Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

2020-03-16 Thread Frank Chau 
External Email - Use Caution

Hi Bruce,

I uploaded the recon-all.log file and the zip file of the entire subject dir to 
my dropbox. Please download them through the following shared link:

Recon-all.log file: 
https://www.dropbox.com/s/sona1xycmdr7jma/Terminal%20Saved%20Output%3B%20exited%20with%20ERROR%2020%20Jan%202020%20.txt?dl=0
 

Zip file of the entire subject dir: 
https://www.dropbox.com/s/r1uvd2ngyap7klp/subject%20dir%20%28exited%20with%20ERRORS%29.zip?dl=0
 

Please take your time. Thank you very much.

Regards

Frank



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: 12 March 2020 22:07
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

Hi Frank

sorry, I've been busy with local deadlines that are over now. Can you send
us the recon-all.log file? Or tar and gzip the entire subject dir and
upload it to our ftp site? Apologies if any of this has been done.

cheers
Bruce


On Thu, 12 Mar 2020, Frank Chau wrote:

>External Email - Use Caution
>
> Dear Douglas ,
>
> How could I find out the root cause of this recon-all "exited with ERRORS"?
> Does it mean there are flaws in the generated output? Or I could ignore this 
> error warning? Thank you.
>
> Regards
>
> Frank
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N. Greve 
> 
> Sent: 11 March 2020 21:52
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
>
> it should not really affect it
>
> On 3/10/2020 10:22 AM, Tim Schäfer wrote:
>>  External Email - Use Caution
>>
>> Maybe Doug or Bruce should comment on that, but afaik that should not affect 
>> your analysis at all: recon-all will resample your data to 256x256x256 (as 
>> part of creating what FreeSurfer calls the 'conformed' version of the image) 
>> anyways.
>>
>> The error you get, if I understand correctly from the logs, is that *after* 
>> the resampling, the FOV *still* is not 256.
>>
>> Best,
>>
>> Tim
>>
>>> On March 9, 2020 at 7:34 PM Frank Chau  wrote:
>>>
>>>
>>>  External Email - Use Caution
>>>
>>> Dear Tim,
>>>
>>> The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will 
>>> affect the process Recon-all? If yes, how would it impact my output results?
>>>
>>> Regards
>>>
>>> Frank
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  on behalf of Frank Chau 
>>> 
>>> Sent: 06 March 2020 22:17
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
>>>
>>>  External Email - Use Caution
>>>
>>> Dear Tim,
>>>
>>> The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will 
>>> affect the process Recon-all? If yes, how would it impact my output results?
>>>
>>> Regards
>>>
>>> Frank
>>>
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  on behalf of Tim Schäfer 
>>> 
>>> Sent: 05 March 2020 2:25
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
>>>
>>>  External Email - Use Caution
>>>
>>> Thanks for providing the image. Looks fine to me as well.
>>>
>>> What is a bit strange is that when running `mri_info` on the file you 
>>> provided, it shows a FOV of 256 (not 284!) for me, so I have no idea why 
>>> this error is triggered in recon-all.
>>>
>>> Maybe somebody else has an idea...
>>>
>>> Tim
>>>
>>>> On March 4, 2020 at 4:47 PM Frank Chau  wrote:
>>>>
>>>>
>>>>  External Email - Use Caution
>>>>
>>>> Dear Tim,
>>>>
>>>> I have checked the orig.mgz file and nothing usual was found (please see 
>>>> the attachment image)
>>>>
>>>> For downloading my orig.mgz: 
>>>> https://www.dropbox.com/s/crkndenx8ev957v/orig.mgz?dl=0
>>>>
>>>> Regards
>>>>
>>>> Frank
>>>>
>>>> 
>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

2020-03-12 Thread Bruce Fischl 

Hi Frank

sorry, I've been busy with local deadlines that are over now. Can you send 
us the recon-all.log file? Or tar and gzip the entire subject dir and 
upload it to our ftp site? Apologies if any of this has been done.


cheers
Bruce


On Thu, 12 Mar 2020, Frank Chau wrote:


   External Email - Use Caution

Dear Douglas ,

How could I find out the root cause of this recon-all "exited with ERRORS"?
Does it mean there are flaws in the generated output? Or I could ignore this 
error warning? Thank you.

Regards

Frank

From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Douglas N. Greve 
Sent: 11 March 2020 21:52
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

it should not really affect it

On 3/10/2020 10:22 AM, Tim Schäfer wrote:

 External Email - Use Caution

Maybe Doug or Bruce should comment on that, but afaik that should not affect 
your analysis at all: recon-all will resample your data to 256x256x256 (as part 
of creating what FreeSurfer calls the 'conformed' version of the image) anyways.

