On Fri, May 8, 2020 at 2:06 PM Zeng, Qi <qi.zeng@icahn.mssm.edu> wrote:

Hi Douglas and Bruce,

I reran the recon-all with freesurfer/MailScanner has detected a possible fraud attempt from "7.0.0" claiming to be MailScanner warning: numerical links are often malicious: 7.0.0. Now it generated more files (57) compared to normal run (81) in SUBJ/surf/ than freesurfer/6.0.0 (12)

The script didn't exit with error but stopped running after about 10hrs. Attached the log file.

The script ends with "

writing registered surface to ../surf/rh.sphere.reg...
registration took 0.35 hours
#VMPC# mris_register VmPeak 3617640
FSRUNTIME@ mris_register 0.3463 hours 1 threads
@#@FSTIME 2020:05:06:22:35:52 mris_register N 6 e 1247.13 S 3.72 U 1239.39 P 99% M 3227664 F 0 R 2401997 W 0 c 128071 w 126 I 5584 O 0 L 19.04 19.01 18.97
@#@FSLOADPOST 2020:05:06:22:56:39 mris_register N 6 17.46 18.04 18.52"

Is it still about topological defects? Attached the white matter surface loading. It seems like there is no clear strip of the brain skull on the right top, is that so?

Thank you so much !

Best,

Qi
On Wed, May 6, 2020 at 12:49 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
Qi, in this context a "defect" is not just a place where the surface is inaccurate. It is a place where the surface is topologically incorrect, ie, a "handle" or a "hole" in the surface. Such defects are quite common and usually fixed by recon-all automatically. Sometimes the defects can be very large. This generally indicates a problem with the skull stripping or otherwise a failure to remove non-cortical regions. Your job is to find where this region is and fix it by fixing the skull strip or the wm.mgz file. Again, this is not going to be a small error in the surface -- it should be large.

See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview for more info

On 5/6/2020 12:30 PM, Zeng, Qi wrote:
        External Email - Use Caution

Hi Bruce,

After examining the sagittal view of the parietal lobe, it is fine including the area.

However, after examining the outputs in surf/, I noticed that after it generated lh.defects, it stopped processing lh.smoothwm and never got a chance to generate rh.defects. Compared to normal subjects that successfully finished, there is a clear mismatch between the inflated.nofix and the brainmask & wm.mgz. Attached below.

Can you help confirm the fact of mismatch and let me know if there is any way to fix this?

Thank you so much !

Best,

Qi

On Wed, May 6, 2020 at 10:12 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Qi

it is not obvious from that one image that something is wrong there. What
does a saggital view look like with the cursor on that region? Also, can
you send an image of the rh.inflated.nofix in 3D mode? Sometime XL
defects are fixable automatically, which may be the case for your
subjects with very large ventricles, but sometimes not

cheers
Bruce
On Tue, 5 May 2020,
Zeng, Qi wrote:

>
>         External Email - Use Caution
>
> Hi Douglas,
>
> Compared to the ones without error, the subject surface misses including
> left parietal lobe. Is that correct? Attached the comparison.
>
> Thank you so much!
> Best,
> Qi
>
> On Tue, May 5, 2020 at 1:58 PM Douglas N. Greve <dgreve@mgh.harvard.edu>
> wrote:
> You should load that volume along with the orig.nofix hemisphere
> that is giving you problems and look for a large area that
> should not be within the surface
>
> On 5/5/2020 1:23 PM, Zeng, Qi wrote:
>
>          External Email - Use Caution
>
> Hi Douglas,
>
> The cerebrum is removed and with no skull attached.
> However, compared to others that run normally, it may have
> problems with white matter segmentation and missing brainstem
> (no clear). Attached the comparison below. Can you help figure
> it out?
>
>
>
> Thank you so much!
> Best,
> Qi
>
> On Tue, May 5, 2020 at 11:36 AM Douglas N. Greve
> <dgreve@mgh.harvard.edu> wrote:
> You should look at the wm.mgz to see where the
> defect is. Probably cerebellum is still attached or
> maybe a big piece of skull.
>
> On 5/4/2020 11:19 PM, Zeng, Qi wrote:
>
>          External Email - Use Caution
>
> Hi,
>
> I've conducted longitudinal T1 recon-all. One
> subject's last-scan ran into error in the first
> independent recon all step: " recon-all -s SUBJ1
> -SUBJ1.nii -all'.
> Error: "CORRECTING DEFECT 0 (vertices=14101, convex
> hull=2297, v0=1419) XL defect detected...". Log file
> attached below.
>
> I've increased the memory usage limit as some
> suggestions did, but no help. Also T1.nii looks
> fine, same parameter setting as first scan, also
> attached below. Subject first scan and all the other
> subjects were finished without errors. Can you help
> figure out what has caused it?
>
> Thank you so much!
> Best,
> Qi
>
> --
>
> Ph.D. candidate
> Icahn School of Medicine at Mount Sinai
>
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