Re: [Freesurfer] trac-all -path errors
Hi,
I am also getting the error where the txt files cannot be opened because they
were not created beforehand. Where does the trac-all -prior step take place?
Does it appear within the trac-all -prep script?
Thank you,
Ammar Moiyadi, BS
Professional Research Assistant
Department of Psychiatry
University of Colorado Anschutz Medical Campus
303-724-5490
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of
freesurfer-requ...@nmr.mgh.harvard.edu [freesurfer-requ...@nmr.mgh.harvard.edu]
Sent: Friday, July 29, 2011 10:00 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 89, Issue 99
Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
freesurfer-requ...@nmr.mgh.harvard.edu
You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. trac-all -path errors (Ping-Hong Yeh)
2. Re: trac-all -path errors (Priti Srinivasan)
--
Message: 1
Date: Fri, 29 Jul 2011 11:09:28 -0400
From: Ping-Hong Yeh
Subject: [Freesurfer] trac-all -path errors
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
Content-Type: text/plain; charset=ISO-8859-1
Hi,
I got the error running "trac-all -path -c configure.txt"
ERROR: Could not open
${SUBJECTS_DIR}/$Subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt
I can only find only image files in the "dlabel/diff" directory, but
not text files.
Which step(s) create the lh.cst_AS_avg33_mni_flt_cpts_5.txt file?
Thanks,
Ping
--
Message: 2
Date: Fri, 29 Jul 2011 11:26:13 -0400 (EDT)
From: "Priti Srinivasan"
Subject: Re: [Freesurfer] trac-all -path errors
To: "Ping-Hong Yeh"
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<42727.132.183.139.239.1311953173.squir...@mail.nmr.mgh.harvard.edu>
Content-Type: text/plain;charset=iso-8859-1
Hi Ping,
The text files get created in the trac-all -prior stage. Maybe something
went wrong in that step. Is this the case for all the tracts or just for
this tract? If you can send us the trac-all.log file under the scripts
directory it'll be easier to troubleshoot as to what went wrong.
-Priti
> Hi,
>
> I got the error running "trac-all -path -c configure.txt"
>
> ERROR: Could not open
> ${SUBJECTS_DIR}/$Subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt
>
>
> I can only find only image files in the "dlabel/diff" directory, but
> not text files.
>
> Which step(s) create the lh.cst_AS_avg33_mni_flt_cpts_5.txt file?
>
> Thanks,
>
> Ping
> ___
> 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
End of Freesurfer Digest, Vol 89, Issue 99
**
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 mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] trac-all -path errors
Hi - I created the text file with gedit in Lucid Ubuntu. I checked my locale
and my lang reads en_US.UTF-8, is this the same for you?
Thank you,
Ammar Moiyadi, BS
Professional Research Assistant
Department of Psychiatry
University of Colorado Anschutz Medical Campus
303-724-5490
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: Wednesday, August 03, 2011 10:25 AM
To: Moiyadi, Ammar
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] trac-all -path errors
Hi Ammar - It looks like it's the same text file formatting issue that
someone else had recently. Did you create this file in excel by any
chance? It can't be read properly under unix.
a.y
On Wed, 3 Aug 2011, Moiyadi, Ammar wrote:
> Hi - The txt files are missing for all the tracts as it turns out trac-all
> -prep exited with errors before getting to -prior. It appears there is a
> problem with my bvec file since the dmri/bvec is reading all 0's. As a
> result, i get this error "Error: bvecs and bvals don't have the same number
> of entries". I have attached my bvec.txt file and trac-all log - any ideas to
> where the problem may lie?
>
> Thank You,
>
> Ammar Moiyadi, BS
> Professional Research Assistant
> Department of Psychiatry
> University of Colorado Anschutz Medical Campus
> 303-724-5490
>
> From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
> Sent: Monday, August 01, 2011 12:32 PM
> To: Moiyadi, Ammar
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] trac-all -path errors
>
> Hi Ammar - Yes, -prior is the last step included in -prep. Are the text
> files missing for all tracts, or specifically for lh.cst?
