[Freesurfer] samseg error: illegal hardware instructions

[Jacky Lee]

External Email - Use Caution

Hi FreeSurfer developers,

I was trying to do lesion segmentation and calculation with FreeSurfer
samseg function on my MS subjects as described here:
https://secure-web.cisco.com/1zAsxk4FzHM5NR_SkitDdzHN3p9YF3oxn6CN---kSGPRsxsLrR96AiAnRJ4jOBVfwNnpls2HBOrLcACGlWeNk4ubbyOH3Yuaqai3T0d3m4Iut9_4u8SzhDHocmEUJ8tdwp6EojeFiGOrG71KL54fAn0cI9eBZB1kt0P6vR2JKJhf0n68xeKDqi5UWhEWLOavmBVKfeBTCCQ4tGTjTIkWZXVjJc-DZGzZhYWJqJLl1tez1958L02hE1RHGxCaPKOo3Y3escE9xPJz-k5p7RgcXuxuUBYLUVXyJ-5p3sRLDyJsnW86ClfYyW-X3Zq-mpOzK5KkuHHviCN-Z_wtEBOUebA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSamseg

I have performed coregistration and reformatting of my FLAIR image. I
proceeded to run_samseg as follows: run_samseg --input 105_t1.nii
105_flairRegT1.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1
--output samsegoutput

Then I encountered this error: zsh: illegal hardware instruction  run_samseg
--input 105_t1.nii 105_flairRegT1.nii --pallidum-separate --lesion

1) FreeSurfer version: freesurfer-darwin-macOS-7.3.1-20220723-115e466
2) Platform: macOS Ventura 13.1 (22c65) [Apple M1 macbook pro]

Please help looking into it. Thanks

Jacky
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Re: [Freesurfer] Manual correction for brainstem module

[Jacky Lee]

Just a short note for other people who may use the matlab script to get
volumes from the corrected hard segmentations. The volume in cubic mm
should be total voxels divided by 8 instead of multiplying by 8.

Cheers,
Jacky

2016-05-12 17:44 GMT+02:00 Eugenio Iglesias <e.igles...@bcbl.eu>:

> Yes! But take all the medulla volumes from the script. In other words: do
> not use the script to compute the medulla volumes of the cases you edited,
> and take the medulla volumes from the text file for all other cases. If you
> do that, you'd be introducing a fairly ugly bias in the study.
> Cheers,
> /E
>
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
> --
> *From: *"Jacky Lee" <cyle...@gmail.com>
> *To: *"Eugenio Iglesias" <e.igles...@bcbl.eu>
> *Cc: *"Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> *Sent: *Thursday, May 12, 2016 4:11:20 PM
>
> *Subject: *Re: [Freesurfer] Manual correction for brainstem module
>
> Hi Eugenio,
>
> Thanks, the script worked.
>
> Actually I only edited the medulla segmentation in 3 out of the 49
> subjects that I have. I suppose the original volumetric estimates for
> midbrain and pons are still valid and I can just calculate and compare the
> new medulla volumes for all subjects. Is that correct?
>
> Jacky
>
> 2016-05-12 12:05 GMT+02:00 Eugenio Iglesias <e.igles...@bcbl.eu>:
>
>> My email client is replacing the combination colon + right parenthesis by
>> a smiley! If the same thing happened to you, please replace the smiley by a
>> colon and a right parenthesis...
>> Next time I'll just attach the code.
>> Sorry for the inconvenience
>>
>> Juan Eugenio Iglesias
>> Postdoctoral researcher BCBL
>> www.jeiglesias.com
>> www.bcbl.eu
>>
>> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>>
>> --
>> *From: *"Eugenio Iglesias" <e.igles...@bcbl.eu>
>> *To: *"Jacky Lee" <cyle...@gmail.com>
>> *Cc: *"Freesurfer support list" <Freesurfer@nmr.mgh.harvard.edu>
>> *Sent: *Thursday, May 12, 2016 5:59:33 AM
>>
>> *Subject: *Re: [Freesurfer] Manual correction for brainstem module
>>
>> Of course! I haven't tested the code below, but I think it should work
>> right away.
>>
>> Let's assume that FreeSurfer is installed in /usr/local/freesurfer/ (if
>> not, replace the location in the code below). Also, you'd need to replace
>> the name of your subject directory.
>> Finally, I have assumed that brainstemSsLabels.v10.mgz was modified and
>> saved as  brainstemSsLabels.v10.edited.mgz  (again, replace as needed).
>>
>>
>> subjectdir='/mysubjectdir/';
>> editedFileName='brainstemSsLabels.v10.edited.mgz';
>>
>> addpath /usr/local/freesurfer/matlab
>>
>> d=dir(subjectdir);
>>
>> for i=1:length(d)
>>
>>   tentativeSegFile=[subjectdir '/' d(i).name '/mri/' editedFileName];
>>
>>   if d(i).isdir && exist(tentativeSegFile,'file')
>>
>> A=MRIread(tentativeSegFile);
>> MidbrainVol=8*sum(A.vol(:)==173);   % the eight is because each voxel
>> of the segmentation has a volume equal to 0.125 cubic mm
>> PonsVol=8*sum(A.vol(:)==174);
>> MedullaVol=8*sum(A.vol(:)==175);
>> SCPvol=8*sum(A.vol(:)==178);
>>
>> disp(['Subject ' d(i).name ', midbrain = ' num2str(MidbrainVol) ',
>> pons = ' num2str(PonsVol) ', medulla = ' num2str(MedullaVol) ', SCP = '
>> num2str(SCPvol)]);
>>
>>   end
>>
>> end
>>
>> One more thing: if you haven't edited anything around the SCP, I would
>> use the original estimate for this structure. The reason is that, because
>> the SCP is very thing, the voxel count is a much poorer approximation for
>> the volume as computed by the code (i.e., using soft segmentations).
>>
>> Cheers,
>>
>> Eugenio
>>
>>
>> Juan Eugenio Iglesias
>> Postdoctoral researcher BCBL
>> www.jeiglesias.com
>> www.bcbl.eu
>>
>> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>>
>> --
>> *From: *"Jacky Lee" <cyle...@gmail.com>
>> *To: *"Freesurfer support list" <Freesurfer@nmr.mgh.harvard.edu>
>> *Cc: *"Eugenio Iglesias" <e.igles...@bcbl.eu>
>> *Sent: *Thursday, May 12, 2016 10:32:24 AM
>> *Subje

[Freesurfer] Manual correction for brainstem module

[Jacky Lee]

Hi freesurfer experts,

I have successfully run the brainstem module for some subjects. On visual
checking, I can see there are voxels with T1 hypointense lesions
mislabelled as non-brainstem tissue. I manually corrected them on the
brainstemSsLabels.v10.mgz on Freeview. Then how do I obtain this new
corrected volume of the brainstem substructures?

Thanks.

Regards,

Jacky
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[Freesurfer] [freesurfer] XL defect correction?

[Jacky Lee]

Dear freesurfer experts,

I have encountered problems running recon-all on some subjects where the
processes were stuck at "CORRECTING DEFECT 5 (vertices=14049, convex
hull=3020) XL defect detected...".

I have read from the mailing list that this is a large defect to be
manually corrected or control points. So does that mean the recon-all
cannot correct this? If that is the case, what are the steps for manual
correction or control points and how should I re-run the recon-all
afterwards with incorporation of this correction?

Regards,

Jacky Lee
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