From minc-development@bic.mni.mcgill.ca Tue Dec 2 20:40:44 2003 From: minc-development@bic.mni.mcgill.ca (Robert VINCENT) Date: Tue, 2 Dec 2003 15:40:44 -0500 Subject: [MINC-development] -version Message-ID: Hi everyone, A quick question about the oft-requested "-version" option for MINC commands. Which version should this print? The overall build version (i.e. 1.2, 1.1, etc.?) -bert From minc-development@bic.mni.mcgill.ca Tue Dec 2 20:46:17 2003 From: minc-development@bic.mni.mcgill.ca (Andrew Janke) Date: Tue, 2 Dec 2003 15:46:17 -0500 Subject: [MINC-development] -version In-Reply-To: Message-ID: On Tue, 2 Dec 2003, Robert VINCENT wrote: > A quick question about the oft-requested "-version" option for MINC > commands. Do it the perl/autoconf way... mincfoo {-version,-v} give a short version 1.2 1.3 etc mincfoo {-Version,-V} gives the long version (IMHO this should be a CVS string but I have been told this isn't good idea) a From minc-development@bic.mni.mcgill.ca Wed Dec 3 03:15:33 2003 From: minc-development@bic.mni.mcgill.ca (Peter NEELIN) Date: Tue, 2 Dec 2003 22:15:33 -0500 Subject: [MINC-development] Re: [MINC-users] Re: [geeks] voxel loop In-Reply-To: <3591.66.131.214.145.1070031144.squirrel@www.cim.mcgill.ca> Message-ID: This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. ---2066828793-1237723228-1070421318=:7013171 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-ID: On Fri, 28 Nov 2003, Maxime Descoteaux wrote: > My problem is that I run out of memory on full brain mr images. I need > help setting things up? I normally have "Volume" data structures lying > around (too many)! Why? > > Well, I do a multiscale vessel extraction. So, at all time and for every > scale, I need six volumes to compute the symmetric Hessian matrix of [...] > > So, I also have 5 other volumes to save the output of the analysis > [...] > This is a lot of volumes lying around.... Is voxel_loop a solution to my > problem? I am not quite familiar with the buffer idea and I am not quite > sure on how to set things up... No. Voxel_loop is not designed for neighbourhood operations. You could probably kludge it to do that, but I don't think that that would be a good idea. You can use volume_io to create temporary volumes that are cached - that essentially swap to disk. You have to either set an environment variable to force caching or make a library call. You also have to play around a bit to make sure that the temp files live where you have disk space (if /tmp is not large enough). I've just had a look - I have an old example that tries to do this. You might want to play around with it. I've attached it. Note that you can do caching in two modes: random access and slice access. Random access caches blocks of data. Unfortunately, reading a single block