>
> Thanks,
> a.y
>
> On Mon, 1 Aug 2011, Moiyadi, Ammar wrote:
>
>> Hi,
>> I am also getting the error where the txt files cannot be opened because
>> they were not created beforehand. Where does the trac-all -prior step take
>> place? Does it appear within the trac-all -prep script?
>>
>> Thank you,
>>
>> Ammar Moiyadi, BS
>> Professional Research Assistant
>> Department of Psychiatry
>> University of Colorado Anschutz Medical Campus
>> 303-724-5490
>>
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of
>> freesurfer-requ...@nmr.mgh.harvard.edu
>> [freesurfer-requ...@nmr.mgh.harvard.edu]
>> Sent: Friday, July 29, 2011 10:00 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Freesurfer Digest, Vol 89, Issue 99
>>
>> Send Freesurfer mailing list submissions to
>>freesurfer@nmr.mgh.harvard.edu
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> or, via email, send a message with subject or body 'help' to
>>freesurfer-requ...@nmr.mgh.harvard.edu
>>
>> You can reach the person managing the list at
>>freesurfer-ow...@nmr.mgh.harvard.edu
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Freesurfer digest..."
>>
>>
>> Today's Topics:
>>
>> 1. trac-all -path errors (Ping-Hong Yeh)
>> 2. Re: trac-all -path errors (Priti Srinivasan)
>>
>>
>> --
>>
>> Message: 1
>> Date: Fri, 29 Jul 2011 11:09:28 -0400
>> From: Ping-Hong Yeh
>> Subject: [Freesurfer] trac-all -path errors
>> To: freesurfer@nmr.mgh.harvard.edu
>> Message-ID:
>>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Hi,
>>
>> I got the error running "trac-all -path -c configure.txt"
>>
>> ERROR: Could not open
>> ${SUBJECTS_DIR}/$Subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt
>>
>>
>> I can only find only image files in the "dlabel/diff" directory, but
>> not text files.
>>
>> Which step(s) create the lh.cst_AS_avg33_mni_flt_cpts_5.txt file?
>>
>> Thanks,
>>
>> Ping
>>
>>
>> --
>>
>> Message: 2
>> Date: Fri, 29 Jul 2011 11:26:13 -0400 (EDT)
>> From: "Priti Srinivasan"
>> Subject: Re: [Freesurfer] trac-all -path errors
>> To: "Ping-Hong Yeh"
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Message-ID:
>><42727.132.183.139.239.1311953173.squir...@mail.nmr.mgh.harvard.edu>
>> Content-Type: text/plain;charset=iso-8859-1
>
Re: [Freesurfer] trac-all -path errors
Thanks Anastasia - I decided to made an entirely new txt file and the proper dmri/bvec file is now being created. Unfortunately now I'm running into a memory allocation problem. Since I'm running on ubuntu I'm not sure its the same problem that mac users are facing. Any suggestions for how to proceed? Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Wednesday, August 03, 2011 10:37 AM To: Moiyadi, Ammar Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] trac-all -path errors Yes, that's the lang that I got, too. But the text file shows up with ^M's where the ends of lines should be on darwin and on centos only the first 2 lines show up. On Wed, 3 Aug 2011, Moiyadi, Ammar wrote: > Hi - I created the text file with gedit in Lucid Ubuntu. I checked my locale > and my lang reads en_US.UTF-8, is this the same for you? > > Thank you, > > Ammar Moiyadi, BS > Professional Research Assistant > Department of Psychiatry > University of Colorado Anschutz Medical Campus > 303-724-5490 > > From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] > Sent: Wednesday, August 03, 2011 10:25 AM > To: Moiyadi, Ammar > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] trac-all -path errors > > Hi Ammar - It looks like it's the same text file formatting issue that > someone else had recently. Did you create this file in excel by any > chance? It can't be read properly under unix. > > a.y > > On Wed, 3 Aug 2011, Moiyadi, Ammar wrote: > >> Hi - The txt files are missing for all the tracts as it turns out trac-all >> -prep exited with errors before getting to -prior. It appears there is a >> problem with my bvec file since the dmri/bvec is reading all 0's. As a >> result, i get this error "Error: bvecs and bvals don't have the same number >> of entries". I have attached my bvec.txt file and trac-all log - any ideas >> to where the problem may lie? >> >> Thank You, >> >> Ammar Moiyadi, BS >> Professional Research Assistant >> Department of Psychiatry >> University of Colorado Anschutz Medical Campus >> 303-724-5490 >> >> From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] >> Sent: Monday, August 01, 2011 12:32 PM >> To: Moiyadi, Ammar >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] trac-all -path errors >> >> Hi Ammar - Yes, -prior is the last step included in -prep. Are the text >> files missing for all tracts, or specifically for lh.cst? >> >> Thanks, >> a.y >> >> On Mon, 1 Aug 2011, Moiyadi, Ammar wrote: >> >>> Hi, >>> I am also getting the error where the txt files cannot be opened because >>> they were not created beforehand. Where does the trac-all -prior step take >>> place? Does it appear within the trac-all -prep script? >>> >>> Thank you, >>> >>> Ammar Moiyadi, BS >>> Professional Research Assistant >>> Department of Psychiatry >>> University of Colorado Anschutz Medical Campus >>> 303-724-5490 >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of >>> freesurfer-requ...@nmr.mgh.harvard.edu >>> [freesurfer-requ...@nmr.mgh.harvard.edu] >>> Sent: Friday, July 29, 2011 10:00 AM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Freesurfer Digest, Vol 89, Issue 99 >>> >>> Send Freesurfer mailing list submissions to >>>freesurfer@nmr.mgh.harvard.edu >>> >>> To subscribe or unsubscribe via the World Wide Web, visit >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> or, via email, send a message with subject or body 'help' to >>>freesurfer-requ...@nmr.mgh.harvard.edu >>> >>> You can reach the person managing the list at >>>freesurfer-ow...@nmr.mgh.harvard.edu >>> >>> When replying, please edit your Subject line so it is more specific >>> than "Re: Contents of Freesurfer digest..." >>> >>> >>> Today's Topics: >>> >>> 1. trac-all -path errors (Ping-Hong Yeh) >>> 2. Re: trac-all -path errors (Priti Srinivasan) >>> >>> >&
[Freesurfer] Trac paths error - bedpost files not found
Hi Freesurfers - I am encountering an error in trac-all -paths where it cannot find the mean_dsamples.nii.gz file in my dmri.bedpostX directory since it was not created during the bedpost step. Because I ran the original bedpost (not the Seychelles version) I was wondering if this output file was specific to the other version. I have a feeling bedpost is not getting through its entire process but I don't receive any error messages as feedback - once it reaches 47 slices processed it starts queing the post processing stage and then the program ends. Is it possible that the post processing stage has not completed and as a result the required files are not being created? Currently I have the following files in my bedpost output directory: dyads1.nii.gz dyads2.nii.gz mean_th1samples.nii.gz mean_th2samples.nii.gz mean_f1samples.nii.gz mean_f2samples.nii.gz mean_ph1samples.nii.gz mean_ph2samples.nii.gz merged_th1samples.nii.gz merged_th2samples.nii.gz merged_f1samples.nii.gz merged_f2samples.nii.gz merged_ph1samples.nii.gz merged_ph2samples.nii.gz nodif_brain_mask.nii.gz It appears I am missing both the mean_dsample and dyads_dispersion files. Any ideas why these files haven't been created and when they should have been created during bedpost? Thanks for your help, Ammar Moiyadi ___ 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] Trac paths error - bedpost files not found
I believe I'm running the latest version of fsl for Ubuntu, 4.1.4 Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Thursday, August 18, 2011 10:51 AM To: Moiyadi, Ammar Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Trac paths error - bedpost files not found Was this by any chance an older version of bedpost that you ran? Older versions didn't use to create mean_dsamples.nii.gz. On Thu, 18 Aug 2011, Moiyadi, Ammar wrote: > Hi Freesurfers - I am encountering an error in trac-all -paths where it > cannot find the mean_dsamples.nii.gz file in my dmri.bedpostX directory since > it was not created during the bedpost step. Because I ran the original > bedpost (not the Seychelles version) I was wondering if this output file was > specific to the other version. I have a feeling bedpost is not getting > through its entire process but I don't receive any error messages as feedback > - once it reaches 47 slices processed it starts queing the post processing > stage and then the program ends. Is it possible that the post processing > stage has not completed and as a result the required files are not being > created? > Currently I have the following files in my bedpost output directory: > dyads1.nii.gz > dyads2.nii.gz > mean_th1samples.nii.gz > mean_th2samples.nii.gz > mean_f1samples.nii.gz > mean_f2samples.nii.gz > mean_ph1samples.nii.gz > mean_ph2samples.nii.gz > merged_th1samples.nii.gz > merged_th2samples.nii.gz > merged_f1samples.nii.gz > merged_f2samples.nii.gz > merged_ph1samples.nii.gz > merged_ph2samples.nii.gz > nodif_brain_mask.nii.gz > > It appears I am missing both the mean_dsample and dyads_dispersion files. Any > ideas why these files haven't been created and when they should have been > created during bedpost? > > Thanks for your help, > > Ammar Moiyadi > ___ > 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Tracula Memory Requirements
Hi Freesurfers, I've been getting a memory allocation error (below) when running trac prep and trac paths on my computer with 6 gb ram. Since I was able to run these steps on a computer with 16 gb, I want to know, what is the minimum memory requirement for running tracula? Is the memory allocation error resulting from a lack of memory or is there something else going on that I am not aware of? Error: Loading BEDPOST parameter samples from /usr/local/freesurfer5.1/subjects/1052/dmri.bedpostX MRIalloc(256, 256, 50): could not allocate 262144 bytes for 431th slice Thanks always, Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 ___ 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] Tracula Memory Requirements
Hi Anastasia, These are both linux ubuntu 10.04 lts machines. The DICOM images are 1300 slices each 140 KB. Thanks, Ammar From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Friday, September 23, 2011 10:30 AM To: Moiyadi, Ammar Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula Memory Requirements Hi Ammar - Are these macos or linux machines and what is the size of your diffusion images? a.y On Fri, 23 Sep 2011, Moiyadi, Ammar wrote: > Hi Freesurfers, > > I've been getting a memory allocation error (below) when running trac > prep and trac paths on my computer with 6 gb ram. Since I was able to > run these steps on a computer with 16 gb, I want to know, what is the > minimum memory requirement for running tracula? Is the memory > allocation error resulting from a lack of memory or is there something > else going on that I am not aware of? > > Error: > > Loading BEDPOST parameter samples from > /usr/local/freesurfer5.1/subjects/1052/dmri.bedpostX MRIalloc(256, 256, > 50): could not allocate 262144 bytes for 431th slice > > Thanks always, > > Ammar Moiyadi, BS > Professional Research Assistant > Department of Psychiatry > University of Colorado Anschutz Medical Campus > 303-724-5490 > ___ > 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Tracula Memory Requirements
Hi - The voxel dimensions are 1.0156 x 1.0156 x 2.6 mm in the merged_f1 bedpost output and the total number of voxels in the nodif_brain_mask is 3,276,800. Ammar From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Friday, September 23, 2011 11:41 AM To: Moiyadi, Ammar Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula Memory Requirements Hi Ammar - Can you check the voxel dimensions of one of the merged_* files in the bedpost directory, and also how many voxels are included in the mask that was used for bedpost? It seems to be failing when loading the bedpost outputs, which is before it reads any tracula-specific inputs. a.y On Fri, 23 Sep 2011, Moiyadi, Ammar wrote: > Hi Anastasia, > > These are both linux ubuntu 10.04 lts machines. The DICOM images are 1300 > slices each 140 KB. > > Thanks, > > Ammar > > From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] > Sent: Friday, September 23, 2011 10:30 AM > To: Moiyadi, Ammar > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Tracula Memory Requirements > > Hi Ammar - Are these macos or linux machines and what is the size of your > diffusion images? > > a.y > > On Fri, 23 Sep 2011, Moiyadi, Ammar wrote: > >> Hi Freesurfers, >> >> I've been getting a memory allocation error (below) when running trac >> prep and trac paths on my computer with 6 gb ram. Since I was able to >> run these steps on a computer with 16 gb, I want to know, what is