Hi all - By popular demand we've posted the dmri_* executables compiled on snow leopard here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz
This is not the entire FS distribution, just the commands that are called by trac-all. If you are a mac user with snow leopard and have been running into memory issues with the leopard version, you can download this, copy the new files into your $FREESURFER_HOME/bin, and try rerunning the part of the analysis that had errored out.
Let us know if there are any problems, a.y
Dear Anastasia,
Thanks a lot for the upload. The procedure now runs perfectly, except for that last message at the end of trac-all -path :
Merging volume 18 of 18... Threshold: 68.1 Name: Right Uncinate Fasciculus dmri_mergepaths(26008) malloc: *** mmap(size=18446744073709543424) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Done in 2.433 sec. dmri_mergepaths done #------------------------------------- trac-paths finished without error at Do 18 Aug 2011 11:39:42 CEST
This however does not seem to affect the pipeline, as all the expected outputs seem to be present and valid.
Dr. David Coynel Division of Cognitive Neuroscience
University of Basel Birmannsgasse 8 4055 Basel - Switzerland
david.coynel@unibas.ch tel: +41(0)612.670.240
Am 17.08.2011 um 23:44 schrieb Anastasia Yendiki:
Hi all - By popular demand we've posted the dmri_* executables compiled on snow leopard here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz
This is not the entire FS distribution, just the commands that are called by trac-all. If you are a mac user with snow leopard and have been running into memory issues with the leopard version, you can download this, copy the new files into your $FREESURFER_HOME/bin, and try rerunning the part of the analysis that had errored out.
Let us know if there are any problems, a.y
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.
Hi David - Glad to hear things are working! I can look into dmri_mergepaths and see if something is wrong with the snow leopard build. Have you by any chance kept the original leopard build of it? If you haven't overwritten it, it'd be useful to run the same thing with that version and see if it works. Thanks!
a.y
On Tue, 23 Aug 2011, David Coynel wrote:
Dear Anastasia,
Thanks a lot for the upload. The procedure now runs perfectly, except for that last message at the end of trac-all -path :
Merging volume 18 of 18... Threshold: 68.1 Name: Right Uncinate Fasciculus dmri_mergepaths(26008) malloc: *** mmap(size=18446744073709543424) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Done in 2.433 sec. dmri_mergepaths done #------------------------------------- trac-paths finished without error at Do 18 Aug 2011 11:39:42 CEST
This however does not seem to affect the pipeline, as all the expected outputs seem to be present and valid.
Dr. David Coynel Division of Cognitive Neuroscience
University of Basel Birmannsgasse 8 4055 Basel - Switzerland
david.coynel@unibas.ch tel: +41(0)612.670.240
Am 17.08.2011 um 23:44 schrieb Anastasia Yendiki:
Hi all - By popular demand we've posted the dmri_* executables compiled on snow leopard here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz
This is not the entire FS distribution, just the commands that are called by trac-all. If you are a mac user with snow leopard and have been running into memory issues with the leopard version, you can download this, copy the new files into your $FREESURFER_HOME/bin, and try rerunning the part of the analysis that had errored out.
Let us know if there are any problems, a.y
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
Hi Anastasia,
Thanks for your answer. Unfortunately I overwrote the executables (I could still retrieve them from the website distribution ?). Interestingly this message does not show up when selecting only a subset of the pathways, as for example ( lh.ccg rh.ccg lh.unc rh.unc ), however the merged_avg33_mni file only appears to contain the first pathway (lh.ccg).
David
Am 23.08.2011 um 17:06 schrieb Anastasia Yendiki:
Hi David - Glad to hear things are working! I can look into dmri_mergepaths and see if something is wrong with the snow leopard build. Have you by any chance kept the original leopard build of it? If you haven't overwritten it, it'd be useful to run the same thing with that version and see if it works. Thanks!
a.y
On Tue, 23 Aug 2011, David Coynel wrote:
Dear Anastasia,
Thanks a lot for the upload. The procedure now runs perfectly, except for that last message at the end of trac-all -path :
Merging volume 18 of 18... Threshold: 68.1 Name: Right Uncinate Fasciculus dmri_mergepaths(26008) malloc: *** mmap(size=18446744073709543424) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Done in 2.433 sec. dmri_mergepaths done #------------------------------------- trac-paths finished without error at Do 18 Aug 2011 11:39:42 CEST
This however does not seem to affect the pipeline, as all the expected outputs seem to be present and valid.
