Re: [Freesurfer] Qdec error in analysis

[Douglas N Greve]

Can you send the command line, your key strokes and button presses, and 
the terminal output leading up to the error message?


On 07/06/2017 12:27 AM, AYUSHI SHUKLA wrote:
> Hi,
>
> Thank you for your response.
>
> Yes, I checked, and I do have the permission to read the file.
>
> Warm Regards
>
> Ayushi
>
> On Thu, 6 Jul 2017 at 09:42, Douglas Greve  > wrote:
>
> Do you have read permission to that file?
>
>
> On 6/29/17 7:04 AM, AYUSHI SHUKLA wrote:
>> Hi,
>>
>> I'm a new user of qdec and I'm trying to run a cortical thickness
>> analysis in qdec between Schizophrenic patients and healthy
>> controls.
>> I have run "recon-all -i" and "recon-all -s  -qcache" on
>> my data and it says that this has run successfully without any
>> errors.
>>
>> But when I hit analyze on the qdec GUI, I get the following
>> error-  "Error in Analyze: Couldn't open
>> 
>> /Applications/freesurfer/subjects/5/surf/lh.thickness.fwhm10.fsaverage.mgz
>> or .mgh file."
>>
>> I went through the old questions with the same issue, however I
>> could not figure a solution for my problem as when I check in the
>> directory, the file is present. I have tried to re-run recon-all
>> and recon-all -s as well, but it is still giving the same error.
>> I was wondering if someone could help me with this issue.
>>
>>
>> Warm Regards
>>
>> Ayushi Shukla
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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>
>
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> whom it is
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> dispose of the e-mail.
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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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Qdec error in analysis

[AYUSHI SHUKLA]

Hi,

Thank you for your response.

Yes, I checked, and I do have the permission to read the file.

Warm Regards

Ayushi

On Thu, 6 Jul 2017 at 09:42, Douglas Greve 
wrote:

> Do you have read permission to that file?
>
> On 6/29/17 7:04 AM, AYUSHI SHUKLA wrote:
>
> Hi,
>
> I'm a new user of qdec and I'm trying to run a cortical thickness analysis
> in qdec between Schizophrenic patients and healthy controls.
> I have run "recon-all -i" and "recon-all -s  -qcache" on my data
> and it says that this has run successfully without any errors.
>
> But when I hit analyze on the qdec GUI, I get the following error-  "Error
> in Analyze: Couldn't open
> /Applications/freesurfer/subjects/5/surf/lh.thickness.fwhm10.fsaverage.mgz
> or .mgh file."
>
> I went through the old questions with the same issue, however I could not
> figure a solution for my problem as when I check in the directory, the file
> is present. I have tried to re-run recon-all and recon-all -s as well, but
> it is still giving the same error. I was wondering if someone could help me
> with this issue.
>
>
> Warm Regards
>
> Ayushi Shukla
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> 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
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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Re: [Freesurfer] Qdec error in analysis

[Douglas Greve]

Do you have read permission to that file?


On 6/29/17 7:04 AM, AYUSHI SHUKLA wrote:

Hi,

I'm a new user of qdec and I'm trying to run a cortical thickness 
analysis in qdec between Schizophrenic patients and healthy controls.
I have run "recon-all -i" and "recon-all -s  -qcache" on my 
data and it says that this has run successfully without any errors.


But when I hit analyze on the qdec GUI, I get the following error- 
 "Error in Analyze: Couldn't open 
/Applications/freesurfer/subjects/5/surf/lh.thickness.fwhm10.fsaverage.mgz 
or .mgh file."


I went through the old questions with the same issue, however I could 
not figure a solution for my problem as when I check in the directory, 
the file is present. I have tried to re-run recon-all and recon-all -s 
as well, but it is still giving the same error. I was wondering if 
someone could help me with this issue.



Warm Regards

Ayushi Shukla


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but does not contain patient information, please contact the sender and properly
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[Freesurfer] Qdec error in analysis

[AYUSHI SHUKLA]

Hi,

I'm a new user of qdec and I'm trying to run a cortical thickness analysis
in qdec between Schizophrenic patients and healthy controls.
I have run "recon-all -i" and "recon-all -s  -qcache" on my data
and it says that this has run successfully without any errors.

