From smiile-lists5281@mailzoo.com Wed Sep 1 17:45:05 2004 From: smiile-lists5281@mailzoo.com (Jon Frederick) Date: Wed Sep 1 16:45:05 2004 Subject: [MINC-users] problem installing N3 on Mac G5 Message-ID: Hello, I seem to be able to configure with no problem, but I get errors involving "evaluate field", "all recursive", and ld: undefined symbol: _dsysv_ Here's the output of make. Any clues? Thanks in advance, Jon Frederick University of Texas Houston Health Science Center Making all in testing make[1]: Nothing to be done for `all'. if gcc -DHAVE_CONFIG_H -I. -I. -I./include -DUSE_COMPMAT -DUSE_DBLMAT -I/usr/local/mni/include -g -O2 -MT src/MincProg/print_version.o -MD -MP -MF "src/MincProg/.deps/print_version.Tpo" \ -c -o src/MincProg/print_version.o `test -f 'src/MincProg/print_version.c' || echo './'`src/MincProg/print_version.c; \ then mv "src/MincProg/.deps/print_version.Tpo" "src/MincProg/.deps/print_version.Po"; \ else rm -f "src/MincProg/.deps/print_version.Tpo"; exit 1; \ fi rm -f libmincprog.a ar cru libmincprog.a src/MincProg/print_version.o ranlib libmincprog.a if g++ -DHAVE_CONFIG_H -I. -I. -I./include -DUSE_COMPMAT -DUSE_DBLMAT -I/usr/local/mni/include -g -O2 -MT src/EvaluateField/evaluateFieldArgs.o -MD -MP -MF "src/EvaluateField/.deps/evaluateFieldArgs.Tpo" \ -c -o src/EvaluateField/evaluateFieldArgs.o `test -f 'src/EvaluateField/evaluateFieldArgs.cc' || echo './'`src/EvaluateField/evaluateFieldArgs.cc; \ then mv "src/EvaluateField/.deps/evaluateFieldArgs.Tpo" "src/EvaluateField/.deps/evaluateFieldArgs.Po"; \ else rm -f "src/EvaluateField/.deps/evaluateFieldArgs.Tpo"; exit 1; \ fi g++ -g -O2 -L/usr/local/mni/lib -o evaluate_field src/EvaluateField/evaluateField.o src/EvaluateField/evaluateFieldArgs.o src/SplineSmooth/fieldIO.o libmincprog.a -lvolume_io -lminc -lnetcdf -lm -lEBTKS -lvolume_io -lminc -lnetcdf -lm -lEBTKS ld: warning table of contents of library: /usr/local/mni/lib/libminc.a not sorted slower link editing will result (use the ranlib(1) -s option) ld: warning table of contents of library: /usr/local/mni/lib/libminc.a not sorted slower link editing will result (use the ranlib(1) -s option) ld: Undefined symbols: _dsysv_ make[1]: *** [evaluate_field] Error 1 make: *** [all-recursive] Error 1 From smiile-lists5281@mailzoo.com Wed Sep 1 20:17:04 2004 From: smiile-lists5281@mailzoo.com (Jon Frederick) Date: Wed Sep 1 19:17:04 2004 Subject: [MINC-users] problem installing N3 on Mac G5 In-Reply-To: References: Message-ID: Aha! You were right. We were using ./configure --with-build-path=/usr/local/mni There was an old version of libEBTKS.a in /usr/local/mni/lib Replacing it with the one we recently installed in /usr/local/lib solved the problem. Thanks! JON On Wed, 1 Sep 2004, Robert VINCENT wrote: > Jon, > > Thanks. The dsysv() function should be present in the EBTKS library as of > 1.3. Can you check your version of libEBTKS.a and confirm that it > contains an object file named dsysv.o and symbol named dsysv_ or _dsysv_? > You might also want to verify that there isn't an older version of > libEBTKS.a somewhere on the system. > > -bert > > > On Wed, 1 Sep 2004, Jon Frederick wrote: > >> Hi Bert, >> our version of EBTKS is 1.3. >> configure confirms seeing the EBTKS library when running. >> >> We are running a Mac G5 with Mac OS X (Darwin). >> >> thanks, >> JON >> >> On Wed, 1 Sep 2004, Robert VINCENT wrote: >> >>> Hi Jon, >>> >>> I'm not sure what is happening, but it could be that your EBTKS >>> library is out of date. Which version of the EBTKS library have you >>> installed? >>> >>> Also, what type of computer and operating system are you using? >>> >>> -bert >>> >>> On Wed, 1 Sep 2004, Jon Frederick wrote: >>> >>>> Hello, >>>> I seem to be able to configure with no problem, but I get errors involving >>>> "evaluate field", "all recursive", and ld: undefined symbol: _dsysv_ >>>> >>>> Here's the output of make. Any clues? >>>> >>>> Thanks in advance, >>>> Jon Frederick >>>> University of Texas Houston Health Science Center >>>> >>>> >>>> Making all in testing >>>> make[1]: Nothing to be done for `all'. >>>> if gcc -DHAVE_CONFIG_H -I. -I. -I./include -DUSE_COMPMAT -DUSE_DBLMAT >>>> -I/usr/local/mni/include -g -O2 -MT src/MincProg/print_version.o -MD -MP >>>> -MF "src/MincProg/.deps/print_version.Tpo" \ >>>> -c -o src/MincProg/print_version.o `test -f >>>> 'src/MincProg/print_version.c' || echo './'`src/MincProg/print_version.c; >>>> \ >>>> then mv "src/MincProg/.deps/print_version.Tpo" >>>> "src/MincProg/.deps/print_version.Po"; \ >>>> else rm -f "src/MincProg/.deps/print_version.Tpo"; exit 1; \ >>>> fi >>>> rm -f libmincprog.a >>>> ar cru libmincprog.a src/MincProg/print_version.o >>>> ranlib libmincprog.a >>>> if g++ -DHAVE_CONFIG_H -I. -I. -I./include -DUSE_COMPMAT -DUSE_DBLMAT >>>> -I/usr/local/mni/include -g -O2 -MT src/EvaluateField/evaluateFieldArgs.o >>>> -MD -MP -MF "src/EvaluateField/.deps/evaluateFieldArgs.Tpo" \ >>>> -c -o src/EvaluateField/evaluateFieldArgs.o `test -f >>>> 'src/EvaluateField/evaluateFieldArgs.cc' || echo >>>> './'`src/EvaluateField/evaluateFieldArgs.cc; \ >>>> then mv "src/EvaluateField/.deps/evaluateFieldArgs.Tpo" >>>> "src/EvaluateField/.deps/evaluateFieldArgs.Po"; \ >>>> else rm -f "src/EvaluateField/.deps/evaluateFieldArgs.Tpo"; exit 1; \ >>>> fi >>>> g++ -g -O2 -L/usr/local/mni/lib -o evaluate_field >>>> src/EvaluateField/evaluateField.o src/EvaluateField/evaluateFieldArgs.o >>>> src/SplineSmooth/fieldIO.o libmincprog.a -lvolume_io -lminc -lnetcdf -lm >>>> -lEBTKS -lvolume_io -lminc -lnetcdf -lm -lEBTKS >>>> ld: warning table of contents of library: /usr/local/mni/lib/libminc.a not >>>> sorted slower link editing will result (use the ranlib(1) -s option) >>>> ld: warning table of contents of library: /usr/local/mni/lib/libminc.a not >>>> sorted slower link editing will result (use the ranlib(1) -s option) >>>> ld: Undefined symbols: >>>> _dsysv_ >>>> make[1]: *** [evaluate_field] Error 1 >>>> make: *** [all-recursive] Error 1 >>>> >>>> _______________________________________________ >>>> MINC-users@bic.mni.mcgill.ca >>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>>> >>> >>> >> > > From smiile-lists5281@mailzoo.com Mon Sep 6 19:27:04 2004 From: smiile-lists5281@mailzoo.com (Jon