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---++ <font color=#0c860c>ADNI PET Core</font> ---++++PET Core News *Data Recall Advisory* From time to time, our PET Quality Control process identifies data as faulty that have already been posted and downloaded by users. We are not able to notify individual investigators of these problems. Therefore, any investigators working with PET data should regularly check the following site for notification of faulty data, and this data should be removed from all analyses until it has been corrected and reposted. *For more information on PET scan advisories contact: Robert Koeppe, ADNI PET Core QC Coordinator (koeppe@umich.edu)* --- --- ---+++ *<font color=#dd0000>New warnings:</font>* *Replacement scan for 033_S_1285* This subject originally had a scan on 8/28/08. This scan was acquired incorrectly at 18m (since this subject is not an MCI subject and hence should not have had an 18m scan). At that time it was decided to use this scan instead of the 24m PET scan. Hence, we initially passed this scan as this subject's 24m FDG scan with the plan was to skip the scan at 24 months. However, the site scanned the subject again at 24m anyway (scan date 2/23/09). This scan has been QC'd and is now the official 24m FDG scan for this subject. The previous scan from 8/28/09 has now been failed, and is no longer accessible from LONI. The new 24M FDG scan for 033_S_1285 was approved on March 12th, 2009. If this scan was downloaded before March 13, 2009, please download again and replace. Downloads March 13, 2009 or after will give the newer scan. -- Main.BobKoeppe - 20 April 2009 --- --- ---+++ *<font color=#ff6600> _Excel file_ available with listing of all PET scans considered to have potential issues that may effect results of image analysis.</font>* ---+++++<font color=#117711> The _Excel File_ now contains two additional pages with specific information for !BioGraph !HiRez and HRRT scans that have been reworked. The _Excel file_ contains both Series UID and Image UID for all scans to insure proper identification of the PET scans that should be analyzed.</font> This Excel file can be downloaded using the link at the bottom of this page. It is sorted by site, then subject, then PET visit (BV, 6m, 12m, etc.) and contains both FDG and PIB information. An updated version of this file will be available for download the first of each month. New information about problem scans will be placed at the top of the file and clearly marked. After one month, this 'new' information will be sorted and moved below, so only information from the previous month will be listed at the top. *All PET users are strongly encouraged to bookmark this page, and download the file each month. Any questions about particular sites, scanners, or individual PET scans, and the potential ramifications of the specific issues can be directed to Bob Koeppe.* -- Main.BobKoeppe - 01 Nov 2007 --- --- ---+++ <font color=#1111cc>Old warnings:</font> ---++++ New Site with PET scanner change: Four more ADNI sites have just replaced their PET scanners (the other sites are listed under "Old Warnings"). As mentioned below, investigators should be aware of resolution differences between scanners, hence should consider analyzing the PET data that has been matched for resolution. This is the 4th of the 4 pre-processed image files that get uploaded to LONI by the QC group. These have a uniform 160x160x96 1.5 mm3 grid and isotropic ~8mm FWHM resolution. Another important consideration is that the apparent size of the brain can be different for different scanners. For example, '20 cm' in size on the older Siemens Accel and Exact is smaller than '20' cm in the newer !BioGraph !HiRez scanner. As with the previous PET scanner replacements, all "pre-processed" images for the new scanner have been adjusted to correct for these differences. This is important for within-subject analyses. *Site 009 Baylor: All prior scans were done on a Siemens Ecat Exact 47-slice scanner. Their new scanner is a GE Discovery ST 47-slice scanner For the new Discovery ST scans, the x,y voxel size is reduced from 2.00 mm to 1.945 mm to match the size of the Exact scanner. The z dimension of the scans for these subjects are reduced from 3.27 to 3.24 mm. *Site 021 Baylor: All prior scans were done on a GE Advance 35-slice scanner. Their new scanner is a GE Discovery STE 47-slice scanner There are no changes in voxel sizes. *Site 057 and 126 (St. Joe and Parkwood (sharing scanner): All prior scans were done on a GE Discovery LS 35-slice scanner. Their new scanner is a GE Discovery STE 47-slice scanner There are no changes in voxel sizes. A fourth ADNI site has just replaced their PET scanner (the other 3 sites are listed under "Old Warnings"). As mentioned below, investigators should be aware of resolution differences between scanners, hence should consider analyzing the PET data that has been matched for resolution. This is the 4th of the 4 