Hi Freesurfers,
I tried different ways to compile freesurfer for support cuda 9.1. Unfortunately, I still cannot get it work. While I tried to compile a specific module freesurfer/utils where the errors generated, I got the error message. Any suggestions would be appreciated!
gcc -DHAVE_CONFIG_H -I. -I.. -I../include -I../include/dicom -I../xml2 -I../include/NrrdIO -DTEEM_DIO=0 -DTEEM_32BIT=0 -DTEEM_QNANHIBIT=1 -DTEEM_ENDIAN=1234 -I../jpeg -I../tiff -I../expat -I/home/bc/software /environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit -I/home/bc/softwa re/environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit/Algorithms -I/h ome/bc/software/environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit/Ba sicFilters -I/home/bc/software/environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/In sightToolkit/Common -I/home/bc/software/environment/freesurfer_src/centos6-x86_64-packages/itk/current/i nclude/InsightToolkit/IO -I/home/bc/software/environment/freesurfer_src/centos6-x86_64-packages/itk/curr ent/include/InsightToolkit/Numerics -I/home/bc/software/environment/freesurfer_src/centos6-x86_64-packag es/itk/current/include/InsightToolkit/Numerics/Statistics -I/home/bc/software/environment/freesurfer_src /centos6-x86_64-packages/itk/current/include/InsightToolkit/Review -I/home/bc/software/environment/frees urfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit/Review/Statistics -I/home/bc/softwa re/environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit/SpatialObject - I/home/bc/software/environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit /Utilities -DHAVE_ITK_LIBS -I../glut -DHAVE_GLUT_LIBS -I/home/bc/software/environment/freesurfer_src/c entos6-x86_64-packages/vxl/current/include/vxl/core -I/home/bc/software/environment/freesurfer_src/cento s6-x86_64-packages/vxl/current/include/vxl/vcl -I/home/bc/software/environment/freesurfer_src/centos6-x8 6_64-packages/vxl/current/include/vxl/v3p/netlib -I/home/bc/software/environment/freesurfer_src/centos6- x86_64-packages/vxl/current/include/vxl/v3p/netlib/opt -I/usr/local/cuda/include -DHAVE_ZLIB -g -O3 -mss e2 -mfpmath=sse -Wall -Wno-unused-but-set-variable -DUSE_SSE_MATHFUN -fopenmp -DHAVE_OPENMP -m64 -DLinx -DANSI -fdata-sections -ffunction-sections -Wl,--gc-sections -I/home/bc/software/environment/freesurfe r_src/centos6-x86_64-packages/mni/current/include -DFS_CUDA -I/usr/local/cuda/include -MT libutils_cud a_a-mrishash.o -MD -MP -MF .deps/libutils_cuda_a-mrishash.Tpo -c -o libutils_cuda_a-mrishash.o `test -f 'mrishash.c' || echo './'`mrishash.c mrifilter.c: In function ‘MRIconvolveGaussian’: mrifilter.c:2618:7: error: ‘width’ undeclared (first use in this function) if (width <= 1 || height <= 1 || depth <= 1) ^ mrifilter.c:2618:7: note: each undeclared identifier is reported only once for each function it appears in mrifilter.c:2618:21: error: ‘height’ undeclared (first use in this function) if (width <= 1 || height <= 1 || depth <= 1) ^ mrifilter.c:2618:36: error: ‘depth’ undeclared (first use in this function) if (width <= 1 || height <= 1 || depth <= 1) ^ Makefile:4419: recipe for target 'libutils_cuda_a-mrifilter.o' failed make[3]: *** [libutils_cuda_a-mrifilter.o] Error 1 make[3]: *** Waiting for unfinished jobs.... mv -f .deps/libutils_cuda_a-mriprob.Tpo .deps/libutils_cuda_a-mriprob.Po mv -f .deps/libutils_cuda_a-mrisbiorthogonalwavelets.Tpo .deps/libutils_cuda_a-mrisbiorthogonalwavelets. Po mv -f .deps/libutils_cuda_a-mrisegment.Tpo .deps/libutils_cuda_a-mrisegment.Po mv -f .deps/libutils_cuda_a-mrishash.Tpo .deps/libutils_cuda_a-mrishash.Po mv -f .deps/libutils_cuda_a-mrinorm.Tpo .deps/libutils_cuda_a-mrinorm.Po mv -f .deps/libutils_cuda_a-mripolv.Tpo .deps/libutils_cuda_a-mripolv.Po mv -f .deps/libutils_cuda_a-mriset.Tpo .deps/libutils_cuda_a-mriset.Po make[3]: Leaving directory '/home/bc/software/environment/freesurfer_src/freesurfer/utils' Makefile:6230: recipe for target 'all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory '/home/bc/software/environment/freesurfer_src/freesurfer/utils' Makefile:1060: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/home/bc/software/environment/freesurfer_src/freesurfer' Makefile:970: recipe for target 'all' failed make: *** [all] Error 2
Best, Foucault
Dear Freesurfers,
I made some modification and finally can compile freesurfer that gets recon-all with cuda9.1 support. However, I am sure if the modification would incur unexpected results. The modification I made is as following: 1. taking out comments in the file mrifilter.c to declare the width, height, and depth variable 2. a little hack that makes `priors[i] = gcaSample[i].prior;` to `priors[i] = 1;` in the file utils/gcasgpu.cu (I am not sure what this line means, just a quick hack to get it pass errors, which is gcaSample[i].prior didn’t exist) 3. explicitly specify the NVIDIA_ARCH="sm_50" and CUDA_DIR="/usr/local/cuda" in configure.in
Any suggestions would be appreciated!
Best, Foucault
On Sat, Jan 13, 2018 at 9:39 AM zuxfoucault Wong zuxfoucault@gmail.com wrote:
Hi Freesurfers,
I tried different ways to compile freesurfer for support cuda 9.1. Unfortunately, I still cannot get it work. While I tried to compile a specific module freesurfer/utils where the errors generated, I got the error message. Any suggestions would be appreciated!
gcc -DHAVE_CONFIG_H -I. -I.. -I../include -I../include/dicom -I../xml2 -I../include/NrrdIO -DTEEM_DIO=0 -DTEEM_32BIT=0 -DTEEM_QNANHIBIT=1 -DTEEM_ENDIAN=1234 -I../jpeg -I../tiff -I../expat -I/home/bc/software /environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit -I/home/bc/softwa re/environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit/Algorithms -I/h
ome/bc/software/environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit/Ba sicFilters -I/home/bc/software/environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/In sightToolkit/Common -I/home/bc/software/environment/freesurfer_src/centos6-x86_64-packages/itk/current/i nclude/InsightToolkit/IO -I/home/bc/software/environment/freesurfer_src/centos6-x86_64-packages/itk/curr ent/include/InsightToolkit/Numerics -I/home/bc/software/environment/freesurfer_src/centos6-x86_64-packag es/itk/current/include/InsightToolkit/Numerics/Statistics -I/home/bc/software/environment/freesurfer_src /centos6-x86_64-packages/itk/current/include/InsightToolkit/Review -I/home/bc/software/environment/frees urfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit/Review/Statistics -I/home/bc/softwa re/environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit/SpatialObject
I/home/bc/software/environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit /Utilities -DHAVE_ITK_LIBS -I../glut -DHAVE_GLUT_LIBS -I/home/bc/software/environment/freesurfer_src/c entos6-x86_64-packages/vxl/current/include/vxl/core -I/home/bc/software/environment/freesurfer_src/cento s6-x86_64-packages/vxl/current/include/vxl/vcl -I/home/bc/software/environment/freesurfer_src/centos6-x8 6_64-packages/vxl/current/include/vxl/v3p/netlib -I/home/bc/software/environment/freesurfer_src/centos6- x86_64-packages/vxl/current/include/vxl/v3p/netlib/opt -I/usr/local/cuda/include -DHAVE_ZLIB -g -O3 -mss e2 -mfpmath=sse -Wall -Wno-unused-but-set-variable -DUSE_SSE_MATHFUN -fopenmp -DHAVE_OPENMP -m64 -DLinx -DANSI -fdata-sections -ffunction-sections -Wl,--gc-sections -I/home/bc/software/environment/freesurfe r_src/centos6-x86_64-packages/mni/current/include -DFS_CUDA -I/usr/local/cuda/include -MT libutils_cud a_a-mrishash.o -MD -MP -MF .deps/libutils_cuda_a-mrishash.Tpo -c -o libutils_cuda_a-mrishash.o `test -f 'mrishash.c' || echo './'`mrishash.c mrifilter.c: In function ‘MRIconvolveGaussian’: mrifilter.c:2618:7: error: ‘width’ undeclared (first use in this function) if (width <= 1 || height <= 1 || depth <= 1) ^ mrifilter.c:2618:7: note: each undeclared identifier is reported only once for each function it appears in mrifilter.c:2618:21: error: ‘height’ undeclared (first use in this function) if (width <= 1 || height <= 1 || depth <= 1) ^ mrifilter.c:2618:36: error: ‘depth’ undeclared (first use in this function) if (width <= 1 || height <= 1 || depth <= 1) ^ Makefile:4419: recipe for target 'libutils_cuda_a-mrifilter.o' failed make[3]: *** [libutils_cuda_a-mrifilter.o] Error 1 make[3]: *** Waiting for unfinished jobs.... mv -f .deps/libutils_cuda_a-mriprob.Tpo .deps/libutils_cuda_a-mriprob.Po mv -f .deps/libutils_cuda_a-mrisbiorthogonalwavelets.Tpo .deps/libutils_cuda_a-mrisbiorthogonalwavelets. Po mv -f .deps/libutils_cuda_a-mrisegment.Tpo .deps/libutils_cuda_a-mrisegment.Po mv -f .deps/libutils_cuda_a-mrishash.Tpo .deps/libutils_cuda_a-mrishash.Po mv -f .deps/libutils_cuda_a-mrinorm.Tpo .deps/libutils_cuda_a-mrinorm.Po mv -f .deps/libutils_cuda_a-mripolv.Tpo .deps/libutils_cuda_a-mripolv.Po mv -f .deps/libutils_cuda_a-mriset.Tpo .deps/libutils_cuda_a-mriset.Po make[3]: Leaving directory '/home/bc/software/environment/freesurfer_src/freesurfer/utils' Makefile:6230: recipe for target 'all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory '/home/bc/software/environment/freesurfer_src/freesurfer/utils' Makefile:1060: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/home/bc/software/environment/freesurfer_src/freesurfer' Makefile:970: recipe for target 'all' failed make: *** [all] Error 2
Best, Foucault
On 13 January 2018 at 06:11, zuxfoucault Wong zuxfoucault@gmail.com wrote:
I made some modification and finally can compile freesurfer that gets recon-all with cuda9.1 support.