Frederick) Date: Mon Sep 6 18:27:04 2004 Subject: [MINC-users] losing bytes when converting to/from minc Message-ID: Hello, when we convert our raw file to minc and back to raw with the following commands, our image browser complains that it has reached the end of the file and, in fact, the output of minctoraw is 16 bytes shorter. Any idea where these bytes are going? # dd conv=swab if=eih0060t1.al0 | rawtominc -coronal -byte -unsigned -ystep 1 -zstep 1 -xstep 1 -mri -origin 0 0 0 -range 0 255 -real_range 0 255 -clobber temp.mnc 256 256 256 32768+1 records in 32768+1 records out 16777232 bytes transferred in 0.771042 secs (21759164 bytes/sec) total 98376 # minctoraw -range 0 255 -normalize temp.mnc | dd conv=swab of=temp.al0 32768+0 records in 32768+0 records out 16777216 bytes transferred in 0.714025 secs (23496678 bytes/sec) nal7:/private/var/root/nucorrect.dir root# ls -l -rw-r--r-- 1 root wheel 16777232 1 Sep 17:33 eih0060t1.al0 -rw-r--r-- 1 root wheel 16777216 6 Sep 17:17 temp.al0 -rw-r--r-- 1 root wheel 16783884 6 Sep 17:17 temp.mnc From sylvain@bic.mni.mcgill.ca Mon Sep 6 21:51:04 2004 From: sylvain@bic.mni.mcgill.ca (Sylvain MILOT) Date: Mon Sep 6 20:51:04 2004 Subject: [MINC-users] losing bytes when converting to/from minc In-Reply-To: Message-ID: Hello, I would suggest that your assumption about the size of your volume's dimensions is wrong since 256*256*256 = 16777216, hence rawtominc did exactly what you asked it to do, it stored 16777216 raw bytes + a header (and dropped the last 16 bytes). Sylvain On Mon, 6 Sep 2004, Jon Frederick wrote: > Hello, > when we convert our raw file to minc and back to raw with the following > commands, our image browser complains that it has reached the end of the > file and, in fact, the output of minctoraw is 16 bytes shorter. Any idea > where these bytes are going? > > # dd conv=swab if=eih0060t1.al0 | rawtominc -coronal -byte -unsigned > -ystep 1 -zstep 1 -xstep 1 -mri -origin 0 0 0 -range 0 255 -real_range 0 > 255 -clobber temp.mnc 256 256 256 > > 32768+1 records in > 32768+1 records out > 16777232 bytes transferred in 0.771042 secs (21759164 bytes/sec) > > total 98376 > # minctoraw -range 0 255 -normalize temp.mnc | dd conv=swab of=temp.al0 > > 32768+0 records in > 32768+0 records out > 16777216 bytes transferred in 0.714025 secs (23496678 bytes/sec) > > nal7:/private/var/root/nucorrect.dir root# ls -l > -rw-r--r-- 1 root wheel 16777232 1 Sep 17:33 eih0060t1.al0 > -rw-r--r-- 1 root wheel 16777216 6 Sep 17:17 temp.al0 > -rw-r--r-- 1 root wheel 16783884 6 Sep 17:17 temp.mnc > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > --- Sylvain Milot (sylvain@bic.mni.mcgill.ca) (trinity@bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute Webster 2B, Room 208 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, 1996 Fax: 8948 Mobile : (514) 712-1768 Office : 527 Pine, room 204 From rotor@cmr.uq.edu.au Mon Sep 6 22:09:04 2004 From: rotor@cmr.uq.edu.au (Andrew Janke) Date: Mon Sep 6 21:09:04 2004 Subject: [MINC-users] losing bytes when converting to/from minc In-Reply-To: References: Message-ID: > On Mon, 6 Sep 2004, Jon Frederick wrote: > > > # dd conv=swab if=eih0060t1.al0 | rawtominc -coronal -byte -unsigned > > -ystep 1 -zstep 1 -xstep 1 -mri -origin 0 0 0 -range 0 255 -real_range 0 > > 255 -clobber temp.mnc 256 256 256 You may also be interested to note that in later releases of MINC 1.x (and 2.x) you could achieve the same result as above without dd via the -swap_bytes option in rawtominc. ie: # rawtominc -coronal -byte -unsigned -ystep 1 -zstep 1 -xstep 1 \ -mri -origin 0 0 0 -range 0 255 -real_range 0 255 \ -clobber -swap_bytes -input eih0060t1.al0 \ temp.mnc 256 256 256 -- Andrew Janke (rotor@cmr.uq.edu DOT au || www.cmr.uq.edu.au/~rotor) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3232 7254 || H: +61 7 3879 0374 || M: +61 4 2138 8581 From bert@bic.mni.mcgill.ca Tue Sep 7 17:10:04 2004 From: bert@bic.mni.mcgill.ca (Robert VINCENT) Date: Tue Sep 7 16:10:04 2004 Subject: [MINC-users] Display 1.3.9 and Register 1.3.5 Message-ID: Hi everyone, I've posted new source distributions for Display 1.3.9 and Register 1.3.5. The changes are minor, primarily intended to fix build issues with FreeGLUT. The only used-visible change is that Register should now permit saving a slice viewport on any system with ImageMagick installed. The file will be saved as a TIFF. Please send all comments/questions to me, -bert From smiile-lists5281@mailzoo.com Sun Sep 12 19:19:04 2004 From: smiile-lists5281@mailzoo.com (Jon Frederick) Date: Sun Sep 12 18:19:04 2004 Subject: [MINC-users] proper use of nu_correct Message-ID: Hello, We're hoping someone can explain what we're doing wrong with nu_correct. We introduced an artificial bias field into a 256x256x256 MRI image, that increased by one (on a pixel intensity scale of zero to 256) with each coronal slice (only in the masked area of the brain... the unmasked area remained black or zero). We ran nu_correct -iterations 150 -stop .00001 temp.mnc -clobber temp-corr.mnc After converting the output image back to raw and putting our header back on, the bias field could still easily be seen in the sagittal or axial views. nu_estimate of the uncorrected file returns c.v of field change=7.6 e-5. For the corrected file, the value is 2.5 e-5. Are both of these numbers rather small? John Sled's dissertation shows graphs with c.v.'s on the scale of 0.01. Could the problem be related to our conversion to minc format? I.e., dd conv=swab if=temp.raw | rawtominc -coronal -byte -unsigned -ystep 1 -zstep 1 -xstep 1 -mri -origin 0 0 0 -range 0 255 -real_range 0 255 -clobber temp.mnc 256 256 256 Apologies in advance if this is a really dumb question. Thanks in advance, Jon Frederick, Ph.D. University of Texas Health Science Center From jason@bic.mni.mcgill.ca Mon Sep 13 10:53:04 2004 From: jason@bic.mni.mcgill.ca (Jason Lerch) Date: Mon Sep 13 09:53:04 2004 Subject: [MINC-users] proper use of nu_correct In-Reply-To: References: Message-ID: <0226F7AE-058C-11D9-A098-000A95DBBFD8@bic.mni.mcgill.ca> First question: what version of N3 are you using? We did have some bugs recently, so you should make sure to grab the latest sources of the web-age - I believe the most up-to-date release is 1.09. Let