Dr. David Coynel Division of Cognitive Neuroscience
University of Basel Birmannsgasse 8 4055 Basel - Switzerland
david.coynel@unibas.ch tel: +41(0)612.670.240
Am 17.08.2011 um 23:44 schrieb Anastasia Yendiki:
Hi all - By popular demand we've posted the dmri_* executables compiled on snow leopard here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz
This is not the entire FS distribution, just the commands that are called by trac-all. If you are a mac user with snow leopard and have been running into memory issues with the leopard version, you can download this, copy the new files into your $FREESURFER_HOME/bin, and try rerunning the part of the analysis that had errored out.
Let us know if there are any problems, a.y
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi David - Thanks for catching this. There was something wrong with the new snow leopard build of dmri_mergepaths. (The original from the 5.1 distribution didn't have this problem). Sorry about that!
I've now updated the snow leopard tar file, so if you download it again you should not get this error any more.
As before it's here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz
Let me know how it goes, a.y
On Tue, 23 Aug 2011, David Coynel wrote:
Hi Anastasia,
Thanks for your answer. Unfortunately I overwrote the executables (I could still retrieve them from the website distribution ?). Interestingly this message does not show up when selecting only a subset of the pathways, as for example ( lh.ccg rh.ccg lh.unc rh.unc ), however the merged_avg33_mni file only appears to contain the first pathway (lh.ccg).
David
Am 23.08.2011 um 17:06 schrieb Anastasia Yendiki:
Hi David - Glad to hear things are working! I can look into dmri_mergepaths and see if something is wrong with the snow leopard build. Have you by any chance kept the original leopard build of it? If you haven't overwritten it, it'd be useful to run the same thing with that version and see if it works. Thanks!
a.y
On Tue, 23 Aug 2011, David Coynel wrote:
Dear Anastasia,
Thanks a lot for the upload. The procedure now runs perfectly, except for that last message at the end of trac-all -path :
Merging volume 18 of 18... Threshold: 68.1 Name: Right Uncinate Fasciculus dmri_mergepaths(26008) malloc: *** mmap(size=18446744073709543424) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Done in 2.433 sec. dmri_mergepaths done #------------------------------------- trac-paths finished without error at Do 18 Aug 2011 11:39:42 CEST
This however does not seem to affect the pipeline, as all the expected outputs seem to be present and valid.
Dr. David Coynel Division of Cognitive Neuroscience
University of Basel Birmannsgasse 8 4055 Basel - Switzerland
david.coynel@unibas.ch tel: +41(0)612.670.240
Am 17.08.2011 um 23:44 schrieb Anastasia Yendiki:
Hi all - By popular demand we've posted the dmri_* executables compiled on snow leopard here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz
This is not the entire FS distribution, just the commands that are called by trac-all. If you are a mac user with snow leopard and have been running into memory issues with the leopard version, you can download this, copy the new files into your $FREESURFER_HOME/bin, and try rerunning the part of the analysis that had errored out.
Let us know if there are any problems, a.y
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 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
Yes, there are no more malloc issues, thanks for the update.
However I still have a question, related to the merged_avg33_mni file. It still only contains the first path that was passed as an input to dmri_mergepaths. If I understand correctly I should see all generated paths, thresholded and merged into this file ?
David
Am 23.08.2011 um 21:28 schrieb Anastasia Yendiki:
Hi David - Thanks for catching this. There was something wrong with the new snow leopard build of dmri_mergepaths. (The original from the 5.1 distribution didn't have this problem). Sorry about that!
I've now updated the snow leopard tar file, so if you download it again you should not get this error any more.
