Re: [Freesurfer] Correcting defect problem after checking skull stripped and editing wm.mgz

[Jiun Wei Chen]

External Email - Use Caution

Hi Bruce

Thanks so much for your quick reply.
I had overlaid the ?h.defect_labels on the inflated.nofix and orig.nofix. I
adjusted the threshold to focus on the largest defect. Although I could
look at the defect, I couldn't figure how to fix it manually because the
defect is too large.
In addition, I separately overlaid the ?h.defect_labels on the
inflated.nofix and orig.nofix but I actually don't know how to use
inflated.nofix to look for the defect. I don't know the difference between
defect_labels overlaid on the inflated.nofix and orig.nofix.

Excuse me, I also want to ask another question. Because I also check the
aseg.auto and aseg.presurf and find there is bad segmentation, can I
only modify segmentation results manually or is there another approach to
solve the bad segmentation problem? In some cases, the contrast of the
image is not obvious and thus modifying segmentation results manually is
hard.

I have put these two subject directories named Stroke_subject001.tar.gz and
Stroke_subject001.tar.gz on your ftp.

Thank you so much for your help.

Best regards,

Jiun-Wei

On Mon, 9 Sep 2019 at 20:39, Bruce Fischl 
wrote:

> Hi Jiun-Wei
>
> have you looked at the ?h.defect_labels overlaid on the inflated.nofix
> and orig.nofix surfaces? That will tell you where the defect is that is
> causing you trouble. If you have lesions they may be the source of the
> issue. If you can't sort it out you can tar and gzip the entire subject
> directory and put it on our ftp site for us to have a look
> cheers
> Bruce
> On Mon, 9 Sep
> 2019, Jiun Wei Chen wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear freesurfer experts,
> > When executing recon-all in two subjects with brain lesions, the
> recon-all
> > process stopped at CORRECTING DEFECT 13 (vertices=49319, convex
> hull=12973,
> > v0=65403) and
> > CORRECTING DEFECT 6 (vertices=23529, convex hull=6740, v0=16029),
> > respectively.
> >
> > After reading the relevant problem from freesufer mailing list, I had
> > checked the skull and cerebellum not attached to the surface, two
> > hemispheres are separated using freeview. In addition, I also load
> > the brain.mgz, wm.mgz, ?h.orig.nofix and ?h.inflated.nofix and separately
> > overlap the ?h.defect_label onto ?h.orig.nofix  , ?h.inflated.nofix to
> edit
> > wm.mgz to solve this problem.
> >
> > However, after editing wm.mgz in two subjects, the recon-all process
> still
> > stopped at CORRECTING DEFECT 0 (vertices=32853, convex hull=7926) and
> > CORRECTING DEFECT 6 (vertices=16533, convex hull= 4510) , respectively.
> >
> > Although I try to erase the non-white matter and label voxels as white
> > matter as much as possible, there are too many voxels I think I need to
> > label, which may cause the failure.
> >
> > I can't figure out how to continue to solve this problem. I use
> freesurfer
> > version 6.0.0.
> >
> > I really appreciate your help. Thanks a lot.
> >
> > Best regards,
> >
> > Jiun-Wei
> >
> >
> >
> >
> >
> >___
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Re: [Freesurfer] Correcting defect problem after checking skull stripped and editing wm.mgz

[Bruce Fischl]

Hi Jiun-Wei

have you looked at the ?h.defect_labels overlaid on the inflated.nofix 
and orig.nofix surfaces? That will tell you where the defect is that is 
causing you trouble. If you have lesions they may be the source of the 
issue. If you can't sort it out you can tar and gzip the entire subject 
directory and put it on our ftp site for us to have a look

cheers
Bruce
On Mon, 9 Sep 
2019, Jiun Wei Chen wrote:




External Email - Use Caution

Dear freesurfer experts,
When executing recon-all in two subjects with brain lesions, the recon-all
process stopped at CORRECTING DEFECT 13 (vertices=49319, convex hull=12973,
v0=65403) and 
CORRECTING DEFECT 6 (vertices=23529, convex hull=6740, v0=16029),
respectively.

After reading the relevant problem from freesufer mailing list, I had
checked the skull and cerebellum not attached to the surface, two
hemispheres are separated using freeview. In addition, I also load
the brain.mgz, wm.mgz, ?h.orig.nofix and ?h.inflated.nofix and separately
overlap the ?h.defect_label onto ?h.orig.nofix  , ?h.inflated.nofix to edit
wm.mgz to solve this problem.

However, after editing wm.mgz in two subjects, the recon-all process still
stopped at CORRECTING DEFECT 0 (vertices=32853, convex hull=7926) and
CORRECTING DEFECT 6 (vertices=16533, convex hull= 4510) , respectively.

Although I try to erase the non-white matter and label voxels as white
matter as much as possible, there are too many voxels I think I need to
label, which may cause the failure. 

I can't figure out how to continue to solve this problem. I use freesurfer
version 6.0.0.

I really appreciate your help. Thanks a lot.

Best regards,

Jiun-Wei





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[Freesurfer] Correcting defect problem after checking skull stripped and editing wm.mgz

[Jiun Wei Chen]

External Email - Use Caution

Dear freesurfer experts,

When executing recon-all in two subjects with brain lesions, the recon-all
process stopped at CORRECTING DEFECT 13 (vertices=49319, convex hull=12973,
v0=65403) and
CORRECTING DEFECT 6 (vertices=23529, convex hull=6740, v0=16029),
respectively.

After reading the relevant problem from freesufer mailing list, I had
checked the skull and cerebellum not attached to the surface, two
hemispheres are separated using freeview. In addition, I also load
the brain.mgz, wm.mgz, ?h.orig.nofix and ?h.inflated.nofix and separately
overlap the ?h.defect_label onto ?h.orig.nofix  , ?h.inflated.nofix to edit
wm.mgz to solve this problem.

However, after editing wm.mgz in two subjects, the recon-all process still
stopped at CORRECTING DEFECT 0 (vertices=32853, convex hull=7926) and
CORRECTING DEFECT 6 (vertices=16533, convex hull= 4510) , respectively.

Although I try to erase the non-white matter and label voxels as white
matter as much as possible, there are too many voxels I think I need to
label, which may cause the failure.

I can't figure out how to continue to solve this problem. I use freesurfer
version 6.0.0.

I really appreciate your help. Thanks a lot.

Best regards,

Jiun-Wei
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Re: [Freesurfer] CORRECTING DEFECT

[Balken, Brendan]

External Email - Use Caution

Bruce,

Awesome! I'll try that!

Thanks,
Brendan

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Friday, August 09, 2019 11:40 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] CORRECTING DEFECT

CAUTION: External

Hi Brendan

usually defects that are that big don't get corrected properly. I would look at 
the wm.mgz and the lh.orig.nofix to understand what is causing the large 
defects and correct them manually

cheers
Bruce


On Fri, 9 Aug 2019, Balken, Brendan wrote:

>External Email - Use Caution
>
> Bruce,
>
> Oh okay I understand now. This has been very enlightening! So, you think if I 
> let it keep running it will eventually correct the defects? And then I just 
> need to double check the result to make sure it corrected them properly? When 
> I got the overlay to work, I could see two big defects on the left hemisphere 
> (30 and 41) so I guess it'll probably get stuck again on 40. Also, is there 
> anything I can do to make it faster?
>
> Thanks,
> Brendan
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
> Fischl
> Sent: Friday, August 9, 2019 11:21 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] CORRECTING DEFECT
>
> CAUTION: External
>
> yes, because that is the total # of defects. The 29th or 30th isn't the last 
> one, just what it got stuck on. The #30 should look much bigger though 
> (you'll need to change the overlay thresholds) On Fri, 9 Aug 2019, Balken, 
> Brendan wrote:
>
>>External Email - Use Caution
>>
>> Bruce,
>>
>> I just imported lh.defect_labels as an overlay over the lh.inflated.nofix 
>> but the values aren't 1-30 they're 0 - 160 roughly. I'm not sure why...
>>
>>
>> Thanks!
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
>> Fischl
>> Sent: Friday, August 9, 2019 11:00 AM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] CORRECTING DEFECT
>>
>> CAUTION: External
>>
>> they are an overlay not a surface. Load the surface first then load them as 
>> an overlay on top of it (e.g. the lh.inflated.nofix) On Fri, 9 Aug 2019, 
>> Balken, Brendan wrote:
>>
>>>External Email - Use Caution
>>>
>>> Bruce,
>>>
>>> Thanks so much for the quick response! I don't know how to load the defect 
>>> labels. When I try to load them as a surface, I get an error. I'm doing 
>>> this in freeview gui. Also, I checked the cerebellum and it's not attached.
>>>
>>> Thanks,
>>> Brendan
>>>
>>> -Original Message-
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
>>> Fischl
>>> Sent: Friday, August 9, 2019 10:27 AM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] CORRECTING DEFECT
>>>
>>> CAUTION: External
>>>
>>> Hi Brendan
>>>
>>> the time to correct goes with the square of the size of the defect 
>>> (actually the convex hull of the defect) so it can take a very long time 
>>> for big ones. More importantly, if the defect is that large it may not be 
>>> corrected in the anatomically desired manner. You should take a look at it 
>>> and see what is causing it. Is skull left over? Cerebellum attached?
>>> Hemispheres connected? Usually the big ones are due to something dramatic.
>>> Look at the ?h.orig.nofix and the ?h.inflated.nofix. YOu can load the 
>>> ?h.defect_labels on top of the surfaces and brain.mgz and the wm.mgz to see 
>>> which one is 29 (note that they defect_labels file is probably 1-based so 
>>> you would need to look for 30 in it).
>>>
>>> If you can't sort it out gzip and tar your subject and put it on our 
>>> ftp site and we will take a look for you cheers Bruce
>>>
>>> On Fri, 9 Aug 2019, Balken, Brendan wrote:
>>>
>>>>
>>>> External Email - Use Caution
>>>>
>>>> Hello!
>>>>
>>>>
>>>>
>>>> So I am attempting to use freesurfer’s recon-all script but for one 
>>>> of our subjects I keep getting stuck at this point: “CORRECTING 
>&g

Re: [Freesurfer] CORRECTING DEFECT

[Bruce Fischl]

Hi Brendan

usually defects that are that big don't get corrected properly. I would 
look at the wm.mgz and the lh.orig.nofix to understand what is causing the 
large defects and correct them manually


cheers
Bruce


On Fri, 9 Aug 2019, Balken, Brendan wrote:


   External Email - Use Caution

Bruce,

Oh okay I understand now. This has been very enlightening! So, you think if I 
let it keep running it will eventually correct the defects? And then I just 
need to double check the result to make sure it corrected them properly? When I 
got the overlay to work, I could see two big defects on the left hemisphere (30 
and 41) so I guess it'll probably get stuck again on 40. Also, is there 
anything I can do to make it faster?

