When you ran mri_glmfit the first time, you had to specify a file with the --y flag. It is looking for that file now. Does that file still exist in the location where it was when you ran mri_glmfit?
On 11/03/2015 04:50 PM, smcl@u.washington.edu wrote:
Thanks. But it is still unsuccessfully looking for "rh.cope7.mgh" in [mydata}/cope7ACroi_rh.osgm.rfx.
There are a lot of .mgh files in there (ar1, beta, mask, rstd, rvar, sar1), and even more .mgh files in cope7ACroi_rh.osgm.rfx/osgm (cnr, F, gamma, gammavar, mask, and sig) but no rh.cope7.mgh.
Thanks for going back and forth about this,
Susan
On Tue, 3 Nov 2015, Douglas N Greve wrote:
The correct command line is
--cache 4 neg --cache-label AC
On 11/03/2015 03:36 PM, smcl@u.washington.edu wrote:
Hi Doug,
So if I pass cope7ACroi_rh.osgm.rfx and get rid of the --grf (cannot find any documentation about what to put instead of --grf), as in
mri_glmfit-sim --glmdir /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx --cache-label AC 4 neg --cwpvalthresh 0.05 --2spaces
I get back "ERROR: Flag 4 is unrecognized."
If I try just --cache instead of --cache-label AC, I get back "ERROR: cannot find /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/rh.cope7.mgh"
Any thoughts?
Many thanks, Susan
On Tue, 3 Nov 2015, Douglas N Greve wrote:
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, smcl@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, smcl@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, smcl@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, smcl@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: smcl@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 >>>> greve@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 >> greve@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
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Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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/
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