Hello,
I have been successfully running FreeSurfer 4.5 on my MacOSX 10.5.8 with no issues. I recently installed FreeSurfer 5.1 to a separate directory on the same laptop to analyze a new dataset and I am now having various issues with both FreeSurfer versions.
1. For Version 4.5, I path the freesurfer directories as follows (identical to before installing new program):
setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir source $FREESURFER_HOME/SetUpFreeSurfer.csh
--------- freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir MNI_DIR /Applications/freesurfer/mni
The issue is that now various commands are no longer found in version 4.5. For example when typing tkmedit, tksurfer or qdec, I get the following type of error:
tkmedit.bin: Command not found.
Is it possible that, although I installed version 5.1 in a separate directory, that some files were deleted or moved in version 4.5? Is my 4.5 license no longer valid now that I have installed version 5.1 with a new license? It is confusing since some commands appear to function, such as mri_convert and recon-all, but anything involving a GUI seems not to function.
2. For version 5.1, I believe the program is successfully installed and pathed. I have been able to use it to convert files to mgz, tkmedit and tksurfer work fine, however, I get the same error each time I run recon-all with each participant (one of which was previously successfully processed using version 4.5). The recon-all error occurs early during motion correction of the 2 structural runs:
Resolution: 0 S( 512 512 352 ) T( 512 512 352 ) Iteration(f): 1 (subsample 200) mri_robust_template(3271) malloc: *** mmap(size=1048576) failed (error code=12)*** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(512, 512, 352): could not allocate 1048576 bytes for 258th slice
Cannot allocate memory Darwin jennifer-phillipss-macbook-pro.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
recon-all -s SS002 exited with ERRORS at Fri Nov 4 10:04:46 EDT 2011
Any ideas on what might be causing this error? I have 4 GB memory.
thanks, Jennifer Addicks University of Ottawa
Hi Jennifer
for question 2. You run out of memory. How many within session inputs are you trying to motion correct?
You can a) try downsample your hi-res images before processing b) try to only select a single input to recon-all instead of averaging inputs.
Best, Martin
On Tue, 2011-11-08 at 13:35 -0500, Jennifer Addicks wrote:
Hello,
I have been successfully running FreeSurfer 4.5 on my MacOSX 10.5.8 with no issues. I recently installed FreeSurfer 5.1 to a separate directory on the same laptop to analyze a new dataset and I am now having various issues with both FreeSurfer versions.
- For Version 4.5, I path the freesurfer directories as follows
(identical to before installing new program):
setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir source $FREESURFER_HOME/SetUpFreeSurfer.csh
--------- freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir MNI_DIR /Applications/freesurfer/mni
The issue is that now various commands are no longer found in version 4.5. For example when typing tkmedit, tksurfer or qdec, I get the following type of error:
tkmedit.bin: Command not found.
Is it possible that, although I installed version 5.1 in a separate directory, that some files were deleted or moved in version 4.5? Is my 4.5 license no longer valid now that I have installed version 5.1 with a new license? It is confusing since some commands appear to function, such as mri_convert and recon-all, but anything involving a GUI seems not to function.
- For version 5.1, I believe the program is successfully installed
and pathed. I have been able to use it to convert files to mgz, tkmedit and tksurfer work fine, however, I get the same error each time I run recon-all with each participant (one of which was previously successfully processed using version 4.5). The recon-all error occurs early during motion correction of the 2 structural runs:
Resolution: 0 S( 512 512 352 ) T( 512 512 352 ) Iteration(f): 1 (subsample 200) mri_robust_template(3271) malloc: *** mmap(size=1048576) failed (error code=12)*** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(512, 512, 352): could not allocate 1048576 bytes for 258th slice
Cannot allocate memory Darwin jennifer-phillipss-macbook-pro.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
recon-all -s SS002 exited with ERRORS at Fri Nov 4 10:04:46 EDT 2011
Any ideas on what might be causing this error? I have 4 GB memory.
thanks, Jennifer Addicks University of Ottawa
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry for incremental updates:
c) you can pass the -flirt-motioncor flag to recon all to revert to the old way (using flirt)
If your scans are decent quality I would recommend b) as it is unclear if averaging actually helps.