Thanks,
Brendan

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Friday, August 9, 2019 11:21 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT

CAUTION: External

yes, because that is the total # of defects. The 29th or 30th isn't the last 
one, just what it got stuck on. The #30 should look much bigger though (you'll 
need to change the overlay thresholds) On Fri, 9 Aug 2019, Balken, Brendan 
wrote:


   External Email - Use Caution

Bruce,

I just imported lh.defect_labels as an overlay over the lh.inflated.nofix but 
the values aren't 1-30 they're 0 - 160 roughly. I'm not sure why...


Thanks!

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
Fischl
Sent: Friday, August 9, 2019 11:00 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT

CAUTION: External

they are an overlay not a surface. Load the surface first then load them as an 
overlay on top of it (e.g. the lh.inflated.nofix) On Fri, 9 Aug 2019, Balken, 
Brendan wrote:


   External Email - Use Caution

Bruce,

Thanks so much for the quick response! I don't know how to load the defect 
labels. When I try to load them as a surface, I get an error. I'm doing this in 
freeview gui. Also, I checked the cerebellum and it's not attached.

Thanks,
Brendan

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
Fischl
Sent: Friday, August 9, 2019 10:27 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT

CAUTION: External

Hi Brendan

the time to correct goes with the square of the size of the defect (actually 
the convex hull of the defect) so it can take a very long time for big ones. 
More importantly, if the defect is that large it may not be corrected in the 
anatomically desired manner. You should take a look at it and see what is 
causing it. Is skull left over? Cerebellum attached?
Hemispheres connected? Usually the big ones are due to something dramatic.
Look at the ?h.orig.nofix and the ?h.inflated.nofix. YOu can load the 
?h.defect_labels on top of the surfaces and brain.mgz and the wm.mgz to see 
which one is 29 (note that they defect_labels file is probably 1-based so you 
would need to look for 30 in it).

If you can't sort it out gzip and tar your subject and put it on our
ftp site and we will take a look for you cheers Bruce

On Fri, 9 Aug 2019, Balken, Brendan wrote:



External Email - Use Caution

Hello!



So I am attempting to use freesurfer’s recon-all script but for one
of our subjects I keep getting stuck at this point: “CORRECTING
DEFECT 29 (vertices=19321, convex hull=4029, v0=32423) XL defect
detected...” It has already corrected 28 defects, but they were much
smaller. It has been running for about 48 hours on a very powerful
machine and I’m wondering how long I should wait. Will it eventually
move on? If no, what is my contingency plan for processing this? I’m
using the output anatomy folder in brainstorm for source analysis.
Any guidance or information would be greatly appreciated.



Thanks a million!

Brendan





Here’s what the lh and rh.inflated.nofix look like (is that the defect?):



[IMAGE]





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Re: [Freesurfer] CORRECTING DEFECT

[Balken, Brendan]

External Email - Use Caution

Bruce,

Oh okay I understand now. This has been very enlightening! So, you think if I 
let it keep running it will eventually correct the defects? And then I just 
need to double check the result to make sure it corrected them properly? When I 
got the overlay to work, I could see two big defects on the left hemisphere (30 
and 41) so I guess it'll probably get stuck again on 40. Also, is there 
anything I can do to make it faster?

Thanks,
Brendan

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Friday, August 9, 2019 11:21 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT

CAUTION: External

yes, because that is the total # of defects. The 29th or 30th isn't the last 
one, just what it got stuck on. The #30 should look much bigger though (you'll 
need to change the overlay thresholds) On Fri, 9 Aug 2019, Balken, Brendan 
wrote:

>External Email - Use Caution
>
> Bruce,
>
> I just imported lh.defect_labels as an overlay over the lh.inflated.nofix but 
> the values aren't 1-30 they're 0 - 160 roughly. I'm not sure why...
>
>
> Thanks!
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
> Fischl
> Sent: Friday, August 9, 2019 11:00 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] CORRECTING DEFECT
>
> CAUTION: External
>
> they are an overlay not a surface. Load the surface first then load them as 
> an overlay on top of it (e.g. the lh.inflated.nofix) On Fri, 9 Aug 2019, 
> Balken, Brendan wrote:
>
>>External Email - Use Caution
>>
>> Bruce,
>>
>> Thanks so much for the quick response! I don't know how to load the defect 
>> labels. When I try to load them as a surface, I get an error. I'm doing this 
>> in freeview gui. Also, I checked the cerebellum and it's not attached.
>>
>> Thanks,
>> Brendan
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
>> Fischl
>> Sent: Friday, August 9, 2019 10:27 AM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] CORRECTING DEFECT
>>
>> CAUTION: External
>>
>> Hi Brendan
>>
>> the time to correct goes with the square of the size of the defect (actually 
>> the convex hull of the defect) so it can take a very long time for big ones. 
>> More importantly, if the defect is that large it may not be corrected in the 
>> anatomically desired manner. You should take a look at it and see what is 
>> causing it. Is skull left over? Cerebellum attached?
>> Hemispheres connected? Usually the big ones are due to something dramatic.
>> Look at the ?h.orig.nofix and the ?h.inflated.nofix. YOu can load the 
>> ?h.defect_labels on top of the surfaces and brain.mgz and the wm.mgz to see 
>> which one is 29 (note that they defect_labels file is probably 1-based so 
>> you would need to look for 30 in it).
>>
>> If you can't sort it out gzip and tar your subject and put it on our 
>> ftp site and we will take a look for you cheers Bruce
>>
>> On Fri, 9 Aug 2019, Balken, Brendan wrote:
>>
>>>
>>> External Email - Use Caution
>>>
>>> Hello!
>>>
>>>
>>>
>>> So I am attempting to use freesurfer’s recon-all script but for one 
>>> of our subjects I keep getting stuck at this point: “CORRECTING 
>>> DEFECT 29 (vertices=19321, convex hull=4029, v0=32423) XL defect 
>>> detected...” It has already corrected 28 defects, but they were much 
>>> smaller. It has been running for about 48 hours on a very powerful 
>>> machine and I’m wondering how long I should wait. Will it eventually 
>>> move on? If no, what is my contingency plan for processing this? I’m 
>>> using the output anatomy folder in brainstorm for source analysis.
>>> Any guidance or information would be greatly appreciated.
>>>
>>>
>>>
>>> Thanks a million!
>>>
>>> Brendan
>>>
>>>
>>>
>>>
>>>
>>> Here’s what the lh and rh.inflated.nofix look like (is that the defect?):
>>>
>>>
>>>
>>> [IMAGE]
>>>
>>>
>>>
>>
>> ___
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>>
>>
>>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

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Re: [Freesurfer] CORRECTING DEFECT

[Bruce Fischl]

yes, because that is the total # of defects. The 29th or 30th isn't the 
last one, just what it got stuck on. The #30 should look much bigger 
though (you'll need to change the overlay thresholds)
On Fri, 9 Aug 2019, 
Balken, Brendan wrote:



   External Email - Use Caution

Bruce,

I just imported lh.defect_labels as an overlay over the lh.inflated.nofix but 
the values aren't 1-30 they're 0 - 160 roughly. I'm not sure why...


Thanks!

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Friday, August 9, 2019 11:00 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT

CAUTION: External

they are an overlay not a surface. Load the surface first then load them as an 
overlay on top of it (e.g. the lh.inflated.nofix) On Fri, 9 Aug 2019, Balken, 
Brendan wrote:


   External Email - Use Caution

Bruce,

Thanks so much for the quick response! I don't know how to load the defect 
labels. When I try to load them as a surface, I get an error. I'm doing this in 
freeview gui. Also, I checked the cerebellum and it's not attached.

Thanks,
Brendan

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
Fischl
Sent: Friday, August 9, 2019 10:27 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT

CAUTION: External

Hi Brendan

the time to correct goes with the square of the size of the defect (actually 
the convex hull of the defect) so it can take a very long time for big ones. 
More importantly, if the defect is that large it may not be corrected in the 
anatomically desired manner. You should take a look at it and see what is 
causing it. Is skull left over? Cerebellum attached?
Hemispheres connected? Usually the big ones are due to something dramatic.
Look at the ?h.orig.nofix and the ?h.inflated.nofix. YOu can load the 
?h.defect_labels on top of the surfaces and brain.mgz and the wm.mgz to see 
which one is 29 (note that they defect_labels file is probably 1-based so you 
would need to look for 30 in it).

If you can't sort it out gzip and tar your subject and put it on our
ftp site and we will take a look for you cheers Bruce

On Fri, 9 Aug 2019, Balken, Brendan wrote:



External Email - Use Caution

Hello!



So I am attempting to use freesurfer’s recon-all script but for one
of our subjects I keep getting stuck at this point: “CORRECTING
DEFECT 29 (vertices=19321, convex hull=4029, v0=32423) XL defect
detected...” It has already corrected 28 defects, but they were much
smaller. It has been running for about 48 hours on a very powerful
machine and I’m wondering how long I should wait. Will it eventually
move on? If no, what is my contingency plan for processing this? I’m
using the output anatomy folder in brainstorm for source analysis.
Any guidance or information would be greatly appreciated.



Thanks a million!

Brendan





Here’s what the lh and rh.inflated.nofix look like (is that the defect?):



[IMAGE]





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Re: [Freesurfer] CORRECTING DEFECT

[Balken, Brendan]

External Email - Use Caution

Bruce,

I just imported lh.defect_labels as an overlay over the lh.inflated.nofix but 
the values aren't 1-30 they're 0 - 160 roughly. I'm not sure why...


Thanks!