the >> minimum memory requirement for running tracula? Is the memory >> allocation error resulting from a lack of memory or is there something >> else going on that I am not aware of? >> >> Error: >> >> Loading BEDPOST parameter samples from >> /usr/local/freesurfer5.1/subjects/1052/dmri.bedpostX MRIalloc(256, 256, >> 50): could not allocate 262144 bytes for 431th slice >> >> Thanks always, >> >> Ammar Moiyadi, BS >> Professional Research Assistant >> Department of Psychiatry >> University of Colorado Anschutz Medical Campus >> 303-724-5490 >> ___ >> 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. > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Tracula Memory Requirements
Hi - After upgrading my total RAM to 12 gb (from 6) I am continuing to run into memory allocation problems running tracula preproc and paths with the error messages as follows: 1. preproc error Loading cortex mask from /usr/local/freesurfer5.1/trctrain/trc010/dlabel/mni/cortex+2mm.nii.gz MRIalloc(218, 182, 182): could not allocate 872 bytes for 112th slice Cannot allocate memory Linux coolguy 2.6.38-10-generic-pae #46~lucid1-Ubuntu SMP Wed Jul 6 20:34:59 UTC 2011 i686 GNU/Linux trac-preproc exited with ERRORS at Fri Oct 7 12:33:56 MDT 2011 2. paths error Loading BEDPOST parameter samples from /usr/local/freesurfer5.1/subjects/1052/dmri.bedpostX MRIalloc(256, 256, 50): could not allocate 262144 bytes for 431th slice Cannot allocate memory Linux coolguy 2.6.38-10-generic-pae #46~lucid1-Ubuntu SMP Wed Jul 6 20:34:59 UTC 2011 i686 GNU/Linux trac-paths exited with ERRORS at Tue Oct 11 12:54:59 MDT 2011 *** Has anyone else had these memory errors with their machines? I am running on a linux box ubuntu 10.04. When the code exits, the script is only utilizing about 20 percent of the memory so I am certain that the problem lies within my machine reading the code or within the code itself. Thank you in advance for any suggestions in solving this problem. Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 From: Moiyadi, Ammar Sent: Friday, September 23, 2011 12:31 PM To: Anastasia Yendiki Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula Memory Requirements Hi - The voxel dimensions are 1.0156 x 1.0156 x 2.6 mm in the merged_f1 bedpost output and the total number of voxels in the nodif_brain_mask is 3,276,800. Ammar From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Friday, September 23, 2011 11:41 AM To: Moiyadi, Ammar Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula Memory Requirements Hi Ammar - Can you check the voxel dimensions of one of the merged_* files in the bedpost directory, and also how many voxels are included in the mask that was used for bedpost? It seems to be failing when loading the bedpost outputs, which is before it reads any tracula-specific inputs. a.y On Fri, 23 Sep 2011, Moiyadi, Ammar wrote: > Hi Anastasia, > > These are both linux ubuntu 10.04 lts machines. The DICOM images are 1300 > slices each 140 KB. > > Thanks, > > Ammar > > From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] > Sent: Friday, September 23, 2011 10:30 AM > To: Moiyadi, Ammar > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Tracula Memory Requirements > > Hi Ammar - Are these macos or linux machines and what is the size of your > diffusion images? > > a.y > > On Fri, 23 Sep 2011, Moiyadi, Ammar wrote: > >> Hi Freesurfers, >> >> I've been getting a memory allocation error (below) when running trac >> prep and trac paths on my computer with 6 gb ram. Since I was able to >> run these steps on a computer with 16 gb, I want to know, what is the >> minimum memory requirement for running tracula? Is the memory >> allocation error resulting from a lack of memory or is there something >> else going on that I am not aware of? >> >> Error: >> >> Loading BEDPOST parameter samples from >> /usr/local/freesurfer5.1/subjects/1052/dmri.bedpostX MRIalloc(256, 256, >> 50): could not allocate 262144 bytes for 431th slice >> >> Thanks always, >> >> Ammar Moiyadi, BS >> Professional Research Assistant >> Department of Psychiatry >> University of Colorado Anschutz Medical Campus >> 303-724-5490 >> ___ >> 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. > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Tracula Memory Requirements
