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Few clusters survive glm fit. No clusters seem to survive glm-fit-sim (when
visualizing). However, I'm not sure if I should also see this in a text file.
Opening cache.th40(or 30).abs.sig.cluster.summary it seems to have found no
clusters. At least, under the line ClusterNo Max VtxMax Size MNIX MNIY etc.
nothing is written.
But does a lack of significant clusters also explain the weird messages of
"colortable with 1 entries read (originally none)" (& "CTABisEntryValid: index
-1 was OOB" & "Resource temporarily unavailable") that show up in the terminal?
Thanks very much, Caroline
-Oorspronkelijk bericht-
Van: freesurfer-boun...@nmr.mgh.harvard.edu
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Verzonden: dinsdag 9 oktober 2018 18:00
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Freesurfer Digest, Vol 176, Issue 9
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Today's Topics:
1. FW: RE: error glm-fit-sim (Caroline Beelen)
2. Re: output values of vertices on surface into a textfile
(Sims, Sara A)
3. Re: output values of vertices on surface into a textfile
(Bruce Fischl)
4. Re: output values of vertices on surface into a textfile
(Sims, Sara A)
5. Re: Hippocampal segmentation with an additional scan ERROR
kvlGEMSMatlab (Pradeep)
6. Re: Hippocampal segmentation with an additional scan ERROR
kvlGEMSMatlab (Iglesias Gonzalez, Eugenio)
7. hippocampal subfields (Marcel Heers)
8. Re: hippocampal subfields (Iglesias Gonzalez, Eugenio)
9. Re: Difference between 6.0.1 and 6.0.0 (Dicamillo, Robert)
10. Talairach failed in monkey brain (Frehiwot Woldeyes)
11. Re: FW: RE: error glm-fit-sim (Greve, Douglas N.,Ph.D.)
12. Mri Convert Help (Justin Arnett)
13. Re: Mri Convert Help (Greve, Douglas N.,Ph.D.)
14. Re: Recon-all with/without T2 give the same stats
(Greve, Douglas N.,Ph.D.)
15. Re: Recon-all with/without T2 give the same stats (Jianzhong Chen)
16. m.khalil...@sutech.ac.ir sent you files via WeTransfer
(WeTransfer)
17. very bad result using "mris_ca_train" and "mris_ca_label"
(Maedeh Khalilian)
18. Re: Talairach failed in monkey brain (Greve, Douglas N.,Ph.D.)
19. Re: Recon-all with/without T2 give the same stats
(Greve, Douglas N.,Ph.D.)
20. Re: very bad result using "mris_ca_train" and "mris_ca_label"
(Bruce Fischl)
21. Re: Extract individual vertex thickness values from cortical
parcellations (Greve, Douglas N.,Ph.D.)
22. Re: nu_correct disk i/o issues (Greve, Douglas N.,Ph.D.)
23. Re: masking cortical thickness (Greve, Douglas N.,Ph.D.)
--
Message: 1
Date: Mon, 8 Oct 2018 16:12:06 +
From: Caroline Beelen
Subject: [Freesurfer] FW: RE: error glm-fit-sim
To: "freesurfer-boun...@nmr.mgh.harvard.edu"
,
"freesurfer@nmr.mgh.harvard.edu"
Message-ID:
<4051d561c94b40e0b641202b7bad7...@icts-s-exmbx25.luna.kuleuven.be>
Content-Type: text/plain; charset="us-ascii"
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