pre-processed image files that get uploaded to LONI by the QC group. These have a uniform 160x160x96 1.5 mm3 grid and isotropic ~8mm FWHM resolution. Another important consideration is that the apparent size of the brain can be different for different scanners. For example, '20 cm' in size on the older Siemens Accel and Exact is smaller than '20' cm in the newer !BioGraph !HiRez scanner. As with the previous 3 PET scanner replacements, all "pre-processed" images for the new scanner have been adjusted to correct for these differences. This is important for within-subject analyses. *Site 003 USC: All scans acquired prior to 2008 were performed on an Siemens !BioGraph LSO scanner, the older 47 slice model. Their new scanner is a !BioGraph LSO !HiRez 81 slice scanner, and was brought on-line in March 2008. To date (April 2, 2008), two scans have been uploaded to LONI, 003_S_1057 (12m scan) and 003_S_1074 (12m scan). For the new !BioGraph !HiRez scans, the x,y voxel size is unchanged, while the z dimension of the scans for subjects that have earlier scans on the old scanner has been reduced from 2.0205 to 1.995 mm. -- Main.BobKoeppe - 02 Apr 2008 ---+++++ Recalled ADNI PET scans replaced with new re-worked images The original raw and processed PET images for the BV visit _FDG_ scan for subjects 128_S_1407 and 128_S_1408 contained reconstruction artifacts resulting from a problematic attenuation correction. When the 6m _FDG_ scans were received for these subjects, QC determined mismatchs between BV and 6m scans bad enough to warrant re-processing of the BV scans. Both "raw" and "pre-processed" _FDG_ images for these two subjects downloaded before 2/12/2008 should be deleted and replaced with the new images sets, as the re-worked images sets were approved and "pre-processed" images uploaded to LONI on 2/11/2008. Corrected BV _FDG_ image sets for subject 128_S_1407 have series UID S41093. The corrected raw images have image UID I90029. *<font color=#0000DD>(Original raw images NOT TO BE USED have image UID I77122)</font>* Corrected BV _FDG_ image sets for subject 128_S_1408 have series UID S42724. The corrected raw images have image UID I90030. *<font color=#0000DD>(Original raw images NOT TO BE USED have image UID I82093)</font>* -- Main.BobKoeppe - 12 Feb 2008 The original raw and processed PET images for the 12m visit _PIB_ scan on subject 128_S_0188 contained time framing errors (frames were not from 50-70 min post-injection). Both raw and processed PET PIB images for this subject downloaded before 12/18/2007 should be deleted. Corrected 12m _PIB_ images for subject 128_S_0188 have series UID S35089. The corrected raw images have image UID I85224. *<font color=#0000DD>(Original raw images NOT TO BE USED have image UID I60256)</font>* -- Main.BobKoeppe - 04 Jan 2008 ---+++++ Incorrect Subject The baseline PET FDG scan for ADNI subject 109_S_1343 has been determined to be the wrong subject. At the time of the 6m PET scan on 109_S_1343, the PET FDG image sets were found not to match, i.e. they were from different subjects. The site has determined that it was the baseline scan that was in error. The baseline FDG scan for this subject has been processed and reuploaded. All investigators will need to replace the baseline PET for this subject in their analyses. (See also the November PET Scan issues file) -- Main.BobKoeppe - 01 Nov 2007 ---++++ PET Sites with scanner changes: Three sites have replaced their PET scanner during the ADNI project. Investigators should be aware of resolution differences between scanners, and should consider analyzing the PET data that has been matched for resolution. This is the 4th of the pre-processed image files that get uploaded to LONI. These have a uniform 160x160x96 1.5 mm3 grid and isotropic 8mm FWHM resolution. Another important consideration is that the apparent size of the brain can be different for different scanners. For example, '20 cm' in size on the older Siemens Accel and Exact is smaller than '20' cm in the newer !BioGraph !HiRez scanner. In each case the voxel size of scans from the replacement scanner has been adjusted to match that of the *earlier* scans if there was a scanner change for the subject. * Site 016 Wien: subjects 0354 and 0359 had their BV scans on an Siemens Accel. Their 6m and 12m scans were acquired on a Siemens !BioGraph !HiRez scanner. The voxel size of scans for these two subjects acquired on the repalcement scanner have been made smaller, multiplied by 0.965 in the x,y dimensions, and by 0.970 in the z dimension. * Site 100 Boston: subjects 0047 BV, 6m, 12m; 0743 BV and 6m; 0747 BV and 6m; 0892 BV; 0930 BV; 0995 BV; 1062 BV, and 1154 BV were performed on a Siemens !BioGraph. Subjects 0747 12m; 0892 6m; 0930 6m; 0995 6m; 1062 6m, and 1154 6m have been performed on a GE Discovery STE scanner. The x,y voxel size is unchanged. The z dimension of the STE scans for subjects that have earlier !BioGraph scans has been reduced to 0.325 cm. * Site 