The error you get, if I understand correctly from the logs, is that *after* the 
resampling, the FOV *still* is not 256.

Best,

Tim


On March 9, 2020 at 7:34 PM Frank Chau  wrote:


 External Email - Use Caution

Dear Tim,

The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will 
affect the process Recon-all? If yes, how would it impact my output results?

Regards

Frank

From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Frank Chau 
Sent: 06 March 2020 22:17
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

 External Email - Use Caution

Dear Tim,

The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will 
affect the process Recon-all? If yes, how would it impact my output results?

Regards

Frank



From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Tim Schäfer 
Sent: 05 March 2020 2:25
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

 External Email - Use Caution

Thanks for providing the image. Looks fine to me as well.

What is a bit strange is that when running `mri_info` on the file you provided, 
it shows a FOV of 256 (not 284!) for me, so I have no idea why this error is 
triggered in recon-all.

Maybe somebody else has an idea...

Tim


On March 4, 2020 at 4:47 PM Frank Chau  wrote:


 External Email - Use Caution

Dear Tim,

I have checked the orig.mgz file and nothing usual was found (please see the 
attachment image)

For downloading my orig.mgz: 
https://www.dropbox.com/s/crkndenx8ev957v/orig.mgz?dl=0

Regards

Frank


From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Tim Schäfer 
Sent: 04 March 2020 23:27
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

 External Email - Use Caution

Dear Frank,

if you search the log in your Dropbox for 'error', this comes up:


ERROR! FOV=284.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.


Did you have a look at the orig.mgz?

Best,

Tim



On March 4, 2020 at 2:59 PM Frank Chau  wrote:


 External Email - Use Caution

Hello FreeSurfer Developers,

I ran a recon-all on a recent batch of T1 Nifti files and all ended with "exited with 
ERRORS". For example: "recon-all -s Chan_Pui_Kim_42M_T1 exited with ERRORS at Sat Jan 11 
01:32:55 HKT 2020".

I've searched the email archive list and I found other researcher encountered same 
problem before. However, I am quite sure their root causes are not same as my case. 3 
possible causes were found in the email archive which about "exited with 
ERRORS":

   1.  The version of freesurfer (I have already used the latest 6.0.0 version)
   2.  Hard disk space (My computer have enough hard disk space)
   3.  sharing folder between virtual machine and original platform. (I use 
freesurfer in Mac OS which do not have this problem)

I uploaded the recon-all.log to my dropbox in case it's of any use.


1) FreeSurfer version: Darwin-OSX-stable-pub-v6.0.0-2beb96c

2) Platform: MAC OS X 10.11.6

3) uname -a: Darwin PFCs-MacBook-Pro.local 15.6.0 Darwin Kernel Version 15.6.0: 
Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 x86_64

4) recon-all.log, please download at:

https://www.dropbox.com/s/bxb2vyhz3koo83s/recon-all.log-%20Terminal%20Output%20log%2020%20Jan%202020%20.txt?dl=0



Regards

Frank

---

FRANK  C Y CHAU



Research assistant

Division of Neurology

Department of Medicine



Tel: +852 6340 2553

Fax: 2872 5828



E-mail : cyfr...@hku.hk&

Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

2020-03-12 Thread Frank Chau 
External Email - Use Caution

Dear Douglas ,

How could I find out the root cause of this recon-all "exited with ERRORS"? 
Does it mean there are flaws in the generated output? Or I could ignore this 
error warning? Thank you.

Regards

Frank

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: 11 March 2020 21:52
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