But when I hit analyze on the qdec GUI, I get the following error-  "Error
in Analyze: Couldn't open
/Applications/freesurfer/subjects/5/surf/lh.thickness.fwhm10.fsaverage.mgz
or .mgh file."

I went through the old questions with the same issue, however I could not
figure a solution for my problem as when I check in the directory, the file
is present. I have tried to re-run recon-all and recon-all -s as well, but
it is still giving the same error. I was wondering if someone could help me
with this issue.


Warm Regards

Ayushi Shukla
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
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.

[Freesurfer] QDEC Error in Analysis

[AYUSHI SHUKLA]

Hi,

I'm a new user of qdec and I'm trying to run a cortical thickness analysis
in qdec between Schizophrenic patients and healthy controls.
I have run "recon-all -i" and "recon-all -s  -qcache" on my data
and it says that this has run successfully without any errors.

But when I hit analyze on the qdec GUI, I get the following error-  "Error
in Analyze: Couldn't open
/Applications/freesurfer/subjects/5/surf/lh.thickness.fwhm10.fsaverage.mgz
or .mgh file."

I went through the old questions with the same issue, however I could not
figure a solution for my problem as when I check in the directory, the file
is present. I have tried to re-run recon-all and recon-all -s as well, but
it is still giving the same error. I was wondering if someone could help me
with this issue.


Warm Regards

Ayushi Shukla
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
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.

[Freesurfer] QDEC error and analysis termination during 'concatenating volumes' and different results from Monte Carlo Simulation from QDEC Command line

[Isotalus, Hanna]

Dear Doug, 

Thanks for the quick response. I will try running the analyses on the command 
line. I've put the whole error message here if that is of any use and sheds any 
light to the problem? https://www.dropbox.com/s/1h1wzwidt3k1scu/ErrorMessage.txt

Also, when I try to plot the stats tables using QDEC I get the following error:
X Error of failed request: BadAlloc (insufficient resources for operation)
I've a screenshot of this error 
here:https://www.dropbox.com/s/1jf9vd4bms0zv99/x%20error.pdf
I get this when I try to plot stats tables for those subjects on whom the 
analysis works on QDEC. Could this be related to my initial problem? I haven't 
tried generating these stats tables on the command line yet. 

I also have an additional question. When I run the analysis on QDEC (for those 
subjects it works for) I get one cluster after correcting for multiple 
comparisons but when I correct for multiple comparisons using the same settings 
(?) on the command line I get three clusters. The settings I chose on QDEC were 
Monte Carlo Null Z at 1.3 (0.05) and with the abs setting. The first of these 
three clusters matches the one I get on QDEC. I used the following command:

mri_glmfit-sim --glmdir directory --cache 1.3 abs --sim-sign abs

Why am I getting different results? 

Thank you so much for your time and help.

Best wishes, 

Hanna

--

Date: Mon, 28 Jul 2014 12:22:16 -0400
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] QDEC error and analysis termination during
'concatenating volumes'
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 53d678b8.7060...@nmr.mgh.harvard.edu
Content-Type: text/plain; charset=UTF-8; format=flowed


I can't make anything out of the error msg gif. Somewhere in there,
there should be a mris_preproc command line. Can you try cutting and
pasting that into a shell? Trying to do this in the context of qdec will
be difficult
doug

On 07/25/2014 05:09 AM, Isotalus, Hanna wrote:

 Dear FreeSurfer gurus,


 I am using QDEC to run my analyses on a large data set. The analysis
 works fine with up to 1224 subjects but as soon as I add subject 1225
 I get an error and the analysis stops. The error displays during
 'concatenating volumes' and it just displays file names. When I try to
 run the analysis on the remaining subjects (around 360 of them) the
 analysis runs fine ? so I am inclined to think there's nothing wrong
 with the data files. I've tried rotating the order of subjects and it
 just doesn't seem to allow me to run the analysis on all of them. Do
 you have any suggestions?



 Here's a link to a screenshot of the error I get:

 https://www.dropbox.com/s/08pqnmgep6crmr5/error%20message.gif

 I can't actually see all of the error message, here's it from the
 beginning of what I can see and it continues like that ? displaying
 all file names I think.


