From gabriel.devenyi at mcgill.ca Fri Jun 7 12:26:47 2019 From: gabriel.devenyi at mcgill.ca (Gabriel Allan Devenyi, Dr) Date: Fri, 7 Jun 2019 16:26:47 +0000 Subject: [MINC-users] Mincview and register launch issues In-Reply-To: <441fe1f334eb438da01bb7cc4fb4957a@YTBPR01MB3070.CANPRD01.PROD.OUTLOOK.COM> References: <441fe1f334eb438da01bb7cc4fb4957a@YTBPR01MB3070.CANPRD01.PROD.OUTLOOK.COM> Message-ID: Hi Colm, The MINC display tools use OpenGL (GLUT) as part of their rendering and as such, X forwarding doesn't work properly. Sorry. -- Gabriel A. Devenyi B.Eng. Ph.D. Research Computing Associate Computational Brain Anatomy Laboratory Cerebral Imaging Center Douglas Mental Health University Institute Affiliate, Department of Psychiatry McGill University t: 514.761.6131x4781 e: gabriel.devenyi at mcgill.ca On Mon, 15 Apr 2019 at 10:00, McGinnity, Colm > wrote: Dear Minc Users, I am new to the Minc toolkit, and was wondering if anyone could help me with these little issues: 1. Mincview yields these errors: "Dimensions of start or count vectors not equal to dimensions in file"; "Unknown argument: -monitor". 2. Register seems to open ok when I launch it from my Ubuntu desktop, but when I try to open it remotely via MobaXterm (from Windows) I get: "X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 146 (GLX) Minor opcode of failed request: 168 () Serial number of failed request: 39 Current serial number in output stream: 39" Does anyone have any suggestions? I apologise if these issues have already been answered in another email thread. Many thanks and best wishes, Colm Colm J. McGinnity MBChB PhD School of Biomedical Engineering & Imaging Sciences King's College London & KCL/GSTT PET Centre 4th Floor Lambeth Wing St. Thomas' Hospital Westminster Bridge Road London SE1 7EH colm.mcginnity at kcl.ac.uk> 020-7188-9259 _______________________________________________ MINC-users at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users From ekuama at kaist.ac.kr Fri Jun 21 01:45:49 2019 From: ekuama at kaist.ac.kr (Antoinette Deborah Martin) Date: Fri, 21 Jun 2019 14:45:49 +0900 Subject: [MINC-users] Save Register transform Message-ID: I have two images in .mnc form and a tag file. I used register image1.minc image2.mic landmarks.tag to view the two images and the transformed image. I will like to save the transformed image. Please, how do I do this? Thank you for your help in advance. Regards. From eskild at gmail.com Fri Jun 21 03:58:36 2019 From: eskild at gmail.com (Simon Eskildsen) Date: Fri, 21 Jun 2019 09:58:36 +0200 Subject: [MINC-users] Save Register transform In-Reply-To: References: Message-ID: First you need to decide the transformation type. You select that by hitting the 'Transform Type' button on the left hand panel in register. After you have selected the type, say 3 translations, 3 rotations, and 1 scale parameter, you can save the transformation matrix using the button 'Save Transform' in the panel on the left. If you type in a filename in the field just below and hit the save button, the transformation is saved as an xfm file with that name. Now you can transform and resample your image using the saved transformation. You can do that using mincresample or itk_resample. Their syntax is very similar, the main difference being that they offer different ways for interpolation. For example, this performs transformation and trilinear interpolation: mincresample -like image2.mnc -transformation image1toimage2.xfm -trilinear image1.mnc image1_transformed.mnc The -like option provides the resampling parameters using a model. I.e. the sampling of the transformed image1.mnc becomes the same as image2.mnc See mincresample -help or itk_resample --help for more options. Hope this helps. - Simon On Fri, Jun 21, 2019 at 7:46 AM Antoinette Deborah Martin < ekuama at kaist.ac.kr> wrote: > I have two images in .mnc form and a tag file. > I used register image1.minc image2.mic landmarks.tag to view the two images > and the transformed image. > I will like to save the transformed image. > Please, how do I do this? > > Thank you for your help in advance. > > Regards. > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users >