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Friday, August 9, 2019 11:00 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT

CAUTION: External

they are an overlay not a surface. Load the surface first then load them as an 
overlay on top of it (e.g. the lh.inflated.nofix) On Fri, 9 Aug 2019, Balken, 
Brendan wrote:

>External Email - Use Caution
>
> Bruce,
>
> Thanks so much for the quick response! I don't know how to load the defect 
> labels. When I try to load them as a surface, I get an error. I'm doing this 
> in freeview gui. Also, I checked the cerebellum and it's not attached.
>
> Thanks,
> Brendan
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
> Fischl
> Sent: Friday, August 9, 2019 10:27 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] CORRECTING DEFECT
>
> CAUTION: External
>
> Hi Brendan
>
> the time to correct goes with the square of the size of the defect (actually 
> the convex hull of the defect) so it can take a very long time for big ones. 
> More importantly, if the defect is that large it may not be corrected in the 
> anatomically desired manner. You should take a look at it and see what is 
> causing it. Is skull left over? Cerebellum attached?
> Hemispheres connected? Usually the big ones are due to something dramatic.
> Look at the ?h.orig.nofix and the ?h.inflated.nofix. YOu can load the 
> ?h.defect_labels on top of the surfaces and brain.mgz and the wm.mgz to see 
> which one is 29 (note that they defect_labels file is probably 1-based so you 
> would need to look for 30 in it).
>
> If you can't sort it out gzip and tar your subject and put it on our 
> ftp site and we will take a look for you cheers Bruce
>
> On Fri, 9 Aug 2019, Balken, Brendan wrote:
>
>>
>> External Email - Use Caution
>>
>> Hello!
>>
>>
>>
>> So I am attempting to use freesurfer’s recon-all script but for one 
>> of our subjects I keep getting stuck at this point: “CORRECTING 
>> DEFECT 29 (vertices=19321, convex hull=4029, v0=32423) XL defect 
>> detected...” It has already corrected 28 defects, but they were much 
>> smaller. It has been running for about 48 hours on a very powerful 
>> machine and I’m wondering how long I should wait. Will it eventually 
>> move on? If no, what is my contingency plan for processing this? I’m 
>> using the output anatomy folder in brainstorm for source analysis. 
>> Any guidance or information would be greatly appreciated.
>>
>>
>>
>> Thanks a million!
>>
>> Brendan
>>
>>
>>
>>
>>
>> Here’s what the lh and rh.inflated.nofix look like (is that the defect?):
>>
>>
>>
>> [IMAGE]
>>
>>
>>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

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Re: [Freesurfer] CORRECTING DEFECT

[Bruce Fischl]

they are an overlay not a surface. Load the surface first then load them 
as an overlay on top of it (e.g. the lh.inflated.nofix)
On Fri, 9 Aug 2019, 
Balken, Brendan wrote:



   External Email - Use Caution

Bruce,

Thanks so much for the quick response! I don't know how to load the defect 
labels. When I try to load them as a surface, I get an error. I'm doing this in 
freeview gui. Also, I checked the cerebellum and it's not attached.

Thanks,
Brendan

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Friday, August 9, 2019 10:27 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT

CAUTION: External

Hi Brendan

the time to correct goes with the square of the size of the defect (actually 
the convex hull of the defect) so it can take a very long time for big ones. 
More importantly, if the defect is that large it may not be corrected in the 
anatomically desired manner. You should take a look at it and see what is 
causing it. Is skull left over? Cerebellum attached?
Hemispheres connected? Usually the big ones are due to something dramatic.
Look at the ?h.orig.nofix and the ?h.inflated.nofix. YOu can load the 
?h.defect_labels on top of the surfaces and brain.mgz and the wm.mgz to see 
which one is 29 (note that they defect_labels file is probably 1-based so you 
would need to look for 30 in it).

If you can't sort it out gzip and tar your subject and put it on our ftp site 
and we will take a look for you cheers Bruce

On Fri, 9 Aug 2019, Balken, Brendan wrote:



External Email - Use Caution

Hello!



So I am attempting to use freesurfer’s recon-all script but for one of
our subjects I keep getting stuck at this point: “CORRECTING DEFECT 29
(vertices=19321, convex hull=4029, v0=32423) XL defect detected...” It
has already corrected 28 defects, but they were much smaller. It has
been running for about 48 hours on a very powerful machine and I’m
wondering how long I should wait. Will it eventually move on? If no,
what is my contingency plan for processing this? I’m using the output
anatomy folder in brainstorm for source analysis. Any guidance or
information would be greatly appreciated.



Thanks a million!

Brendan





Here’s what the lh and rh.inflated.nofix look like (is that the defect?):



[IMAGE]





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Re: [Freesurfer] CORRECTING DEFECT

[Balken, Brendan]

External Email - Use Caution

Bruce,

Thanks so much for the quick response! I don't know how to load the defect 
labels. When I try to load them as a surface, I get an error. I'm doing this in 
freeview gui. Also, I checked the cerebellum and it's not attached.

Thanks,
Brendan

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Friday, August 9, 2019 10:27 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT

CAUTION: External

Hi Brendan

the time to correct goes with the square of the size of the defect (actually 
the convex hull of the defect) so it can take a very long time for big ones. 
More importantly, if the defect is that large it may not be corrected in the 
anatomically desired manner. You should take a look at it and see what is 
causing it. Is skull left over? Cerebellum attached?
Hemispheres connected? Usually the big ones are due to something dramatic.
Look at the ?h.orig.nofix and the ?h.inflated.nofix. YOu can load the 
?h.defect_labels on top of the surfaces and brain.mgz and the wm.mgz to see 
which one is 29 (note that they defect_labels file is probably 1-based so you 
would need to look for 30 in it).

If you can't sort it out gzip and tar your subject and put it on our ftp site 
and we will take a look for you cheers Bruce

On Fri, 9 Aug 2019, Balken, Brendan wrote:

>
> External Email - Use Caution
>
> Hello!
>
>
>
> So I am attempting to use freesurfer’s recon-all script but for one of 
> our subjects I keep getting stuck at this point: “CORRECTING DEFECT 29 
> (vertices=19321, convex hull=4029, v0=32423) XL defect detected...” It 
> has already corrected 28 defects, but they were much smaller. It has 
> been running for about 48 hours on a very powerful machine and I’m 
> wondering how long I should wait. Will it eventually move on? If no, 
> what is my contingency plan for processing this? I’m using the output 
> anatomy folder in brainstorm for source analysis. Any guidance or 
> information would be greatly appreciated.
>
>
>
> Thanks a million!
>
> Brendan
>
>
>
>
>
> Here’s what the lh and rh.inflated.nofix look like (is that the defect?):
>
>
>
> [IMAGE]
>
>
>

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Re: [Freesurfer] CORRECTING DEFECT

[Bruce Fischl]

Hi Brendan

the time to correct goes with the square of the size of the defect 
(actually the convex hull of the defect) so it can take a very long time 
for big ones. More importantly, if the defect is that large it may not be 
corrected in the anatomically desired manner. You should take a look at it 
and see what is causing it. Is skull left over? Cerebellum attached? 
Hemispheres connected? Usually the big ones are due to something dramatic. 
Look at the ?h.orig.nofix and the ?h.inflated.nofix. YOu can load the 
?h.defect_labels on top of the surfaces and brain.mgz and the wm.mgz to see 
which one is 29 (note that they defect_labels file is probably 1-based so 
you would need to look for 30 in it).


If you can't sort it out gzip and tar your subject and put it on our ftp 
site and we will take a look for you

cheers
Bruce

On Fri, 9 Aug 2019, Balken, Brendan wrote:



External Email - Use Caution

Hello!

 

So I am attempting to use freesurfer’s recon-all script but for one of our
subjects I keep getting stuck at this point: “CORRECTING DEFECT 29
(vertices=19321, convex hull=4029, v0=32423) XL defect detected...” It has
already corrected 28 defects, but they were much smaller. It has been
running for about 48 hours on a very powerful machine and I’m wondering how
long I should wait. Will it eventually move on? If no, what is my
contingency plan for processing this? I’m using the output anatomy folder in
brainstorm for source analysis. Any guidance or information would be greatly
appreciated.

 

Thanks a million!

Brendan

 

 

Here’s what the lh and rh.inflated.nofix look like (is that the defect?):

 

[IMAGE]


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Re: [Freesurfer] CORRECTING DEFECT 1 problem

[Pradeepa Ruwan]

External Email - Use Caution

Hello,
Have you got some time to check my data?
I appreciate if you can give me some advices.
Thank you very much.

Ruwan

On Tue, Apr 23, 2019 at 7:41 PM Pradeepa Ruwan <
pradee.wanniarach...@gmail.com> wrote:

> Dear Prof.Bruce,
>
> I am sending my raw data and the images that you requested to send.
> I have two datasets that I got trouble with.
> I appreciate if you can take a look at this data.
> Thank you very much in advance.
>
> Best regards,
> Ruwan
>  Freesurfer-ruwan.zip
> 
>
>
>
>
> On Mon, Apr 22, 2019 at 10:38 PM Bruce Fischl 
> wrote:
>
>> Hi Ruwan
>>
>> have you looked at the data? Can you tell us what the acquisition
>> parameters are or send us a 3-plane image of the norm.mgz with the
>> lh.orig.nofix and rh.orig.nofix surfaces? The big defects are usually a
>> symptom of something else
>>
>> cheers
>> Bruce
>> On Mon, 22 Apr 2019, Pradeepa
>> Ruwan
>> wrote:
>>
>> >
>> > External Email - Use Caution
>> >
>> > Dear Freesurfer experts,
>> > I frequently get correcting defect error. It seems freezing the
>> recon-all after the defect and it
>> > won't run thereafter.
>> > Due to this error, I can not use most of the data for connectome
>> analysis.
>> > Can you please tell me how to get rid of this?
>> >
>> > I have attached a picture FYI.
>> >
>> > Best regards,
>> > Ruwan
>> >
>> > On Mon, Apr 22, 2019 at 11:10 AM Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu> wrote:
>> >   sorry, I've been traveling
>> >   On Mon, 22 Apr 2019, Abby tang wrote:
>> >
>> >   >
>> >   > External Email - Use Caution
>> >   >
>> >   > Hi BruceI did't get your reply message  yet. I have send the
>> subject file to you.
>> >   Could you give me
>> >   > your advises?
>> >   > Thank you for your help.
>> >   > Abby
>> >   >
>> >   > Abby tang  于2019年4月19日周五 上午8:32写道：
>> >   >   Hello，BruceI attached my subjects. Please help me.
>> >   > Thank you.
>> >   > Abby
>> >   > [icon_10_generic_list.png]  2851A_T1_w4.nii[IMAGE]
>> >   >
>> >   > Bruce Fischl  于2019年4月18日周四
>> 下午10:53写道：
>> >   >   Hi Abby
>> >   >
>> >   >   it's hard to tell from the image, but it looks like there
>> is a big I/S
>> >   >   bias field as well as large amounts of pathology.
>> >   >
>> >   >   If you upload the subject to our ftp site we will take a
>> look
>> >   >
>> >   >   cheers
>> >   >   Bruce
>> >   >   On Thu, 18 Apr
>> >   >   2019, Abby
>> >   >   tang wrote:
>> >   >
>> >   >   >
>> >   >   > External Email - Use Caution
>> >   >   >
>> >   >   > Hello FreeSurfer Developers,
>> >   >   >
>> >   >   > I'm attempting to recon_all my subjects which is .nii
>> file. But I usually meet
>> >   >   this error.
>> >   >   >
>> >   >   > CORRECTING DEFECT 0 (vertices=67, convex hull=73,
>> v0=950)
>> >   >   > After retessellation of defect 0 (v0=950), euler #=20
>> (87340,255044,167724) :
>> >   >   difference with theory
>> >   >   >  (-32) = -52
>> >   >   >
>> >   >   > CORRECTING DEFECT 1 (vertices=46367, convex hull=8524,
>> v0=962)
>> >   >   > Segmentation fault (core dumped)
>> >   >   > Linux abby-virtual-machine 4.15.0-47-generic #50-Ubuntu
>> SMP Wed Mar 13
>> >   10:44:52
>> >   >   UTC 2019 x86_64 x86_
>> >   >   > 64 x86_64 GNU/Linux
>> >   >   >
>> >   >   > recon-all -s 2851A_T1_w4 exited with ERRORS at Thu Apr
>> 18 20:25:16 CST 2019
>> >   >   >
>> >   >   > To report a problem, see
>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> >   >   >
>> >   >   > I check files in blow command and attached picture.
>> >   >   >
>> >   >   > freeview -v 2851A_T1_w4/mri/norm.mgz -f
>> 2851A_T1_w4/surf/lh.orig.nofix
>> >   >   2851A_T1_w4/surf/lh.inflated.
>> >   >   > nofix
>> >   >   >
>> >   >   > almost all of subjects go wrong. I need your help.
>> >   >   >
>> >   >   > please give some advises with program statements in
>> detail.
>> >   >   >
>> >   >   > I really appreciate your help
>> >   >   >
>> >   >   > 1) FreeSurfer version:
>> freesurfer-linux-centos7_x86_64-dev.tar.gz
>> >   >   > 2) Platform: ubuntu 18
>> >   >   > 3) recon-all.log:see attached
>> >   >   >
>> >   >   >___
>> >   >   Freesurfer mailing list
>> >   >   Freesurfer@nmr.mgh.harvard.edu
>> >   >
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >   >
>> >   >
>> >   >___
>> 

