01:41 PM, s...@u.washington.edu wrote: >>>>> Hi Doug, >>>>> >>>>> Do you mean: >>>>> >>>>> mri_glmfit-sim --debug --glmdir >>>>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm >>>>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee >>>>> doug.log? >>>>> >>>>> When I tried running the same code with |& tee doug.log at the end, >>>>> I kept getting: >>>>> >>>>> syntax error near unexpected token `&' >>>>> >>>>> Thanks, >>>>> Susan >>>>> >>>>> On Tue, 3 Nov 2015, Douglas N Greve wrote: >>>>> >>>>>> Can you run >>>>>> >>>>>> mri_glmfit-sim --debug --glmdir [my data >>>>>> dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg >>>>>> --cwpvalthresh 0.05 --2space |& tee doug.log >>>>>> >>>>>> and send me doug.log? >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 11/02/2015 05:08 PM, s...@u.washington.edu wrote: >>>>>>> Hi experts, >>>>>>> >>>>>>> I am having trouble performing a Monte Carlo correction using >>>>>>> mri_glmfit-sim. >>>>>>> >>>>>>> My data were sampled to fsaverage and smoothed at fwhm 5, using >>>>>>> mris_preproc. I then ran mri_glmfit on the data. >>>>>>> >>>>>>> I want to do my analysis/correction only in auditory cortex (AC) >>>>>>> so I did my own simulation in AC of each hemisphere using >>>>>>> mri_mcsim (as per >>>>>>> http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo). >>>>>>> >>>>>>> So far, so good. >>>>>>> >>>>>>> But when I try to run: >>>>>>> >>>>>>> mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm >>>>>>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space >>>>>>> >>>>>>> I get "fwhm: Undefined variable." I tried adding --fwhm-override >>>>>>> 5, but it didn't help. >>>>>>> >>>>>>> Any thoughts? Also, can you clarify which comparison neg vs pos >>>>>>> will give me? >>>>>>> >>>>>>> Thank you, >>>>>>> >>>>>>> Susan McLaughlin, PhD >>>>>>> Research Scientist >>>>>>> Laboratory for Auditory Brain Sciences & Neuroengineering >>>>>>> Institute for Learning & Brain Sciences (I-LABS) >>>>>>> Portage Bay Bldg. Room 204 >>>>>>> University of Washington, Box 357988 >>>>>>> Seattle, WA 98195-7988 >>>>>>> >>>>>>> Ph: (206) 616-0102 Fx: (206) 221-6472 >>>>>>> Cell: 206-850-8638 >>>>>>> E-mail: s...@uw.edu >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>> -- >>>>>> Douglas N. Greve, Ph.D. >>>>>> MGH-NMR Center >>>>>> gr...@nmr.mgh.harvard.edu >>>>>> Phone Number: 617-724-2358 >>>>>> Fax: 617-726-7422 >>>>>> >>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> Outgoing: >>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> gr...@nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> >>>> _______________________________________________ >>>> 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 >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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 > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