I will try to make time to find out if there are still compile issues. It's been a while since I tried a recompile.
However, I am sure if the modification would incur unexpected results.
That's entirely possible, and there aren't any automated tests to examine this. The best test is to run a comparison between the CPU and GPU, and see if the final segmentations are significantly different (that they will be different is a given).
Richard
Dear experts, Is the corpus callosum volume included in the 'cortical White matter' volume?
Thank you, Best, Elisabetta
Get Outlook for iOShttps://aka.ms/o0ukef ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of R Edgar freesurfer.rge@gmail.com Sent: Monday, January 15, 2018 7:25:47 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer compilation for supporting cuda9.1
On 13 January 2018 at 06:11, zuxfoucault Wong zuxfoucault@gmail.com wrote:
I made some modification and finally can compile freesurfer that gets recon-all with cuda9.1 support.
I will try to make time to find out if there are still compile issues. It's been a while since I tried a recompile.
However, I am sure if the modification would incur unexpected results.
That's entirely possible, and there aren't any automated tests to examine this. The best test is to run a comparison between the CPU and GPU, and see if the final segmentations are significantly different (that they will be different is a given).
Richard _______________________________________________ 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.
Hello Elisabetta -
The Corpus callosal volumes are included in the ASEG output and not in the WM files. They are titled CC_Anterior, CC_Midbody etc.
Best,
Alan
On Mon, Jan 15, 2018 at 2:11 PM, Del Re, Elisabetta < Elisabetta_DelRe@hms.harvard.edu> wrote:
Dear experts, Is the corpus callosum volume included in the 'cortical White matter' volume?
Thank you, Best, Elisabetta
Get Outlook for iOS https://aka.ms/o0ukef
Alan,
thank you.
Of course, but my question was different:
Is the volume of the corpus callosum included in the calculation of the volume of the 'cerebral white matter'? Or does the volume of the cerebral white matter not include the volume of the corpus?
My understanding is that the volume of the corpus is included in the calculation of the volume of the cerebral white matter.
Can you confirm?
Thank you,
Elisabetta
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alan Francis alandarkenergy@gmail.com Sent: Tuesday, January 16, 2018 11:42 AM To: Freesurfer support list Subject: Re: [Freesurfer] Cortical White matter/corpus callisum
Hello Elisabetta -
The Corpus callosal volumes are included in the ASEG output and not in the WM files. They are titled CC_Anterior, CC_Midbody etc.
Best,
Alan
On Mon, Jan 15, 2018 at 2:11 PM, Del Re, Elisabetta <Elisabetta_DelRe@hms.harvard.edumailto:Elisabetta_DelRe@hms.harvard.edu> wrote: Dear experts, Is the corpus callosum volume included in the 'cortical White matter' volume?
Thank you, Best, Elisabetta
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Alan N. Francis PhD Instructor - Imaging Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf@bwh.harvard.edumailto:ezra_wegbreit@brown.edu afrancis@mclean.harvard.edumailto:afrancis@mclean.harvard.edu
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Hi Elisabetta -
Yes it is included in the calculation of the cerebral WM. Since the CC is a WM tract comprising the Forceps Minor and Major, it is part of the WM calculation.
best,
Alan
On Tue, Jan 16, 2018 at 11:58 AM, Del Re, Elisabetta < Elisabetta_DelRe@hms.harvard.edu> wrote:
Alan,
thank you.
Of course, but my question was different:
Is the volume of the corpus callosum included in the calculation of the volume of the 'cerebral white matter'? Or does the volume of the cerebral white matter not include the volume of the corpus?
My understanding is that the volume of the corpus is included in the calculation of the volume of the cerebral white matter.
Can you confirm?
Thank you,
Elisabetta
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alan Francis < alandarkenergy@gmail.com> *Sent:* Tuesday, January 16, 2018 11:42 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Cortical White matter/corpus callisum
Hello Elisabetta -
The Corpus callosal volumes are included in the ASEG output and not in the WM files. They are titled CC_Anterior, CC_Midbody etc.
Best,
Alan
On Mon, Jan 15, 2018 at 2:11 PM, Del Re, Elisabetta < Elisabetta_DelRe@hms.harvard.edu> wrote:
Dear experts, Is the corpus callosum volume included in the 'cortical White matter' volume?
Thank you, Best, Elisabetta
-- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
- Alan N. Francis PhD*
Instructor - Imaging Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf@bwh.harvard.edu ezra_wegbreit@brown.edu afrancis@mclean.harvard.edu
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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