Re: [Freesurfer] CORRECTING DEFECT 1 problem

[Pradeepa Ruwan]

External Email - Use Caution

Dear Prof.Bruce,

I am sending my raw data and the images that you requested to send.
I have two datasets that I got trouble with.
I appreciate if you can take a look at this data.
Thank you very much in advance.

Best regards,
Ruwan
 Freesurfer-ruwan.zip





On Mon, Apr 22, 2019 at 10:38 PM Bruce Fischl 
wrote:

> Hi Ruwan
>
> have you looked at the data? Can you tell us what the acquisition
> parameters are or send us a 3-plane image of the norm.mgz with the
> lh.orig.nofix and rh.orig.nofix surfaces? The big defects are usually a
> symptom of something else
>
> cheers
> Bruce
> On Mon, 22 Apr 2019, Pradeepa
> Ruwan
> wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Freesurfer experts,
> > I frequently get correcting defect error. It seems freezing the
> recon-all after the defect and it
> > won't run thereafter.
> > Due to this error, I can not use most of the data for connectome
> analysis.
> > Can you please tell me how to get rid of this?
> >
> > I have attached a picture FYI.
> >
> > Best regards,
> > Ruwan
> >
> > On Mon, Apr 22, 2019 at 11:10 AM Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> >   sorry, I've been traveling
> >   On Mon, 22 Apr 2019, Abby tang wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > Hi BruceI did't get your reply message  yet. I have send the
> subject file to you.
> >   Could you give me
> >   > your advises?
> >   > Thank you for your help.
> >   > Abby
> >   >
> >   > Abby tang  于2019年4月19日周五 上午8:32写道：
> >   >   Hello，BruceI attached my subjects. Please help me.
> >   > Thank you.
> >   > Abby
> >   > [icon_10_generic_list.png]  2851A_T1_w4.nii[IMAGE]
> >   >
> >   > Bruce Fischl  于2019年4月18日周四
> 下午10:53写道：
> >   >   Hi Abby
> >   >
> >   >   it's hard to tell from the image, but it looks like there
> is a big I/S
> >   >   bias field as well as large amounts of pathology.
> >   >
> >   >   If you upload the subject to our ftp site we will take a
> look
> >   >
> >   >   cheers
> >   >   Bruce
> >   >   On Thu, 18 Apr
> >   >   2019, Abby
> >   >   tang wrote:
> >   >
> >   >   >
> >   >   > External Email - Use Caution
> >   >   >
> >   >   > Hello FreeSurfer Developers,
> >   >   >
> >   >   > I'm attempting to recon_all my subjects which is .nii
> file. But I usually meet
> >   >   this error.
> >   >   >
> >   >   > CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950)
> >   >   > After retessellation of defect 0 (v0=950), euler #=20
> (87340,255044,167724) :
> >   >   difference with theory
> >   >   >  (-32) = -52
> >   >   >
> >   >   > CORRECTING DEFECT 1 (vertices=46367, convex hull=8524,
> v0=962)
> >   >   > Segmentation fault (core dumped)
> >   >   > Linux abby-virtual-machine 4.15.0-47-generic #50-Ubuntu
> SMP Wed Mar 13
> >   10:44:52
> >   >   UTC 2019 x86_64 x86_
> >   >   > 64 x86_64 GNU/Linux
> >   >   >
> >   >   > recon-all -s 2851A_T1_w4 exited with ERRORS at Thu Apr
> 18 20:25:16 CST 2019
> >   >   >
> >   >   > To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >   >   >
> >   >   > I check files in blow command and attached picture.
> >   >   >
> >   >   > freeview -v 2851A_T1_w4/mri/norm.mgz -f
> 2851A_T1_w4/surf/lh.orig.nofix
> >   >   2851A_T1_w4/surf/lh.inflated.
> >   >   > nofix
> >   >   >
> >   >   > almost all of subjects go wrong. I need your help.
> >   >   >
> >   >   > please give some advises with program statements in
> detail.
> >   >   >
> >   >   > I really appreciate your help
> >   >   >
> >   >   > 1) FreeSurfer version:
> freesurfer-linux-centos7_x86_64-dev.tar.gz
> >   >   > 2) Platform: ubuntu 18
> >   >   > 3) recon-all.log:see attached
> >   >   >
> >   >   >___
> >   >   Freesurfer mailing list
> >   >   Freesurfer@nmr.mgh.harvard.edu
> >   >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >   >
> >   >
> >   >___
> >   Freesurfer mailing list
> >   Freesurfer@nmr.mgh.harvard.edu
> >   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] CORRECTING DEFECT 1 problem

[Bruce Fischl]

Hi Ruwan

have you looked at the data? Can you tell us what the acquisition 
parameters are or send us a 3-plane image of the norm.mgz with the 
lh.orig.nofix and rh.orig.nofix surfaces? The big defects are usually a 
symptom of something else


cheers
Bruce
On Mon, 22 Apr 2019, Pradeepa 
Ruwan 
wrote:




External Email - Use Caution

Dear Freesurfer experts,
I frequently get correcting defect error. It seems freezing the recon-all after 
the defect and it
won't run thereafter.
Due to this error, I can not use most of the data for connectome analysis.
Can you please tell me how to get rid of this?

I have attached a picture FYI.

Best regards,
Ruwan

On Mon, Apr 22, 2019 at 11:10 AM Bruce Fischl  
wrote:
  sorry, I've been traveling
  On Mon, 22 Apr 2019, Abby tang wrote:

  >
  > External Email - Use Caution
  >
  > Hi BruceI did't get your reply message  yet. I have send the subject 
file to you.
  Could you give me
  > your advises?
  > Thank you for your help.
  > Abby
  >
  > Abby tang  于2019年4月19日周五 上午8:32写道：
  >       Hello，BruceI attached my subjects. Please help me.
  > Thank you.
  > Abby
  > [icon_10_generic_list.png]  2851A_T1_w4.nii[IMAGE]
  >
  > Bruce Fischl  于2019年4月18日周四 下午10:53写道：
  >       Hi Abby
  >
  >       it's hard to tell from the image, but it looks like there is a 
big I/S
  >       bias field as well as large amounts of pathology.
  >
  >       If you upload the subject to our ftp site we will take a look
  >
  >       cheers
  >       Bruce
  >       On Thu, 18 Apr
  >       2019, Abby
  >       tang wrote:
  >
  >       >
  >       > External Email - Use Caution
  >       >
  >       > Hello FreeSurfer Developers,
  >       >
  >       > I'm attempting to recon_all my subjects which is .nii file. But 
I usually meet
  >       this error.
  >       >
  >       > CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950)
  >       > After retessellation of defect 0 (v0=950), euler #=20 
(87340,255044,167724) :
  >       difference with theory
  >       >  (-32) = -52
  >       >
  >       > CORRECTING DEFECT 1 (vertices=46367, convex hull=8524, v0=962)
  >       > Segmentation fault (core dumped)
  >       > Linux abby-virtual-machine 4.15.0-47-generic #50-Ubuntu SMP Wed 
Mar 13
  10:44:52
  >       UTC 2019 x86_64 x86_
  >       > 64 x86_64 GNU/Linux
  >       >
  >       > recon-all -s 2851A_T1_w4 exited with ERRORS at Thu Apr 18 
20:25:16 CST 2019
  >       >
  >       > To report a problem, see 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
  >       >
  >       > I check files in blow command and attached picture.
  >       >
  >       > freeview -v 2851A_T1_w4/mri/norm.mgz -f 
2851A_T1_w4/surf/lh.orig.nofix
  >       2851A_T1_w4/surf/lh.inflated.
  >       > nofix
  >       >
  >       > almost all of subjects go wrong. I need your help.
  >       >
  >       > please give some advises with program statements in detail.
  >       >
  >       > I really appreciate your help
  >       >
  >       > 1) FreeSurfer version: 
freesurfer-linux-centos7_x86_64-dev.tar.gz
  >       > 2) Platform: ubuntu 18
  >       > 3) recon-all.log:see attached
  >       >
  >       >___
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  >
  >
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Re: [Freesurfer] CORRECTING DEFECT 1 problem

[Pradeepa Ruwan]

External Email - Use Caution

Dear Freesurfer experts,

I frequently get correcting defect error. It seems freezing the recon-all
after the defect and it won't run thereafter.
Due to this error, I can not use most of the data for connectome analysis.
Can you please tell me how to get rid of this?

I have attached a picture FYI.

