The command:
gop@gop-linux:~/freesurfer$ freeview -f $SUBJECTS_DIR/avgsubject/surf/lh.inflated:overlay=lh.area.glmdir/groupeffect/cache.th40.abs.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.area.glmdir/groupeffect/cache.th40.abs.sig.ocn.annot
-viewport 3d
The output:
reading colortable from annotation file...
colortable with 1 entries read (originally none)
colortable with 1 entries read (originally none)
CTABisEntryValid: index -1 was OOB
Resource temporarily unavailable
Resource temporarily unavailable
B
ginally none)
CTABisEntryValid: index -1 was OOB
Resource temporarily unavailable
Resource temporarily unavailable
B
ginally none)
CTABisEntryValid: index -1 was OOB
Resource temporarily unavailable
Resource temporarily unavailable
B
ginally none)
The command with a bit less strict significance level:
gop@gop-linux:~/freesurfer$ freeview -f $SUBJECTS_DIR/avgsubject/surf/lh.inflated:overlay=lh.area.glmdir/groupeffect/cache.th40.abs.sig.cluster.mgh:overlay_threshold=3,5:annot=lh.area.glmdir/groupeffect/cache.th40.abs.sig.ocn.annot
-viewport 3d
The output:
reading colortable from annotation file...
colortable with 1 entries read (originally none)
colortable with 1 entries read (originally none)
(and then it says no more).
Both commands visualize the data, but no clusters are found.
Is this how it should be? Does it mean that there is a problem with reading colortables or not?
Best, Caroline
Message: 2
Date: Mon, 1 Oct 2018 17:10:28 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] error glm-fit-sim
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <504d6069-399f-163d-39a9-dcc6c02d32f9@mgh.harvard.edu>
Content-Type: text/plain; charset="Windows-1252"
What says that? What command are you running? What is the other terminal
On 10/01/2018 04:54 AM, Caroline Beelen wrote:
>
> ????????External Email - Use Caution
>
> Dear FS,
>
> I followed the group analysis page for glm analysis and it worked fine
> until the final step. I?m using version 5.3.
After performing
> glm-fit-sim it says ?glm-fit done? (for all files), but when trying to
> open these it says:
>
> ?Reading colortable from annotation file?
>
> Colortable with 1 entries read (originally none)
>
> Colortable with 1 entries read (originally none)
>
> CTABisentryvalid: index -1 was 00B
>
> Resource temporarily unavailable
>
> CTABisentryvalid: index -1 was 00B
>
> Resource temporarily unavailable
>
> Resource temporarily unavailable?
>
> (etc..)
>
> It opens, but nothing is visible and I have the feeling it cannot open
> color files??
>
> MRI glmfit gives positive clusters for some values. I therefore used
> the abs sign for glm-fit-sim.
>
> What might be wrong?
>
> Thanks. Caroline