External Email - Use Caution
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.edumailto:DGREVE@mgh.harvard.edu> Subject: Re: [Freesurfer] error glm-fit-sim To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <504d6069-399f-163d-39a9-dcc6c02d32f9@mgh.harvard.edumailto: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 output?
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