Best regards,
Ruwan

On Mon, Apr 22, 2019 at 11:10 AM Bruce Fischl 
wrote:

> sorry, I've been traveling
> On Mon, 22 Apr 2019, Abby tang wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi BruceI did't get your reply message  yet. I have send the subject
> file to you. Could you give me
> > your advises?
> > Thank you for your help.
> > Abby
> >
> > Abby tang  于2019年4月19日周五 上午8:32写道：
> >   Hello，BruceI attached my subjects. Please help me.
> > Thank you.
> > Abby
> > [icon_10_generic_list.png]  2851A_T1_w4.nii[IMAGE]
> >
> > Bruce Fischl  于2019年4月18日周四 下午10:53写道：
> >   Hi Abby
> >
> >   it's hard to tell from the image, but it looks like there is a big
> I/S
> >   bias field as well as large amounts of pathology.
> >
> >   If you upload the subject to our ftp site we will take a look
> >
> >   cheers
> >   Bruce
> >   On Thu, 18 Apr
> >   2019, Abby
> >   tang wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > Hello FreeSurfer Developers,
> >   >
> >   > I'm attempting to recon_all my subjects which is .nii file. But
> I usually meet
> >   this error.
> >   >
> >   > CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950)
> >   > After retessellation of defect 0 (v0=950), euler #=20
> (87340,255044,167724) :
> >   difference with theory
> >   >  (-32) = -52
> >   >
> >   > CORRECTING DEFECT 1 (vertices=46367, convex hull=8524, v0=962)
> >   > Segmentation fault (core dumped)
> >   > Linux abby-virtual-machine 4.15.0-47-generic #50-Ubuntu SMP Wed
> Mar 13 10:44:52
> >   UTC 2019 x86_64 x86_
> >   > 64 x86_64 GNU/Linux
> >   >
> >   > recon-all -s 2851A_T1_w4 exited with ERRORS at Thu Apr 18
> 20:25:16 CST 2019
> >   >
> >   > To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >   >
> >   > I check files in blow command and attached picture.
> >   >
> >   > freeview -v 2851A_T1_w4/mri/norm.mgz -f
> 2851A_T1_w4/surf/lh.orig.nofix
> >   2851A_T1_w4/surf/lh.inflated.
> >   > nofix
> >   >
> >   > almost all of subjects go wrong. I need your help.
> >   >
> >   > please give some advises with program statements in detail.
> >   >
> >   > I really appreciate your help
> >   >
> >   > 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev.tar.gz
> >   > 2) Platform: ubuntu 18
> >   > 3) recon-all.log:see attached
> >   >
> >   >___
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> >   Freesurfer@nmr.mgh.harvard.edu
> >   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >___
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Re: [Freesurfer] CORRECTING DEFECT 1 problem

[Bruce Fischl]

sorry, I've been traveling
On Mon, 22 Apr 2019, Abby tang wrote:



External Email - Use Caution

Hi BruceI did't get your reply message  yet. I have send the subject file to 
you. Could you give me
your advises?
Thank you for your help.
Abby

Abby tang  于2019年4月19日周五 上午8:32写道：
  Hello，BruceI attached my subjects. Please help me.
Thank you.
Abby
[icon_10_generic_list.png]  2851A_T1_w4.nii[IMAGE]

Bruce Fischl  于2019年4月18日周四 下午10:53写道：
  Hi Abby

  it's hard to tell from the image, but it looks like there is a big I/S
  bias field as well as large amounts of pathology.

  If you upload the subject to our ftp site we will take a look

  cheers
  Bruce
  On Thu, 18 Apr
  2019, Abby
  tang wrote:

  >
  > External Email - Use Caution
  >
  > Hello FreeSurfer Developers,
  >
  > I'm attempting to recon_all my subjects which is .nii file. But I 
usually meet
  this error.
  >
  > CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950)
  > After retessellation of defect 0 (v0=950), euler #=20 
(87340,255044,167724) :
  difference with theory
  >  (-32) = -52
  >
  > CORRECTING DEFECT 1 (vertices=46367, convex hull=8524, v0=962)
  > Segmentation fault (core dumped)
  > Linux abby-virtual-machine 4.15.0-47-generic #50-Ubuntu SMP Wed Mar 13 
10:44:52
  UTC 2019 x86_64 x86_
  > 64 x86_64 GNU/Linux
  >
  > recon-all -s 2851A_T1_w4 exited with ERRORS at Thu Apr 18 20:25:16 CST 
2019
  >
  > To report a problem, see 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
  >
  > I check files in blow command and attached picture.
  >
  > freeview -v 2851A_T1_w4/mri/norm.mgz -f 2851A_T1_w4/surf/lh.orig.nofix
  2851A_T1_w4/surf/lh.inflated.
  > nofix
  >
  > almost all of subjects go wrong. I need your help.
  >
  > please give some advises with program statements in detail.
  >
  > I really appreciate your help
  >
  > 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev.tar.gz
  > 2) Platform: ubuntu 18
  > 3) recon-all.log:see attached
  >
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Re: [Freesurfer] CORRECTING DEFECT 1 problem

[Abby tang]

External Email - Use Caution

Hi Bruce
I did't get your reply message  yet. I have send the subject file to you.
Could you give me your advises?
Thank you for your help.
Abby

Abby tang  于2019年4月19日周五 上午8:32写道：

> Hello，Bruce
> I attached my subjects. Please help me.
> Thank you.
> Abby
>  2851A_T1_w4.nii
> 
>
> Bruce Fischl  于2019年4月18日周四 下午10:53写道：
>
>> Hi Abby
>>
>> it's hard to tell from the image, but it looks like there is a big I/S
>> bias field as well as large amounts of pathology.
>>
>> If you upload the subject to our ftp site we will take a look
>>
>> cheers
>> Bruce
>> On Thu, 18 Apr
>> 2019, Abby
>> tang wrote:
>>
>> >
>> > External Email - Use Caution
>> >
>> > Hello FreeSurfer Developers,
>> >
>> > I'm attempting to recon_all my subjects which is .nii file. But I
>> usually meet this error.
>> >
>> > CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950)
>> > After retessellation of defect 0 (v0=950), euler #=20
>> (87340,255044,167724) : difference with theory
>> >  (-32) = -52
>> >
>> > CORRECTING DEFECT 1 (vertices=46367, convex hull=8524, v0=962)
>> > Segmentation fault (core dumped)
>> > Linux abby-virtual-machine 4.15.0-47-generic #50-Ubuntu SMP Wed Mar 13
>> 10:44:52 UTC 2019 x86_64 x86_
>> > 64 x86_64 GNU/Linux
>> >
>> > recon-all -s 2851A_T1_w4 exited with ERRORS at Thu Apr 18 20:25:16 CST
>> 2019
>> >
>> > To report a problem, see
>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> >
>> > I check files in blow command and attached picture.
>> >
>> > freeview -v 2851A_T1_w4/mri/norm.mgz -f 2851A_T1_w4/surf/lh.orig.nofix
>> 2851A_T1_w4/surf/lh.inflated.
>> > nofix
>> >
>> > almost all of subjects go wrong. I need your help.
>> >
>> > please give some advises with program statements in detail.
>> >
>> > I really appreciate your help
>> >
>> > 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev.tar.gz
>> > 2) Platform: ubuntu 18
>> > 3) recon-all.log:see attached
>> >
>> >___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] CORRECTING DEFECT 1 problem

[Abby tang]

External Email - Use Caution

Hello，Bruce
I attached my subjects. Please help me.
Thank you.
Abby
 2851A_T1_w4.nii


Bruce Fischl  于2019年4月18日周四 下午10:53写道：

> Hi Abby
>
> it's hard to tell from the image, but it looks like there is a big I/S
> bias field as well as large amounts of pathology.
>
> If you upload the subject to our ftp site we will take a look
>
> cheers
> Bruce
> On Thu, 18 Apr
> 2019, Abby
> tang wrote:
>
> >
> > External Email - Use Caution
> >
> > Hello FreeSurfer Developers,
> >
> > I'm attempting to recon_all my subjects which is .nii file. But I
> usually meet this error.
> >
> > CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950)
> > After retessellation of defect 0 (v0=950), euler #=20
> (87340,255044,167724) : difference with theory
> >  (-32) = -52
> >
> > CORRECTING DEFECT 1 (vertices=46367, convex hull=8524, v0=962)
> > Segmentation fault (core dumped)
> > Linux abby-virtual-machine 4.15.0-47-generic #50-Ubuntu SMP Wed Mar 13
> 10:44:52 UTC 2019 x86_64 x86_
> > 64 x86_64 GNU/Linux
> >
> > recon-all -s 2851A_T1_w4 exited with ERRORS at Thu Apr 18 20:25:16 CST
> 2019
> >
> > To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >
> > I check files in blow command and attached picture.
> >
> > freeview -v 2851A_T1_w4/mri/norm.mgz -f 2851A_T1_w4/surf/lh.orig.nofix
> 2851A_T1_w4/surf/lh.inflated.
> > nofix
> >
> > almost all of subjects go wrong. I need your help.
> >
> > please give some advises with program statements in detail.
> >
> > I really appreciate your help
> >
> > 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev.tar.gz
> > 2) Platform: ubuntu 18
> > 3) recon-all.log:see attached
> >
> >___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] CORRECTING DEFECT 1 problem

[Bruce Fischl]

Hi Abby

it's hard to tell from the image, but it looks like there is a big I/S 
bias field as well as large amounts of pathology.


If you upload the subject to our ftp site we will take a look

cheers
Bruce
On Thu, 18 Apr 
2019, Abby 
tang wrote:




External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to recon_all my subjects which is .nii file. But I usually meet 
this error.

CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950)
After retessellation of defect 0 (v0=950), euler #=20 (87340,255044,167724) : 
difference with theory
 (-32) = -52 


CORRECTING DEFECT 1 (vertices=46367, convex hull=8524, v0=962)
Segmentation fault (core dumped)
Linux abby-virtual-machine 4.15.0-47-generic #50-Ubuntu SMP Wed Mar 13 10:44:52 
UTC 2019 x86_64 x86_
64 x86_64 GNU/Linux

recon-all -s 2851A_T1_w4 exited with ERRORS at Thu Apr 18 20:25:16 CST 2019

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

I check files in blow command and attached picture. 


freeview -v 2851A_T1_w4/mri/norm.mgz -f 2851A_T1_w4/surf/lh.orig.nofix 
2851A_T1_w4/surf/lh.inflated.
nofix

almost all of subjects go wrong. I need your help. 


please give some advises with program statements in detail.

I really appreciate your help

1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev.tar.gz
2) Platform: ubuntu 18
3) recon-all.log:see attached

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Re: [Freesurfer] Correcting Defect error

[Greve, Douglas N.,Ph.D.]

That looks pretty awful. You should check the orig.nofix surfaces. I bet 
your data is extremely noisy

On 2/28/19 11:37 AM, Miguel Ángel Rivas Fernández wrote:
>
> External Email - Use Caution
>
>
> Dear Freesurfer devs,
>
>
> I ran the recon-all in one subject and and this process was stopped in 
> the topology correction. In particular during the "CORRECTING DEFECT 
> 36 (vertices=19847, convex hull=5892, v0=94733)". I reviewed the 
> lh.inflated.nofix and the lh.orig.nofix files in Freeview and I 
> noticed that the this error would be located in the lh.inflated.nofix 
> file. How can I fix this problem?
>
> I sent to you a screenshot of the lh.inflated.nofix file as well as 
> the recon-all.log file if you want take a look.
>
>
>
> Best regards,
>
> -- 
> *Miguel Ángel Rivas Fernández*
>
> ___
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Re: [Freesurfer] Correcting defect

[Douglas Greve]

This is not necessarily a problem. Do the surfaces look ok? You can 
always check the defect fixing using the defect-seg script. Run it with 
--help to get more info



On 12/27/17 12:28 AM, shi yao wang wrote:

Dear FS experts,
I am running FS 6.0. There is a error message like this.