requires reading much more than the block since files are organized by rows. Slice access caches rows and so it does not thrash so badly. Random access will be better on memory in the general case, but really needs an underlying data organization that has a similar block structure (not yet supported in minc). So use slice access. You will probably be iterating over rows anyway, so it should work for you. Just for comparison, one test case that I ran took 55 seconds without caching, 97 seconds with slice access and 430 seconds with random access. This was with 85 MB of image data on a 64 MB machine, so obviously it was faster to let the machine swap than do caching. (Hmmm... that's not very encouraging!) Anyway, play with it and see how it goes - much depends on how you access the data. Have fun! Peter ---- Peter Neelin (neelin@bic.mni.mcgill.ca) ---2066828793-1237723228-1070421318=:7013171 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII; NAME="volio_cachetest.c" Content-Transfer-Encoding: BASE64 Content-ID: Content-Description: Content-Disposition: ATTACHMENT; FILENAME="volio_cachetest.c" LyogLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0gTU5JIEhlYWRlciAt LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLQ0KQE5BTUUgICAg ICAgOiB2b2xpb19zbGljZXRlc3QNCkBJTlBVVCAgICAgIDogaW5wdXQgZmls ZW5hbWUNCkBPVVRQVVQgICAgIDogdGVtcG9yYXJ5IGZpbGVuYW1lIGJhc2Ug YW5kIG91dHB1dCBuYW1lDQpAREVTQ1JJUFRJT046IFByb2dyYW0gdG8gdGVz dCB2b2x1bWUgY2FjaGluZy4NCkBNRVRIT0QgICAgIDogDQpAR0xPQkFMUyAg ICA6IA0KQENSRUFURUQgICAgOiBNYXJjaCAyMywgMjAwMSAoUGV0ZXIgTmVl bGluKQ0KQE1PRElGSUVEICAgOiANCi0tLS0tLS0tLS0tLS0tLS0tLS0tLS0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0t LS0tLS0tLS0gKi8NCg0KI2luY2x1ZGUgPHN0ZGlvLmg+DQojaW5jbHVkZSA8 c3RkbGliLmg+DQojaW5jbHVkZSA8dW5pc3RkLmg+DQojaW5jbHVkZSA8bGlt aXRzLmg+DQojaW5jbHVkZSA8ZmxvYXQuaD4NCiNpbmNsdWRlIDx2b2x1bWVf aW8uaD4NCg0KI2RlZmluZSBOVk9MUyAxMA0KDQojZGVmaW5lIERFRkFVTFRf Q0FDSEVfVEhSRVNIT0xEICg4MCoxMDI0KjEwMjQpDQoNCiNkZWZpbmUgQ0FD SEVfU0laRSAoMioxMDI0KjEwMjQpDQoNCiNkZWZpbmUgQ0FDSEVfQUNDRVNT IFNMSUNFX0FDQ0VTUw0KLyogI2RlZmluZSBDQUNIRV9BQ0NFU1MgUkFORE9N X1ZPTFVNRV9BQ0NFU1MgKi8NCg0KaW50IG1haW4oaW50IGFyZ2MsIGNoYXIg KmFyZ3ZbXSkNCnsNCiAgIGNoYXIgKnByb2c7DQogICBjaGFyICppbnB1dF9m aWxlbmFtZTsNCiAgIGNoYXIgKnRlbXBfcHJlZml4Ow0KICAgY2hhciAqb3V0 cHV0X2ZpbGVuYW1lOw0KICAgVm9sdW1lIGludm9sdW1lLCB0ZW1wdm9sdW1l W05WT0xTXSwgb3V0dm9sdW1lOw0KICAgY2hhciAqZGltZW5zaW9uX25hbWVf bGlzdFtdID0geyIiLCAiIiwgIiJ9Ow0KICAgaW50IGl2b2w7DQogICBpbnQg c2l6ZXNbM107DQogICBSZWFsIHZhbHVlLCB0ZW1wdmFsdWU7DQogICBkb3Vi bGUgcGFyYW1ldGVyc1tdID0gezEuMCwgMi4wLCAzLjAsIDEuMCwgMi4wLCAz LjAsIDEuMCwgMi4wLCAzLjAsIDEuMH07DQogICBkb3VibGUgbWluaW11bSwg bWF4aW11bTsNCiAgIG5jX3R5cGUgZGF0YV90eXBlOw0KICAgaW50IHNpZ25l ZF9mbGFnOw0KICAgUmVhbCB2b3hlbF9taW4sIHZveGVsX21heDsNCiAgIGNo