us know if the problems you are encountering are indeed with that version. Cheers, Jason On Sep 12, 2004, at 6:47 PM, Jon Frederick wrote: > Hello, > We're hoping someone can explain what we're doing wrong with > nu_correct. > > We introduced an artificial bias field into a 256x256x256 MRI image, > that increased by one (on a pixel intensity scale of zero to 256) with > each coronal slice (only in the masked area of the brain... the > unmasked area remained black or zero). > > We ran > nu_correct -iterations 150 -stop .00001 temp.mnc -clobber temp-corr.mnc > > After converting the output image back to raw and putting our header > back on, the bias field could still easily be seen in the sagittal or > axial views. > > nu_estimate of the uncorrected file returns c.v of field change=7.6 > e-5. For the corrected file, the value is 2.5 e-5. Are both of these > numbers rather small? John Sled's dissertation shows graphs with > c.v.'s on the scale of 0.01. > > Could the problem be related to our conversion to minc format? I.e., > dd conv=swab if=temp.raw | rawtominc -coronal -byte -unsigned -ystep 1 > -zstep 1 -xstep 1 -mri -origin 0 0 0 -range 0 255 -real_range 0 255 > -clobber temp.mnc 256 256 256 > > Apologies in advance if this is a really dumb question. > > Thanks in advance, > > Jon Frederick, Ph.D. > University of Texas Health Science Center > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From vsingh@bic.mni.mcgill.ca Mon Sep 13 11:46:04 2004 From: vsingh@bic.mni.mcgill.ca (Vivek SINGH) Date: Mon Sep 13 10:46:04 2004 Subject: [MINC-users] proper use of nu_correct In-Reply-To: Message-ID: Hi Jon, Remember that N3 expects the RF imhomogeneity to be multiplicative and slowly varying across the image. For example, a 60% imhomogeneity field (fairly high) has values ranging from about 0.5 to 1.3. In your case, the values exceed this variation within a couple of slices. Maybe trying a bias field varying within a 0.5 to 1.5 range from the top to the bottom of the image might be a better test. Hope that helps, Vivek On Sun, 12 Sep 2004, Jon Frederick wrote: > Hello, > We're hoping someone can explain what we're doing wrong with nu_correct. > > We introduced an artificial bias field into a 256x256x256 MRI image, that > increased by one (on a pixel intensity scale of zero to 256) with each > coronal slice (only in the masked area of the brain... the unmasked area > remained black or zero). > > We ran > nu_correct -iterations 150 -stop .00001 temp.mnc -clobber temp-corr.mnc > > After converting the output image back to raw and putting our header back > on, the bias field could still easily be seen in the sagittal or axial > views. > > nu_estimate of the uncorrected file returns c.v of field change=7.6 e-5. > For the corrected file, the value is 2.5 e-5. Are both of these numbers > rather small? John Sled's dissertation shows graphs with c.v.'s on the > scale of 0.01. > > Could the problem be related to our conversion to minc format? I.e., > dd conv=swab if=temp.raw | rawtominc -coronal -byte -unsigned -ystep 1 > -zstep 1 -xstep 1 -mri -origin 0 0 0 -range 0 255 -real_range 0 255 > -clobber temp.mnc 256 256 256 > > Apologies in advance if this is a really dumb question. > > Thanks in advance, > > Jon Frederick, Ph.D. > University of Texas Health Science Center > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From haytham@umich.edu Mon Sep 13 13:53:05 2004 From: haytham@umich.edu (haytham@umich.edu) Date: Mon Sep 13 12:53:05 2004 Subject: [MINC-users] Install mni_autoreg-0.98r In-Reply-To: <200409131601.i8DG15PT21059402@shadow.bic.mni.mcgill.ca> References: <200409131601.i8DG15PT21059402@shadow.bic.mni.mcgill.ca> Message-ID: <1095094343.4145d0478989f@web.mail.umich.edu> I am getting the following error when performing "make" on mni_autoreg-0.98r. The reason I am installing mni_autoreg-0.98r is because of errors with minctracc I had on some volumes. Making all in Numerical make[3]: Entering directory `/mni/install/mni_autoreg-0.98r/minctracc/Numerical' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/mni/install/mni_autoreg-0.98r/minctracc/Numerical' Making all in Optimize make[3]: Entering directory `/mni/install/mni_autoreg-0.98r/minctracc/Optimize' gcc -DHAVE_CONFIG_H -I. -I. -I../.. -I./../Include -I../../Proglib -I/usr/local/mni/include -g -O2 -c do_nonlinear.c do_nonlinear.c: In function `do_non_linear_optimization': do_nonlinear.c:862: incompatible type for argument 2 of `format_time' do_nonlinear.c:862: too many arguments to function `format_time' do_nonlinear.c:1195: incompatible type for argument 2 of `format_time' do_nonlinear.c:1195: too many arguments to function `format_time' do_nonlinear.c:1221: incompatible type for argument 2 of `format_time' do_nonlinear.c:1221: too many arguments to function `format_time' do_nonlinear.c:1411: incompatible type for argument 2 of `format_time' do_nonlinear.c:1411: too many arguments to function `format_time' make[3]: *** [do_nonlinear.o] Error 1 make[3]: Leaving directory `/mni/install/mni_autoreg-0.98r/minctracc/Optimize' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/mni/install/mni_autoreg-0.98r/minctracc' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/mni/install/mni_autoreg-0.98r' make: *** [all-recursive-am] Error 2 any ideas of what I can do? -haytham From haytham@umich.edu Mon Sep 13 14:50:04 2004 From: haytham@umich.edu (haytham@umich.edu) Date: Mon Sep 13 13:50:04 2004 Subject: [MINC-users] Missing target volumes In-Reply-To: <200409131601.i8DG15PT21059402@shadow.bic.mni.mcgill.ca> References: <200409131601.i8DG15PT21059402@shadow.bic.mni.mcgill.ca> Message-ID: <1095097779.4145ddb3db4d0@web.mail.umich.edu> mritotal (from mni_autoreg-0.98r) is calling for average_305_16_mask.mnc average_305_8_mask.mnc how do I create these volumes? Thanks in advance From louis@bic.mni.mcgill.ca Mon Sep 13 15:12:04 2004 From: louis@bic.mni.mcgill.ca (D. Louis Collins) Date: Mon Sep 13 14:12:04 2004 Subject: [MINC-users] Missing target volumes In-Reply-To: <1095097779.4145ddb3db4d0@web.mail.umich.edu> References: <200409131601.i8DG15PT21059402@shadow.bic.mni.mcgill.ca> <1095097779.4145ddb3db4d0@web.mail.umich.edu> Message-ID: <60353890-05B0-11D9-8BDF-000D93520AA0@bic.mni.mcgill.ca> Haytham, These