As before it's here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz
Let me know how it goes, a.y
On Tue, 23 Aug 2011, David Coynel wrote:
Hi Anastasia,
Thanks for your answer. Unfortunately I overwrote the executables (I could still retrieve them from the website distribution ?). Interestingly this message does not show up when selecting only a subset of the pathways, as for example ( lh.ccg rh.ccg lh.unc rh.unc ), however the merged_avg33_mni file only appears to contain the first pathway (lh.ccg).
David
Am 23.08.2011 um 17:06 schrieb Anastasia Yendiki:
Hi David - Glad to hear things are working! I can look into dmri_mergepaths and see if something is wrong with the snow leopard build. Have you by any chance kept the original leopard build of it? If you haven't overwritten it, it'd be useful to run the same thing with that version and see if it works. Thanks!
a.y
On Tue, 23 Aug 2011, David Coynel wrote:
Dear Anastasia,
Thanks a lot for the upload. The procedure now runs perfectly, except for that last message at the end of trac-all -path :
Merging volume 18 of 18... Threshold: 68.1 Name: Right Uncinate Fasciculus dmri_mergepaths(26008) malloc: *** mmap(size=18446744073709543424) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Done in 2.433 sec. dmri_mergepaths done #------------------------------------- trac-paths finished without error at Do 18 Aug 2011 11:39:42 CEST
This however does not seem to affect the pipeline, as all the expected outputs seem to be present and valid.
Dr. David Coynel Division of Cognitive Neuroscience
University of Basel Birmannsgasse 8 4055 Basel - Switzerland
david.coynel@unibas.ch tel: +41(0)612.670.240
Am 17.08.2011 um 23:44 schrieb Anastasia Yendiki:
Hi all - By popular demand we've posted the dmri_* executables compiled on snow leopard here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz
This is not the entire FS distribution, just the commands that are called by trac-all. If you are a mac user with snow leopard and have been running into memory issues with the leopard version, you can download this, copy the new files into your $FREESURFER_HOME/bin, and try rerunning the part of the analysis that had errored out.
Let us know if there are any problems, a.y
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 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
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Yes, it should be a concatenation of all existing pathway reconstructions under dpath/... If you open it with trackvis --tv, you should be able to see a 3d view of all the pathways. Sometimes the default threshold might be too high for some pathways and you might need to adjust it individually in freeview to be able to see them.
Does the output of dmri_mergepaths show you that it's found multiple pathways or just ccg?
Yes, there are no more malloc issues, thanks for the update.
However I still have aays question, related to the merged_avg33_mni
file. It
still only contains the first path that was passed as an input to dmri_mergepaths. If I understand correctly I should see all generated paths, thresholded and merged into this file ?
David
Am 23.08.2011 um 21:28 schrieb Anastasia Yendiki:
Hi David - Thanks for catching this. There was something wrong with the new snow leopard build of dmri_mergepaths. (The original from the 5.1 distribution didn't have this problem). Sorry about that!
I've now updated the snow leopard tar file, so if you download it again you should not get this error any more.
As before it's here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz
Let me know how it goes, a.y
On Tue, 23 Aug 2011, David Coynel wrote:
Hi Anastasia,
Thanks for your answer. Unfortunately I overwrote the executables (I could still retrieve them from the website distribution ?). Interestingly this message does not show up when selecting only a subset of the pathways, as for example ( lh.ccg rh.ccg lh.unc rh.unc ), however the merged_avg33_mni file only appears to contain the first pathway (lh.ccg).
David
Am 23.08.2011 um 17:06 schrieb Anastasia Yendiki:
Hi David - Glad to hear things are working! I can look into dmri_mergepaths and see if something is wrong with the snow leopard build. Have you by any chance kept the original leopard build of it? If you haven't overwritten it, it'd be useful to run the same thing with that version and see if it works. Thanks!
a.y
On Tue, 23 Aug 2011, David Coynel wrote:
Dear Anastasia,
Thanks a lot for the upload. The procedure now runs perfectly, except for that last message at the end of trac-all -path :
Merging volume 18 of 18... Threshold: 68.1 Name: Right Uncinate Fasciculus dmri_mergepaths(26008) malloc: *** mmap(size=18446744073709543424) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Done in 2.433 sec. dmri_mergepaths done #------------------------------------- trac-paths finished without error at Do 18 Aug 2011 11:39:42 CEST
This however does not seem to affect the pipeline, as all the expected outputs seem to be present and valid.