114 CWRU: subjects 0173 BV; 0228 BV; 0374 BV; 0378 BV; 0410 BV; 0416 BV were performed on a Philips Allergo scanner. All other scans at this site have been performed on a Philips Gemini-TF scanner. The voxel sizes for the new scanner did not need to be adjusted, and are unchanged. -- Main.BobKoeppe - 03 Oct 2007 ---++++ Updates for Siemens HRRT and Siemens !BioGraph !HiRez PET scan warnings: ---+++++ HRRT issue: see previous comments below, dated May 8, 2007 All HRRT PET scans from sites 029 and 128 performed prior to the posted data recall advisory have been reworked. One HRRT PET scan has been reworked from site 032. While most of the problem scans are reduced or eliminated, there are a few scans that remain suspicous. A summary of individual scan concerns can be downloaded in the Excel "PET Image Issues" file available from this web-page. ---+++++ Current Advice (October 1, 2007): 1. The following scans have been reprocessed and the latest versions should be downloaded from LONI, whether one is using the raw uploaded image files or any of the pre-processed image files available from !LONI. If there are any questions or doubt about whether you have the latest version of a particular scan, the image files should be downloaded again and the xml UIDs can be checked to make sure. * Site 029 subjects: 0836 BV and 6m; 0843 BV; 0845 BV; 0866 BV; 0914 BV; 1038 BV; 1056 BV; 1073 BV * Site 032 subject : 0400 BV * Site 128 subjects: 0135 BV, 6m, 12m; 0138 BV, 6m, 12m; 0167 BV, 6m, 12m; 0188 BV, 6m, 12m; 0200 BV, 6m ; 0205 BV, 6m; 0216 BV, 6m; 0225 BV, 6m; 0227 BV; 0230 BV, 6m, 12m; 0258 BV, 6m; 0266 BV, 6m; 0272 BV, 6m, 12m; 0500 BV, 6m; 0522 BV, 6m; 0608 BV, 6m; 0715 BV, 6m; 0740 BV, 6m; 0770 BV; 0863 BV; 0947 BV; 1043 BV -- Main.BobKoeppe - 01 Oct 2007 ---+++++ !BioGraph !HiRez issue: (sites 016 since 2007, 020, 037, 062, 072, 082, 130): see previous comments below, dated May 8, 2007 Siemens has provided all !BioGraph !HiRez sites with a software patch to correct the problem described previously. Listed below is the status of scans for all the sites. Scans that have been reworked following installation of the patch should be downloaded again from LONI, whether one is using the raw uploaded image files or any of the pre-processed image files. ---+++++ Current Advice (October 1, 2007): 1. The following scans have been reprocessed and the latest versions should be downloaded from LONI, whether one is using the raw uploaded image files or any of the pre-processed image files. If there are any questions or doubt about whether you have the latest version of a particular scan, the image files should be downloaded again and the xml UIDs can be checked to make sure. * Site 016 subjects: all scans since the scanner change to the !BioGraph !HiRez were reconstructed with software routines that did not contain the software bug. No new downloads needed * Site 020 subjects: 0097 12m; 0213 12m have been reworked following software patch and *must be downloaded again*. 0097 BV, 6m, and 0213 BV, 6m scan raw data were found to be corrupted and these images still contain asymmetries. *Use these with caution*. 0883 was scanned after software patch so is acceptable. * Site 037 subjects: 0150 12m; 0566 6m; 0627 6m have been reworked following software patch and *must be downloaded again*. All other scans were either processed with software version before the problem, or after the software patch was installed, and were acceptable. * Site 062 subjects: site did NOT save any scan sinogram data, hence no scans can be reworked. Software patch to fix problem was installed on 6/4/07. All scans performed before this date potentially have asymmetry artifact. *Use these with caution*. Scans after this date should be acceptable. * Site 072 subjects: software version used at this site is older, and is pre version 4.xx which had the bug. All images are acceptable. No new downloads needed. * Site 082 subjects: site has not reworked any images at this time, but site only has two BV scans. * Site 130 subjects: 0232 6m, 12m; 0285 6m, 12m; 0289 6m, 12m; 0783 BV, 6m; 1200 BV; 1201 BV; 1290 BV have been reworked following software patch and *must be downloaded again*. All other scans were either processed with the software version before the problem, or after the software patch was installed, and are acceptable. -- Main.BobKoeppe - 01 Oct 2007 --- --- ---++++ Siemens HRRT PET scan warnings: ---+++++ Sites with HRRT scanners: 029, 032, 053, 128 ---+++++ Summary of warnings: Two issues exist with Siemens HRRT PET images. 