YXIgdGVtcF9maWxlX25hbWVbMjU2XTsNCiAgIGNoYXIgKnRlbXBfZmlsZV9z dWZmaXg7DQogICBpbnQgaXgsIGl5LCBpejsNCg0KICAgLyogQ2hlY2sgYXJn dW1lbnRzICovDQogICBwcm9nID0gYXJndlswXTsNCiAgIGlmIChhcmdjICE9 IDQpIHsNCiAgICAgICh2b2lkKSBmcHJpbnRmKHN0ZGVyciwgIlVzYWdlOiAl cyBpbmZpbGUubW5jIHRlbXBwcmVmaXggb3V0ZmlsZS5tbmNcbiIsDQogICAg ICAgICAgICAgICAgICAgICBwcm9nKTsNCiAgICAgIHJldHVybiBFWElUX0ZB SUxVUkU7DQogICB9DQogICBpbnB1dF9maWxlbmFtZSA9IGFyZ3ZbMV07DQog ICB0ZW1wX3ByZWZpeCA9IGFyZ3ZbMl07DQogICBvdXRwdXRfZmlsZW5hbWUg PSBhcmd2WzNdOw0KDQogICAvKiBSZWFkIGluIHRoZSBpbnB1dCB2b2x1bWUg Ki8NCiAgICh2b2lkKSBwcmludGYoIlJlYWRpbmcgaW5wdXQgdm9sdW1lXG4i KTsNCiAgIGlmIChpbnB1dF92b2x1bWUoaW5wdXRfZmlsZW5hbWUsIDMsIGRp bWVuc2lvbl9uYW1lX2xpc3QsIA0KICAgICAgICAgICAgICAgICAgICBOQ19G TE9BVCwgVFJVRSwgMC4wLCAwLjAsIA0KICAgICAgICAgICAgICAgICAgICBU UlVFLCAmaW52b2x1bWUsIE5VTEwpICE9IE9LKSB7DQogICAgICAodm9pZCkg ZnByaW50ZihzdGRlcnIsICIlczogRXJyb3IgcmVhZGluZyB2b2x1bWUgJXNc biIsDQogICAgICAgICAgICAgICAgICAgICBwcm9nLCBpbnB1dF9maWxlbmFt ZSk7DQogICAgICByZXR1cm4gRVhJVF9GQUlMVVJFOw0KICAgfQ0KDQogICAv KiBDcmVhdGUgdGhlIHByZWZpeCBmb3IgdGVtcG9yYXJ5IGZpbGUgbmFtZXMg Ki8NCiAgICh2b2lkKSBzcHJpbnRmKHRlbXBfZmlsZV9uYW1lLCAiJXNfJWQi LCB0ZW1wX3ByZWZpeCwgKGludCkgZ2V0cGlkKCkpOw0KICAgdGVtcF9maWxl X3N1ZmZpeCA9ICZ0ZW1wX2ZpbGVfbmFtZVtzdHJsZW4odGVtcF9maWxlX25h bWUpXTsNCg0KICAgLyogQ3JlYXRlIHRoZSB0ZW1wb3Jhcnkgdm9sdW1lcyAq Lw0KI2lmbmRlZiBOT0NBQ0hFDQogICAodm9pZCkgcHJpbnRmKCJTZXR0aW5n IHVwIGNhY2hlZCB0ZW1wIHZvbHVtZXNcbiIpOw0KICAgc2V0X25fYnl0ZXNf Y2FjaGVfdGhyZXNob2xkKDApOw0KICAgc2V0X2RlZmF1bHRfbWF4X2J5dGVz X2luX2NhY2hlKENBQ0hFX1NJWkUpOw0KICAgc2V0X2NhY2hlX2Jsb2NrX3Np emVzX2hpbnQoQ0FDSEVfQUNDRVNTKTsNCiNlbHNlDQogICAodm9pZCkgcHJp bnRmKCJTZXR0aW5nIHVwIHRlbXAgdm9sdW1lcyBpbiBtZW1vcnlcbiIpOw0K I2VuZGlmDQogICBmb3IgKGl2b2w9MDsgaXZvbCA8IE5WT0xTOyBpdm9sKysp IHsNCiAgICAgIHRlbXB2b2x1bWVbaXZvbF0gPSANCiAgICAgICAgIGNvcHlf dm9sdW1lX2RlZmluaXRpb24oaW52b2x1bWUsIE5DX0ZMT0FULCBUUlVFLCAw LjAsIDAuMCk7DQojaWZuZGVmIE5PQ0FDSEUNCiAgICAgICh2b2lkKSBzcHJp bnRmKHRlbXBfZmlsZV9zdWZmaXgsICJfJWQubW5jIiwgaXZvbCk7DQogICAg ICAodm9pZCkgcHJpbnRmKCJDYWNoaW5nIHZvbHVtZSB0byAlc1xuIiwgdGVt cF9maWxlX25hbWUpOw0KICAgICAgc2V0X2NhY2hlX291dHB1dF92b2x1bWVf cGFyYW1ldGVycyh0ZW1wdm9sdW1lW2l2b2xdLA0KICAgICAgICAgICAgICAg ICAgICAgICAgICAgICAgICAgICAgICAgICB0ZW1wX2ZpbGVfbmFtZSwNCiAg ICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgTkNfRkxP QVQsIFRSVUUsIDAuMCwgMC4wLA0KICAgICAgICAgICAgICAgICAgICAgICAg ICAgICAgICAgICAgICAgICBpbnB1dF9maWxlbmFtZSwgDQogICAgICAgICAg ICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICJ2b2xpbyB0ZXN0IHRl bXBvcmFyeSBmaWxlIiwNCiAgICAgICAgICAgICAgICAgICAgICAgICAgICAg ICAgICAgICAgICAgTlVMTCk7DQojZW5kaWYNCiAgIH0NCg0KICAgLyogUmVz ZXQgdGhlIGNhY2hlIHRocmVzaG9sZCAqLw0KI2lmbmRlZiBOT0NBQ0hFDQog ICBzZXRfbl9ieXRlc19jYWNoZV90aHJlc2hvbGQoREVGQVVMVF9DQUNIRV9U SFJFU0hPTEQpOw0KI2VuZGlmDQoNCiAgIC8qIEdldCBzaXplIG9mIGRpbWVu c2lvbnMgKi8NCiAgIGdldF92b2x1bWVfc2l6ZXMoaW52b2x1bWUsIHNpemVz KTsNCg0KICAgLyogTG9vcCBvdmVyIHZveGVscywgY2FsY3VsYXRpbmcgdGVt cG9yYXJ5IHZvbHVtZXMgKi8NCiAgICh2b2lkKSBwcmludGYoIkNhbGN1bGF0 aW5nIHRlbXBvcmFyeSB2b2x1bWVzXG4iKTsNCiAgIGZvciAoaXo9MDsgaXog PCBzaXplc1swXTsgaXorKykgew0KICAgICAgZm9yIChpeT0wOyBpeSA8IHNp emVzWzFdOyBpeSsrKSB7DQogICAgICAgICBmb3IgKGl4PTA7IGl4IDwgc2l6 ZXNbMl07IGl4KyspIHsNCg0KICAgICAgICAgICAgdmFsdWUgPSBnZXRfdm9s dW1lX3JlYWxfdmFsdWUoaW52b2x1bWUsIGl6LCBpeSwgaXgsIDAsIDApOw0K DQogICAgICAgICAgICAvKiBDYWxjdWxhdGUgdGhlIHRlbXBvcmFyeSB2YWx1 ZXMgKi8NCiAgICAgICAgICAgIGZvciAoaXZvbD0wOyBpdm9sIDwgTlZPTFM7 IGl2b2wrKykgew0KICAgICAgICAgICAgICAgdGVtcHZhbHVlID0gc2luKHZh bHVlICogKGl2b2wrMS4wKSk7DQogICAgICAgICAgICAgICBzZXRfdm9sdW1l X3JlYWxfdmFsdWUodGVtcHZvbHVtZVtpdm9sXSwgaXosIGl5LCBpeCwgMCwg MCwgDQogICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgdGVt cHZhbHVlKTsNCiAgICAgICAgICAgIH0NCiAgICAgICAgIH0NCiAgICAgIH0N CiAgIH0NCg0KICAgLyogQ3JlYXRlIHRoZSBvdXRwdXQgdm9sdW1lICovDQog ICBvdXR2b2x1bWUgPSBjb3B5X3ZvbHVtZV9kZWZpbml0aW9uKGludm9sdW1l LCBOQ19GTE9BVCwgVFJVRSwgMC4wLCAwLjApOw0KDQogICAvKiBMb29wIG92 ZXIgdm94ZWxzIGFnYWluLCBjYWxjdWxhdGluZyBvdXRwdXQgdmFsdWVzICov DQogICAodm9pZCkgcHJpbnRmKCJDYWxjdWxhdGluZyBvdXRwdXQgdm9sdW1l XG4iKTsNCiAgIG1pbmltdW0gPSBEQkxfTUFYOw0KICAgbWF4aW11bSA9IC1E QkxfTUFYOw0KICAgZm9yIChpej0wOyBpeiA8IHNpemVzWzBdOyBpeisrKSB7 DQogICAgICBmb3IgKGl5PTA7IGl5IDwgc2l6ZXNbMV07IGl5KyspIHsNCiAg ICAgICAgIGZvciAoaXg9MDsgaXggPCBzaXplc1syXTsgaXgrKykgew0KDQog ICAgICAgICAgICAvKiBDYWxjdWxhdGUgdGhlIG91dHB1dCB2YWx1ZSAqLw0K ICAgICAgICAgICAgdmFsdWUgPSAwLjA7DQogICAgICAgICAgICBmb3IgKGl2 b2w9MDsgaXZvbCA8IE5WT0xTOyBpdm9sKyspIHsNCiAgICAgICAgICAgICAg IHRlbXB2YWx1ZSA9IA0KICAgICAgICAgICAgICAgICAgZ2V0X3ZvbHVtZV9y ZWFsX3ZhbHVlKHRlbXB2b2x1bWVbaXZvbF0sIGl6LCBpeSwgaXgsIDAsIDAp Ow0KICAgICAgICAgICAgICAgdmFsdWUgKz0gcGFyYW1ldGVyc1tpdm9sXSAq IHRlbXB2YWx1ZTsNCiAgICAgICAgICAgIH0NCg0KICAgICAgICAgICAgLyog U2F2ZSB0aGUgdmFsdWUgKi8NCiAgICAgICAgICAgIHNldF92b2x1bWVfcmVh bF92YWx1ZShvdXR2b2x1bWUsIGl6LCBpeSwgaXgsIDAsIDAsIHZhbHVlKTsN Cg0KICAgICAgICAgICAgLyogS2VlcCB0cmFjayBvZiB0aGUgcmFuZ2UgKi8N CiAgICAgICAgICAgIGlmICh2YWx1ZSA8IG1pbmltdW0pIG1pbmltdW0gPSB2 YWx1ZTsNCiAgICAgICAgICAgIGlmICh2YWx1ZSA+IG1heGltdW0pIG1heGlt dW0gPSB2YWx1ZTsNCg0KICAgICAgICAgfQ0KICAgICAgfQ0KICAgfQ0KDQog ICAvKiBTZXQgdGhlIHJhbmdlIG9mIHRoZSBkYXRhICovDQogICBzZXRfdm9s dW1lX3JlYWxfcmFuZ2Uob3V0dm9sdW1lLCBtaW5pbXVtLCBtYXhpbXVtKTsN Cg0KICAgLyogU2F2ZSB0aGUgZmlsZSwgY29weWluZyB0aGUgZGF0YSB0eXBl IGFuZCByYW5nZSBmcm9tIHRoZSBpbnB1dA0KICAgICAgdm9sdW1lICovDQog ICBkYXRhX3R5cGUgPSBnZXRfdm9sdW1lX25jX2RhdGFfdHlwZShpbnZvbHVt ZSwgJnNpZ25lZF9mbGFnKTsNCiAgIHZveGVsX21pbiA9IGdldF92b2x1bWVf dm94ZWxfbWluKGludm9sdW1lKTsNCiAgIHZveGVsX21heCA9IGdldF92b2x1 bWVfdm94ZWxfbWF4KGludm9sdW1lKTsNCiAgICh2b2lkKSBwcmludGYoIlNh