it should not really affect it

On 3/10/2020 10:22 AM, Tim Schäfer wrote:
>  External Email - Use Caution
>
> Maybe Doug or Bruce should comment on that, but afaik that should not affect 
> your analysis at all: recon-all will resample your data to 256x256x256 (as 
> part of creating what FreeSurfer calls the 'conformed' version of the image) 
> anyways.
>
> The error you get, if I understand correctly from the logs, is that *after* 
> the resampling, the FOV *still* is not 256.
>
> Best,
>
> Tim
>
>> On March 9, 2020 at 7:34 PM Frank Chau  wrote:
>>
>>
>>  External Email - Use Caution
>>
>> Dear Tim,
>>
>> The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will 
>> affect the process Recon-all? If yes, how would it impact my output results?
>>
>> Regards
>>
>> Frank
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Frank Chau 
>> 
>> Sent: 06 March 2020 22:17
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
>>
>>  External Email - Use Caution
>>
>> Dear Tim,
>>
>> The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will 
>> affect the process Recon-all? If yes, how would it impact my output results?
>>
>> Regards
>>
>> Frank
>>
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Tim Schäfer 
>> 
>> Sent: 05 March 2020 2:25
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
>>
>>  External Email - Use Caution
>>
>> Thanks for providing the image. Looks fine to me as well.
>>
>> What is a bit strange is that when running `mri_info` on the file you 
>> provided, it shows a FOV of 256 (not 284!) for me, so I have no idea why 
>> this error is triggered in recon-all.
>>
>> Maybe somebody else has an idea...
>>
>> Tim
>>
>>> On March 4, 2020 at 4:47 PM Frank Chau  wrote:
>>>
>>>
>>>  External Email - Use Caution
>>>
>>> Dear Tim,
>>>
>>> I have checked the orig.mgz file and nothing usual was found (please see 
>>> the attachment image)
>>>
>>> For downloading my orig.mgz: 
>>> https://www.dropbox.com/s/crkndenx8ev957v/orig.mgz?dl=0
>>>
>>> Regards
>>>
>>> Frank
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  on behalf of Tim Schäfer 
>>> 
>>> Sent: 04 March 2020 23:27
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
>>>
>>>  External Email - Use Caution
>>>
>>> Dear Frank,
>>>
>>> if you search the log in your Dropbox for 'error', this comes up:
>>>
>>> 
>>> ERROR! FOV=284.000 > 256
>>> Include the flag -cw256 with recon-all!
>>> Inspect orig.mgz to ensure the head is fully visible.
>>> 
>>>
>>> Did you have a look at the orig.mgz?
>>>
>>> Best,
>>>
>>> Tim
>>>
>>>
>>>> On March 4, 2020 at 2:59 PM Frank Chau  wrote:
>>>>
>>>>
>>>>  External Email - Use Caution
>>>>
>>>> Hello FreeSurfer Developers,
>>>>
>>>> I ran a recon-all on a recent batch of T1 Nifti files and all ended with 
>>>> "exited with ERRORS". For example: "recon-all -s Chan_Pui_Kim_42M_T1 
>>>> exited with ERRORS at Sat Jan 11 01:32:55 HKT 2020".
>>>>
>>>> I've searched the email archive list and I found other researcher 
>>>> encountered same problem before. However, I am quite sure their root 
>>>> causes are not

Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

2020-03-11 Thread Douglas N. Greve 
it should not really affect it

On 3/10/2020 10:22 AM, Tim Schäfer wrote:
>  External Email - Use Caution
>
> Maybe Doug or Bruce should comment on that, but afaik that should not affect 
> your analysis at all: recon-all will resample your data to 256x256x256 (as 
> part of creating what FreeSurfer calls the 'conformed' version of the image) 
> anyways.
>
> The error you get, if I understand correctly from the logs, is that *after* 
> the resampling, the FOV *still* is not 256.
>
> Best,
>
> Tim
>
>> On March 9, 2020 at 7:34 PM Frank Chau  wrote:
>>
>>
>>  External Email - Use Caution
>>
>> Dear Tim,
>>
>> The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will 
>> affect the process Recon-all? If yes, how would it impact my output results?
>>
>> Regards
>>
>> Frank
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Frank Chau 
>> 
>> Sent: 06 March 2020 22:17
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
>>
>>  External Email - Use Caution
>>
>> Dear Tim,
>>
>> The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will 
>> affect the process Recon-all? If yes, how would it impact my output results?
>>
>> Regards
>>
>> Frank
>>
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Tim Schäfer 
>> 
>> Sent: 05 March 2020 2:25
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
>>
>>  External Email - Use Caution
>>
>> Thanks for providing the image. Looks fine to me as well.
>>
>> What is a bit strange is that when running `mri_info` on the file you 
>> provided, it shows a FOV of 256 (not 284!) for me, so I have no idea why 
>> this error is triggered in recon-all.
>>
>> Maybe somebody else has an idea...
>>
>> Tim
>>
>>> On March 4, 2020 at 4:47 PM Frank Chau  wrote:
>>>
>>>
>>>  External Email - Use Caution
>>>
>>> Dear Tim,
>>>
>>> I have checked the orig.mgz file and nothing usual was found (please see 
>>> the attachment image)
>>>
>>> For downloading my orig.mgz: 
>>> https://www.dropbox.com/s/crkndenx8ev957v/orig.mgz?dl=0
>>>
>>> Regards
>>>
>>> Frank
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  on behalf of Tim Schäfer 
>>> 
>>> Sent: 04 March 2020 23:27
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
>>>
>>>  External Email - Use Caution
>>>
>>> Dear Frank,
>>>
>>> if you search the log in your Dropbox for 'error', this comes up:
>>>
>>> 
>>> ERROR! FOV=284.000 > 256
>>> Include the flag -cw256 with recon-all!
>>> Inspect orig.mgz to ensure the head is fully visible.
>>> 
>>>
>>> Did you have a look at the orig.mgz?
>>>
>>> Best,
>>>
>>> Tim
>>>
>>>
>>>> On March 4, 2020 at 2:59 PM Frank Chau  wrote:
>>>>
>>>>
>>>>  External Email - Use Caution
>>>>
>>>> Hello FreeSurfer Developers,
>>>>
>>>> I ran a recon-all on a recent batch of T1 Nifti files and all ended with 
>>>> "exited with ERRORS". For example: "recon-all -s Chan_Pui_Kim_42M_T1 
>>>> exited with ERRORS at Sat Jan 11 01:32:55 HKT 2020".
>>>>
>>>> I've searched the email archive list and I found other researcher 
>>>> encountered same problem before. However, I am quite sure their root 
>>>> causes are not same as my case. 3 possible causes were found in the email 
>>>> archive which about "exited with ERRORS":
>>>>
>>>>1.  The version of freesurfer (I have already used the latest 6.0.0 
>>>> version)
>>>>2.  Hard disk space (My computer have enough hard disk space)
>>>>3.  sharing folder between virtual machine and original platform. (I 
>>>> use freesurfer in Mac OS which do not have this problem)
>>>>
>>>> I upload

Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

2020-03-10 Thread Tim Schäfer 
External Email - Use Caution

Maybe Doug or Bruce should comment on that, but afaik that should not affect 
your analysis at all: recon-all will resample your data to 256x256x256 (as part 
of creating what FreeSurfer calls the 'conformed' version of the image) anyways.

The error you get, if I understand correctly from the logs, is that *after* the 
resampling, the FOV *still* is not 256.

Best,

Tim

> On March 9, 2020 at 7:34 PM Frank Chau  wrote:
> 
> 
> External Email - Use Caution
> 
> Dear Tim,
> 
> The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will 
> affect the process Recon-all? If yes, how would it impact my output results?
> 
> Regards
> 
> Frank
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Frank Chau 
> 
> Sent: 06 March 2020 22:17
> To: Freesurfer support list
> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
> 
> External Email - Use Caution
> 
> Dear Tim,
> 
> The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will 
> affect the process Recon-all? If yes, how would it impact my output results?
> 
> Regards
> 
> Frank
> 
> 
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Tim Schäfer 
> 
> Sent: 05 March 2020 2:25
> To: Freesurfer support list
> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
> 
> External Email - Use Caution
> 
> Thanks for providing the image. Looks fine to me as well.
> 
> What is a bit strange is that when running `mri_info` on the file you 
> provided, it shows a FOV of 256 (not 284!) for me, so I have no idea why this 
> error is triggered in recon-all.
> 
> Maybe somebody else has an idea...
> 
> Tim
> 
> > On March 4, 2020 at 4:47 PM Frank Chau  wrote:
> >
> >
> > External Email - Use Caution
> >
> > Dear Tim,
> >
> > I have checked the orig.mgz file and nothing usual was found (please see 
> > the attachment image)
> >
> > For downloading my orig.mgz: 
> > https://www.dropbox.com/s/crkndenx8ev957v/orig.mgz?dl=0
> >
> > Regards
> >
> > Frank
> >
> > 
> > From: freesurfer-boun...@nmr.mgh.harvard.edu 
> >  on behalf of Tim Schäfer 
> > 
> > Sent: 04 March 2020 23:27
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
> >
> > External Email - Use Caution
> >
> > Dear Frank,
> >
> > if you search the log in your Dropbox for 'error', this comes up:
> >
> > 
> > ERROR! FOV=284.000 > 256
> > Include the flag -cw256 with recon-all!
> > Inspect orig.mgz to ensure the head is fully visible.
> > 
> >
> > Did you have a look at the orig.mgz?
> >
> > Best,
> >
> > Tim
> >
> >
> > > On March 4, 2020 at 2:59 PM Frank Chau  wrote:
> > >
> > >
> > > External Email - Use Caution
> > >
> > > Hello FreeSurfer Developers,
> > >
> > > I ran a recon-all on a recent batch of T1 Nifti files and all ended with 
> > > "exited with ERRORS". For example: "recon-all -s Chan_Pui_Kim_42M_T1 
> > > exited with ERRORS at Sat Jan 11 01:32:55 HKT 2020".
> > >
> > > I've searched the email archive list and I found other researcher 
> > > encountered same problem before. However, I am quite sure their root 
> > > causes are not same as my case. 3 possible causes were found in the email 
> > > archive which about "exited with ERRORS":
> > >
> > >   1.  The version of freesurfer (I have already used the latest 6.0.0 
> > > version)
> > >   2.  Hard disk space (My computer have enough hard disk space)
> > >   3.  sharing folder between virtual machine and original platform. (I 
> > > use freesurfer in Mac OS which do not have this problem)
> > >
> > > I uploaded the recon-all.log to my dropbox in case it's of any use.
> > >
> > >
> > > 1) FreeSurfer version: Darwin-OSX-stable-pub-v6.0.0-2beb96c
> > >
> > > 2) Platform: MAC OS X 10.11.6
> > >
> > > 3) uname -a: Darwin PFCs-MacBook-Pro.local 15.6.0 Darwin Kernel Version 
> > > 15.6.0: Thu Jun 21 20:07:40 PDT 2018; 
> > > root:xnu-3248.73.11~1/RELEASE_X86_64 x86_64
> > >
> > > 4) recon-all.log

Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

2020-03-09 Thread Frank Chau 
External Email - Use Caution

Dear Tim,

The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will 
affect the process Recon-all? If yes, how would it impact my output results?

Regards

Frank

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Frank Chau 

Sent: 06 March 2020 22:17
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

External Email - Use Caution

Dear Tim,

The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will 
affect the process Recon-all? If yes, how would it impact my output results?

Regards

Frank



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Tim Schäfer 

Sent: 05 March 2020 2:25
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

External Email - Use Caution

Thanks for providing the image. Looks fine to me as well.

What is a bit strange is that when running `mri_info` on the file you provided, 
it shows a FOV of 256 (not 284!) for me, so I have no idea why this error is 
triggered in recon-all.

Maybe somebody else has an idea...

Tim

> On March 4, 2020 at 4:47 PM Frank Chau  wrote:
>
>
> External Email - Use Caution
>
> Dear Tim,
>
> I have checked the orig.mgz file and nothing usual was found (please see the 
> attachment image)
>
> For downloading my orig.mgz: 
> https://www.dropbox.com/s/crkndenx8ev957v/orig.mgz?dl=0
>
> Regards
>
> Frank
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Tim Schäfer 
> 
> Sent: 04 March 2020 23:27
> To: Freesurfer support list
> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
>
> External Email - Use Caution
>
> Dear Frank,
>
> if you search the log in your Dropbox for 'error', this comes up:
>
> 
> ERROR! FOV=284.000 > 256
> Include the flag -cw256 with recon-all!
> Inspect orig.mgz to ensure the head is fully visible.
> 
>
> Did you have a look at the orig.mgz?
>
> Best,
>
> Tim
>
>
> > On March 4, 2020 at 2:59 PM Frank Chau  wrote:
> >
> >
> > External Email - Use Caution
> >
> > Hello FreeSurfer Developers,
> >
> > I ran a recon-all on a recent batch of T1 Nifti files and all ended with 
> > "exited with ERRORS". For example: "recon-all -s Chan_Pui_Kim_42M_T1 exited 
> > with ERRORS at Sat Jan 11 01:32:55 HKT 2020".
> >
> > I've searched the email archive list and I found other researcher 
> > encountered same problem before. However, I am quite sure their root causes 
> > are not same as my case. 3 possible causes were found in the email archive 
> > which about "exited with ERRORS":
> >
> >   1.  The version of freesurfer (I have already used the latest 6.0.0 
> > version)
> >   2.  Hard disk space (My computer have enough hard disk space)
> >   3.  sharing folder between virtual machine and original platform. (I use 
> > freesurfer in Mac OS which do not have this problem)
> >
> > I uploaded the recon-all.log to my dropbox in case it's of any use.
> >
> >
> > 1) FreeSurfer version: Darwin-OSX-stable-pub-v6.0.0-2beb96c
> >
> > 2) Platform: MAC OS X 10.11.6
> >
> > 3) uname -a: Darwin PFCs-MacBook-Pro.local 15.6.0 Darwin Kernel Version 
> > 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 
> > x86_64
> >
> > 4) recon-all.log, please download at:
> >
> > https://www.dropbox.com/s/bxb2vyhz3koo83s/recon-all.log-%20Terminal%20Output%20log%2020%20Jan%202020%20.txt?dl=0
> >
> >
> >
> > Regards
> >
> > Frank
> >
> > ---
> >
> > FRANK  C Y CHAU
> >
> >
> >
> > Research assistant
> >
> > Division of Neurology
> >
> > Department of Medicine
> >
> >
> >
> > Tel: +852 6340 2553
> >
> > Fax: 2872 5828
> >
> >
> >
> > E-mail : cyfr...@hku.hk<mailto:cyfr...@hku.hk>
> >
> >
> >
> >
> >
> > Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, 
> > Hong Kong
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard

Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

2020-03-06 Thread Frank Chau 
External Email - Use Caution

Dear Tim,

The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will 
affect the process Recon-all? If yes, how would it impact my output results?

Regards

Frank



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Tim Schäfer 

Sent: 05 March 2020 2:25
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

External Email - Use Caution

Thanks for providing the image. Looks fine to me as well.

What is a bit strange is that when running `mri_info` on the file you provided, 
it shows a FOV of 256 (not 284!) for me, so I have no idea why this error is 
triggered in recon-all.

Maybe somebody else has an idea...

Tim

> On March 4, 2020 at 4:47 PM Frank Chau  wrote:
>
>
> External Email - Use Caution
>
> Dear Tim,
>
> I have checked the orig.mgz file and nothing usual was found (please see the 
> attachment image)
>
> For downloading my orig.mgz: 
> https://www.dropbox.com/s/crkndenx8ev957v/orig.mgz?dl=0
>
> Regards
>
> Frank
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Tim Schäfer 
> 
> Sent: 04 March 2020 23:27
> To: Freesurfer support list
> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
>
> External Email - Use Caution
>
> Dear Frank,
>
> if you search the log in your Dropbox for 'error', this comes up:
>
> 
> ERROR! FOV=284.000 > 256
> Include the flag -cw256 with recon-all!
> Inspect orig.mgz to ensure the head is fully visible.
> 
>
> Did you have a look at the orig.mgz?
>
> Best,
>
> Tim
>
>
> > On March 4, 2020 at 2:59 PM Frank Chau  wrote:
> >
> >
> > External Email - Use Caution
> >
> > Hello FreeSurfer Developers,
> >
> > I ran a recon-all on a recent batch of T1 Nifti files and all ended with 
> > "exited with ERRORS". For example: "recon-all -s Chan_Pui_Kim_42M_T1 exited 
> > with ERRORS at Sat Jan 11 01:32:55 HKT 2020".
> >
> > I've searched the email archive list and I found other researcher 
> > encountered same problem before. However, I am quite sure their root causes 
> > are not same as my case. 3 possible causes were found in the email archive 
> > which about "exited with ERRORS":
> >
> >   1.  The version of freesurfer (I have already used the latest 6.0.0 
> > version)
> >   2.  Hard disk space (My computer have enough hard disk space)
> >   3.  sharing folder between virtual machine and original platform. (I use 
> > freesurfer in Mac OS which do not have this problem)
> >
> > I uploaded the recon-all.log to my dropbox in case it's of any use.
> >
> >
> > 1) FreeSurfer version: Darwin-OSX-stable-pub-v6.0.0-2beb96c
> >
> > 2) Platform: MAC OS X 10.11.6
> >
> > 3) uname -a: Darwin PFCs-MacBook-Pro.local 15.6.0 Darwin Kernel Version 
> > 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 
> > x86_64
> >
> > 4) recon-all.log, please download at:
> >
> > https://www.dropbox.com/s/bxb2vyhz3koo83s/recon-all.log-%20Terminal%20Output%20log%2020%20Jan%202020%20.txt?dl=0
> >
> >
> >
> > Regards
> >
> > Frank
> >
> > ---
> >
> > FRANK  C Y CHAU
> >
> >
> >
> > Research assistant
> >
> > Division of Neurology
> >
> > Department of Medicine
> >
> >
> >
> > Tel: +852 6340 2553
> >
> > Fax: 2872 5828
> >
> >
> >
> > E-mail : cyfr...@hku.hk<mailto:cyfr...@hku.hk>
> >
> >
> >
> >
> >
> > Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, 
> > Hong Kong
> >
> >
> > ___
> > 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
> 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
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

2020-03-05 Thread Frank Chau 
External Email - Use Caution

Dear Tim,

Is it the FOV of my T1 image will affect the process Recon-all? If yes, how 
would it impact my output results?

Regards

Frank


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Tim Schäfer 

Sent: 05 March 2020 2:25
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

External Email - Use Caution

Thanks for providing the image. Looks fine to me as well.

