Hi Doug,
thank you - using this new version changed everything back to "normal"
(small clusters, few results), so it may indeed have been a problem with
that particular version.
Thanks again,
Nicola
On 7/22/2016 8:22 PM, Douglas N Greve wrote:
>
> That version may have had a bug. Try this on
That version may have had a bug. Try this one
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit
btw, you should not be using the dev version of recon-all
On 07/22/2016 02:01 PM, Nicola Toschi wrote:
> Hi,
>
> it's a dev version downloaded on Jan 17th 2016.
>
> As mentioned
Hi,
it's a dev version downloaded on Jan 17th 2016.
As mentioned in my other mail, I have uploaded a full glmdir at
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=akbem4mthlv
thanks for your time,
Nicola
On 7/22/2016 6:35 PM, Douglas N Greve wrote:
> what version does it fail on? If a dev versi
Hi,
I have uploaded it and the link should be
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=akbem4mthlv
Thanks!
Nicola
On 7/22/2016 6:31 PM, Douglas N Greve wrote:
> Can you tar up the glmdir and send it to me on our filedrop? The first
> warning is not a problem. Not sure about the 2nd.
> do
what version does it fail on? If a dev version, when did you download it?
On 07/22/2016 12:15 PM, Nicola Toschi wrote:
> Hi Again,
>
> (apologies for the many posts): I should add that none of this
> happens (and everything works fine - no warning and small clusters
> which look reasonable) if
Can you tar up the glmdir and send it to me on our filedrop? The first
warning is not a problem. Not sure about the 2nd.
doug
On 07/22/2016 08:10 AM, Nicola Toschi wrote:
> Hi,
>
> thanks - I tried using "abs" as well as a higher threshold, however
> the large, whole-brain cluster (as well as th
Hi Again,
(apologies for the many posts): I should add that none of this happens
(and everything works fine - no warning and small clusters which look
reasonable) if I use version 5.3.
Thank you,
Nicola
On 7/22/2016 2:10 PM, Nicola Toschi wrote:
> Hi,
>
> thanks - I tried using "abs" as wel
Hi,
thanks - I tried using "abs" as well as a higher threshold, however the
large, whole-brain cluster (as well as the warning messages) still remains.
Do the warnings:
WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
WARNING: 251446 NaNs found in volume
give any clues?
The strange
Try using abs instead of pos. abs (absolute) is more appropriate since
an F test is unsigned. Also, I would go with a threshold of 2 and not
1.3. I'm just now finding out that such a low threshold can cause a lot
of false postives on real data.
On 07/21/2016 05:32 PM, Nicola Toschi wrote:
> Hi
Hi,
thanks for your reply. The mri_glmfit-sim was pasted below, here it is
the dereferenced version:
/usr/local/freesurfer6dev/bin/mri_glmfit-sim --glmdir
design_3groups_AgeGenderIq_area_lh_fwhm0_pial --cache 1.3 pos
thanks again,
Nicola
On 7/21/2016 11:13 PM, Douglas N Greve wrote:
> That
That is the mri_glmfit command, I need the mri_glmfit-sim. Also, please
do not include variables, just the full command with all dereferenced args
On 07/21/2016 03:28 PM, Nicola Toschi wrote:
> Hi,
>
> here it is (I also pasted the mri_glmfit line):
>
> /odir=${prefix}_${meas}_${h}_fwhm${s}_${sur
Hi,
here it is (I also pasted the mri_glmfit line):
/odir=${prefix}_${meas}_${h}_fwhm${s}_${surf} #name output directory//
//
//mri_glmfit --y ${h}.fwhm${s}.${list}.${meas}.mgh --X ${matrix} \//
//--C ${C1} \//
//--glmdir ${odir} --surf fsaverage ${h} ${surf}//
//
//*/usr/local/freesurfer6dev/bi
what is your mri_glmfit-sim command line?
On 07/20/2016 05:56 PM, Nicola Toschi wrote:
> Hi List,
>
> I am getting a couple of strange error when running a 3-group F-test.
>
> WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
> WARNING: 251446 NaNs found in volume
> analysis/Ftest/cache.t
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