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Thanks Steve so in that case do I need to interfere manually to correct for any registration problems, if so how to take care of this for the rest of the batch processing steps i.e. do I need to change anything in the log files which are created by running batch processing commands so that the following/next processing steps will take this changes (that I made manually) into effect. Is there anywhere I can find guidelines how to do this i.e. if there is a manual intereference in one of the processing steps how to incorporate those changes into the log files so that next batch processing commands can go on . Thanks Venkateswaran ________________________________ From: FSL - FMRIB's Software Library on behalf of Stephen Smith Sent: Tue 10/26/2010 11:38 PM To: [log in to unmask] Subject: Re: [FSL] VBM results in white matter Hi - where you see such VBM effects at the edges of average GM then yes that suggests that the result is an alignment artefact and to be treated with caution. Cheers. On 26 Oct 2010, at 19:22, Rajagopalan, Venkateswaran wrote: Dear All, I did VBM analysis using FSL-VBM I am seeing significant differences in white matter, what am i doing wrong here. Screeshot attached. Thanks Venkateswaran =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org <http://www.clevelandclinic.org/> for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. <vbm_gm_results.JPG> --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve --------------------------------------------------------------------------- =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.