Inline image 1

are there any way to modify it?

thanks
Lawrence

Radiology Department
Emory University


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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
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Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

[Diamond, Bram Ryder]

Hi Martin,


I will have to defer to Bruce or Doug regarding the validity of analyzing 
FreeSurfer output for your subject - although I would not recommend any 
analysis on the current state of your subject's surfaces.  After glancing at 
your data, I have a few recommendations:


  1.  You seem to be using an excessive number of control points.  Control 
points are designed for diffuse intensity normalize - using too many control 
points is unnecessary and possibly counterproductive.  See 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPointsV6.0?highlight=%28control%29%7C%28point%29
 for more information on control points.
  2.  I've noticed that your brainmask.mgz is missing a large portion of your 
subject's cerebellum.  This most likely caused some issues down the recon-all 
pipeline so you should address this issue first.  You can change the watershed 
value to adjust the brain extraction.  See 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFixV6.0 for 
information of fixing a bad skull strip.
  3.  Since the wm.mgz has done such a poor job of identifying white matter, I 
would suggest directly editing the wm.mgz.  Of course, only edit the wm.mgz 
after first attempting to use (fewer) control points on a better skull-stripped 
brainmask.mgz.  See 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0 for 
information on editing the wm.mgz.


Best,

Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Loeffler, Martin 
<martin.loeff...@zi-mannheim.de>
Sent: Saturday, December 23, 2017 4:26:15 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst


Dear Bruce,

Dear Bram,



Thanks a lot for having a look. Unfortunately the left hemisphere is equally 
important as the right one for our question of interest. With a lot of patience 
the recon-all has finished and the result looks surprisingly ok. I have 
additionally re-run it (recon-all -autorecon2-cp -autorecon3 -s Case) after 
setting control points to correct errors in the wm.mgz. Some errors were 
corrected, but not all. Next I would like to correct the surfaces.

My questions:

-  I know that recon-all is not designed for such a subject. But is 
there any argument against continuing the analysis now?

-  What can I do for those errors where the wm.mgz is still false, 
despite control points?

I have uploaded the respective files.



Best,

Martin





Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Diamond, Bram 
Ryder
Gesendet: Mittwoch, 13. Dezember 2017 23:23
An: Freesurfer support list
Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst



Hi Martin,



We've taken a look at the scans you uploaded, and unfortunately it won't be 
possible to run the standard recon-all on your subject.  Recon-all is not 
designed to work on scans with such large lesions.  If you are interested, 
there may be a way to generate a reasonable model of the right hemisphere.



Best,

Bram



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Loeffler, Martin 
<martin.loeff...@zi-mannheim.de<mailto:martin.loeff...@zi-mannheim.de>>
Sent: Tuesday, December 12, 2017 11:57:36 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst



Dear Bruce,
I have uploaded the respective files. If there is something missing let me know.
Cheers,
Martin


-Ursprüngliche Nachricht-
Von: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Dienstag, 12. Dezember 2017 16:35
An: Freesurfer support list
Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Hi Martin

we are happy to take a look, but can't really tell much from a screenshot.
Feel free to upload the subject to our ftp site if you want us to help

cheers
Bruce

On Tue, 12 Dec 2017, Loeffler, Martin wrote:

> Dear Bruce,
>
> thanks for the quick reply! You are right, of course. I do find errors in 
> lh.inflated.nofix.
> I have attached a screenshot of the biggest errors I found..
> Can you maybe guide me a little how to fix the issue? Do I just cancel the 
> running recon-all process, and set control points and run again? Investing 
> some time in manual editing would be fine as it's a case study...
>
> Thanks for your help,
> Martin
>
>
> 
> Von: 
> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> [freesurfer-boun...@nmr.mgh.harv

[Freesurfer] Correcting defect

[shi yao wang]

Dear FS experts,
I am running FS 6.0. There is a error message like this.

[image: Inline image 1]

are there any way to modify it?

thanks
Lawrence

Radiology Department
Emory University
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

[Loeffler, Martin]

Dear Bruce,
Dear Bram,

Thanks a lot for having a look. Unfortunately the left hemisphere is equally 
important as the right one for our question of interest. With a lot of patience 
the recon-all has finished and the result looks surprisingly ok. I have 
additionally re-run it (recon-all -autorecon2-cp -autorecon3 -s Case) after 
setting control points to correct errors in the wm.mgz. Some errors were 
corrected, but not all. Next I would like to correct the surfaces.
My questions:

-  I know that recon-all is not designed for such a subject. But is 
there any argument against continuing the analysis now?

-  What can I do for those errors where the wm.mgz is still false, 
despite control points?
I have uploaded the respective files.

Best,
Martin


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Diamond, Bram 
Ryder
Gesendet: Mittwoch, 13. Dezember 2017 23:23
An: Freesurfer support list
Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst


Hi Martin,



We've taken a look at the scans you uploaded, and unfortunately it won't be 
possible to run the standard recon-all on your subject.  Recon-all is not 
designed to work on scans with such large lesions.  If you are interested, 
there may be a way to generate a reasonable model of the right hemisphere.



Best,

Bram


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Loeffler, Martin 
<martin.loeff...@zi-mannheim.de<mailto:martin.loeff...@zi-mannheim.de>>
Sent: Tuesday, December 12, 2017 11:57:36 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Dear Bruce,
I have uploaded the respective files. If there is something missing let me know.
Cheers,
Martin


-Ursprüngliche Nachricht-
Von: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Dienstag, 12. Dezember 2017 16:35
An: Freesurfer support list
Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Hi Martin

we are happy to take a look, but can't really tell much from a screenshot.
Feel free to upload the subject to our ftp site if you want us to help

cheers
Bruce

On Tue, 12 Dec 2017, Loeffler, Martin wrote:

> Dear Bruce,
>
> thanks for the quick reply! You are right, of course. I do find errors in 
> lh.inflated.nofix.
> I have attached a screenshot of the biggest errors I found..
> Can you maybe guide me a little how to fix the issue? Do I just cancel the 
> running recon-all process, and set control points and run again? Investing 
> some time in manual editing would be fine as it's a case study...
>
> Thanks for your help,
> Martin
>
>
> 
> Von: 
> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> [freesurfer-boun...@nmr.mgh.harvard.edu] im Auftrag von
> Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Gesendet: Montag, 11. Dezember 2017 22:47
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
>
> Hi Martin
>
> a defect that large means that something big went wrong (skull or dura
> attached, etc...). Try looking at the ?h.orig.nofix and/or the
> ?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find
> defect 9
>
> cheers
> Bruce
>
>
> On Mon, 11 Dec 2017, Loeffler, Martin wrote:
>
>>
>> Dear FreeSurfer team,
>>
>>
>>
>> For a case report I'm running recon-all on a patient with a giant
>> arachnoid cyst in the left hemisphere. It gets stuck at this point (last 
>> message):
>>
>> CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849)
>>
>> XL defect detected...
>>
>> It is stuck here since a whole day now, so I'm not expecting it to
>> advance.
>>
>> Following this post:
>> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I 
>> looked at the wm.mgz, but did not find huge errors.
>>
>> Do you have any ideas what the problem might be or what I can do to work 
>> around it?
>>
>>
>>
>> Thanks,
>>
>> Martin
>>
>>
>>
>>
>>
>>
>>

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Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

[Diamond, Bram Ryder]

Hi Martin,


We've taken a look at the scans you uploaded, and unfortunately it won't be 
possible to run the standard recon-all on your subject.  Recon-all is not 
designed to work on scans with such large lesions.  If you are interested, 
there may be a way to generate a reasonable model of the right hemisphere.


Best,

Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Loeffler, Martin 
<martin.loeff...@zi-mannheim.de>
Sent: Tuesday, December 12, 2017 11:57:36 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Dear Bruce,
I have uploaded the respective files. If there is something missing let me know.
Cheers,
Martin


-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Dienstag, 12. Dezember 2017 16:35
An: Freesurfer support list
Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Hi Martin

we are happy to take a look, but can't really tell much from a screenshot.
Feel free to upload the subject to our ftp site if you want us to help

cheers
Bruce

On Tue, 12 Dec 2017, Loeffler, Martin wrote:

> Dear Bruce,
>
> thanks for the quick reply! You are right, of course. I do find errors in 
> lh.inflated.nofix.
> I have attached a screenshot of the biggest errors I found..
> Can you maybe guide me a little how to fix the issue? Do I just cancel the 
> running recon-all process, and set control points and run again? Investing 
> some time in manual editing would be fine as it's a case study...
>
> Thanks for your help,
> Martin
>
>
> 
> Von: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] im Auftrag von
> Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Gesendet: Montag, 11. Dezember 2017 22:47
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
>
> Hi Martin
>
> a defect that large means that something big went wrong (skull or dura
> attached, etc...). Try looking at the ?h.orig.nofix and/or the
> ?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find
> defect 9
>
> cheers
> Bruce
>
>
> On Mon, 11 Dec 2017, Loeffler, Martin wrote:
>
>>
>> Dear FreeSurfer team,
>>
>>
>>
>> For a case report I'm running recon-all on a patient with a giant
>> arachnoid cyst in the left hemisphere. It gets stuck at this point (last 
>> message):
>>
>> CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849)
>>
>> XL defect detected...
>>
>> It is stuck here since a whole day now, so I'm not expecting it to
>> advance.
>>
>> Following this post:
>> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I 
>> looked at the wm.mgz, but did not find huge errors.
>>
>> Do you have any ideas what the problem might be or what I can do to work 
>> around it?
>>
>>
>>
>> Thanks,
>>
>> Martin
>>
>>
>>
>>
>>
>>
>>

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Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

[Loeffler, Martin]

Dear Bruce,
I have uploaded the respective files. If there is something missing let me know.
Cheers,
Martin


-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Dienstag, 12. Dezember 2017 16:35
An: Freesurfer support list
Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Hi Martin

we are happy to take a look, but can't really tell much from a screenshot. 
Feel free to upload the subject to our ftp site if you want us to help

cheers
Bruce

On Tue, 12 Dec 2017, Loeffler, Martin wrote:

> Dear Bruce,
>
> thanks for the quick reply! You are right, of course. I do find errors in 
> lh.inflated.nofix.
> I have attached a screenshot of the biggest errors I found..
> Can you maybe guide me a little how to fix the issue? Do I just cancel the 
> running recon-all process, and set control points and run again? Investing 
> some time in manual editing would be fine as it's a case study...
>
> Thanks for your help,
> Martin
>
>
> 
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] im Auftrag von 
> Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Gesendet: Montag, 11. Dezember 2017 22:47
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
>
> Hi Martin
>
> a defect that large means that something big went wrong (skull or dura 
> attached, etc...). Try looking at the ?h.orig.nofix and/or the 
> ?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find 
> defect 9
>
> cheers
> Bruce
>
>
> On Mon, 11 Dec 2017, Loeffler, Martin wrote:
>
>>
>> Dear FreeSurfer team,
>>
>>
>>
>> For a case report I'm running recon-all on a patient with a giant 
>> arachnoid cyst in the left hemisphere. It gets stuck at this point (last 
>> message):
>>
>> CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849)
>>
>> XL defect detected...
>>
>> It is stuck here since a whole day now, so I'm not expecting it to 
>> advance.
>>
>> Following this post: 
>> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I 
>> looked at the wm.mgz, but did not find huge errors.
>>
>> Do you have any ideas what the problem might be or what I can do to work 
>> around it?
>>
>>
>>
>> Thanks,
>>
>> Martin
>>
>>
>>
>>
>>
>>
>>

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Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

[Bruce Fischl]

Hi Martin

we are happy to take a look, but can't really tell much from a screenshot. 
Feel free to upload the subject to our ftp site if you want us to help


cheers
Bruce

On Tue, 12 Dec 2017, Loeffler, Martin wrote:


Dear Bruce,

thanks for the quick reply! You are right, of course. I do find errors in 
lh.inflated.nofix.
I have attached a screenshot of the biggest errors I found..
Can you maybe guide me a little how to fix the issue? Do I just cancel the 
running recon-all process, and set control points and run again? Investing some 
time in manual editing would be fine as it's a case study...