used to be created with the make_model script. Check the script - if there is no command to do so, simply link the brain mask volume to these two filenames. -Louis On Sep 13, 2004, at 1:49 PM, haytham@umich.edu wrote: > mritotal (from mni_autoreg-0.98r) is calling for > average_305_16_mask.mnc > average_305_8_mask.mnc > > how do I create these volumes? > > Thanks in advance > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From haytham@umich.edu Mon Sep 13 15:29:03 2004 From: haytham@umich.edu (haytham@umich.edu) Date: Mon Sep 13 14:29:03 2004 Subject: [MINC-users] Mritotal objective function value In-Reply-To: <60353890-05B0-11D9-8BDF-000D93520AA0@bic.mni.mcgill.ca> References: <200409131601.i8DG15PT21059402@shadow.bic.mni.mcgill.ca> <1095097779.4145ddb3db4d0@web.mail.umich.edu> <60353890-05B0-11D9-8BDF-000D93520AA0@bic.mni.mcgill.ca> Message-ID: <1095100137.4145e6e9baa71@web.mail.umich.edu> I am running the new mritotal to do some nonlinear registration: mritotal -nonlinear in.mnc -transformation in_lin.xfm in_nonlin.xfm -clobber I keep getting Initial objective function val = nan Final objective function value = nan after minctracc finish running. The minctracc command that mritotal calls for is as follows: minctracc -clobber /tmp/in_8_blur.mnc average_305_8_blur.mnc /tmp/in_16_nl.xfm -transformation in_lin.xfm -nonlinear -xcorr -step 8 8 8 -sub_lattice 6 -similarity 0.5 -iterations 12 -weight 0.5 -stiffness 0.5 -super 2 I used in_nonlin.xfm with mincresample to see the transformed volume with register and it's not right. Does anyone know what could be causing the "nan's". Is there a specific way in modifying the parameters. Note, the in.mnc has the following header image: unsigned byte 0 to 255 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 256 -0.856018 -109.57 yspace 124 -1.4879 -92.25 xspace 256 -0.856018 -109.57 Thanks in advance. Hopefull, this would be my last question for the day. From rotor@cmr.uq.edu.au Tue Sep 14 04:13:03 2004 From: rotor@cmr.uq.edu.au (Andrew Janke) Date: Tue Sep 14 03:13:03 2004 Subject: [MINC-users] Install mni_autoreg-0.98r In-Reply-To: <1095094343.4145d0478989f@web.mail.umich.edu> References: <200409131601.i8DG15PT21059402@shadow.bic.mni.mcgill.ca> <1095094343.4145d0478989f@web.mail.umich.edu> Message-ID: On Mon, 13 Sep 2004 haytham@umich.edu wrote: > do_nonlinear.c: In function `do_non_linear_optimization': > do_nonlinear.c:862: incompatible type for argument 2 of `format_time' > do_nonlinear.c:862: too many arguments to function `format_time' > > any ideas of what I can do? Which platform are you compiling this on? a From haytham@umich.edu Tue Sep 14 09:12:05 2004 From: haytham@umich.edu (haytham@umich.edu) Date: Tue Sep 14 08:12:05 2004 Subject: [MINC-users] Install mni_autoreg-0.98r In-Reply-To: References: <200409131601.i8DG15PT21059402@shadow.bic.mni.mcgill.ca> <1095094343.4145d0478989f@web.mail.umich.edu> Message-ID: <1095163883.4146dfeb851b8@web.mail.umich.edu> Linux with a 2.4 kernel Quoting Andrew Janke : > On Mon, 13 Sep 2004 haytham@umich.edu wrote: > > > do_nonlinear.c: In function `do_non_linear_optimization': > > do_nonlinear.c:862: incompatible type for argument 2 of `format_time' > > do_nonlinear.c:862: too many arguments to function `format_time' > > > > any ideas of what I can do? > > Which platform are you compiling this on? > > > a > > > From dwagne@bic.mni.mcgill.ca Tue Sep 14 12:30:06 2004 From: dwagne@bic.mni.mcgill.ca (Dylan WAGNER) Date: Tue Sep 14 11:30:06 2004 Subject: [MINC-users] Resampling 2mm MRI to 1MM Message-ID: Hi Minc-users, I expect this is child's play for most but I can't seem to find any details in the archives on how we resample our 7 minute anatomicals to match the 15 minute globals. I already have high-res mris for my subjects, now I want to boost up the low-res mris I took in another session. I'm thinking something along the lines of: mincresample -like highres_session1_mri.mnc lowres_session2_mri.mnc highres_session1_mri.mnc Seems too simple somehow but the result looks alright. Also once the lowres mri is resampled can we then treat it as we would any other mri? Ie: use it to generate an xfm for transforming the fmri volumes to tal? Thanks, From jason@bic.mni.mcgill.ca Tue Sep 14 12:55:05 2004 From: jason@bic.mni.mcgill.ca (Jason Lerch) Date: Tue Sep 14 11:55:05 2004 Subject: [MINC-users] Resampling 2mm MRI to 1MM In-Reply-To: References: Message-ID: <60962C89-0666-11D9-A098-000A95DBBFD8@bic.mni.mcgill.ca> This should work: autocrop -isostep 1 input_2mm.mnc output_1mm.mnc Though your mincresample call provides the same functionality - except that, in your case, you would overwrite the highres_session1_mri.mnc file (well, actually, it would complain that the output file already exists), which is probably not what you want. Cheers, Jason On Sep 14, 2004, at 11:29 AM, Dylan WAGNER wrote: > Hi Minc-users, > > I expect this is child's play for most but I can't seem to find > any > details in the archives on how we resample our 7 minute anatomicals > to match the 15 minute globals. > > I already have high-res mris for my subjects, now I want to > boost up > the low-res mris I took in another session. > > I'm thinking something along the lines of: > > mincresample -like highres_session1_mri.mnc lowres_session2_mri.mnc > highres_session1_mri.mnc > > Seems too simple somehow but the result looks alright. > > Also once the lowres mri is resampled can we then treat it as we > would any other mri? Ie: use it to generate an xfm for transforming the > fmri volumes to tal? > > Thanks, > > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From dwagne@bic.mni.mcgill.ca Tue Sep 14 13:05:04 2004 From: dwagne@bic.mni.mcgill.ca (Dylan WAGNER) Date: Tue Sep 14 12:05:04 2004 Subject: [MINC-users] Resampling 2mm MRI to 1MM In-Reply-To: <60962C89-0666-11D9-A098-000A95DBBFD8@bic.mni.mcgill.ca> Message-ID: Slight typo, I meant to write session 2. However I'll try the autocrop instead, it's shorter! Thanks, On Tue, 14 Sep 2004, Jason Lerch wrote: > This should work: > > autocrop -isostep 1 input_2mm.mnc output_1mm.mnc > > Though your mincresample call provides the same functionality - except > that, in your case, you would overwrite the highres_session1_mri.mnc > file (well, actually, it would complain that the output file already > exists), which is probably not what you want. > > Cheers, > > Jason > From haytham@umich.edu Tue Sep 14 17:25:05 2004 From: haytham@umich.edu (haytham@umich.edu) Date: Tue Sep 14 16:25:05 2004 Subject: [MINC-users] Minctracc In-Reply-To: <200409141601.i8EG16PT20819069@shadow.bic.mni.mcgill.ca> References: <200409141601.i8EG16PT20819069@shadow.bic.mni.mcgill.ca> Message-ID: <1095193446.4147536622172@web.mail.umich.edu> When doing linear registration with mritotal on certain volumes, I get the following error from minctracc: Error in /usr/local/mni/bin/minctracc in file init_params.c, line 576 Cannot calculate the COG or COV of volume 1. mritotal: crashed while running minctracc (exit status=65280) any ideas? -haytham From rotor@cmr.uq.edu.au Wed Sep 15 00:54:03 2004 From: rotor@cmr.uq.edu.au (Andrew Janke) Date: Tue Sep 14 23:54:03 2004 Subject: [MINC-users] Install mni_autoreg-0.98r In-Reply-To: <1095163883.4146dfeb851b8@web.mail.umich.edu> References: <200409131601.i8DG15PT21059402@shadow.bic.mni.mcgill.ca> <1095094343.4145d0478989f@web.mail.umich.edu> <1095163883.4146dfeb851b8@web.mail.umich.edu> Message-ID: On Tue, 14 Sep 2004 haytham@umich.edu wrote: > Linux with a 2.4 kernel Redhat? a From smiile-lists5281@mailzoo.com Fri Sep 17 18:51:04 2004 From: smiile-lists5281@mailzoo.com (Jon Frederick) Date: Fri Sep 17 17:51:04 2004 Subject: [MINC-users] validating nu_correct Message-ID: I'm trying to prove to myself that nu_correct is working. My results are not encouraging. Can anyone suggest what I might be doing wrong? My method was to introduce an artificial bias field using (slice number from 0 to 255) * (1.0/256.0) + 0.5 to get a fractional number between 0.5 and 1.5, and multiplying the pixel intensity at each slice by that number. The bias was clearly visible in the sagittal and axial views (brighter in the frontal lobes). However, this did not visibly change after running nu_correct -stop .000001 -iterations 200 Here are my rawtominc and minctoraw steps (after stripping the headers): dd conv=swab if=tempbias.raw | rawtominc -coronal -byte -unsigned -ystep 1 -zstep 1 -xstep 1 -mri -origin 0 0 0 -range 0 255 -real_range 0 255 -clobber tempbias.mnc 256 256 256 minctoraw -range 0 255 -normalize tempcorr.mnc | dd conv=swab of=tempcorr.raw From rebecca@loni.ucla.edu Sun Sep 19 21:09:04 2004 From: rebecca@loni.ucla.edu (Rebecca Blanton) Date: Sun Sep 19 20:09:04 2004 Subject: [MINC-users] file transfer Message-ID: <200409131926.i8DJQ3W9250806@hethor.loni.ucla.edu> Hi, To whom it may concern, We are in the midst of trying to download some files from a unix system to a pc and the files do not retain the .obj suffix when we use a secure shell to transfer over to the pc. We have tried both using an ascii file transfer and also a binary file transfer. Any suggestions would be appreciated. Thank you. Rebecca From rotor@cmr.uq.edu.au Thu Sep 23 08:59:04 2004 From: rotor@cmr.uq.edu.au (Andrew Janke) Date: Thu Sep 23 07:59:04 2004 Subject: [MINC-users] file transfer In-Reply-To: <200409131926.i8DJQ3W9250806@hethor.loni.ucla.edu> References: <200409131926.i8DJQ3W9250806@hethor.loni.ucla.edu> Message-ID: On Mon, 13 Sep 2004, Rebecca Blanton wrote: > We are in the midst of trying to download some files from a unix system to a > pc and the files do not retain the .obj suffix when we use a secure shell to > transfer over to the pc. We have tried both using an ascii file transfer and > also a binary file transfer. Rebecca, I think you will find that the file extensions do indeed exist on the windows machine, it is just that they are hidden. If you look under Tols->Folder Options you should be able to turn on an option to show the file extensions. -- Andrew Janke (rotor@cmr.uq.edu DOT au || www.cmr.uq.edu.au/~rotor) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3232 7254 || H: +61 7 3879 0374 || M: +61 4 2138 8581 From rotor@cmr.uq.edu.au Thu Sep 23 09:05:04 2004 From: rotor@cmr.uq.edu.au (Andrew Janke) Date: Thu Sep 23 08:05:04 2004 Subject: [MINC-users] Minctracc In-Reply-To: <1095193446.4147536622172@web.mail.umich.edu> References: <200409141601.i8EG16PT20819069@shadow.bic.mni.mcgill.ca> <1095193446.4147536622172@web.mail.umich.edu> Message-ID: On Tue, 14 Sep 2004 haytham@umich.edu wrote: > When doing linear registration with mritotal on certain volumes, I get the > following error from minctracc: > > Error in /usr/local/mni/bin/minctracc in file init_params.c, line 576 > Cannot calculate the COG or COV of volume 1. > mritotal: crashed while running minctracc (exit status=65280) Haytham, This typically happens when minctracc can't find a suitable threshold (background/image). Do the images you are registering have what you would call a "typical" intensity profile? Andrew Janke (rotor@cmr.uq.edu DOT au || www.cmr.uq.edu.au/~rotor) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3232 7254 || H: +61 7 3879 0374 || M: +61 4 2138 8581 From yalingy@usc.edu Fri Sep 24 00:03:04 2004 From: yalingy@usc.edu (yaling yang) Date: Thu Sep 23 23:03:04 2004 Subject: [MINC-users] mincmask program Message-ID: <009101c4a1e2$fd554040$6401a8c0@YALINGYANG> This is a multi-part message in MIME format. --Boundary_(ID_nyMOaDPGR1EmXc+QdLgCbw) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT Dear All, Does any one know where to get the MincMask? Our lab were using that for a year. But since we updated and change some of the setting on our server, we accidentally lost the program and I couldn't find it on any MINC distribution website. Is there anyone who know how to get this program? Cause our project has been using that for half of the subjects' MRI data so I really need to get it back. Or any suggestion on other program that does the same thing? (Also read the raw + the label and create the object model) Any information would be more than appreciated. Thank you. Best, yaling Yaling Yang Brain and Cognitive Science Program University of Southern California --Boundary_(ID_nyMOaDPGR1EmXc+QdLgCbw) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: 7BIT
Dear All,
 
Does any one know where to get the MincMask?
 