Dr. David Coynel Division of Cognitive Neuroscience
University of Basel Birmannsgasse 8 4055 Basel - Switzerland
david.coynel@unibas.ch tel: +41(0)612.670.240
Am 17.08.2011 um 23:44 schrieb Anastasia Yendiki:
Hi all - By popular demand we've posted the dmri_* executables compiled on snow leopard here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz
This is not the entire FS distribution, just the commands that are called by trac-all. If you are a mac user with snow leopard and have been running into memory issues with the leopard version, you can download this, copy the new files into your $FREESURFER_HOME/bin, and try rerunning the part of the analysis that had errored out.
Let us know if there are any problems, a.y
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.
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Everything looks to be running fine. Wether I look at the merged file with freeview or fslview, I still have only one tract. Here's an extract of the outputs :
Input files: lh.ccg_PP_avg33_mni_flt/path.pd.nii.gz lh.unc_AS_avg33_mni_flt/path.pd.nii.gz rh.ccg_PP_avg33_mni_flt/path.pd.nii.gz rh.unc_AS_avg33_mni_flt/path.pd.nii.gz Lower threshold for display: 0.150000 Merging volume 1 of 4... Threshold: 111 Name: Left Cingulum - Cingulate Gyrus Merging volume 2 of 4... Threshold: 74.85 Name: Left Uncinate Fasciculus Merging volume 3 of 4... Threshold: 87.9 Name: Right Cingulum - Cingulate Gyrus Merging volume 4 of 4... Threshold: 57.6 Name: Right Uncinate Fasciculus Done in 0.621 sec. dmri_mergepaths done
It remains the same if I take a very low threshold (0.001).
David
Am 24.08.2011 um 16:49 schrieb ayendiki@nmr.mgh.harvard.edu:
Yes, it should be a concatenation of all existing pathway reconstructions under dpath/... If you open it with trackvis --tv, you should be able to see a 3d view of all the pathways. Sometimes the default threshold might be too high for some pathways and you might need to adjust it individually in freeview to be able to see them.
Does the output of dmri_mergepaths show you that it's found multiple pathways or just ccg?
Yes, there are no more malloc issues, thanks for the update.
However I still have aays question, related to the merged_avg33_mni
file. It
still only contains the first path that was passed as an input to dmri_mergepaths. If I understand correctly I should see all generated paths, thresholded and merged into this file ?
David
Am 23.08.2011 um 21:28 schrieb Anastasia Yendiki:
Hi David - Thanks for catching this. There was something wrong with the new snow leopard build of dmri_mergepaths. (The original from the 5.1 distribution didn't have this problem). Sorry about that!
I've now updated the snow leopard tar file, so if you download it again you should not get this error any more.
As before it's here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz
Let me know how it goes, a.y
On Tue, 23 Aug 2011, David Coynel wrote:
Hi Anastasia,
Thanks for your answer. Unfortunately I overwrote the executables (I could still retrieve them from the website distribution ?). Interestingly this message does not show up when selecting only a subset of the pathways, as for example ( lh.ccg rh.ccg lh.unc rh.unc ), however the merged_avg33_mni file only appears to contain the first pathway (lh.ccg).