 Thank you and best wishes,

 ?




 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
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] QDEC error and analysis termination during 'concatenating volumes' and different results from Monte Carlo Simulation from QDEC Command line

[Douglas N Greve]

On 07/29/2014 06:26 AM, Isotalus, Hanna wrote:
 Dear Doug,

 Thanks for the quick response. I will try running the analyses on the command 
 line. I've put the whole error message here if that is of any use and sheds 
 any light to the problem? 
 https://www.dropbox.com/s/1h1wzwidt3k1scu/ErrorMessage.txt
Unforunately, this does not shed any light. It could be that you are 
running out of memory. Try that mri_concat command line from the 
terminal. If that fails, send the full terminal output.

 Also, when I try to plot the stats tables using QDEC I get the following 
 error:
 X Error of failed request: BadAlloc (insufficient resources for operation)
 I've a screenshot of this error 
 here:https://www.dropbox.com/s/1jf9vd4bms0zv99/x%20error.pdf
 I get this when I try to plot stats tables for those subjects on whom the 
 analysis works on QDEC. Could this be related to my initial problem? I 
 haven't tried generating these stats tables on the command line yet.
Check the aseg.stats file that it is having a problem with. It may be 
that recon-all failed for that subject (which might explain the 
mri_concat failure too).

 I also have an additional question. When I run the analysis on QDEC (for 
 those subjects it works for) I get one cluster after correcting for multiple 
 comparisons but when I correct for multiple comparisons using the same 
 settings (?) on the command line I get three clusters. The settings I chose 
 on QDEC were Monte Carlo Null Z at 1.3 (0.05) and with the abs setting. The 
 first of these three clusters matches the one I get on QDEC. I used the 
 following command:

 mri_glmfit-sim --glmdir directory --cache 1.3 abs --sim-sign abs

 Why am I getting different results?
I'm not sure. Is the voxel-wise threshold 1.3 in QDEC? Can you take a 
screen shot?
doug

 Thank you so much for your time and help.

 Best wishes,

 Hanna

 --

 Date: Mon, 28 Jul 2014 12:22:16 -0400
 From: Douglas N Greve gr...@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] QDEC error and analysis termination during
  'concatenating volumes'
 To: freesurfer@nmr.mgh.harvard.edu
 Message-ID: 53d678b8.7060...@nmr.mgh.harvard.edu
 Content-Type: text/plain; charset=UTF-8; format=flowed


 I can't make anything out of the error msg gif. Somewhere in there,
 there should be a mris_preproc command line. Can you try cutting and
 pasting that into a shell? Trying to do this in the context of qdec will
 be difficult
 doug

 On 07/25/2014 05:09 AM, Isotalus, Hanna wrote:
 Dear FreeSurfer gurus,


 I am using QDEC to run my analyses on a large data set. The analysis
 works fine with up to 1224 subjects but as soon as I add subject 1225
 I get an error and the analysis stops. The error displays during
 'concatenating volumes' and it just displays file names. When I try to
 run the analysis on the remaining subjects (around 360 of them) the
 analysis runs fine ? so I am inclined to think there's nothing wrong
 with the data files. I've tried rotating the order of subjects and it
 just doesn't seem to allow me to run the analysis on all of them. Do
 you have any suggestions?



 Here's a link to a screenshot of the error I get:

 https://www.dropbox.com/s/08pqnmgep6crmr5/error%20message.gif

 I can't actually see all of the error message, here's it from the
 beginning of what I can see and it continues like that ? displaying
 all file names I think.


 Thank you and best wishes,

 ?




 ___
 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



-- 
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
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] Freesurfer] QDEC error and analysis termination during 'concatenating volumes'

[Douglas N Greve]

I'm still not sure what is going on. I can run it with 2000 files, so I 
still suspect a memory problem. Try running it with /usr/bin/time, ie,

/usr/bin/time mri_concat ...

SEnd me the last line


On 07/28/2014 03:24 PM, Isotalus, Hanna wrote:
 Dear FreeSurfer experts, Bruce/Doug,

 I am running my analysis on a server. I have a total of 128 GB RAM, when I 
 run my analysis and when it stops I'm consuming ~44, having about 83 free.

