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(1) The AC is the anterior commissure. Open up a copy of your image, then put the cursor on the cross hair. There will be an x y z coordinate listed below the display window (mm:). Put the negative of each of these numbers in the right, forward, up boxes. Now make sure that the brain is rotated similar to the template. If not adjust the rotations. You only need a small amount (.05 or .1 at the most). (2) Resampling: I always use AFNI's 3dresample command with -dxyz option. Perhaps there is a quicker way in SPM. (3) The functional data is separate from the anatomical. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Wed, Mar 2, 2011 at 10:22 PM, Carolina Valencia <[log in to unmask]>wrote: > Thanks for your replay > > Sorry for the dumb questions, but I'm very new using spm > (1) How I know the coordinates for the AC (anterior comissure I guess)? > This coordinates will be the ones in x, y and z position? > (2) How I resample my data? Do I need to resample the functional MRI too? > > Best regards, > > Carolina > > 2011/3/2 MCLAREN, Donald <[log in to unmask]> > > (1) You need to make sure the origin on the AC. You can use the display >> function to change the origin with the reorient button after change the x y >> z position. >> >> (2) You should resample your data to 1x1x1 mm. There is no need for .5 mm >> voxels and this is what is taking up the memory. >> >> >> Best Regards, Donald McLaren >> ================= >> D.G. McLaren, Ph.D. >> Postdoctoral Research Fellow, GRECC, Bedford VA >> Research Fellow, Department of Neurology, Massachusetts General Hospital >> and Harvard Medical School >> Office: (773) 406-2464 >> ===================== >> This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED >> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is >> intended only for the use of the individual or entity named above. If the >> reader of the e-mail is not the intended recipient or the employee or agent >> responsible for delivering it to the intended recipient, you are hereby >> notified that you are in possession of confidential and privileged >> information. Any unauthorized use, disclosure, copying or the taking of any >> action in reliance on the contents of this information is strictly >> prohibited and may be unlawful. If you have received this e-mail >> unintentionally, please immediately notify the sender via telephone at (773) >> 406-2464 or email. >> >> >> On Wed, Mar 2, 2011 at 10:03 PM, Carolina Valencia < >> [log in to unmask]> wrote: >> >>> Thanks for the responses >>> I tried the solution using the spm Dicom importer (image attached) and >>> then re run the segmentation and once I get a poor result (image attached) >>> and tried several times to run it again but now, I have memory problems with >>> this error: >>> ------------------------------------------------------------------------ >>> Running job #1 >>> ------------------------------------------------------------------------ >>> Running 'Segment' >>> Failed 'Segment' >>> Out of memory. Type HELP MEMORY for your options. >>> In file "C:\spm8\spm_prep2sn.m" (v1143), function "create_def" at line >>> 188. >>> In file "C:\spm8\spm_prep2sn.m" (v1143), function "spm_prep2sn" at line >>> 20. >>> In file "C:\spm8\config\spm_run_preproc.m" (v2312), function >>> "spm_run_preproc" at line 20. >>> >>> The following modules did not run: >>> Failed: Segment >>> >>> Best regards, >>> >>> Carolina >>> >>> >>> 2011/3/2 John Ashburner <[log in to unmask]> >>> >>> It looks like your images were acquired sagittally, but the headers >>>> encode an axial orientation. Before trying to segment the images, >>>> you'll need to correct the orientation using the Display button. >>>> You'll need to enter various +/- 90 degree rotations (ie pi/2 >>>> rotations, because Display works in radians) until you get the right >>>> ones. Once you've done this, hit the reorient images button and apply >>>> the same transformation to all images that have the same wrong >>>> information in their headers. >>>> >>>> You may also need to try to figure out which is the left or right side >>>> of the brain. If the headers are wrong, then there's no way that SPM >>>> can work out which is left and which is right. If you use DICOM >>>> conversion routines that support NIfTI, then the headers should be >>>> written correctly. >>>> >>>> Best regards, >>>> -John >>>> >>>> On 2 March 2011 03:01, Carolina Valencia <[log in to unmask]> >>>> wrote: >>>> > Hi all, >>>> > >>>> > I am having problems with the segmentation step within SPM8. I have >>>> gotten deformed images (please see attached jpeg images). I have tried to >>>> adjust some of the segmentation defaults (gaussian, space), but have gotten >>>> similar results in each case. >>>> > >>>> > Thanks in advance, >>>> > >>>> > Carollina >>>> > >>>> >>> >>> >>> >> > > >