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, s...@u.washington.edu wrote:
> Thanks. But it is still unsuccessfully l
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.
The correct command line is
--cache 4 neg --cache-label AC
On 11/03/2015 03:36 PM, s...@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
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$cope.mgh
>
It's:
mri_glmfit --y
/Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/lh.cope$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 i
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.e
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
O
I am using bash. I am trying to google the bash equivalent of tcsh |&, but if
anybody knows it, please let me know.
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 inste
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
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
get
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
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
12 matches
Mail list logo