 I can run 1224 subjects but no more than that. As soon as I have 1225 
 subjects the analysis won't run (but it does run for all the remaining 
 subjects if I run them separately).​ I tried to run the analysis on different 
 servers, some that had 72GB and some that had 128GB and the pattern stayed 
 the same; none of  the 12 servers could run 1225 subjects but all could run 
 1224 subjects. This may mean it's not a memory problem (?) but it doesn't 
 seem to be a problem with subject files either as all of them work, just not 
 all at the same time.

 All the servers I have access to have a 24-core processor, if that's 
 important.

 Any further suggestions on what might be going on?

 Best wishes,

 Hanna

 --

 Date: Fri, 25 Jul 2014 09:50:51 -0400 (EDT)
 From: Bruce Fischl fis...@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] QDEC error and analysis termination during
  'concatenating volumes'
 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
 Message-ID: alpine.lrh.2.03.1407250949560.20...@nmr.mgh.harvard.edu
 Content-Type: text/plain; charset=utf-8

 Hi Hanna

 seems like you are running out of memory. How much RAM do you have on
 your machine? Are there other things running on it that you can kill, or
 is there a larger RAM machine you can use?

 Doug will be back next week and perhaps will comment also. If you don't
 hear from him you should repost.

 cheers
 Bruce

 On Fri, 25 Jul 2014, Isotalus,
 Hanna wrote:

 Dear FreeSurfer gurus,


 I am using QDEC to run my analyses on a large data set. The analysis works
 fine with up to 1224 subjects but as soon as I add subject 1225 I get an
 error and the analysis stops. The error displays during 'concatenating
 volumes' and it just displays file names. When I try to run the analysis on
 the remaining subjects (around 360 of them) the analysis runs fine ? so I am
 inclined to think there's nothing wrong with the data files. I've tried
 rotating the order of subjects and it just doesn't seem to allow me to run
 the analysis on all of them. Do you have any suggestions?



 Here's a link to a screenshot of the error I get:

 https://www.dropbox.com/s/08pqnmgep6crmr5/error%20message.gif

 I can't actually see all of the error message, here's it from the beginning
 of what I can see and it continues like that ? displaying all file names I
 think.


 Thank you and best wishes,
 Hanna
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
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
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] QDEC error and analysis termination during 'concatenating volumes'

[Douglas N Greve]

I can't make anything out of the error msg gif. Somewhere in there, 
there should be a mris_preproc command line. Can you try cutting and 
pasting that into a shell? Trying to do this in the context of qdec will 
be difficult
doug

On 07/25/2014 05:09 AM, Isotalus, Hanna wrote:

 Dear FreeSurfer gurus,


 I am using QDEC to run my analyses on a large data set. The analysis 
 works fine with up to 1224 subjects but as soon as I add subject 1225 
 I get an error and the analysis stops. The error displays during 
 'concatenating volumes' and it just displays file names. When I try to 
 run the analysis on the remaining subjects (around 360 of them) the 
 analysis runs fine – so I am inclined to think there's nothing wrong 
 with the data files. I've tried rotating the order of subjects and it 
 just doesn't seem to allow me to run the analysis on all of them. Do 
 you have any suggestions?



 Here's a link to a screenshot of the error I get:

 https://www.dropbox.com/s/08pqnmgep6crmr5/error%20message.gif

 I can't actually see all of the error message, here's it from the 
 beginning of what I can see and it continues like that – displaying 
 all file names I think.


 Thank you and best wishes,

 ​




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

-- 
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
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
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Freesurfer] QDEC error and analysis termination during 'concatenating volumes'

[Isotalus, Hanna]

Dear FreeSurfer experts, Bruce/Doug, 

I am running my analysis on a server. I have a total of 128 GB RAM, when I run 
my analysis and when it stops I'm consuming ~44, having about 83 free.