David
Am 23.08.2011 um 17:06 schrieb Anastasia Yendiki:
Hi David - Glad to hear things are working! I can look into dmri_mergepaths and see if something is wrong with the snow leopard build. Have you by any chance kept the original leopard build of it? If you haven't overwritten it, it'd be useful to run the same thing with that version and see if it works. Thanks!
a.y
On Tue, 23 Aug 2011, David Coynel wrote:
Dear Anastasia,
Thanks a lot for the upload. The procedure now runs perfectly, except for that last message at the end of trac-all -path :
Merging volume 18 of 18... Threshold: 68.1 Name: Right Uncinate Fasciculus dmri_mergepaths(26008) malloc: *** mmap(size=18446744073709543424) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Done in 2.433 sec. dmri_mergepaths done #------------------------------------- trac-paths finished without error at Do 18 Aug 2011 11:39:42 CEST
This however does not seem to affect the pipeline, as all the expected outputs seem to be present and valid.
Dr. David Coynel Division of Cognitive Neuroscience
University of Basel Birmannsgasse 8 4055 Basel - Switzerland
david.coynel@unibas.ch tel: +41(0)612.670.240
Am 17.08.2011 um 23:44 schrieb Anastasia Yendiki:
> > Hi all - By popular demand we've posted the dmri_* executables > compiled on > snow leopard here: > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz > > This is not the entire FS distribution, just the commands that are > called > by trac-all. If you are a mac user with snow leopard and have been > running > into memory issues with the leopard version, you can download this, > copy > the new files into your $FREESURFER_HOME/bin, and try rerunning the > part > of the analysis that had errored out. > > Let us know if there are any problems, > a.y > > _______________________________________________ > 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. >
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Hi David,
Can you visualize these tracts individually?
type in freeview -v lh.ccg_PP_avg33_mni_flt/path.pd.nii.gz
and to visualize the merged you could try
freeview -tv merged_avg33_mni_flt.nii.gz
If both of these do not work you can try running dmri_mergepaths seperately using the following command and see if that works for you:
dmri_mergepaths --indir <main input dir> --in <path to all the path.pd.nii.gz files> --out <path to outputdir/merged_avg32_mni_flt.mgz> --ctab /usr/local/freesurfer/dev/FreeSurferColorLUT.txt --thresh .15
You should have a copy of this command in your log file you can copy paste that on to the terminal as well.
Can you try these things to see if it solves your problem?
-Priti
Everything looks to be running fine. Wether I look at the merged file with freeview or fslview, I still have only one tract. Here's an extract of the outputs :
Input files: lh.ccg_PP_avg33_mni_flt/path.pd.nii.gz lh.unc_AS_avg33_mni_flt/path.pd.nii.gz rh.ccg_PP_avg33_mni_flt/path.pd.nii.gz rh.unc_AS_avg33_mni_flt/path.pd.nii.gz Lower threshold for display: 0.150000 Merging volume 1 of 4... Threshold: 111 Name: Left Cingulum - Cingulate Gyrus Merging volume 2 of 4... Threshold: 74.85 Name: Left Uncinate Fasciculus Merging volume 3 of 4... Threshold: 87.9 Name: Right Cingulum - Cingulate Gyrus Merging volume 4 of 4... Threshold: 57.6 Name: Right Uncinate Fasciculus Done in 0.621 sec. dmri_mergepaths done
It remains the same if I take a very low threshold (0.001).
David
Am 24.08.2011 um 16:49 schrieb ayendiki@nmr.mgh.harvard.edu:
Yes, it should be a concatenation of all existing pathway reconstructions under dpath/... If you open it with trackvis --tv, you should be able to see a 3d view of all the pathways. Sometimes the default threshold might be too high for some pathways and you might need to adjust it individually in freeview to be able to see them.
Does the output of dmri_mergepaths show you that it's found multiple pathways or just ccg?
Yes, there are no more malloc issues, thanks for the update.
However I still have aays question, related to the merged_avg33_mni
file. It
still only contains the first path that was passed as an input to dmri_mergepaths. If I understand correctly I should see all generated paths, thresholded and merged into this file ?
David
Am 23.08.2011 um 21:28 schrieb Anastasia Yendiki:
Hi David - Thanks for catching this. There was something wrong with the new snow leopard build of dmri_mergepaths. (The original from the 5.1 distribution didn't have this problem). Sorry about that!
I've now updated the snow leopard tar file, so if you download it again you should not get this error any more.