What is a bit strange is that when running `mri_info` on the file you provided, 
it shows a FOV of 256 (not 284!) for me, so I have no idea why this error is 
triggered in recon-all.

Maybe somebody else has an idea...

Tim

> On March 4, 2020 at 4:47 PM Frank Chau  wrote:
>
>
> External Email - Use Caution
>
> Dear Tim,
>
> I have checked the orig.mgz file and nothing usual was found (please see the 
> attachment image)
>
> For downloading my orig.mgz: 
> https://www.dropbox.com/s/crkndenx8ev957v/orig.mgz?dl=0
>
> Regards
>
> Frank
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Tim Schäfer 
> 
> Sent: 04 March 2020 23:27
> To: Freesurfer support list
> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
>
> External Email - Use Caution
>
> Dear Frank,
>
> if you search the log in your Dropbox for 'error', this comes up:
>
> 
> ERROR! FOV=284.000 > 256
> Include the flag -cw256 with recon-all!
> Inspect orig.mgz to ensure the head is fully visible.
> 
>
> Did you have a look at the orig.mgz?
>
> Best,
>
> Tim
>
>
> > On March 4, 2020 at 2:59 PM Frank Chau  wrote:
> >
> >
> > External Email - Use Caution
> >
> > Hello FreeSurfer Developers,
> >
> > I ran a recon-all on a recent batch of T1 Nifti files and all ended with 
> > "exited with ERRORS". For example: "recon-all -s Chan_Pui_Kim_42M_T1 exited 
> > with ERRORS at Sat Jan 11 01:32:55 HKT 2020".
> >
> > I've searched the email archive list and I found other researcher 
> > encountered same problem before. However, I am quite sure their root causes 
> > are not same as my case. 3 possible causes were found in the email archive 
> > which about "exited with ERRORS":
> >
> >   1.  The version of freesurfer (I have already used the latest 6.0.0 
> > version)
> >   2.  Hard disk space (My computer have enough hard disk space)
> >   3.  sharing folder between virtual machine and original platform. (I use 
> > freesurfer in Mac OS which do not have this problem)
> >
> > I uploaded the recon-all.log to my dropbox in case it's of any use.
> >
> >
> > 1) FreeSurfer version: Darwin-OSX-stable-pub-v6.0.0-2beb96c
> >
> > 2) Platform: MAC OS X 10.11.6
> >
> > 3) uname -a: Darwin PFCs-MacBook-Pro.local 15.6.0 Darwin Kernel Version 
> > 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 
> > x86_64
> >
> > 4) recon-all.log, please download at:
> >
> > https://www.dropbox.com/s/bxb2vyhz3koo83s/recon-all.log-%20Terminal%20Output%20log%2020%20Jan%202020%20.txt?dl=0
> >
> >
> >
> > Regards
> >
> > Frank
> >
> > ---
> >
> > FRANK  C Y CHAU
> >
> >
> >
> > Research assistant
> >
> > Division of Neurology
> >
> > Department of Medicine
> >
> >
> >
> > Tel: +852 6340 2553
> >
> > Fax: 2872 5828
> >
> >
> >
> > E-mail : cyfr...@hku.hk<mailto:cyfr...@hku.hk>
> >
> >
> >
> >
> >
> > Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, 
> > Hong Kong
> >
> >
> > ___
> > 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
> 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
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

2020-03-04 Thread Tim Schäfer 
External Email - Use Caution

Thanks for providing the image. Looks fine to me as well. 

What is a bit strange is that when running `mri_info` on the file you provided, 
it shows a FOV of 256 (not 284!) for me, so I have no idea why this error is 
triggered in recon-all. 

Maybe somebody else has an idea...