I can run 1224 subjects but no more than that. As soon as I have 1225 subjects 
the analysis won't run (but it does run for all the remaining subjects if I run 
them separately).​ I tried to run the analysis on different servers, some that 
had 72GB and some that had 128GB and the pattern stayed the same; none of  the 
12 servers could run 1225 subjects but all could run 1224 subjects. This may 
mean it's not a memory problem (?) but it doesn't seem to be a problem with 
subject files either as all of them work, just not all at the same time. 

All the servers I have access to have a 24-core processor, if that's important. 

Any further suggestions on what might be going on?

Best wishes, 

Hanna

--

Date: Fri, 25 Jul 2014 09:50:51 -0400 (EDT)
From: Bruce Fischl fis...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] QDEC error and analysis termination during
'concatenating volumes'
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Message-ID: alpine.lrh.2.03.1407250949560.20...@nmr.mgh.harvard.edu
Content-Type: text/plain; charset=utf-8

Hi Hanna

seems like you are running out of memory. How much RAM do you have on
your machine? Are there other things running on it that you can kill, or
is there a larger RAM machine you can use?

Doug will be back next week and perhaps will comment also. If you don't
hear from him you should repost.

cheers
Bruce

On Fri, 25 Jul 2014, Isotalus,
Hanna wrote:


 Dear FreeSurfer gurus,


 I am using QDEC to run my analyses on a large data set. The analysis works
 fine with up to 1224 subjects but as soon as I add subject 1225 I get an
 error and the analysis stops. The error displays during 'concatenating
 volumes' and it just displays file names. When I try to run the analysis on
 the remaining subjects (around 360 of them) the analysis runs fine ? so I am
 inclined to think there's nothing wrong with the data files. I've tried
 rotating the order of subjects and it just doesn't seem to allow me to run
 the analysis on all of them. Do you have any suggestions?



 Here's a link to a screenshot of the error I get:

 https://www.dropbox.com/s/08pqnmgep6crmr5/error%20message.gif

 I can't actually see all of the error message, here's it from the beginning
 of what I can see and it continues like that ? displaying all file names I
 think.


 Thank you and best wishes,
Hanna

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[Freesurfer] QDEC error and analysis termination during 'concatenating volumes'

[Isotalus, Hanna]

Dear FreeSurfer gurus,

I am using QDEC to run my analyses on a large data set. The analysis works fine 
with up to 1224 subjects but as soon as I add subject 1225 I get an error and 
the analysis stops. The error displays during 'concatenating volumes' and it 
just displays file names. When I try to run the analysis on the remaining 
subjects (around 360 of them) the analysis runs fine - so I am inclined to 
think there's nothing wrong with the data files. I've tried rotating the order 
of subjects and it just doesn't seem to allow me to run the analysis on all of 
them. Do you have any suggestions?



Here's a link to a screenshot of the error I get:

https://www.dropbox.com/s/08pqnmgep6crmr5/error%20message.gif

I can't actually see all of the error message, here's it from the beginning of 
what I can see and it continues like that - displaying all file names I think.


Thank you and best wishes,

?

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
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
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] QDEC error and analysis termination during 'concatenating volumes'

[Bruce Fischl]

Hi Hanna

seems like you are running out of memory. How much RAM do you have on 
your machine? Are there other things running on it that you can kill, or 
is there a larger RAM machine you can use?


Doug will be back next week and perhaps will comment also. If you don't 
hear from him you should repost.


cheers
Bruce

On Fri, 25 Jul 2014, Isotalus, 
Hanna wrote:




Dear FreeSurfer gurus,


I am using QDEC to run my analyses on a large data set. The analysis works
fine with up to 1224 subjects but as soon as I add subject 1225 I get an
error and the analysis stops. The error displays during 'concatenating
volumes' and it just displays file names. When I try to run the analysis on
the remaining subjects (around 360 of them) the analysis runs fine – so I am
inclined to think there's nothing wrong with the data files. I've tried
rotating the order of subjects and it just doesn't seem to allow me to run
the analysis on all of them. Do you have any suggestions?



Here's a link to a screenshot of the error I get:

https://www.dropbox.com/s/08pqnmgep6crmr5/error%20message.gif

I can't actually see all of the error message, here's it from the beginning
of what I can see and it continues like that – displaying all file names I
think.


Thank you and best wishes,




​___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
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
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.