As before it's here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz
Let me know how it goes, a.y
On Tue, 23 Aug 2011, David Coynel wrote:
Hi Anastasia,
Thanks for your answer. Unfortunately I overwrote the executables (I could still retrieve them from the website distribution ?). Interestingly this message does not show up when selecting only a subset of the pathways, as for example ( lh.ccg rh.ccg lh.unc rh.unc ), however the merged_avg33_mni file only appears to contain the first pathway (lh.ccg).
David
Am 23.08.2011 um 17:06 schrieb Anastasia Yendiki:
Hi David - Glad to hear things are working! I can look into dmri_mergepaths and see if something is wrong with the snow leopard build. Have you by any chance kept the original leopard build of it? If you haven't overwritten it, it'd be useful to run the same thing with that version and see if it works. Thanks!
a.y
On Tue, 23 Aug 2011, David Coynel wrote:
> Dear Anastasia, > > Thanks a lot for the upload. The procedure now runs perfectly, > except > for that last message at the end of trac-all -path : > > > Merging volume 18 of 18... > Threshold: 68.1 Name: Right Uncinate Fasciculus > dmri_mergepaths(26008) malloc: *** mmap(size=18446744073709543424) > failed (error code=12) > *** error: can't allocate region > *** set a breakpoint in malloc_error_break to debug > Done in 2.433 sec. > dmri_mergepaths done > #------------------------------------- > trac-paths finished without error at Do 18 Aug 2011 11:39:42 CEST > > > This however does not seem to affect the pipeline, as all the > expected outputs seem to be present and valid. > > Dr. David Coynel > Division of Cognitive Neuroscience > > University of Basel > Birmannsgasse 8 > 4055 Basel - Switzerland > > david.coynel@unibas.ch > tel: +41(0)612.670.240 > > Am 17.08.2011 um 23:44 schrieb Anastasia Yendiki: > >> >> Hi all - By popular demand we've posted the dmri_* executables >> compiled on >> snow leopard here: >> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz >> >> This is not the entire FS distribution, just the commands that are >> called >> by trac-all. If you are a mac user with snow leopard and have been >> running >> into memory issues with the leopard version, you can download >> this, >> copy >> the new files into your $FREESURFER_HOME/bin, and try rerunning >> the >> part >> of the analysis that had errored out. >> >> Let us know if there are any problems, >> a.y >> >> _______________________________________________ >> 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Priti and Anastasia,
Indeed, I was expecting a single volume in the merged file with all the tracts, whereas there is a single volume for each of them. Thanks for the help.
David
Am 24.08.2011 um 17:53 schrieb Priti Srinivasan:
Hi David,
Can you visualize these tracts individually?
type in freeview -v lh.ccg_PP_avg33_mni_flt/path.pd.nii.gz
and to visualize the merged you could try
freeview -tv merged_avg33_mni_flt.nii.gz
If both of these do not work you can try running dmri_mergepaths seperately using the following command and see if that works for you:
dmri_mergepaths --indir <main input dir> --in <path to all the path.pd.nii.gz files> --out <path to outputdir/merged_avg32_mni_flt.mgz> --ctab /usr/local/freesurfer/dev/FreeSurferColorLUT.txt --thresh .15
You should have a copy of this command in your log file you can copy paste that on to the terminal as well.
Can you try these things to see if it solves your problem?
-Priti
Everything looks to be running fine. Wether I look at the merged file with freeview or fslview, I still have only one tract. Here's an extract of the outputs :
Input files: lh.ccg_PP_avg33_mni_flt/path.pd.nii.gz lh.unc_AS_avg33_mni_flt/path.pd.nii.gz rh.ccg_PP_avg33_mni_flt/path.pd.nii.gz rh.unc_AS_avg33_mni_flt/path.pd.nii.gz Lower threshold for display: 0.150000 Merging volume 1 of 4... Threshold: 111 Name: Left Cingulum - Cingulate Gyrus Merging volume 2 of 4... Threshold: 74.85 Name: Left Uncinate Fasciculus Merging volume 3 of 4... Threshold: 87.9 Name: Right Cingulum - Cingulate Gyrus Merging volume 4 of 4... Threshold: 57.6 Name: Right Uncinate Fasciculus Done in 0.621 sec. dmri_mergepaths done
It remains the same if I take a very low threshold (0.001).
David
Am 24.08.2011 um 16:49 schrieb ayendiki@nmr.mgh.harvard.edu:
Yes, it should be a concatenation of all existing pathway reconstructions under dpath/... If you open it with trackvis --tv, you should be able to see a 3d view of all the pathways. Sometimes the default threshold might be too high for some pathways and you might need to adjust it individually in freeview to be able to see them.
Does the output of dmri_mergepaths show you that it's found multiple pathways or just ccg?
Yes, there are no more malloc issues, thanks for the update.
However I still have aays question, related to the merged_avg33_mni
file. It
still only contains the first path that was passed as an input to dmri_mergepaths. If I understand correctly I should see all generated paths, thresholded and merged into this file ?
David
Am 23.08.2011 um 21:28 schrieb Anastasia Yendiki:
Hi David - Thanks for catching this. There was something wrong with the new snow leopard build of dmri_mergepaths. (The original from the 5.1 distribution didn't have this problem). Sorry about that!
I've now updated the snow leopard tar file, so if you download it again you should not get this error any more.
As before it's here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz
Let me know how it goes, a.y
On Tue, 23 Aug 2011, David Coynel wrote:
Hi Anastasia,
Thanks for your answer. Unfortunately I overwrote the executables (I could still retrieve them from the website distribution ?). Interestingly this message does not show up when selecting only a subset of the pathways, as for example ( lh.ccg rh.ccg lh.unc rh.unc ), however the merged_avg33_mni file only appears to contain the first pathway (lh.ccg).
David
Am 23.08.2011 um 17:06 schrieb Anastasia Yendiki:
> > Hi David - Glad to hear things are working! I can look into > dmri_mergepaths and see if something is wrong with the snow leopard > build. > Have you by any chance kept the original leopard build of it? If you > haven't overwritten it, it'd be useful to run the same thing with > that > version and see if it works. Thanks! > > a.y > > On Tue, 23 Aug 2011, David Coynel wrote: > >> Dear Anastasia, >> >> Thanks a lot for the upload. The procedure now runs perfectly, >> except >> for that last message at the end of trac-all -path : >> >> >> Merging volume 18 of 18... >> Threshold: 68.1 Name: Right Uncinate Fasciculus >> dmri_mergepaths(26008) malloc: *** mmap(size=18446744073709543424) >> failed (error code=12) >> *** error: can't allocate region >> *** set a breakpoint in malloc_error_break to debug >> Done in 2.433 sec. >> dmri_mergepaths done >> #------------------------------------- >> trac-paths finished without error at Do 18 Aug 2011 11:39:42 CEST >> >> >> This however does not seem to affect the pipeline, as all the >> expected outputs seem to be present and valid. >> >> Dr. David Coynel >> Division of Cognitive Neuroscience >> >> University of Basel >> Birmannsgasse 8 >> 4055 Basel - Switzerland >> >> david.coynel@unibas.ch >> tel: +41(0)612.670.240 >> >> Am 17.08.2011 um 23:44 schrieb Anastasia Yendiki: >> >>> >>> Hi all - By popular demand we've posted the dmri_* executables >>> compiled on >>> snow leopard here: >>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz >>> >>> This is not the entire FS distribution, just the commands that are >>> called >>> by trac-all. If you are a mac user with snow leopard and have been >>> running >>> into memory issues with the leopard version, you can download >>> this, >>> copy >>> the new files into your $FREESURFER_HOME/bin, and try rerunning >>> the >>> part >>> of the analysis that had errored out. >>> >>> Let us know if there are any problems, >>> a.y >>> >>> _______________________________________________ >>> 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 mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-
Anastasia Yendiki -
ayendiki＠nmr.mgh.harvard.edu
-
David Coynel -
Priti Srinivasan