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Thank you very much Dr.Steve, you are right our data was acquired at 1*1*1 and resampled to 0.5*0.5*1 by the scanner. I will use a computer with better memory than mine. Thanks again, venkateswaran -----Original Message----- From: FSL - FMRIB's Software Library on behalf of Steve Smith Sent: Wed 9/9/2009 2:41 AM To: [log in to unmask] Subject: Re: [FSL] template list creation in FSL VBM Hi - we don't normally recommend downsampling/resampling data before running segmentation - however 1mm is still pretty good so that's not too bad. However I suspect that maybe your data was only actually acquired at lower resolution than 0.5mm in the first place, and upsampled on the scanner - so a much better solution would be to get the non-resampled data from your scanner if that's the case. It would also be a good idea to try to get more RAM and swap for your computer, and make sure you're using a 64-bit OS and 64-bit version of FSL. Cheers. On 8 Sep 2009, at 14:48, Rajagopalan, Venkateswaran wrote: > Thanks very much Dr.Steve for your kind help. One more question i > would like to ask, i am using VBM for structural image studies, our > MPRAGE T1-W sequence has a dimension of 512*512 and 1 mm thick > slices, my computer has only 2GB RAM so this becomes problem in case > of FAST (FAST runs out of memory) and once i was using FNIRT on this > data for some other purpose and it also had memory problems. Is it > advisable to resample my 0.5*0.5*1 mm images to lower resolution, > will this affect tissue segmentation (FAST) and eventually the VBM > results. Any input regarding this is greatly appreciated. > > Thanks again > > venkateswaran > > > -----Original Message----- > From: FSL - FMRIB's Software Library on behalf of Steve Smith > Sent: Sat 9/5/2009 2:02 AM > To: [log in to unmask] > Subject: Re: [FSL] template list creation in FSL VBM > > Hi - I guess you're not using bash or sh as your shell, so this syntax > would be wrong? > > You can just create this text file by hand using any text editor, or > even just > > ls -1 CON_04.nii.gz CON_08.nii.gz CON_10.nii.gz CON_13.nii.gz > CON_19.nii.gz PAT_02.nii.gz PAT_05.nii.gz PAT_11.nii.gz PAT_18.nii.gz > PAT_19.nii.gz > template_list > > Cheers > > > > > On 4 Sep 2009, at 22:48, Rajagopalan, Venkateswaran wrote: > >> >> Dear FSL Users, >> >> I am new to Linux OS. I tried the following >> >> "for g in CON_04.nii.gz CON_08.nii.gz CON_10.nii.gz CON_13.nii.gz >> CON_19.nii.gz \ >> PAT_02.nii.gz PAT_05.nii.gz PAT_11.nii.gz PAT_18.nii.gz >> PAT_19.nii.gz; do >> echo $g >> template_list >> done" >> >> to create a template list of my data set as described in FSL_VBM >> documentation page. I typed this in the terminal window and it gives >> me the following error "g undefined variable "for" command not >> found. I don't have much programming experience too. Can you pleas >> tell me the mistake i am making here. >> >> Thanks >> >> venkat >> >> >> =================================== >> 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 (2008). >> 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. >> > > > --------------------------------------------------------------------------- > 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 (2008). > 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. > --------------------------------------------------------------------------- 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 (2008). 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.