Hi - dmripaths used about 30 percent of the 16gb at max and than lowered to 6 percent. Dmri train uses about 25 percent of the 16gb throughout its process. Would running the 32bit version of freesurfer have something to do with the problem? I have a PAE kernel installed to take advantage of the extra memory that the 32bit OS would otherwise not use. Is anyone else with a 32b linux box having memory errors? Thanks, Ammar From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Tuesday, October 11, 2011 1:23 PM To: Moiyadi, Ammar Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula Memory Requirements Hi Ammar - You mentioned that you were able to run things fine on another computer with 16 Gb of RAM. How much memory was being utilized on that computer by these processes (dmri_train and dmri_paths)? a.y On Tue, 11 Oct 2011, Moiyadi, Ammar wrote: > Hi - After upgrading my total RAM to 12 gb (from 6) I am continuing to run > into memory allocation problems running tracula preproc and paths with the > error messages as follows: > > > 1. preproc error > > Loading cortex mask from > /usr/local/freesurfer5.1/trctrain/trc010/dlabel/mni/cortex+2mm.nii.gz > MRIalloc(218, 182, 182): could not allocate 872 bytes for 112th slice > > Cannot allocate memory > Linux coolguy 2.6.38-10-generic-pae #46~lucid1-Ubuntu SMP Wed Jul 6 20:34:59 > UTC 2011 i686 GNU/Linux > > trac-preproc exited with ERRORS at Fri Oct 7 12:33:56 MDT 2011 > > 2. paths error > > Loading BEDPOST parameter samples from > /usr/local/freesurfer5.1/subjects/1052/dmri.bedpostX > MRIalloc(256, 256, 50): could not allocate 262144 bytes for 431th slice > > Cannot allocate memory > Linux coolguy 2.6.38-10-generic-pae #46~lucid1-Ubuntu SMP Wed Jul 6 20:34:59 > UTC 2011 i686 GNU/Linux > > trac-paths exited with ERRORS at Tue Oct 11 12:54:59 MDT 2011 > > *** > > Has anyone else had these memory errors with their machines? I am running on > a linux box ubuntu 10.04. When the code exits, the script is only utilizing > about 20 percent of the memory so I am certain that the problem lies within > my machine reading the code or within the code itself. Thank you in advance > for any suggestions in solving this problem. > > Ammar Moiyadi, BS > Professional Research Assistant > Department of Psychiatry > University of Colorado Anschutz Medical Campus > 303-724-5490 > > From: Moiyadi, Ammar > Sent: Friday, September 23, 2011 12:31 PM > To: Anastasia Yendiki > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] Tracula Memory Requirements > > Hi - The voxel dimensions are 1.0156 x 1.0156 x 2.6 mm in the merged_f1 > bedpost output and the total number of voxels in the nodif_brain_mask is > 3,276,800. > > Ammar > > From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] > Sent: Friday, September 23, 2011 11:41 AM > To: Moiyadi, Ammar > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] Tracula Memory Requirements > > Hi Ammar - Can you check the voxel dimensions of one of the merged_* files > in the bedpost directory, and also how many voxels are included in the > mask that was used for bedpost? It seems to be failing when loading the > bedpost outputs, which is before it reads any tracula-specific inputs. > > a.y > > On Fri, 23 Sep 2011, Moiyadi, Ammar wrote: > >> Hi Anastasia, >> >> These are both linux ubuntu 10.04 lts machines. The DICOM images are 1300 >> slices each 140 KB. >> >> Thanks, >> >> Ammar >> >> From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] >> Sent: Friday, September 23, 2011 10:30 AM >> To: Moiyadi, Ammar >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Tracula Memory Requirements >> >> Hi Ammar - Are these macos or linux machines and what is the size of your >> diffusion images? >> >> a.y >> >> On Fri, 23 Sep 2011, Moiyadi, Ammar wrote: >> >>> Hi Freesurfers, >>> >>> I've been getting a memory allocation error (below) when running trac >>> prep and trac paths on my computer with 6 gb ram. Since I was able to >>> run these steps on a computer with 16 gb, I want to know, what is the >>> minimum memory requirement for running tracula? Is the memory >>> allocation error resulting from a lack of memory or is there something >>> else going on that I am not aware of? >>> >>> Error: >>> >>> Loading BEDPOST parameter samples from >>>
