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
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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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