Our lab were using that for a year. But since we updated and change some of the setting on our server, we accidentally lost the program and I couldn't find it on any MINC distribution website. Is there anyone who know how to get this program? Cause our project has been using that for half of the subjects' MRI data so I really need to get it back.
 
Or any suggestion on other program that does the same thing? (Also read the raw + the label and create the object model)
 
Any information would be more than appreciated.
Thank you.
 
Best,
yaling
 
Yaling Yang
Brain and Cognitive Science Program
University of Southern California
 
--Boundary_(ID_nyMOaDPGR1EmXc+QdLgCbw)-- From rotor@cmr.uq.edu.au Fri Sep 24 05:30:05 2004 From: rotor@cmr.uq.edu.au (Andrew Janke) Date: Fri Sep 24 04:30:05 2004 Subject: [MINC-users] mincmask program In-Reply-To: <009101c4a1e2$fd554040$6401a8c0@YALINGYANG> References: <009101c4a1e2$fd554040$6401a8c0@YALINGYANG> Message-ID: On Thu, 23 Sep 2004, yaling yang wrote: > Does any one know where to get the MincMask? do you mean MincMask or mincmask? If you mean mincmask, I'll assume you are talking about a extra little program that louis collins of the MNI wrote for some of his own processing. It has never been part of the core MINC distribution. Essentially the logic of mincmask can be very easily encapsulated in a quick shell script: ie: mincmask converts to: mincresample -like .tmp mincmath -mult .tmp > Or any suggestion on other program that does the same thing? (Also read the > raw + the label and create the object model) This question would lead me to believe that MincMask is something that someone at your local lab has written..... -- Andrew Janke (rotor@cmr.uq.edu DOT au || www.cmr.uq.edu.au/~rotor) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3232 7254 || H: +61 7 3879 0374 || M: +61 4 2138 8581 From yves.roy@umontreal.ca Fri Sep 24 19:19:04 2004 From: yves.roy@umontreal.ca (Roy Yves) Date: Fri Sep 24 18:19:04 2004 Subject: [MINC-users] ana2mnc error Message-ID: hello: plain and simply: ana2mnc image.hdr image.mnc Unknown data type: 1024 I know my analyse image is OK for I display it correctly with SPM. Why the error? PS. I am running the ana2mnc on bullcalf. Thanks Yves From rotor@cmr.uq.edu.au Sun Sep 26 10:51:04 2004 From: rotor@cmr.uq.edu.au (Andrew Janke) Date: Sun Sep 26 09:51:04 2004 Subject: [MINC-users] ana2mnc error In-Reply-To: References: Message-ID: On Fri, 24 Sep 2004, Roy Yves wrote: > ana2mnc image.hdr image.mnc > Unknown data type: 1024 > > I know my analyse image is OK for I display it correctly with SPM. 1024 is not a defined analyze data type. Did you happen to transfer this file from one computer to another before running the conversion? ie: from a linux box to bullcalf? If so, I'd guess your problem is that your analyze header has been byte-swapped along the way. -- Andrew Janke (rotor@cmr.uq.edu DOT au || www.cmr.uq.edu.au/~rotor) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3232 7254 || H: +61 7 3879 0374 || M: +61 4 2138 8581 From yves.roy@umontreal.ca Tue Sep 28 17:44:05 2004 From: yves.roy@umontreal.ca (Roy Yves) Date: Tue Sep 28 16:44:05 2004 Subject: [MINC-users] problem with ana2mnc Message-ID: This is a multi-part message in MIME format. ------_=_NextPart_001_01C4A59B.DEA79C2B Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Thanks.... I was about to try to correct the situation with dd: dd if=3Dfoo.hdr of=3Dfoo.swap.hdr conv=3Dswab but now ana2mnc doesn't cooperate: bullcalf 102% ana2mnc -help Can't locate warnings.pm in @INC (@INC contains: = /usr/share/lib/perl5/irix-n32/5.00405 /usr/share/lib/perl5 = /usr/share/lib/perl5/site_perl/irix-n32 /usr/share/lib/perl5/site_perl = /usr/share/lib/perl5/sgi_perl .) at /usr/local/mni/bin/ana2mnc line 29. BEGIN failed--compilation aborted at /usr/local/mni/bin/ana2mnc line 29. Thanks Yves -----Original Message----- From: minc-users-admin@bic.mni.mcgill.ca on behalf of = minc-users-request@bic.mni.mcgill.ca Sent: Sun 9/26/2004 12:01 PM To: minc-users@bic.mni.mcgill.ca Cc:=09 Subject: MINC-users digest, Vol 1 #198 - 1 msg Send MINC-users mailing list submissions to minc-users@bic.mni.mcgill.ca To subscribe or unsubscribe via the World Wide Web, visit http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users or, via email, send a message with subject or body 'help' to minc-users-request@bic.mni.mcgill.ca You can reach the person managing the list at minc-users-admin@bic.mni.mcgill.ca When replying, please edit your Subject line so it is more specific than "Re: Contents of MINC-users digest..." Today's Topics: 1. Re: ana2mnc error (Andrew Janke) --__--__-- Message: 1 Date: Sun, 26 Sep 2004 23:49:55 +1000 From: Andrew Janke To: Roy Yves cc: minc-users@bic.mni.mcgill.ca Subject: Re: [MINC-users] ana2mnc error On Fri, 24 Sep 2004, Roy Yves wrote: > ana2mnc image.hdr image.mnc > Unknown data type: 1024 > > I know my analyse image is OK for I display it correctly with SPM. 1024 is not a defined analyze data type. Did you happen to transfer = this file from one computer to another before running the conversion? ie: from a = linux box to bullcalf? If so, I'd guess your problem is that your analyze header has been = byte-swapped along the way. -- Andrew Janke (rotor@cmr.uq.edu DOT au || www.cmr.uq.edu.au/~rotor) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3232 7254 || H: +61 7 3879 0374 || M: +61 4 2138 8581 --__--__-- _______________________________________________ MINC-users mailing list MINC-users@bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users End of MINC-users Digest ------_=_NextPart_001_01C4A59B.DEA79C2B Content-Type: application/ms-tnef; name="winmail.dat" Content-Transfer-Encoding: base64 eJ8+IjgUAQaQCAAEAAAAAAABAAEAAQeQBgAIAAAA5AQAAAAAAADoAAEIgAcAGAAAAElQTS5NaWNy b3NvZnQgTWFpbC5Ob3RlADEIAQ2ABAACAAAAAgACAAEEgAEAFQAAAHByb2JsZW0gd2l0aCBhbmEy bW5jAI0HAQWAAwAOAAAA1AcJABwAEAArADYAAgBzAQEggAMADgAAANQHCQAcABAAKwA2AAIAcwEB CYABACEAAAA3RDE4MTUxRkYxQzdEMTQyOUEyODk4NEU4NEUyRTY0MQAeBwEDkAYA0A0AADcAAAAD ACYAAAAAAAMANgAAAAAAQAA5ACucp96bpcQBHgA9AAEAAAABAAAAAAAAAAIBRwABAAAAMQAAAGM9 Q0E7YT0gO3A9VU1vbnRyZWFsO2w9RVROQS0wNDA5MjgyMDQzNTRaLTExMDE3NQAAAAAeAEkAAQAA ACYAAABNSU5DLXVzZXJzIGRpZ2VzdCwgVm9sIDEgIzE5OCAtIDEgbXNnAAAAQABOAADgfAbio8QB HgBaAAEAAAAjAAAAbWluYy11c2Vycy1hZG1pbkBiaWMubW5pLm1jZ2lsbC5jYQAAAgFbAAEAAABj