-Martin
On Tue, 2011-11-08 at 13:45 -0500, Martin Reuter wrote:
Hi Jennifer
for question 2. You run out of memory. How many within session inputs are you trying to motion correct?
You can a) try downsample your hi-res images before processing b) try to only select a single input to recon-all instead of averaging inputs.
Best, Martin
On Tue, 2011-11-08 at 13:35 -0500, Jennifer Addicks wrote:
Hello,
I have been successfully running FreeSurfer 4.5 on my MacOSX 10.5.8 with no issues. I recently installed FreeSurfer 5.1 to a separate directory on the same laptop to analyze a new dataset and I am now having various issues with both FreeSurfer versions.
- For Version 4.5, I path the freesurfer directories as follows
(identical to before installing new program):
setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir source $FREESURFER_HOME/SetUpFreeSurfer.csh
--------- freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir MNI_DIR /Applications/freesurfer/mni
The issue is that now various commands are no longer found in version 4.5. For example when typing tkmedit, tksurfer or qdec, I get the following type of error:
tkmedit.bin: Command not found.
Is it possible that, although I installed version 5.1 in a separate directory, that some files were deleted or moved in version 4.5? Is my 4.5 license no longer valid now that I have installed version 5.1 with a new license? It is confusing since some commands appear to function, such as mri_convert and recon-all, but anything involving a GUI seems not to function.
- For version 5.1, I believe the program is successfully installed
and pathed. I have been able to use it to convert files to mgz, tkmedit and tksurfer work fine, however, I get the same error each time I run recon-all with each participant (one of which was previously successfully processed using version 4.5). The recon-all error occurs early during motion correction of the 2 structural runs:
Resolution: 0 S( 512 512 352 ) T( 512 512 352 ) Iteration(f): 1 (subsample 200) mri_robust_template(3271) malloc: *** mmap(size=1048576) failed (error code=12)*** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(512, 512, 352): could not allocate 1048576 bytes for 258th slice
Cannot allocate memory Darwin jennifer-phillipss-macbook-pro.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
recon-all -s SS002 exited with ERRORS at Fri Nov 4 10:04:46 EDT 2011
Any ideas on what might be causing this error? I have 4 GB memory.
thanks, Jennifer Addicks University of Ottawa
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
I see you have only two inputs. 4GB should be enough. Are you running a lot of other stuff that takes up memory?
-Martin
On Tue, 2011-11-08 at 13:35 -0500, Jennifer Addicks wrote:
Hello,
I have been successfully running FreeSurfer 4.5 on my MacOSX 10.5.8 with no issues. I recently installed FreeSurfer 5.1 to a separate directory on the same laptop to analyze a new dataset and I am now having various issues with both FreeSurfer versions.
- For Version 4.5, I path the freesurfer directories as follows
(identical to before installing new program):
setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir source $FREESURFER_HOME/SetUpFreeSurfer.csh
--------- freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir MNI_DIR /Applications/freesurfer/mni
The issue is that now various commands are no longer found in version 4.5. For example when typing tkmedit, tksurfer or qdec, I get the following type of error:
tkmedit.bin: Command not found.
Is it possible that, although I installed version 5.1 in a separate directory, that some files were deleted or moved in version 4.5? Is my 4.5 license no longer valid now that I have installed version 5.1 with a new license? It is confusing since some commands appear to function, such as mri_convert and recon-all, but anything involving a GUI seems not to function.
- For version 5.1, I believe the program is successfully installed
and pathed. I have been able to use it to convert files to mgz, tkmedit and tksurfer work fine, however, I get the same error each time I run recon-all with each participant (one of which was previously successfully processed using version 4.5). The recon-all error occurs early during motion correction of the 2 structural runs:
Resolution: 0 S( 512 512 352 ) T( 512 512 352 ) Iteration(f): 1 (subsample 200) mri_robust_template(3271) malloc: *** mmap(size=1048576) failed (error code=12)*** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(512, 512, 352): could not allocate 1048576 bytes for 258th slice
Cannot allocate memory Darwin jennifer-phillipss-macbook-pro.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
recon-all -s SS002 exited with ERRORS at Fri Nov 4 10:04:46 EDT 2011
Any ideas on what might be causing this error? I have 4 GB memory.
thanks, Jennifer Addicks University of Ottawa
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Jennifer Addicks -
Martin Reuter