Hi Anastasia,
Thanks for your help. We updated to version 5.3 and received this error: INFO: Distances between consecutive points in test subject's space are 5 5 6 5 Writing output files to /BrainLabDocs/studies/nicotine_mj_ecstasy_study/data/MRI/N1064/data/freesurfer/dlabel/mni/lh.ccg_PP_avg23_mni_flt_* dmri_train(44276) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice
Cannot allocate memory
We use Mac OS X 10.6.8 Snowleopard.
Best, Skyler
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 3, 2013 1:19:55 AM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
Hi Skyler - I would *highly* recommend using the version of tracula in 5.3, as there have been improvements in both performance and speed.
You can check the DWI to anatomical registration by overlaying the aparc+aseg from the dlabel/diff directory (which is in diffusion space) on the FA map. Does that look ok?
a.y
On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote:
Hi Anastasia,
We're using 5.1. It's likely poor registration. The aparc+aseg. looked fine. Is there anything to do about poor registration?
Thank you for the fast reply. Truly appreciated. Skyler
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: Freesurfer@nmr.mgh.harvard.edu Sent: Monday, December 2, 2013 4:27:37 PM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
Hi Skyler - Are you using freesurfer 5.1 or 5.3?
Most likely this issue is due to poor registration, either from the individual DWI to the individual T1, or from the individual T1 to the template space. Or it could be that there is a problem with the aparc+aseg.
a.y
On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote:
Hi all,
I've been running DTI using tracula (fs version 5) for over 1 week on 2 subjects. It appears that it is having difficulty finding satisfactory control point fit and has attempted over 1600 tries. Any help is greatly appreciated. See error below:
INFO: Distances between consecutive points are 25 24 25 26 WARN: Could not find satisfactory control point fit - try 1665 Finding center streamline INFO: Step is 4 voxels WARN: Turning off FA check for center streamline INFO: Step is 4 voxels WARN: Turning off deviation check for center streamline INFO: Step is 4 voxels INFO: Length of center streamline is 96 voxels Selecting 5 points on center streamline INFO: Step is 4 voxels WARN: Defaulting to equidistant control points INFO: Selected control points are 108 193 84 112 173 72 98 153 75 74 157 75 74 184 86 INFO: Distances between consecutive points are 24 25 24 29 WARN: Could not find satisfactory control point fit - try 1666 Finding center streamline INFO: Step is 4 voxels WARN: Turning off FA check for center streamline INFO: Step is 4 voxels WARN: Turning off deviation check for center streamline INFO: Step is 4 voxels
Best, Skyler
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.
It looks like your running 32bit freesurfer on a 64bit machine with snow leopard installed on it. In this case You will have to install the 64bit version of freesurfer instead of the 32bit version you installed previously.
You can get the version you need from the following link:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg
Sorry for the confusion.
-Zeke
On 12/04/2013 10:34 AM, Skyler Gabriel Shollenbarger wrote:
Hi Anastasia,
Thanks for your help. We updated to version 5.3 and received this error: INFO: Distances between consecutive points in test subject's space are 5 5 6 5 Writing output files to /BrainLabDocs/studies/nicotine_mj_ecstasy_study/data/MRI/N1064/data/freesurfer/dlabel/mni/lh.ccg_PP_avg23_mni_flt_* dmri_train(44276) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice
Cannot allocate memory
We use Mac OS X 10.6.8 Snowleopard.
Best, Skyler
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 3, 2013 1:19:55 AM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
Hi Skyler - I would *highly* recommend using the version of tracula in 5.3, as there have been improvements in both performance and speed.
You can check the DWI to anatomical registration by overlaying the aparc+aseg from the dlabel/diff directory (which is in diffusion space) on the FA map. Does that look ok?
a.y
On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote:
Hi Anastasia,
We're using 5.1. It's likely poor registration. The aparc+aseg. looked fine. Is there anything to do about poor registration?
Thank you for the fast reply. Truly appreciated. Skyler
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: Freesurfer@nmr.mgh.harvard.edu Sent: Monday, December 2, 2013 4:27:37 PM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
Hi Skyler - Are you using freesurfer 5.1 or 5.3?