AAAAAAAAAIErH6S+oxAZnW4A3QEPVAIAAAAAbWluYy11c2Vycy1hZG1pbkBiaWMubW5pLm1jZ2ls bC5jYQBTTVRQAG1pbmMtdXNlcnMtYWRtaW5AYmljLm1uaS5tY2dpbGwuY2EAAAIBXAABAAAAKAAA AFNNVFA6TUlOQy1VU0VSUy1BRE1JTkBCSUMuTU5JLk1DR0lMTC5DQQAeAF0AAQAAACUAAABtaW5j LXVzZXJzLXJlcXVlc3RAYmljLm1uaS5tY2dpbGwuY2EAAAAAAgFeAAEAAABnAAAAAAAAAIErH6S+ oxAZnW4A3QEPVAIAAAAAbWluYy11c2Vycy1yZXF1ZXN0QGJpYy5tbmkubWNnaWxsLmNhAFNNVFAA bWluYy11c2Vycy1yZXF1ZXN0QGJpYy5tbmkubWNnaWxsLmNhAAACAV8AAQAAACoAAABTTVRQOk1J TkMtVVNFUlMtUkVRVUVTVEBCSUMuTU5JLk1DR0lMTC5DQQAAAB4AZgABAAAABQAAAFNNVFAAAAAA HgBnAAEAAAAjAAAAbWluYy11c2Vycy1hZG1pbkBiaWMubW5pLm1jZ2lsbC5jYQAAHgBoAAEAAAAF AAAAU01UUAAAAAAeAGkAAQAAACUAAABtaW5jLXVzZXJzLXJlcXVlc3RAYmljLm1uaS5tY2dpbGwu Y2EAAAAAHgBwAAEAAAAmAAAATUlOQy11c2VycyBkaWdlc3QsIFZvbCAxICMxOTggLSAxIG1zZwAA AAIBcQABAAAAGwAAAAHEo+905NaOWCIrqEw4kL9pYbbs3IcAaulSmQAeAHQAAQAAAB0AAABtaW5j LXVzZXJzQGJpYy5tbmkubWNnaWxsLmNhAAAAAB4AGgwBAAAACQAAAFJveSBZdmVzAAAAAB4AHQ4B AAAAFQAAAHByb2JsZW0gd2l0aCBhbmEybW5jAAAAAAIBCRABAAAAjAYAAIgGAADiCwAATFpGddUx nfQDAAoAcmNwZzEyNeIyA0N0ZXgFQQEDAff/CoACpAPkBxMCgA/zAFAEVj8IVQeyESUOUQMBAgBj aOEKwHNldDIGAAbDESX2MwRGE7cwEiwRMwjvCfe2OxgfDjA1ESIMYGMAUDMLCQFkMzYWUAumIFQh E+Bua3MuHVEgSXggd2EEIAGgCGAFQHRybx5QcnkeUgWhGCBjER5BaGUgAJB0dWEcdGkCIB2wH9Bo IGS8ZDoKogqECoAgoSAGkEI9AhBvLmhkBcBvMyH0A+BhcCJDBaBudi49IwEMMCD5Yh4xbm+DB+AA cGEybW5jIKAybweQbicFQAWgb3AbBJAgAGUg2yTgbGxjgQdAZiAxMDIlJVfSLR+QbHAg5EMAcCYx vxewKAAOsB2xBKALgGcdQAxwbSHQA6BASU5DPCAoK5MjkQGQC4BzOoAgL3Vzci9zE+FAZS9saWIv JpFsCDUvaQUQeC1uMwAyLzUuMDA0MD41LN8t4i8/LeMfwWVfPy3SLicwjzGcMw8xlGdp+TSkLikd 8AVANQMqMjJg0SWgaS9iC4AvJWYtkCJuH6AyOS4g5EJFUkcroCBmC3BsCYAt8i0FoG1wAxAgBB4B ACB/CYA3DzgfOSkg6hz0IORZ3nYHkCDqOpBBMU8FEDZgCyVwAyBNB5BzYWdlO0EzIORGA2Eg0AGR IG0ZC4BjLTUQBJBzLWHKZEPRQD0QYy480UUQdmM2YCfgLigAIoADoGK+ZRPgKCEikEPKGCBxClD0 c3RE32Eg5AZgAjBDdIRTdQOgOS8yNkpgAy7hKEAyOjAxIFA6TT8Vb0N+R/9JBUNjY0N0SRV1Ymof QUN0TR8roUQUIKBBoEfBLCBWgwbwKEAgIzE5OCkQ/VGBbTZQSRchwFApAMADEP8q4TjhR9AfsE9g Q9AEECAh/wQgHmAg5UwfTS8+2R5wVKG/BPJGMCKABcBKIFjodgcwlR9zVwWwbCHAV2kBAHla4GVi UTBacB/BVYloQQJAcDovL3ddYC7/Vu88wDpBA4EtgUfQC4ACEL88wEPnIOQFsFvSReBlU9L/UTAU EFLxReAHgUJCIFRUoVdPgllyBuBkHrAnKTIn71VfRw9W/yD5WQhgHvADkd8YIADQIJAfgiaRcyAx A4H/QlBUEh+CVFMgAGSfRD9m390g5FcfkGiiC1B5KuFRML8LUGjQFBBhQFDQBUB5CGH/SgFjJDjz aZAh0AVABABrsPcFsB+hJpBjBpAN4CDkH4D5A5EiUibgEiECMEmBBCA3RqFQLx1RIj5fS8FkYdx5 JwQgS9A64GMssCDr/XiwMR2Ac5IlZgSQA2AFwFwoQVLwGCAH4EodEWXyKUB8X1971CDqQhUswPsa 8wqARCbCSgJRMEpwBlEGcDkwSrIyMzo0OfI6GmAgKyhQLuBC2RDAGXpZIDwDYB5gckBjQG1yLnVx LgmAdfAuYXU+S3cH8R6wQDIVggB5QEEuA2B5QHXfBGACMGjBRbKDVWNOgFYv120vT0d5A1t0mF15 TCDq9k8DoEMwaX7BStB/FlEw7YQHd4IhJuw+JVcHcEJR7yJDj5QloY6WVR0gJSEDoHd3IAGQHlB5 JpB9oShgNP+OlY6WHaCRYmuwHrAlYW8g52/Rj5Nxwk9LOiAFsR2g/1DQclALYB6wcCEfBW8gIFT+ U0tQPkuScnHCJSBq0SCg7wEQOQE70ZRSeh+gkccdgPwgRFtgcEJc4CMgJpADoPseYwBxZhKBH4Bx 0XKgOmD/IOQDUkXxH6A6sh4wnKIecL8AcIIwH5BjkQEQchJySiDfKtIfcyOSbDEgIT94sAiQTyzA ncNF4DjxdXgkhW/WeB5SJ8Y/IOpJKDBpkOlRMEknIcBnZiEEIHBT/nADYAJgYVBxwnMxcDWZ5n8f kGxwEoET4AQgRjBuwWL6eQ6wLSMCJpALMSECB0D3AiBqRB3AeT5PQRIg5IFLZiiCLpsQT1Qd8Ghg fM58HbBdcYKLL36CI3sFjkE1EJxBLZBhLT6RQG5poPOSEEaSUQpQCfBzdwtgUvCxkENJgXIhlYJN f0JQORAgECXAc5BpkQBwYyWdVVcswCs2SzA3IDcukDLhAcA1StCu0iBIAbWXODc5IDAzNy22lU21 lH+BMbeQIDj8NTh9xXsffC+64Lw/vU//vgl81VM/VEO/HodPSQVc/+9eD18fYCkg6kVS8XRsmyAX UPLG7yE1fcsQHgA1EAEAAABBAAAAPEI1ODM1RTFDQzU5NDdENEY4MUJFQUU2QzY5OTczOThGMDQ1 RkJEMTVAZXRuYS5zaW0udW1vbnRyZWFsLmNhPgAAAAAeAEcQAQAAAA8AAABtZXNzYWdlL3JmYzgy MgAACwDyEAEAAAAfAPMQAQAAADIAAABwAHIAbwBiAGwAZQBtACAAdwBpAHQAaAAgAGEAbgBhADIA bQBuAGMALgBFAE0ATAAAAAAACwD2EAAAAABAAAcwm9MuGpulxAFAAAgwkyWx3pulxAEDAN4/r28A AAMA8T8JBAAAHgD4PwEAAAAJAAAAUm95IFl2ZXMAAAAAAgH5PwEAAABeAAAAAAAAANynQMjAQhAa tLkIACsv4YIBAAAAAAAAAC9PPVVNT05UUkVBTC9PVT1GSVJTVCBBRE1JTklTVFJBVElWRSBHUk9V UC9DTj1SRUNJUElFTlRTL0NOPVJPWVlWAAAAHgD6PwEAAAAVAAAAU3lzdGVtIEFkbWluaXN0cmF0 b3IAAAAAAgH7PwEAAAAeAAAAAAAAANynQMjAQhAatLkIACsv4YIBAAAAAAAAAC4AAAADAP0/5AQA AAMAGUAAAAAAAwAaQAAAAAADAB1AAAAAAAMAHkAAAAAAHgAwQAEAAAAGAAAAUk9ZWVYAAAAeADFA AQAAAAYAAABST1lZVgAAAB4AMkABAAAAIwAAAG1pbmMtdXNlcnMtYWRtaW5AYmljLm1uaS5tY2dp bGwuY2EAAB4AM0ABAAAAJQAAAG1pbmMtdXNlcnMtcmVxdWVzdEBiaWMubW5pLm1jZ2lsbC5jYQAA AAAeADhAAQAAAAYAAABST1lZVgAAAB4AOUABAAAAAgAAAC4AAAALACkAAAAAAAsAIwAAAAAAAwAG EMGeTmwDAAcQSQcAAAMAEBAAAAAAAwAREAAAAAAeAAgQAQAAAGUAAABUSEFOS1NJV0FTQUJPVVRU T1RSWVRPQ09SUkVDVFRIRVNJVFVBVElPTldJVEhERDpERElGPUZPT0hEUk9GPUZPT1NXQVBIRFJD T05WPVNXQUJCVVROT1dBTkEyTU5DRE9FU05UAAAAAAIBfwABAAAAQQAAADxCNTgzNUUxQ0M1OTQ3 RDRGODFCRUFFNkM2OTk3Mzk4RjA0NUZCRDE1QGV0bmEuc2ltLnVtb250cmVhbC5jYT4AAAAAR/I= ------_=_NextPart_001_01C4A59B.DEA79C2B-- From Jean-Francois.Malouin@bic.mni.mcgill.ca Tue Sep 28 18:00:05 2004 From: Jean-Francois.Malouin@bic.mni.mcgill.ca (Jean-Francois Malouin) Date: Tue Sep 28 17:00:05 2004 Subject: [MINC-users] problem with ana2mnc In-Reply-To: References: Message-ID: <20040928205945.GA7379489@shadow.bic.mni.mcgill.ca> * Roy Yves [20040928 16:51]: > Thanks.... I was about to try to correct the situation with dd: > > dd if=foo.hdr of=foo.swap.hdr conv=swab > > but now ana2mnc doesn't cooperate: > > bullcalf 102% ana2mnc -help > Can't locate warnings.pm in @INC (@INC contains: /usr/share/lib/perl5/irix-n32/5.00405 /usr/share/lib/perl5 /usr/share/lib/perl5/site_perl/irix-n32 /usr/share/lib/perl5/site_perl /usr/share/lib/perl5/sgi_perl .) at /usr/local/mni/bin/ana2mnc line 29. > BEGIN failed--compilation aborted at /usr/local/mni/bin/ana2mnc line 29. my mistake. I just updated ana2mnc from the cvs repositary. I've reverted back to the previous script. Andrew, if you read this can you tell us what is the problem? Seems to me that one has to use: /usr/local/unstable/bin/perl5 /usr/local/mni/bin/ana2mnc -help jf > > > Thanks > Yves > > -----Original Message----- > From: minc-users-admin@bic.mni.mcgill.ca on behalf of minc-users-request@bic.mni.mcgill.ca > Sent: Sun 9/26/2004 12:01 PM > To: minc-users@bic.mni.mcgill.ca > Cc: > Subject: MINC-users digest, Vol 1 #198 - 1 msg > Send MINC-users mailing list submissions to > minc-users@bic.mni.mcgill.ca > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > or, via email, send a message with subject or body 'help' to > minc-users-request@bic.mni.mcgill.ca > > You can reach the person managing the list at > minc-users-admin@bic.mni.mcgill.ca > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of MINC-users digest..." > > > Today's