dmluZyB0aGUgb3V0cHV0IHZvbHVtZVxuIik7DQogICBvdXRwdXRfbW9kaWZp ZWRfdm9sdW1lKG91dHB1dF9maWxlbmFtZSwgZGF0YV90eXBlLCBzaWduZWRf ZmxhZywNCiAgICAgICAgICAgICAgICAgICAgICAgICAgdm94ZWxfbWluLCB2 b3hlbF9tYXgsIG91dHZvbHVtZSwNCiAgICAgICAgICAgICAgICAgICAgICAg ICAgaW5wdXRfZmlsZW5hbWUsICJ0ZXN0X3Byb2dyYW0iLCBOVUxMKTsNCg0K ICAgLyogRGVsZXRlIHRoZSB2b2x1bWVzICovDQogICAodm9pZCkgcHJpbnRm KCJDbGVhbmluZyB1cFxuIik7DQogICBkZWxldGVfdm9sdW1lKGludm9sdW1l KTsNCiAgIGRlbGV0ZV92b2x1bWUob3V0dm9sdW1lKTsNCiAgIGZvciAoaXZv bD0wOyBpdm9sIDwgTlZPTFM7IGl2b2wrKykgew0KICAgICAgZGVsZXRlX3Zv bHVtZSh0ZW1wdm9sdW1lW2l2b2xdKTsNCiAgIH0NCg0KICAgLyogRGVsZXRl IHRoZSB0ZW1wb3JhcnkgZmlsZXMgKi8NCiAgIGZvciAoaXZvbD0wOyBpdm9s IDwgTlZPTFM7IGl2b2wrKykgew0KICAgICAgKHZvaWQpIHNwcmludGYodGVt cF9maWxlX3N1ZmZpeCwgIl8lZC5tbmMiLCBpdm9sKTsNCiAgICAgICh2b2lk KSByZW1vdmUodGVtcF9maWxlX25hbWUpOw0KICAgfQ0KDQogICByZXR1cm4g RVhJVF9TVUNDRVNTOw0KfQ0K ---2066828793-1237723228-1070421318=:7013171-- From minc-development@bic.mni.mcgill.ca Tue Dec 9 16:34:07 2003 From: minc-development@bic.mni.mcgill.ca (Andrew Janke) Date: Tue, 9 Dec 2003 11:34:07 -0500 Subject: [MINC-development] vol_io_prototypes.h Message-ID: Is there any reason as to why grid_inverse_transform_point(...) is declared twice? -- Andrew Janke ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3365 4100 || H: +61 7 3800 4042 || M: +61 4 2138 8581 From minc-development@bic.mni.mcgill.ca Tue Dec 9 16:41:35 2003 From: minc-development@bic.mni.mcgill.ca (Robert VINCENT) Date: Tue, 9 Dec 2003 11:41:35 -0500 Subject: [MINC-development] vol_io_prototypes.h In-Reply-To: Message-ID: Just a guess- there are two different implementations of the function in grid_transforms.c, one of which is #ifdef'd out of existence. Perhaps somebody either used an automatic tool to generate the header, or just wasn't paying attention when they typed in the prototypes... -bert On Tue, 9 Dec 2003, Andrew Janke wrote: > > Is there any reason as to why grid_inverse_transform_point(...) is declared > twice? > > > > -- > Andrew Janke ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) > Australia->University of Queensland->Centre for Magnetic Resonance > W: +61 7 3365 4100 || H: +61 7 3800 4042 || M: +61 4 2138 8581 > > _______________________________________________ > MINC-development mailing list > MINC-development@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development > From minc-development@bic.mni.mcgill.ca Tue Dec 9 16:43:55 2003 From: minc-development@bic.mni.mcgill.ca (Steve ROBBINS) Date: Tue, 9 Dec 2003 11:43:55 -0500 Subject: [MINC-development] vol_io_prototypes.h In-Reply-To: ; from bert@bic.mni.mcgill.ca on Tue, Dec 09, 2003 at 11:41:35AM -0500 References: Message-ID: <20031209114355.H85687@shadow.bic.mni.mcgill.ca> On Tue, Dec 09, 2003 at 11:41:35AM -0500, Robert VINCENT wrote: > Just a guess- there are two different implementations of the function in > grid_transforms.c, one of which is #ifdef'd out of existence. > > Perhaps somebody either used an automatic tool to generate the header, or Yes, it was initially generated by a script. -S From minc-development@bic.mni.mcgill.ca Tue Dec 9 16:55:00 2003 From: minc-development@bic.mni.mcgill.ca (Andrew Janke) Date: Tue, 9 Dec 2003 11:55:00 -0500 Subject: [MINC-development] vol_io_prototypes.h In-Reply-To: <20031209114355.H85687@shadow.bic.mni.mcgill.ca> Message-ID: On Tue, 9 Dec 2003, Steve ROBBINS wrote: > On Tue, Dec 09, 2003 at 11:41:35AM -0500, Robert VINCENT wrote: > > Just a guess- there are two different implementations of the function in > > grid_transforms.c, one of which is #ifdef'd out of existence. > > > > Perhaps somebody either used an automatic tool to generate the header, or > > Yes, it was initially generated by a script. ... and whos particular script was that? :) a From minc-development@bic.mni.mcgill.ca Tue Dec 9 17:08:30 2003 From: minc-development@bic.mni.mcgill.ca (Steve ROBBINS) Date: Tue, 9 Dec 2003 12:08:30 -0500 Subject: [MINC-development] vol_io_prototypes.h In-Reply-To: ; from rotor@bic.mni.mcgill.ca on Tue, Dec 09, 2003 at 11:55:00AM -0500 References: <20031209114355.H85687@shadow.bic.mni.mcgill.ca> Message-ID: <20031209120830.I85687@shadow.bic.mni.mcgill.ca> On Tue, Dec 09, 2003 at 11:55:00AM -0500, Andrew Janke wrote: > On Tue, 9 Dec 2003, Steve ROBBINS wrote: > > > On Tue, Dec 09, 2003 at 11:41:35AM -0500, Robert VINCENT wrote: > > > Just a guess- there are two different implementations of the function in > > > grid_transforms.c, one of which is #ifdef'd out of existence. > > > > > > Perhaps somebody either used an automatic tool to generate the header, or > > > > Yes, it was initially generated by a script. I take that back. I was thinking of something else. I don't know how vol_io_prototypes.h was generated. -S From minc-development@bic.mni.mcgill.ca Tue Dec 9 17:13:03 2003 From: minc-development@bic.mni.mcgill.ca (Andrew Janke) Date: Tue, 9 Dec 2003 12:13:03 -0500 Subject: [MINC-development] vol_io_prototypes.h In-Reply-To: <20031209120830.I85687@shadow.bic.mni.mcgill.ca> Message-ID: On Tue, 9 Dec 2003, Steve ROBBINS wrote: > I take that back. I was thinking of something else. > I don't know how vol_io_prototypes.h was generated. OK then.. you are hereby let off the hook. I suggest we just munch the second prototype.. volume_io hasn't undergone much development as of late so I don't see this as being a problem in the future. Perhaps we should just comment out the other #def'ed one out in the .c also. a From minc-development@bic.mni.mcgill.ca Wed Dec 10 03:04:07 2003 From: minc-development@bic.mni.mcgill.ca (Peter NEELIN) Date: Tue, 9 Dec 2003 22:04:07 -0500 Subject: [MINC-development] vol_io_prototypes.h In-Reply-To: <20031209120830.I85687@shadow.bic.mni.mcgill.ca> Message-ID: On Tue, 9 Dec 2003, Steve ROBBINS wrote: > On Tue, Dec 09, 2003 at 11:55:00AM -0500, Andrew Janke wrote: > > On Tue, 9 Dec 2003, Steve ROBBINS wrote: > > > > > On Tue, Dec 09, 2003 at 11:41:35AM -0500, Robert VINCENT wrote: > > > > > > > > Perhaps somebody either used an automatic tool to generate the header, or > > > > > > Yes, it was initially generated by a script. It is possible that it was initially generated with an earlier version of my rather crude extract_functions script (~neelin/bin/extract_functions), but you would have to check with Dave M. to be sure. Peter ---- Peter Neelin (neelin@bic.mni.mcgill.ca) From minc-development@bic.mni.mcgill.ca Mon Dec 15 19:34:32 2003 From: minc-development@bic.mni.mcgill.ca (Vicka Corey) Date: Mon, 15 Dec 2003 14:34:32 -0500 Subject: [MINC-development] minc-patch: fixing check for gunzip In-Reply-To: <20031125113850.I20004@gate.nmr.mgh.harvard.edu>; from vicka@nmr.mgh.harvard.edu on Tue, Nov 25, 2003 at 11:38:51AM -0500 References: <7CB36F8A-1EAB-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124133107.B20004@gate.nmr.mgh.harvard.edu> <48D414B0-1EAD-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124143345.C20004@gate.nmr.mgh.harvard.edu> <20031124150144.D20004@gate.nmr.mgh.harvard.edu> <20031124161858.F20004@gate.nmr.mgh.harvard.edu> <20031124171510.C6769116@shadow.bic.mni.mcgill.ca> <551E346E-1ECC-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031125113850.I20004@gate.nmr.mgh.harvard.edu> Message-ID: <20031215143432.H27238@gate.nmr.mgh.harvard.edu> > On Mon, Nov 24, 2003 at 05:19:55PM -0500, Jason Lerch wrote: > > Or give me another few days and I'll have the updated binary dist which > > fixes this and some of the other problems pointed out. Sorry about all > > these problems, and thanks for the (perhaps unwilling) beta testing! hi -- is this ready yet? and if so can you please send me the url for it? thanks much, --vicka From minc-development@bic.mni.mcgill.ca Tue Dec 16 15:18:39 2003 From: minc-development@bic.mni.mcgill.ca (Jason Lerch) Date: Tue, 16 Dec 2003 10:18:39 -0500 Subject: [MINC-development] minc-patch: fixing check for gunzip In-Reply-To: <20031215143432.H27238@gate.nmr.mgh.harvard.edu> References: <7CB36F8A-1EAB-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124133107.B20004@gate.nmr.mgh.harvard.edu> <48D414B0-1EAD-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124143345.C20004@gate.nmr.mgh.harvard.edu> <20031124150144.D20004@gate.nmr.mgh.harvard.edu> <20031124161858.F20004@gate.nmr.mgh.harvard.edu> <20031124171510.C6769116@shadow.bic.mni.mcgill.ca> <551E346E-1ECC-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031125113850.I20004@gate.nmr.mgh.harvard.edu> <20031215143432.H27238@gate.nmr.mgh.harvard.edu> Message-ID: <20812F64-2FDB-11D8-9C60-000A95DBBFD8@bic.mni.mcgill.ca> On Dec 15, 2003, at 2:34 PM, Vicka Corey wrote: >> On Mon, Nov 24, 2003 at 05:19:55PM -0500, Jason Lerch wrote: >>> Or give me another few days and I'll have the updated binary dist >>> which >>> fixes this and some of the other problems pointed out. Sorry about >>> all >>> these problems, and thanks for the (perhaps unwilling) beta testing! > > hi -- is this ready yet? and if so can you please send me the url for > it? Soon - I'll try to have it before Christmas. My apologies for the delays ... Jason > > thanks much, > --vicka > _______________________________________________ > MINC-development mailing list > MINC-development@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development From rboyes@dementia.ion.ucl.ac.uk Tue Dec 23 10:51:13 2003 From: rboyes@dementia.ion.ucl.ac.uk (Richard Boyes) Date: Tue, 23 Dec 2003 10:51:13 -0000 Subject: [MINC-development] nu_correct on linux Message-ID: hi all, we have a SUN file server here that stores all our analyze images as hilo endian. i'm trying to run nu_correct on a linux machine (lohi endian) using these files, byte swapping them beforehand using dd conv=swab and then converting them to minc using the rawtominc command. the converted minc files appear fine in mincview and i can run all the minc* utilities on them without a problem. when i try nu_correct, it jumps out straight away, saying the field change is 1E-27. this has happened for multiple images with bad bias fields, which doesn't seem correct. dd conv=swab if=/tmp/0_0_1071834373.img | rawtominc -oshort -clobber -mri -coronal -short -xstep 0.9766 -ystep 1.8000 -zstep 0.9766 -scan_range ./00000.mnc 120 256 256 #Mask file - no need to swap bytes rawtominc -byte -obyte -clobber -input ./bmask00000.img -coronal -xstep 0.9766 -ystep 1.8000 -zstep 0.9766 -orange 0 255 ./bmask00000.mnc 120 256 256 nu_correct -clobber -mask ./bmask00000.mnc ./00000.mnc /correct00000.mnc -stop 0.0005 -fwhm 0.075 -distance 100 -iterations 250 -mapping_dir . -shrink 3 Transforming slices:.........................................Done Processing:.........................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 1 CV of field change: 9.80328e-27 Transforming slices:.........................................Done 256+0 records in 256+0 records out Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:..................................................................... ...................................................Done At which point it finishes, without really finding a bias field. Any ideas? Is there a test suite or something i could try my build of nu_correct/MINC/netCDF on?