Tim

> On March 4, 2020 at 4:47 PM Frank Chau  wrote:
> 
> 
> External Email - Use Caution
> 
> Dear Tim,
> 
> I have checked the orig.mgz file and nothing usual was found (please see the 
> attachment image)
> 
> For downloading my orig.mgz: 
> https://www.dropbox.com/s/crkndenx8ev957v/orig.mgz?dl=0
> 
> Regards
> 
> Frank
> 
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Tim Schäfer 
> 
> Sent: 04 March 2020 23:27
> To: Freesurfer support list
> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
> 
> External Email - Use Caution
> 
> Dear Frank,
> 
> if you search the log in your Dropbox for 'error', this comes up:
> 
> 
> ERROR! FOV=284.000 > 256
> Include the flag -cw256 with recon-all!
> Inspect orig.mgz to ensure the head is fully visible.
> 
> 
> Did you have a look at the orig.mgz?
> 
> Best,
> 
> Tim
> 
> 
> > On March 4, 2020 at 2:59 PM Frank Chau  wrote:
> >
> >
> > External Email - Use Caution
> >
> > Hello FreeSurfer Developers,
> >
> > I ran a recon-all on a recent batch of T1 Nifti files and all ended with 
> > "exited with ERRORS". For example: "recon-all -s Chan_Pui_Kim_42M_T1 exited 
> > with ERRORS at Sat Jan 11 01:32:55 HKT 2020".
> >
> > I've searched the email archive list and I found other researcher 
> > encountered same problem before. However, I am quite sure their root causes 
> > are not same as my case. 3 possible causes were found in the email archive 
> > which about "exited with ERRORS":
> >
> >   1.  The version of freesurfer (I have already used the latest 6.0.0 
> > version)
> >   2.  Hard disk space (My computer have enough hard disk space)
> >   3.  sharing folder between virtual machine and original platform. (I use 
> > freesurfer in Mac OS which do not have this problem)
> >
> > I uploaded the recon-all.log to my dropbox in case it's of any use.
> >
> >
> > 1) FreeSurfer version: Darwin-OSX-stable-pub-v6.0.0-2beb96c
> >
> > 2) Platform: MAC OS X 10.11.6
> >
> > 3) uname -a: Darwin PFCs-MacBook-Pro.local 15.6.0 Darwin Kernel Version 
> > 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 
> > x86_64
> >
> > 4) recon-all.log, please download at:
> >
> > https://www.dropbox.com/s/bxb2vyhz3koo83s/recon-all.log-%20Terminal%20Output%20log%2020%20Jan%202020%20.txt?dl=0
> >
> >
> >
> > Regards
> >
> > Frank
> >
> > ---
> >
> > FRANK  C Y CHAU
> >
> >
> >
> > Research assistant
> >
> > Division of Neurology
> >
> > Department of Medicine
> >
> >
> >
> > Tel: +852 6340 2553
> >
> > Fax: 2872 5828
> >
> >
> >
> > E-mail : cyfr...@hku.hk<mailto:cyfr...@hku.hk>
> >
> >
> >
> >
> >
> > Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, 
> > Hong Kong
> >
> >
> > ___
> > 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
> 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

Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

2020-03-04 Thread Tim Schäfer 
External Email - Use Caution

Dear Frank,

if you search the log in your Dropbox for 'error', this comes up:


ERROR! FOV=284.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.


Did you have a look at the orig.mgz?

Best,

Tim


> On March 4, 2020 at 2:59 PM Frank Chau  wrote:
> 
> 
> External Email - Use Caution
> 
> Hello FreeSurfer Developers,
> 
> I ran a recon-all on a recent batch of T1 Nifti files and all ended with 
> "exited with ERRORS". For example: "recon-all -s Chan_Pui_Kim_42M_T1 exited 
> with ERRORS at Sat Jan 11 01:32:55 HKT 2020".
> 
> I've searched the email archive list and I found other researcher encountered 
> same problem before. However, I am quite sure their root causes are not same 
> as my case. 3 possible causes were found in the email archive which about 
> "exited with ERRORS":
> 
>   1.  The version of freesurfer (I have already used the latest 6.0.0 version)
>   2.  Hard disk space (My computer have enough hard disk space)
>   3.  sharing folder between virtual machine and original platform. (I use 
> freesurfer in Mac OS which do not have this problem)
> 
> I uploaded the recon-all.log to my dropbox in case it's of any use.
> 
> 
> 1) FreeSurfer version: Darwin-OSX-stable-pub-v6.0.0-2beb96c
> 
> 2) Platform: MAC OS X 10.11.6
> 
> 3) uname -a: Darwin PFCs-MacBook-Pro.local 15.6.0 Darwin Kernel Version 
> 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 
> x86_64
> 
> 4) recon-all.log, please download at:
> 
> https://www.dropbox.com/s/bxb2vyhz3koo83s/recon-all.log-%20Terminal%20Output%20log%2020%20Jan%202020%20.txt?dl=0
> 
> 
> 
> Regards
> 
> Frank
> 
> ---
> 
> FRANK  C Y CHAU
> 
> 
> 
> Research assistant
> 
> Division of Neurology
> 
> Department of Medicine
> 
> 
> 
> Tel: +852 6340 2553
> 
> Fax: 2872 5828
> 
> 
> 
> E-mail : cyfr...@hku.hk
> 
> 
> 
> 
> 
> Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, 
> Hong Kong
> 
> 
> ___
> 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
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