Thanks for your help,
Martin



Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] im Auftrag von Bruce 
Fischl [fis...@nmr.mgh.harvard.edu]
Gesendet: Montag, 11. Dezember 2017 22:47
An: Freesurfer support list
Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Hi Martin

a defect that large means that something big went wrong (skull or
dura attached, etc...). Try looking at the ?h.orig.nofix and/or the
?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find
defect 9

cheers
Bruce


On Mon, 11 Dec 2017, Loeffler, Martin wrote:



Dear FreeSurfer team,



For a case report I’m running recon-all on a patient with a giant arachnoid 
cyst in the left
hemisphere. It gets stuck at this point (last message):

CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849)

XL defect detected...

It is stuck here since a whole day now, so I’m not expecting it to advance…

Following this post: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I
looked at the wm.mgz, but did not find huge errors.

Do you have any ideas what the problem might be or what I can do to work around 
it?



Thanks,

Martin






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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

[Loeffler, Martin]

Dear Bruce,

thanks for the quick reply! You are right, of course. I do find errors in 
lh.inflated.nofix.
I have attached a screenshot of the biggest errors I found..
Can you maybe guide me a little how to fix the issue? Do I just cancel the 
running recon-all process, and set control points and run again? Investing some 
time in manual editing would be fine as it's a case study...

Thanks for your help,
Martin



Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] im Auftrag von Bruce 
Fischl [fis...@nmr.mgh.harvard.edu]
Gesendet: Montag, 11. Dezember 2017 22:47
An: Freesurfer support list
Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Hi Martin

a defect that large means that something big went wrong (skull or
dura attached, etc...). Try looking at the ?h.orig.nofix and/or the
?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find
defect 9

cheers
Bruce


On Mon, 11 Dec 2017, Loeffler, Martin wrote:

>
> Dear FreeSurfer team,
>
>
>
> For a case report I’m running recon-all on a patient with a giant arachnoid 
> cyst in the left
> hemisphere. It gets stuck at this point (last message):
>
> CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849)
>
> XL defect detected...
>
> It is stuck here since a whole day now, so I’m not expecting it to advance…
>
> Following this post: 
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I
> looked at the wm.mgz, but did not find huge errors.
>
> Do you have any ideas what the problem might be or what I can do to work 
> around it?
>
>
>
> Thanks,
>
> Martin
>
>
>
>
>
>
>
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

[Bruce Fischl]

Hi Martin

a defect that large means that something big went wrong (skull or 
dura attached, etc...). Try looking at the ?h.orig.nofix and/or the 
?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find 
defect 9


cheers
Bruce


On Mon, 11 Dec 2017, Loeffler, Martin wrote:



Dear FreeSurfer team,

 

For a case report I’m running recon-all on a patient with a giant arachnoid 
cyst in the left
hemisphere. It gets stuck at this point (last message):

CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849)

XL defect detected...

It is stuck here since a whole day now, so I’m not expecting it to advance…

Following this post: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I
looked at the wm.mgz, but did not find huge errors.

Do you have any ideas what the problem might be or what I can do to work around 
it?

 

Thanks,

Martin

 

 


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[Freesurfer] CORRECTING DEFECT recon-all giant cyst

[Loeffler, Martin]

Dear FreeSurfer team,

For a case report I'm running recon-all on a patient with a giant arachnoid 
cyst in the left hemisphere. It gets stuck at this point (last message):
CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849)
XL defect detected...
It is stuck here since a whole day now, so I'm not expecting it to advance...
Following this post: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I 
looked at the wm.mgz, but did not find huge errors.
Do you have any ideas what the problem might be or what I can do to work around 
it?

Thanks,
Martin


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dispose of the e-mail.

Re: [Freesurfer] correcting defect

[Bruce Fischl]

Hi Meng

we can't diagnose either of these issues without more information and 
possibly some screen shots. The topology fixer will take a very long time 
if the initial surfaces have large defects. You can view these by 
visualizing the ?h.inflated.nofix and ?h.orig.nofix.


The -openmp flag works for us. Are you sure that you have mutliple threads 
available?


cheers
Bruce

On Thu, 14 Sep 2017, Meng Li wrote:


Hi all,

I tried to use FreeSurfer version 6.0.0 to process fifteen subjects, but half 
of the subjects was
stuck at the ‘Correcting Defect’ step. However, when I changed to FreeSurfer 
version 5.3.0, the
‘Correcting defect’ step finished successfully. Is it possibility that the 
unsuccessful ‘Correcting
Defect’ step is caused by the different versions of Freesurefer?

In addition, when I added the flag -parallel -openmp 30 based on the version 
6.0.0, the recon-all
–all runtime still need 20+ hours. It seems that the parallel processing did 
not reduce the
processing time. I wonder why the parallel processing did’t save time?

Any help would be greatly appreciated.

Meng




 


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[Freesurfer] correcting defect

[Meng Li]

Hi all,

I tried to use FreeSurfer version 6.0.0 to process fifteen subjects, but half 
of the subjects was stuck at the ‘Correcting Defect’ step. However, when I 
changed to FreeSurfer version 5.3.0, the ‘Correcting defect’ step finished 
successfully. Is it possibility that the unsuccessful ‘Correcting Defect’ step 
is caused by the different versions of Freesurefer?

In addition, when I added the flag -parallel -openmp 30 based on the version 
6.0.0, the recon-all –all runtime still need 20+ hours. It seems that the 
parallel processing did not reduce the processing time. I wonder why the 
parallel processing did’t save time?

Any help would be greatly appreciated.

Meng

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[Freesurfer] CORRECTING DEFECT

[maryam koochaki]

Hi Bruce,I am wondering if you saw my last email, about uploading my subject in 
your ftp server.I uploaded the subject  "test_emc_039.tar.gz".I appreciate any 
help.
Thank you, Maryam







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Re: [Freesurfer] CORRECTING DEFECT

[maryam koochaki]

Hi Bruce,Did you get my email regarding to the subject I upload in fft server?
Best,Maryam

 





Regards,Maryam Kouchakidivkolaei 

On Friday, June 3, 2016 10:16 PM, maryam koochaki 
 wrote:
 

 Hi Bruce,I already uploaded it.File name:  test_emc_039.tar.gz
Thanks,Maryam
 





Regards,Maryam Kouchakidivkolaei 

On Friday, June 3, 2016 9:35 PM, Bruce Fischl  
wrote:
 

 Hmmm, that sounds like a bug. If you upload the subject we will take a 
lookCheersBruce
On Jun 3, 2016, at 6:54 PM, maryam koochaki  wrote:


Dear freesurfer experts,I have a subject ending up with this error after 
recon-all.I tried to edit the aseg and run it, but it stuck at topological step.
CORRECTING DEFECT 79 (vertices=54196, convex hull=8490)
error in the retessellation 
normal vector of length zero at vertex 97187 with 0 faces
vertex 97187 has 0 face
No such file or directory
Linux cs-cbl-03 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s test_emc_039 exited with ERRORS .
Could you guide me how I can correct it.Thank you,Maryam 





Regards,Maryam Kouchakidivkolaei

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Re: [Freesurfer] CORRECTING DEFECT

[maryam koochaki]

Hi Bruce,I already uploaded it.File name:  test_emc_039.tar.gz
Thanks,Maryam
 





Regards,Maryam Kouchakidivkolaei 

On Friday, June 3, 2016 9:35 PM, Bruce Fischl  
wrote:
 

 Hmmm, that sounds like a bug. If you upload the subject we will take a 
lookCheersBruce
On Jun 3, 2016, at 6:54 PM, maryam koochaki  wrote:


Dear freesurfer experts,I have a subject ending up with this error after 
recon-all.I tried to edit the aseg and run it, but it stuck at topological step.
CORRECTING DEFECT 79 (vertices=54196, convex hull=8490)
error in the retessellation 
normal vector of length zero at vertex 97187 with 0 faces
vertex 97187 has 0 face
No such file or directory
Linux cs-cbl-03 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s test_emc_039 exited with ERRORS .
Could you guide me how I can correct it.Thank you,Maryam 





Regards,Maryam Kouchakidivkolaei

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Re: [Freesurfer] CORRECTING DEFECT

[Bruce Fischl]

Hmmm, that sounds like a bug. If you upload the subject we will take a look
Cheers
Bruce

> On Jun 3, 2016, at 6:54 PM, maryam koochaki  wrote:
> 
> Dear freesurfer experts,
> I have a subject ending up with this error after recon-all.
> I tried to edit the aseg and run it, but it stuck at topological step.
> 
> CORRECTING DEFECT 79 (vertices=54196, convex hull=8490)
> error in the retessellation 
> normal vector of length zero at vertex 97187 with 0 faces
> vertex 97187 has 0 face
> No such file or directory
> Linux cs-cbl-03 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 
> 2016 x86_64 x86_64 x86_64 GNU/Linux
> 
> recon-all -s test_emc_039 exited with ERRORS .
> 
> Could you guide me how I can correct it.
> Thank you,
> Maryam
>  
> 
> 
> 
> 
> 
> 
> Regards,
> Maryam Kouchakidivkolaei
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[Freesurfer] CORRECTING DEFECT

[maryam koochaki]

Dear freesurfer experts,I have a subject ending up with this error after 
recon-all.I tried to edit the aseg and run it, but it stuck at topological step.
CORRECTING DEFECT 79 (vertices=54196, convex hull=8490)
error in the retessellation 
normal vector of length zero at vertex 97187 with 0 faces
vertex 97187 has 0 face
No such file or directory
Linux cs-cbl-03 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s test_emc_039 exited with ERRORS .
Could you guide me how I can correct it.Thank you,Maryam 





Regards,Maryam Kouchakidivkolaei___
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Re: [Freesurfer] Correcting defect

[Katarina Trojacanec]

Hi Bruce,

I uploaded the subject dirs (base for TP1_4 and TP2_4, as well as the 
cross-sectionally processed time points for TP1, TP2, and TP4). In the 
meantime, one of them, template TP1_4 has finished with error. The other one 
(base TP2_4) is still running.