Topics: > > 1. Re: ana2mnc error (Andrew Janke) > > --__--__-- > > Message: 1 > Date: Sun, 26 Sep 2004 23:49:55 +1000 > From: Andrew Janke > To: Roy Yves > cc: minc-users@bic.mni.mcgill.ca > Subject: Re: [MINC-users] ana2mnc error > > On Fri, 24 Sep 2004, Roy Yves wrote: > > > ana2mnc image.hdr image.mnc > > Unknown data type: 1024 > > > > I know my analyse image is OK for I display it correctly with SPM. > > 1024 is not a defined analyze data type. Did you happen to transfer this file > from one computer to another before running the conversion? ie: from a linux > box to bullcalf? > > If so, I'd guess your problem is that your analyze header has been byte-swapped > along the way. > > > -- > Andrew Janke (rotor@cmr.uq.edu DOT au || www.cmr.uq.edu.au/~rotor) > Australia->University of Queensland->Centre for Magnetic Resonance > W: +61 7 3232 7254 || H: +61 7 3879 0374 || M: +61 4 2138 8581 > > > --__--__-- > > _______________________________________________ > MINC-users mailing list > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > End of MINC-users Digest > > > > -- From yves.roy@umontreal.ca Thu Sep 30 12:31:05 2004 From: yves.roy@umontreal.ca (Roy Yves) Date: Thu Sep 30 11:31:05 2004 Subject: [MINC-users] minc tool to correct orientation Message-ID: Hi: I have 4D minc images of functional runs and the head appears upside down (after a dicom to minc conversion with dcm2mnc). Which minc tool can I run on these 4D images to correct the situation (i.e. to flip the head downside up) ? Many thanks Yves From jason@bic.mni.mcgill.ca Thu Sep 30 12:40:04 2004 From: jason@bic.mni.mcgill.ca (Jason Lerch) Date: Thu Sep 30 11:40:04 2004 Subject: [MINC-users] minc tool to correct orientation In-Reply-To: References: Message-ID: Cheerio, param2xfm to create the transform, and then 'mincresample -tfm_input_sampling' to apply the transform to your volume. Cheers, Jason On Sep 30, 2004, at 11:30 AM, Roy Yves wrote: > Hi: > > I have 4D minc images of functional runs and the head appears upside > down (after a dicom to minc conversion with dcm2mnc). > > Which minc tool can I run on these 4D images to correct the situation > (i.e. to flip the head downside up) ? > > Many thanks > Yves > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From jharlap@bic.mni.mcgill.ca Thu Sep 30 12:49:04 2004 From: jharlap@bic.mni.mcgill.ca (Jonathan HARLAP) Date: Thu Sep 30 11:49:04 2004 Subject: [MINC-users] minc tool to correct orientation In-Reply-To: References: Message-ID: <20040930154812.GM21368@bic.mni.mcgill.ca> I believe you would want mincreshape. A lot of basic information like this is in our wiki at http://wiki.bic.mni.mcgill.ca/ For example, this might well be answered by the MincToolsGuide page in the wiki, at http://wiki.bic.mni.mcgill.ca/index.php/MincToolsGuide Cheers, J On Thu, Sep 30, 2004 at 11:30:43AM -0400, Roy Yves wrote: > Hi: > > I have 4D minc images of functional runs and the head appears upside down (after a dicom to minc conversion with dcm2mnc). > > Which minc tool can I run on these 4D images to correct the situation (i.e. to flip the head downside up) ? > > Many thanks > Yves > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From bert@bic.mni.mcgill.ca Thu Sep 30 13:13:05 2004 From: bert@bic.mni.mcgill.ca (Robert VINCENT) Date: Thu Sep 30 12:13:05 2004 Subject: [MINC-users] minc tool to correct orientation In-Reply-To: Message-ID: Yves, Depending on the exact nature of the error and the coordinate system, it could be as simple as changing the sign of the Z coordinate axis. Suppose you have the following situation: oberon 807% mincinfo bert_20030424_mri.mnc file: bert_20030424_mri.mnc image: signed__ short 0 to 4095 image dimensions: xspace zspace yspace dimension name length step start -------------- ------ ---- ----- xspace 88 2 -88.2412 zspace 256 -1 109.8 yspace 256 -1 167.235 To "flip" the Z axis in this case, I just need to change the step and start values as follows: step(2) = -step(1) start(2) = start(1)-((zlength-1)*step(1)) So in this case the fix becomes: minc_modify_header -dinsert zspace:step=1 -dinsert zspace:start=-145.2 This will exactly invert the sense of the Z direction without actually flipping the data. -bert On Thu, 30 Sep 2004, Roy Yves wrote: > Hi: > > I have 4D minc images of functional runs and the head appears upside down (after a dicom to minc conversion with dcm2mnc). > > Which minc tool can I run on these 4D images to correct the situation (i.e. to flip the head downside up) ? > > Many thanks > Yves > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From bert@bic.mni.mcgill.ca Thu Sep 30 13:16:04 2004 From: bert@bic.mni.mcgill.ca (Robert VINCENT) Date: Thu Sep 30 12:16:04 2004 Subject: [MINC-users] minc tool to correct orientation In-Reply-To: Message-ID: Oops, I got the sign wrong. It should be: step(2) = -step(1) start(2) = start(1)_+_((zlength-1)*step(1)) -bert > On Thu, 30 Sep 2004, Robert VINCENT wrote: > Yves, > > Depending on the exact nature of the error and the coordinate system, it > could be as simple as changing the sign of the Z coordinate axis. > > Suppose you have the following situation: > > oberon 807% mincinfo bert_20030424_mri.mnc > file: bert_20030424_mri.mnc > image: signed__ short 0 to 4095 > image dimensions: xspace zspace yspace > dimension name length step start > -------------- ------ ---- ----- > xspace 88 2 -88.2412 > zspace 256 -1 109.8 > yspace 256 -1 167.235 > > To "flip" the Z axis in this case, I just need to change the step and > start values as follows: > > step(2) = -step(1) > start(2) = start(1)-((zlength-1)*step(1)) > > So in this case the fix becomes: > > minc_modify_header -dinsert zspace:step=1 -dinsert zspace:start=-145.2 > > This will exactly invert the sense of the Z direction without actually > flipping the data. > > -bert > > On Thu, 30 Sep 2004, Roy Yves wrote: > > > Hi: > > > > I have 4D minc images of functional runs and the head appears upside down (after a dicom to minc conversion with dcm2mnc). > > > > Which minc tool can I run on these 4D images to correct the situation (i.e. to flip the head downside up) ? > > > > Many thanks > > Yves > > > > _______________________________________________ > > MINC-users@bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > >