Re: [Freesurfer] error: MatrixMultiply: m1 is null

[Peled, Noam]

Thanks Andrew!
Yes, it seems like something is really wrong with this scan:
/autofs/space/frieda_003/users/valia/epilepsy_clin/5545419_1449/3D/dicom/IM-0001-0001.dcm

I’ll try to find another sequence.
Thanks!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Hoopes, Andrew
Sent: Tuesday, November 24, 2020 11:14 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] error: MatrixMultiply: m1 is null

Hi Noam,

Do the volumes look okay? I’m seeing a lot of ‘non-orthogonal axes’ warnings in 
the log. If that’s not the issue, this could be a bug that’s randomly occurring 
with parallel recons in v7. Although, I’ve never seen it fail during 
mri_convert. Can you try to rerun? It might succeed the second time. If not, 
can you send us the input scan and try again without the -parallel flag.

best
Andrew

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Peled, Noam" 
mailto:npe...@mgh.harvard.edu>>
Reply-To: FS Help 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, November 24, 2020 at 10:10 PM
To: FS Help 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] error: MatrixMultiply: m1 is null

Dear FreeSurfer community,
I encountered a recon-all error where I couldn’t find on the web.
The error message is: “error: MatrixMultiply: m1 is null!”. You can find the 
complete log attached.
I used the stable7.1.1 version.

Thanks,
Noam
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[Freesurfer] (no subject)

[Sara Lyn]

External Email - Use Caution

Hi Freesurfer experts,

I'm doing a surface based volume analysis and wanted to know if there was a
flag to regress out eTIV in the model.

Thank you
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Re: [Freesurfer] Mean Curvature for whole hemisphere

[Fischl, Bruce]

Hi Josue

No real reason. We provide maps of the mean curvature so it would be easy 
enough to average them. Not sure it will have much meaning. I guess it will 
loosely measure how much folding there is (since the less folding the more 
sphere-like the geometry will become)

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Josue Luiz Dalboni Da 
Rocha
Sent: Wednesday, November 25, 2020 10:07 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Mean Curvature for whole hemisphere


External Email - Use Caution

Dear FreeSurfer,



Why an average whole hemispherical value for mean curvature is not provided by 
Qdec?

Is there geometrical reason?



Best regards,

Josue
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[Freesurfer] lme_mass_fit_Rgw will only fit 20 % and then it quits using Matlab 2020b

[Knut J Bjuland]

External Email - Use Caution

Dear freesurfer experts


When I run lme_mass_fit_Rgw it stop fitting after i have runed 20 % as seen 
below. I have listed freesurfer matlab toolbox first in the Matlab 2020b path 
list. I am running on Fedora 33 and the mgh files work when I am running the 
same script on a macbook.
Are there any step I can take to debug this issues?

Region 4214: Convergence at iteration 9. Initial and final likelihoods: 
3004.2484, 3047.3654.
Region 4227: Convergence at iteration 15. Initial and final likelihoods: 
2466.513, 2550.6373.
Region 4234: Convergence at iteration 16. Initial and final likelihoods: 
2091.6167, 2576.1704.
Region 4247: Convergence at iteration 11. Initial and final likelihoods: 
1638.1748, 1830.6099.
Region 4254: Convergence at iteration 11. Initial and final likelihoods: 
1963.5263, 2122.7052.
Region 4267: Convergence at iteration 7. Initial and final likelihoods: 
1917.7245, 1924.1933.
Region 4274: Convergence at iteration 15. Initial and final likelihoods: 
1787.8884, 1895.3745.
Region 4287: Convergence at iteration 6. Initial and final likelihoods: 
1935.1202, 1950.6581.
Region 4294: Convergence at iteration 5. Initial and final likelihoods: 
2173.2547, 2185.9629.
Region 4307: Convergence at iteration 4. Initial and final likelihoods: 
1025.3896, 1058.5496.
Region 4314: Convergence at iteration 13. Initial and final likelihoods: 
1209.8828, 1245.91.
Region 4327: Convergence at iteration 26. Initial and final likelihoods: 
1132.3554, 1321.7057.
Region 4334: Convergence at iteration 9. Initial and final likelihoods: 
1157.4764, 1196.4451.
Region 4347: Convergence at iteration 7. Initial and final likelihoods: 
1432.242, 1437.6161.
Region 4354: Convergence at iteration 11. Initial and final likelihoods: 
1187.0457, 1282.0549.
Region 4367: Convergence at iteration 8. Initial and final likelihoods: 
1340.9078, 1494.0789.
Region 4374: Convergence at iteration 8. Initial and final likelihoods: 
1071.3221, 1095.6163.
Region 4387: Convergence at iteration 11. Initial and final likelihoods: 
1202.6703, 1227.2202.
Region 4394: Convergence at iteration 9. Initial and final likelihoods: 
1067.2966, 1100.0462.
Region 4407: Convergence at iteration 12. Initial and final likelihoods: 
1190.4148, 1221.8727.
Region 4414: Convergence at iteration 5. Initial and final likelihoods: 
1190.0332, 1193.3426.
Region 4427: Convergence at iteration 10. Initial and final likelihoods: 
1295.3867, 1416.8343.
Region 4434: Convergence at iteration 14. Initial and final likelihoods: 
1479.4723, 1498.5227.
Region 4447: Convergence at iteration 4. Initial and final likelihoods: 
492.8232, 495.8952.
Region 4454: Convergence at iteration 4. Initial and final likelihoods: 
345.9289, 350.5215.
Region 4467: Convergence at iteration 4. Initial and final likelihoods: 
420.0601, 420.7848.
Region 4474: Convergence at iteration 5. Initial and final likelihoods: 
543.539, 554.8185.
Region 4487: Convergence at iteration 4. Initial and final likelihoods: 
425.3509, 428.4245.
Region 4494: Convergence at iteration 3. Initial and final likelihoods: 
458.8256, 459.5319.
Region 4507: Convergence at iteration 3. Initial and final likelihoods: 
372.6527, 373.0735.
Region 4514: Convergence at iteration 5. Initial and final likelihoods: 
389.5679, 392.0076.
Aproximate percentage of fitted locations: 100%
Parallel pool using the 'local' profile is shutting down.

Summary:
Algorithm did not converge at 0.022139 percent of the total number of regions.
Elapsed time is 3.7353 minutes.

Saving output ...


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[Freesurfer] PETSurfer voxelwise statistic

[Boris Rauchmann]

External Email - Use Caution

Dear all,

How can I run a voxelwise statistic using grey and white matter uptake?
mgx.ctxgm.nii.gz and the other files in output all only include gm as I
understand.

My goal is to run whole brain volume-based analysis. Like in this example
for subcortical analysis:

mri_vol2vol --mov subctxgm.nii.gz --reg aux/bbpet2anat.lta
--tal --talres 2  --o subctxgm.mni305.2mm.sm00.nii.gz


Thanks,
Boris
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