<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><BLOCKQUOTE type="cite"></BLOCKQUOTE>Frank,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>Thanks for the input; it seems like there are two options : JoinSeriesImageFilter and TileImageFilter, with the latter</DIV><DIV>being more generic. My main concern, and one which you may have already tested, is that the filter not copy the </DIV><DIV>underlying data - if it does, then you essentially double your memory requirements, at least transiently. Of course,</DIV><DIV>there are smarter ways to do it such as preallocation of the 4D volume followed by population one 3D "slice" at a</DIV><DIV>time, but I don't know if that's how these filters actually work... I suppose I should just test it out, though it would be</DIV><DIV>nice for the DICOM reader to gracefully handle the common case of 4D r-t data... </DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Matthias</DIV><DIV><BR><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">Matthias,</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Courier; min-height: 16px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">I to am working with 4D MRI data and prefer to have it as a single 4D</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">volume. The method suggested in the 2004-May post doest work because the</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">ImageSeriesReader has no information about the fourth dimension. It sees</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">one big stack of 2D images.</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Courier; min-height: 16px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">My approach to this is to organize the images in my file system</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">as a series of directories grouped by time index. i.e. all slices from</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">time index 0 in directory 000/, all slices from time index 1 in</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">directory 001/, and so on. I then load the slices from each directory</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">into a 3D volume in the usual way with itk::ImageSeriesReader and use</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">the itk::TileImageFilter to group the 3D volume together into a 4D</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">volume.</SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"> </SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Courier; min-height: 16px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">This solution seems less then ideal but it works.</SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"> </SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">Let me know if you</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">have any questions.</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Courier; min-height: 16px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">Frank</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Courier; min-height: 16px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">On Tue, Feb 06, 2007 at 12:18:27AM -0700, Matthias Schabel wrote:</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">></SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I> As per Luis' suggestion in a previous (fairly old) post (here : </I></SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I> </I></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">></SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I> </I></SPAN></FONT><A href="http://public.kitware.com/pipermail/insight-users/2004-May/008568.html"><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><FONT class="Apple-style-span" color="#0006EC"><I>http://public.kitware.com/pipermail/insight-users/2004-May/008568.html</I></FONT></SPAN></FONT></A><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I>),</I></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">></SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I> I am attempting to get ITK to correctly read a 4D (time+volumetric) </I></SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I> </I></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">></SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I> dynamic MRI data set. With filenames ordered following the suggested</I></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">></SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I> grouping (chunked first by acquisition time, then by slice), when I </I></SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I> </I></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">></SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I> attempt to read, I end up with a 1 x 1620 x 192 x 176 volume. While</I></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">></SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I> the total number of voxels is correct, this should in fact be a 90 x </I></SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I> </I></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">></SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I> 18 x 192 x 176 volume. I have already verified independently that</I></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">></SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I> the time stamps are identical for all slices for each acquisition, so </I></SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I> </I></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">></SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I> this seems to me to be a bug in the DICOM reader. I really would prefer</I></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">></SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I> to have the data in the form of a single 4D volume rather than a </I></SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I> </I></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">></SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I> vector of 3D slices - any suggestions/workarounds?</I></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">></SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I> </I></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">></SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I> Thanks,</I></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">></SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I> </I></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;">></SPAN></FONT><FONT class="Apple-style-span" face="Courier" size="3"><SPAN class="Apple-style-span" style="font-size: 13px;"><I> Matthias</I></SPAN></FONT></DIV><BR></BLOCKQUOTE><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV>----------------------------------------------------------------</DIV><DIV>Matthias Schabel, Ph.D. </DIV><DIV>Assistant Professor, Department of Radiology</DIV><DIV>Utah Center for Advanced Imaging Research</DIV><DIV>729 Arapeen Drive</DIV><DIV>Salt Lake City, UT 84108</DIV><DIV>801-587-9413 (work)</DIV><DIV>801-585-3592 (fax)</DIV><DIV>801-706-5760 (cell)</DIV><DIV>801-484-0811 (home)</DIV><DIV>mschabel at ucair dot med dot utah dot edu</DIV><DIV>----------------------------------------------------------------</DIV><DIV><BR></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN></SPAN> </DIV><BR></DIV></BODY></HTML>