Most likely this issue is due to poor registration, either from the individual DWI to the individual T1, or from the individual T1 to the template space. Or it could be that there is a problem with the aparc+aseg.
a.y
On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote:
Hi all,
I've been running DTI using tracula (fs version 5) for over 1 week on 2 subjects. It appears that it is having difficulty finding satisfactory control point fit and has attempted over 1600 tries. Any help is greatly appreciated. See error below:
INFO: Distances between consecutive points are 25 24 25 26 WARN: Could not find satisfactory control point fit - try 1665 Finding center streamline INFO: Step is 4 voxels WARN: Turning off FA check for center streamline INFO: Step is 4 voxels WARN: Turning off deviation check for center streamline INFO: Step is 4 voxels INFO: Length of center streamline is 96 voxels Selecting 5 points on center streamline INFO: Step is 4 voxels WARN: Defaulting to equidistant control points INFO: Selected control points are 108 193 84 112 173 72 98 153 75 74 157 75 74 184 86 INFO: Distances between consecutive points are 24 25 24 29 WARN: Could not find satisfactory control point fit - try 1666 Finding center streamline INFO: Step is 4 voxels WARN: Turning off FA check for center streamline INFO: Step is 4 voxels WARN: Turning off deviation check for center streamline INFO: Step is 4 voxels
Best, Skyler
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
Hi Zeke,
Thanks for the help. We installed the 64bit version and got the same error.
INFO: Distances between consecutive points in test subject's space are 5 5 6 5 Writing output files to /BrainLabDocs/studies/nicotine_mj_ecstasy_study/data/MRI/N1064/data/freesurfer/dlabel/mni/lh.ccg_PP_avg23_mni_flt_* dmri_train(65940) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice
Cannot allocate memory
I've attached the error log for trac-all in case you need.
Thanks again! Skyler and Jon
----- Original Message ----- From: "Z K" zkaufman@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, December 4, 2013 9:46:37 AM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
It looks like your running 32bit freesurfer on a 64bit machine with snow leopard installed on it. In this case You will have to install the 64bit version of freesurfer instead of the 32bit version you installed previously.
You can get the version you need from the following link:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg
Sorry for the confusion.
-Zeke
On 12/04/2013 10:34 AM, Skyler Gabriel Shollenbarger wrote:
Hi Anastasia,
Thanks for your help. We updated to version 5.3 and received this error: INFO: Distances between consecutive points in test subject's space are 5 5 6 5 Writing output files to /BrainLabDocs/studies/nicotine_mj_ecstasy_study/data/MRI/N1064/data/freesurfer/dlabel/mni/lh.ccg_PP_avg23_mni_flt_* dmri_train(44276) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice
Cannot allocate memory
We use Mac OS X 10.6.8 Snowleopard.
Best, Skyler
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 3, 2013 1:19:55 AM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
Hi Skyler - I would *highly* recommend using the version of tracula in 5.3, as there have been improvements in both performance and speed.
You can check the DWI to anatomical registration by overlaying the aparc+aseg from the dlabel/diff directory (which is in diffusion space) on the FA map. Does that look ok?
a.y
On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote:
Hi Anastasia,
We're using 5.1. It's likely poor registration. The aparc+aseg. looked fine. Is there anything to do about poor registration?
Thank you for the fast reply. Truly appreciated. Skyler
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: Freesurfer@nmr.mgh.harvard.edu Sent: Monday, December 2, 2013 4:27:37 PM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
Hi Skyler - Are you using freesurfer 5.1 or 5.3?
Most likely this issue is due to poor registration, either from the individual DWI to the individual T1, or from the individual T1 to the template space. Or it could be that there is a problem with the aparc+aseg.
a.y
On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote:
Hi all,
I've been running DTI using tracula (fs version 5) for over 1 week on 2 subjects. It appears that it is having difficulty finding satisfactory control point fit and has attempted over 1600 tries. Any help is greatly appreciated. See error below:
INFO: Distances between consecutive points are 25 24 25 26 WARN: Could not find satisfactory control point fit - try 1665 Finding center streamline INFO: Step is 4 voxels WARN: Turning off FA check for center streamline INFO: Step is 4 voxels WARN: Turning off deviation check for center streamline INFO: Step is 4 voxels INFO: Length of center streamline is 96 voxels Selecting 5 points on center streamline INFO: Step is 4 voxels WARN: Defaulting to equidistant control points INFO: Selected control points are 108 193 84 112 173 72 98 153 75 74 157 75 74 184 86 INFO: Distances between consecutive points are 24 25 24 29 WARN: Could not find satisfactory control point fit - try 1666 Finding center streamline INFO: Step is 4 voxels WARN: Turning off FA check for center streamline INFO: Step is 4 voxels WARN: Turning off deviation check for center streamline INFO: Step is 4 voxels
Best, Skyler
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
According to the log file you sent, you are running freesurfer 5.1, leopard version.
And now that I am looking at your previous email, it seems you were running the freesurfer 5.1 leopard version in that case too.
It also looks like you are indeed running a 32bit snow leopard machine so please move (or completely erase) any previously installed version of freesurfer you have on your machine and download and install this one.
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg
-Zeke
On 12/04/2013 03:21 PM, Skyler Gabriel Shollenbarger wrote:
Hi Zeke,
Thanks for the help. We installed the 64bit version and got the same error.
INFO: Distances between consecutive points in test subject's space are 5 5 6 5 Writing output files to /BrainLabDocs/studies/nicotine_mj_ecstasy_study/data/MRI/N1064/data/freesurfer/dlabel/mni/lh.ccg_PP_avg23_mni_flt_* dmri_train(65940) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice
Cannot allocate memory
I've attached the error log for trac-all in case you need.
Thanks again! Skyler and Jon
----- Original Message ----- From: "Z K" zkaufman@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, December 4, 2013 9:46:37 AM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
It looks like your running 32bit freesurfer on a 64bit machine with snow leopard installed on it. In this case You will have to install the 64bit version of freesurfer instead of the 32bit version you installed previously.
You can get the version you need from the following link:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg
Sorry for the confusion.
-Zeke
On 12/04/2013 10:34 AM, Skyler Gabriel Shollenbarger wrote:
Hi Anastasia,
Thanks for your help. We updated to version 5.3 and received this error: INFO: Distances between consecutive points in test subject's space are 5 5 6 5 Writing output files to /BrainLabDocs/studies/nicotine_mj_ecstasy_study/data/MRI/N1064/data/freesurfer/dlabel/mni/lh.ccg_PP_avg23_mni_flt_* dmri_train(44276) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice
Cannot allocate memory
We use Mac OS X 10.6.8 Snowleopard.
Best, Skyler
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 3, 2013 1:19:55 AM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
Hi Skyler - I would *highly* recommend using the version of tracula in 5.3, as there have been improvements in both performance and speed.
You can check the DWI to anatomical registration by overlaying the aparc+aseg from the dlabel/diff directory (which is in diffusion space) on the FA map. Does that look ok?
a.y
On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote:
Hi Anastasia,
We're using 5.1. It's likely poor registration. The aparc+aseg. looked fine. Is there anything to do about poor registration?
Thank you for the fast reply. Truly appreciated. Skyler
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: Freesurfer@nmr.mgh.harvard.edu Sent: Monday, December 2, 2013 4:27:37 PM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
Hi Skyler - Are you using freesurfer 5.1 or 5.3?
Most likely this issue is due to poor registration, either from the individual DWI to the individual T1, or from the individual T1 to the template space. Or it could be that there is a problem with the aparc+aseg.
a.y
On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote:
Hi all,
I've been running DTI using tracula (fs version 5) for over 1 week on 2 subjects. It appears that it is having difficulty finding satisfactory control point fit and has attempted over 1600 tries. Any help is greatly appreciated. See error below:
INFO: Distances between consecutive points are 25 24 25 26 WARN: Could not find satisfactory control point fit - try 1665 Finding center streamline INFO: Step is 4 voxels WARN: Turning off FA check for center streamline INFO: Step is 4 voxels WARN: Turning off deviation check for center streamline INFO: Step is 4 voxels INFO: Length of center streamline is 96 voxels Selecting 5 points on center streamline INFO: Step is 4 voxels WARN: Defaulting to equidistant control points INFO: Selected control points are 108 193 84 112 173 72 98 153 75 74 157 75 74 184 86 INFO: Distances between consecutive points are 24 25 24 29 WARN: Could not find satisfactory control point fit - try 1666 Finding center streamline INFO: Step is 4 voxels WARN: Turning off FA check for center streamline INFO: Step is 4 voxels WARN: Turning off deviation check for center streamline INFO: Step is 4 voxels
Best, Skyler
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
hi zeke,
thanks for the help in the log file, if you look at the last new invocation of trac-all, it indicates that it a runing the freesurefer 5.3 version
Excerpt from Log file:
New invocation of trac-all
Wed Dec 4 12:02:28 CST 2013 /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1064/data /Applications/Freesurfer5.3/bin/trac-all -prep -c dmrirc_single_subject Subject freesurfer SUBJECTS_DIR /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1064/data FREESURFER_HOME /Applications/Freesurfer5.3 Actual FREESURFER_HOME /Applications/Freesurfer5.3
----- Original Message ----- From: "Z K" zkaufman@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu, "Jon Wieser" wieser@uwm.edu Sent: Wednesday, December 4, 2013 2:29:43 PM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
According to the log file you sent, you are running freesurfer 5.1, leopard version.
And now that I am looking at your previous email, it seems you were running the freesurfer 5.1 leopard version in that case too.
It also looks like you are indeed running a 32bit snow leopard machine so please move (or completely erase) any previously installed version of freesurfer you have on your machine and download and install this one.
-Zeke
On 12/04/2013 03:21 PM, Skyler Gabriel Shollenbarger wrote:
Hi Zeke,
Thanks for the help. We installed the 64bit version and got the same error.
INFO: Distances between consecutive points in test subject's space are 5 5 6 5 Writing output files to /BrainLabDocs/studies/nicotine_mj_ecstasy_study/data/MRI/N1064/data/freesurfer/dlabel/mni/lh.ccg_PP_avg23_mni_flt_* dmri_train(65940) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice
Cannot allocate memory
I've attached the error log for trac-all in case you need.
Thanks again! Skyler and Jon
----- Original Message ----- From: "Z K" zkaufman@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, December 4, 2013 9:46:37 AM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
It looks like your running 32bit freesurfer on a 64bit machine with snow leopard installed on it. In this case You will have to install the 64bit version of freesurfer instead of the 32bit version you installed previously.
You can get the version you need from the following link:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg
Sorry for the confusion.
-Zeke
On 12/04/2013 10:34 AM, Skyler Gabriel Shollenbarger wrote:
Hi Anastasia,
Thanks for your help. We updated to version 5.3 and received this error: INFO: Distances between consecutive points in test subject's space are 5 5 6 5 Writing output files to /BrainLabDocs/studies/nicotine_mj_ecstasy_study/data/MRI/N1064/data/freesurfer/dlabel/mni/lh.ccg_PP_avg23_mni_flt_* dmri_train(44276) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice
Cannot allocate memory
We use Mac OS X 10.6.8 Snowleopard.
Best, Skyler
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 3, 2013 1:19:55 AM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
Hi Skyler - I would *highly* recommend using the version of tracula in 5.3, as there have been improvements in both performance and speed.
You can check the DWI to anatomical registration by overlaying the aparc+aseg from the dlabel/diff directory (which is in diffusion space) on the FA map. Does that look ok?
a.y
On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote:
Hi Anastasia,
We're using 5.1. It's likely poor registration. The aparc+aseg. looked fine. Is there anything to do about poor registration?
Thank you for the fast reply. Truly appreciated. Skyler
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: Freesurfer@nmr.mgh.harvard.edu Sent: Monday, December 2, 2013 4:27:37 PM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
Hi Skyler - Are you using freesurfer 5.1 or 5.3?
Most likely this issue is due to poor registration, either from the individual DWI to the individual T1, or from the individual T1 to the template space. Or it could be that there is a problem with the aparc+aseg.
a.y
On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote:
Hi all,
I've been running DTI using tracula (fs version 5) for over 1 week on 2 subjects. It appears that it is having difficulty finding satisfactory control point fit and has attempted over 1600 tries. Any help is greatly appreciated. See error below:
INFO: Distances between consecutive points are 25 24 25 26 WARN: Could not find satisfactory control point fit - try 1665 Finding center streamline INFO: Step is 4 voxels WARN: Turning off FA check for center streamline INFO: Step is 4 voxels WARN: Turning off deviation check for center streamline INFO: Step is 4 voxels INFO: Length of center streamline is 96 voxels Selecting 5 points on center streamline INFO: Step is 4 voxels WARN: Defaulting to equidistant control points INFO: Selected control points are 108 193 84 112 173 72 98 153 75 74 157 75 74 184 86 INFO: Distances between consecutive points are 24 25 24 29 WARN: Could not find satisfactory control point fit - try 1666 Finding center streamline INFO: Step is 4 voxels WARN: Turning off FA check for center streamline INFO: Step is 4 voxels WARN: Turning off deviation check for center streamline INFO: Step is 4 voxels
Best, Skyler
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
Yes, you are correct. I sometimes forget these log files keep appending.
But when I look at the last call of trac-all it says "freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0" which is the 32bit OSX build of FreeSurfer. The 64bit version is called ""freesurfer-Darwin-lion-stable-pub-v5.3.0" and I dont see that referenced anywhere in the log file. So it looks like that solution was never actually attempted.
Im not 100% convinced this will solve your problem, but the error you are getting is almost always solved by using the 64bit version, so please download and install the 64bit version from the link I provided earlier:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg
Hopefully that takes care of it. Make sure that "freesurfer-Darwin-lion-stable-pub-v5.3.0" is referenced in the log file. If you still get the error please contact us again and we'll go from there.
-Zeke
On 12/04/2013 05:55 PM, Jon Wieser wrote:
hi zeke,
thanks for the help in the log file, if you look at the last new invocation of trac-all, it indicates that it a runing the freesurefer 5.3 version
Excerpt from Log file:
New invocation of trac-all
Wed Dec 4 12:02:28 CST 2013 /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1064/data /Applications/Freesurfer5.3/bin/trac-all -prep -c dmrirc_single_subject Subject freesurfer SUBJECTS_DIR /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1064/data FREESURFER_HOME /Applications/Freesurfer5.3 Actual FREESURFER_HOME /Applications/Freesurfer5.3
----- Original Message ----- From: "Z K" zkaufman@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu, "Jon Wieser" wieser@uwm.edu Sent: Wednesday, December 4, 2013 2:29:43 PM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
According to the log file you sent, you are running freesurfer 5.1, leopard version.
And now that I am looking at your previous email, it seems you were running the freesurfer 5.1 leopard version in that case too.
It also looks like you are indeed running a 32bit snow leopard machine so please move (or completely erase) any previously installed version of freesurfer you have on your machine and download and install this one.
-Zeke
On 12/04/2013 03:21 PM, Skyler Gabriel Shollenbarger wrote:
Hi Zeke,
Thanks for the help. We installed the 64bit version and got the same error.
INFO: Distances between consecutive points in test subject's space are 5 5 6 5 Writing output files to /BrainLabDocs/studies/nicotine_mj_ecstasy_study/data/MRI/N1064/data/freesurfer/dlabel/mni/lh.ccg_PP_avg23_mni_flt_* dmri_train(65940) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice
Cannot allocate memory
I've attached the error log for trac-all in case you need.
Thanks again! Skyler and Jon
----- Original Message ----- From: "Z K" zkaufman@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, December 4, 2013 9:46:37 AM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
It looks like your running 32bit freesurfer on a 64bit machine with snow leopard installed on it. In this case You will have to install the 64bit version of freesurfer instead of the 32bit version you installed previously.
You can get the version you need from the following link:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg
Sorry for the confusion.
-Zeke
On 12/04/2013 10:34 AM, Skyler Gabriel Shollenbarger wrote:
Hi Anastasia,
Thanks for your help. We updated to version 5.3 and received this error: INFO: Distances between consecutive points in test subject's space are 5 5 6 5 Writing output files to /BrainLabDocs/studies/nicotine_mj_ecstasy_study/data/MRI/N1064/data/freesurfer/dlabel/mni/lh.ccg_PP_avg23_mni_flt_* dmri_train(44276) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice
Cannot allocate memory
We use Mac OS X 10.6.8 Snowleopard.
Best, Skyler
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 3, 2013 1:19:55 AM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
Hi Skyler - I would *highly* recommend using the version of tracula in 5.3, as there have been improvements in both performance and speed.
You can check the DWI to anatomical registration by overlaying the aparc+aseg from the dlabel/diff directory (which is in diffusion space) on the FA map. Does that look ok?
a.y
On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote:
Hi Anastasia,
We're using 5.1. It's likely poor registration. The aparc+aseg. looked fine. Is there anything to do about poor registration?
Thank you for the fast reply. Truly appreciated. Skyler
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: Freesurfer@nmr.mgh.harvard.edu Sent: Monday, December 2, 2013 4:27:37 PM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
Hi Skyler - Are you using freesurfer 5.1 or 5.3?
Most likely this issue is due to poor registration, either from the individual DWI to the individual T1, or from the individual T1 to the template space. Or it could be that there is a problem with the aparc+aseg.
a.y
On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote:
Hi all,
I've been running DTI using tracula (fs version 5) for over 1 week on 2 subjects. It appears that it is having difficulty finding satisfactory control point fit and has attempted over 1600 tries. Any help is greatly appreciated. See error below:
INFO: Distances between consecutive points are 25 24 25 26 WARN: Could not find satisfactory control point fit - try 1665 Finding center streamline INFO: Step is 4 voxels WARN: Turning off FA check for center streamline INFO: Step is 4 voxels WARN: Turning off deviation check for center streamline INFO: Step is 4 voxels INFO: Length of center streamline is 96 voxels Selecting 5 points on center streamline INFO: Step is 4 voxels WARN: Defaulting to equidistant control points INFO: Selected control points are 108 193 84 112 173 72 98 153 75 74 157 75 74 184 86 INFO: Distances between consecutive points are 24 25 24 29 WARN: Could not find satisfactory control point fit - try 1666 Finding center streamline INFO: Step is 4 voxels WARN: Turning off FA check for center streamline INFO: Step is 4 voxels WARN: Turning off deviation check for center streamline INFO: Step is 4 voxels
Best, Skyler
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
Hi Zeke, thanks for the info. we had installed the 64 bit lion version of freesurfer. perhaps the trac-all was engaged from the wrong (older) directory. I am nuking the old versions. and will try it again
Jon ----- Original Message ----- From: "Z K" zkaufman@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu, "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, December 4, 2013 5:15:47 PM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
Yes, you are correct. I sometimes forget these log files keep appending.
But when I look at the last call of trac-all it says "freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0" which is the 32bit OSX build of FreeSurfer. The 64bit version is called ""freesurfer-Darwin-lion-stable-pub-v5.3.0" and I dont see that referenced anywhere in the log file. So it looks like that solution was never actually attempted.
Im not 100% convinced this will solve your problem, but the error you are getting is almost always solved by using the 64bit version, so please download and install the 64bit version from the link I provided earlier:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg
Hopefully that takes care of it. Make sure that "freesurfer-Darwin-lion-stable-pub-v5.3.0" is referenced in the log file. If you still get the error please contact us again and we'll go from there.
-Zeke
On 12/04/2013 05:55 PM, Jon Wieser wrote:
hi zeke,
thanks for the help in the log file, if you look at the last new invocation of trac-all, it indicates that it a runing the freesurefer 5.3 version
Excerpt from Log file:
New invocation of trac-all
Wed Dec 4 12:02:28 CST 2013 /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1064/data /Applications/Freesurfer5.3/bin/trac-all -prep -c dmrirc_single_subject Subject freesurfer SUBJECTS_DIR /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1064/data FREESURFER_HOME /Applications/Freesurfer5.3 Actual FREESURFER_HOME /Applications/Freesurfer5.3
----- Original Message ----- From: "Z K" zkaufman@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu, "Jon Wieser" wieser@uwm.edu Sent: Wednesday, December 4, 2013 2:29:43 PM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
According to the log file you sent, you are running freesurfer 5.1, leopard version.
And now that I am looking at your previous email, it seems you were running the freesurfer 5.1 leopard version in that case too.
It also looks like you are indeed running a 32bit snow leopard machine so please move (or completely erase) any previously installed version of freesurfer you have on your machine and download and install this one.
-Zeke
On 12/04/2013 03:21 PM, Skyler Gabriel Shollenbarger wrote:
Hi Zeke,
Thanks for the help. We installed the 64bit version and got the same error.
INFO: Distances between consecutive points in test subject's space are 5 5 6 5 Writing output files to /BrainLabDocs/studies/nicotine_mj_ecstasy_study/data/MRI/N1064/data/freesurfer/dlabel/mni/lh.ccg_PP_avg23_mni_flt_* dmri_train(65940) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice
Cannot allocate memory
I've attached the error log for trac-all in case you need.
Thanks again! Skyler and Jon
----- Original Message ----- From: "Z K" zkaufman@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, December 4, 2013 9:46:37 AM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
It looks like your running 32bit freesurfer on a 64bit machine with snow leopard installed on it. In this case You will have to install the 64bit version of freesurfer instead of the 32bit version you installed previously.
You can get the version you need from the following link:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg
Sorry for the confusion.
-Zeke
On 12/04/2013 10:34 AM, Skyler Gabriel Shollenbarger wrote:
Hi Anastasia,
Thanks for your help. We updated to version 5.3 and received this error: INFO: Distances between consecutive points in test subject's space are 5 5 6 5 Writing output files to /BrainLabDocs/studies/nicotine_mj_ecstasy_study/data/MRI/N1064/data/freesurfer/dlabel/mni/lh.ccg_PP_avg23_mni_flt_* dmri_train(44276) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice
Cannot allocate memory
We use Mac OS X 10.6.8 Snowleopard.
Best, Skyler
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 3, 2013 1:19:55 AM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
Hi Skyler - I would *highly* recommend using the version of tracula in 5.3, as there have been improvements in both performance and speed.
You can check the DWI to anatomical registration by overlaying the aparc+aseg from the dlabel/diff directory (which is in diffusion space) on the FA map. Does that look ok?
a.y
On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote:
Hi Anastasia,
We're using 5.1. It's likely poor registration. The aparc+aseg. looked fine. Is there anything to do about poor registration?
Thank you for the fast reply. Truly appreciated. Skyler
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: Freesurfer@nmr.mgh.harvard.edu Sent: Monday, December 2, 2013 4:27:37 PM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
Hi Skyler - Are you using freesurfer 5.1 or 5.3?
Most likely this issue is due to poor registration, either from the individual DWI to the individual T1, or from the individual T1 to the template space. Or it could be that there is a problem with the aparc+aseg.
a.y
On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote:
Hi all,
I've been running DTI using tracula (fs version 5) for over 1 week on 2 subjects. It appears that it is having difficulty finding satisfactory control point fit and has attempted over 1600 tries. Any help is greatly appreciated. See error below:
INFO: Distances between consecutive points are 25 24 25 26 WARN: Could not find satisfactory control point fit - try 1665 Finding center streamline INFO: Step is 4 voxels WARN: Turning off FA check for center streamline INFO: Step is 4 voxels WARN: Turning off deviation check for center streamline INFO: Step is 4 voxels INFO: Length of center streamline is 96 voxels Selecting 5 points on center streamline INFO: Step is 4 voxels WARN: Defaulting to equidistant control points INFO: Selected control points are 108 193 84 112 173 72 98 153 75 74 157 75 74 184 86 INFO: Distances between consecutive points are 24 25 24 29 WARN: Could not find satisfactory control point fit - try 1666 Finding center streamline INFO: Step is 4 voxels WARN: Turning off FA check for center streamline INFO: Step is 4 voxels WARN: Turning off deviation check for center streamline INFO: Step is 4 voxels
Best, Skyler
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@nmr.mgh.harvard.edu
-
Jon Wieser -
Skyler Gabriel Shollenbarger -
Z K