What do you suggest in this situation.

Sorry for the inconvenience.

Cheers.

Katarina Trojacanec, M.Sc.
Teaching and research assistant

Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia



From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl 
<fis...@nmr.mgh.harvard.edu>
Sent: Thursday, May 5, 2016 4:20:31 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correcting defect

Hi Katarina

if you want us to look you need to upload the entire subject dirs (tarred
and gzipped). TO visualize it, look at the inflated.nofix in freeview in 3D
mode and just see what the big defects look like. If you load the
orig.nofix at the same time you can goto a vertex in the big defect you see
on the inflated by typing its index into the info winwo for the orig.nofix.
This will be automated in v6

Bruce


On Thu, 5 May 2016, Katarina Trojacanec wrote:

> Thank you.
> I have uploaded the files (lh.inflated_TP_1_4.nofix and 
> lh.inflated_TP_2_4.nofix).
>
> What should I do as a next step?
>
> Cheers
> Katarina Trojacanec, M.Sc.
> Teaching and research assistant
>
> Faculty of Computer Science and Engineering
> Ss. Cyril and Methodius University - Skopje, Republic of Macedonia
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl 
> <fis...@nmr.mgh.harvard.edu>
> Sent: Wednesday, May 4, 2016 2:35 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Correcting defect
>
> sure. Or you can load the ?h.inflated.nofix and look at it - it should be
> obvious if there is a huge defect (you can also load the file
> ?h.defect_labels as an overlay on that surface and it will show you the
> segmentation of the defects)
>
> cheers
> Bruce
> On Wed, 4 May 2016, Katarina Trojacanec wrote:
>
>>
>> Dear FreeSurfer Team,
>>
>>
>> I have been trying to run creation of template with FreeSurfer. However,
>> for two cases for one patient (case 1: template based on TP1 and TP4, case
>> 2: template based on TP2 and TP4), the correcting defect step is running
>> too long. According to the information in the mail archive, the defects are
>> probably too big, and that is the reason for the long processing.
>>
>>
>> May I send you via ftp the subjects directories so you can help me to
>> proceed with this subject, because I am not able to figure out and correct
>> the problem? Should I send you the base directories in their current state
>> or the cross-sectionally processed time points as well?
>>
>>
>> Best Regards,
>>
>>
>> Katarina Trojacanec, M.Sc.
>> Teaching and research assistant
>>
>> Faculty of Computer Science and Engineering
>> Ss. Cyril and Methodius University - Skopje, Republic of Macedonia
>>
>>
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>
>
>
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Re: [Freesurfer] Correcting defect

[Bruce Fischl]

Hi Katarina

if you want us to look you need to upload the entire subject dirs (tarred 
and gzipped). TO visualize it, look at the inflated.nofix in freeview in 3D 
mode and just see what the big defects look like. If you load the 
orig.nofix at the same time you can goto a vertex in the big defect you see 
on the inflated by typing its index into the info winwo for the orig.nofix. 
This will be automated in v6

Bruce


On Thu, 5 May 2016, Katarina Trojacanec wrote:

> Thank you.
> I have uploaded the files (lh.inflated_TP_1_4.nofix and 
> lh.inflated_TP_2_4.nofix).
>
> What should I do as a next step?
>
> Cheers
> Katarina Trojacanec, M.Sc.
> Teaching and research assistant
>
> Faculty of Computer Science and Engineering
> Ss. Cyril and Methodius University - Skopje, Republic of Macedonia
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl 
> <fis...@nmr.mgh.harvard.edu>
> Sent: Wednesday, May 4, 2016 2:35 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Correcting defect
>
> sure. Or you can load the ?h.inflated.nofix and look at it - it should be
> obvious if there is a huge defect (you can also load the file
> ?h.defect_labels as an overlay on that surface and it will show you the
> segmentation of the defects)
>
> cheers
> Bruce
> On Wed, 4 May 2016, Katarina Trojacanec wrote:
>
>>
>> Dear FreeSurfer Team,
>>
>>
>> I have been trying to run creation of template with FreeSurfer. However,
>> for two cases for one patient (case 1: template based on TP1 and TP4, case
>> 2: template based on TP2 and TP4), the correcting defect step is running
>> too long. According to the information in the mail archive, the defects are
>> probably too big, and that is the reason for the long processing.
>>
>>
>> May I send you via ftp the subjects directories so you can help me to
>> proceed with this subject, because I am not able to figure out and correct
>> the problem? Should I send you the base directories in their current state
>> or the cross-sectionally processed time points as well?
>>
>>
>> Best Regards,
>>
>>
>> Katarina Trojacanec, M.Sc.
>> Teaching and research assistant
>>
>> Faculty of Computer Science and Engineering
>> Ss. Cyril and Methodius University - Skopje, Republic of Macedonia
>>
>>
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> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] Correcting defect

[Katarina Trojacanec]

Thank you.
I have uploaded the files (lh.inflated_TP_1_4.nofix and 
lh.inflated_TP_2_4.nofix). 

What should I do as a next step?

Cheers
Katarina Trojacanec, M.Sc.
Teaching and research assistant

Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia



From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl 
<fis...@nmr.mgh.harvard.edu>
Sent: Wednesday, May 4, 2016 2:35 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correcting defect

sure. Or you can load the ?h.inflated.nofix and look at it - it should be
obvious if there is a huge defect (you can also load the file
?h.defect_labels as an overlay on that surface and it will show you the
segmentation of the defects)

cheers
Bruce
On Wed, 4 May 2016, Katarina Trojacanec wrote:

>
> Dear FreeSurfer Team,
>
>
> I have been trying to run creation of template with FreeSurfer. However,
> for two cases for one patient (case 1: template based on TP1 and TP4, case
> 2: template based on TP2 and TP4), the correcting defect step is running
> too long. According to the information in the mail archive, the defects are
> probably too big, and that is the reason for the long processing.
>
>
> May I send you via ftp the subjects directories so you can help me to
> proceed with this subject, because I am not able to figure out and correct
> the problem? Should I send you the base directories in their current state
> or the cross-sectionally processed time points as well?
>
>
> Best Regards,
>
>
> Katarina Trojacanec, M.Sc.
> Teaching and research assistant
>
> Faculty of Computer Science and Engineering
> Ss. Cyril and Methodius University - Skopje, Republic of Macedonia
>
>
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Re: [Freesurfer] Correcting defect

[Bruce Fischl]

sure. Or you can load the ?h.inflated.nofix and look at it - it should be 
obvious if there is a huge defect (you can also load the file 
?h.defect_labels as an overlay on that surface and it will show you the 
segmentation of the defects)


cheers
Bruce
On Wed, 4 May 2016, Katarina Trojacanec wrote:



Dear FreeSurfer Team,


I have been trying to run creation of template with FreeSurfer. However,
for two cases for one patient (case 1: template based on TP1 and TP4, case
2: template based on TP2 and TP4), the correcting defect step is running
too long. According to the information in the mail archive, the defects are
probably too big, and that is the reason for the long processing. 


May I send you via ftp the subjects directories so you can help me to
proceed with this subject, because I am not able to figure out and correct
the problem? Should I send you the base directories in their current state
or the cross-sectionally processed time points as well?


Best Regards, 


Katarina Trojacanec, M.Sc.
Teaching and research assistant

Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia  

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[Freesurfer] Correcting defect

[Katarina Trojacanec]

Dear FreeSurfer Team,


I have been trying to run creation of template with FreeSurfer. However, for 
two cases for one patient (case 1: template based on TP1 and TP4, case 2: 
template based on TP2 and TP4), the correcting defect step is running too long. 
According to the information in the mail archive, the defects are probably too 
big, and that is the reason for the long processing.


May I send you via ftp the subjects directories so you can help me to proceed 
with this subject, because I am not able to figure out and correct the problem? 
Should I send you the base directories in their current state or the 
cross-sectionally processed time points as well?


Best Regards,


Katarina Trojacanec, M.Sc.
Teaching and research assistant

Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia

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[Freesurfer] CORRECTING DEFECT

[Varghese Chikku]

Dear All,
 I have been trying to recon all a patient and unfortunately nothing is
 happening after 24 hrs of  processing so far .No error messages  are
coming up either .This is the line it  got stuck,CORRECTING DEFECT 10
 vertices 67735 convex hull 9509
 This is a  rerun after  my initial processing failed for the same  data
set ,and patiently  waited 36 hrs at Correcting Defect 10 before logging
off .Do you know  why this is  happening.Does it have some thing to do with
the  data itself.
In Thanks
Chikku
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Re: [Freesurfer] CORRECTING DEFECT

[Douglas N Greve]

Hi Chikku, look at the wm.mgz to see if the cerebellum is still attached
doug


On 02/14/2013 11:22 AM, Varghese Chikku wrote:
 Dear All,
  I have been trying to recon all a patient and unfortunately nothing 
 is  happening after 24 hrs of  processing so far .No error messages 
  are coming up either .This is the line it  got stuck,CORRECTING 
 DEFECT 10  vertices 67735 convex hull 9509
  This is a  rerun after  my initial processing failed for the same 
  data set ,and patiently  waited 36 hrs at Correcting Defect 10 before 
 logging off .Do you know  why this is  happening.Does it have some 
 thing to do with the  data itself.
 In Thanks
 Chikku


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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] CORRECTING DEFECT

[Bruce Fischl]

or if the skull is attached or the two hemis. The time it takes to 
correct a defect is quadratic in the size of the (convex hull of) the 
defect, so small ones are fast, and big ones take forever. Anything over 
15K vertices or so usually means there is something dramatically wrong 
with your data. You can look at the ?h.orig.nofix or ?h.inflated.nofix 
surfaces to get an idea

cheers
Bruce
On Thu, 14 Feb 2013, Douglas N Greve wrote:

 Hi Chikku, look at the wm.mgz to see if the cerebellum is still attached
 doug


 On 02/14/2013 11:22 AM, Varghese Chikku wrote:
 Dear All,
  I have been trying to recon all a patient and unfortunately nothing
 is  happening after 24 hrs of  processing so far .No error messages
  are coming up either .This is the line it  got stuck,CORRECTING
 DEFECT 10  vertices 67735 convex hull 9509
  This is a  rerun after  my initial processing failed for the same
  data set ,and patiently  waited 36 hrs at Correcting Defect 10 before
 logging off .Do you know  why this is  happening.Does it have some
 thing to do with the  data itself.
 In Thanks
 Chikku


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 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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