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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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens freesurfer-request@nmr.mgh.harvard.edu 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.khalilian@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.)

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Message: 1 Date: Mon, 8 Oct 2018 16:12:06 +0000 From: Caroline Beelen caroline.beelen@kuleuven.be Subject: [Freesurfer] FW: RE: error glm-fit-sim To: "freesurfer-bounces@nmr.mgh.harvard.edu" freesurfer-bounces@nmr.mgh.harvard.edu, "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: 4051d561c94b40e0b641202b7bad7192@ICTS-S-EXMBX25.luna.kuleuven.be Content-Type: text/plain; charset="us-ascii"

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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