1. After analysis of the ADNI normal control PET subjects, it has become apparent that the baseline pattern of FDG metabolism is different for subjects scanned on HRRT PET scanners than on other scanners. This is not a resolution effect, since the differences are apparent on images smoothed to a common resolution (8 mm). In general, regions in the lower transaxial slices and in particular regions near the middle of these slices, show relatively lower metabolic activity in HRRT scans than in scans acquired on other scanners. For example, the value of the pons relative to the global mean is 12% lower for HRRT scans on average than for all other scans. While the cause of this is not certain, my best guess is that it is a related to scatter correction (or possibly attenuation correction or a combination of the two). The differences are consistent with the lower transaxial slices (base of the brain down into the neck) having greater scatter subtraction for HRRT scanners than other scanners. One possible reason would be that the axial FOV of HRRT scanners is much larger than most all other scanner models, and hence the correction can account for scatter which comes from the levels of the body (e.g. below the brain) imaged by the HRRT that are out of the axial field-of-view of other scanners. Thus, scatter that can be attributed to these “below-brain” slices imaged with the HRRT is being successfully removed by the scatter correction routine, resulting in relatively lower PET values in these inferior slices. Scatter from these areas of the body would not be accounted for and hence subtracted with other scanners since they are out of the axial FOV and not imaged. This apparent difference between scanner types was not seen in the phantom studies, where the relative values in “pons” or “cerebellar” regions of the Hoffman phantom did not differ significantly between HRRT and other scanners. This result is also consistent with the idea of the difference being due to scatter correction. The Hoffman phantom scans did not have activity in these lower slices and hence there was not additional scatter in the field-of-view that could be removed. There was a torso phantom used with the Hoffman phantom scans (simulating out-of-field scatter), but this was outside the FOV for all scanners including the HRRT. 2. Some HRRT images have reconstruction (attenuation and/or scatter correction induced) artifacts. Some of these are quite subtle that were only noticed or confirmed when the 6 month or 12 month PET scans were obtained and overlaid with the baseline scans. This has resulted in some of the HRRT scans that had originally passed “QC” (and hence available) now being “failed”, and no longer available for download. LONI’s advanced database search can be used to find the current HRRT scans that have passed QC. In some cases these artifacts have caused even greater differences in the relative metabolic values in lower image slices, compounding the issue raised above, where for example pons values are relatively lower than in other scanners. ---+++++ Current Advice (May 8, 2007): 1. At present, scans from HRRT scanners should be considered to produce a different pattern of FDG uptake than other scanners (see below). Analyses that assume comparability across all scanners should consider excluding HRRT scans for the time being (e.g. comparison of individual scans to a normal database). 2. Check to see if any HRRT PET scans that you have downloaded are no longer available. Do not use any HRRT images that are now failed and not available through LONI. ---+++++ Plan: 1. Now that all the baseline PET scans on normal controls have been acquired and uploaded to LONI, we are working on an empirical correction for scanner-specific differences in PET scans such as those described above. Notices will be provided here concerning progress on this front. 2. The HRRT sites have figured out how to deal with most of the artifacts mentioned above. All failed scans from HRRT sites are being reprocessed in an attempt to reduce or remove these artifacts. Re-reconstructed images will be uploaded and QC’d. Notices will be provided here for all re-worked HRRT images that pass QC. After re-reconstruction and re-processing of these “failed”, other HRRT scans that are currently available will be re-reconstructed with the new processing stream, to make sure all subjects have optimal images over time. -- Main.BobKoeppe - 08 May 2007 ---++++ Siemens !BioGraph !HiRez PET scan warning: ---+++++ Sites with !BioGraph !HiRez scanners: 016 (since 2007), 020, 037, 062, 072, 082, 130 ---+++++ Summary of warning: There exists a software bug in OSEM reconstruction for Siemens !BioGraph !HiRez PET/CT scanners. Depending upon the circumstances, this artifact can be quite minor or can be quite substantial. Siemens is aware of this, has developed a patch for the problem, and is in the process of distributing the patch to the !BioGraph !HiRez sites. We will be asking all !HiRez sites to re-reconstruct all of their PET images once the site has the software patch installed and tested. The problem involves an error in the Siemens image reconstruction algorithm that may produce an artifactual asymmetry in the PET images. The actual asymmetry depends on how the patient is positioned in the scanner. These asymmetries may produce data analytic results that appear as if brain activity is higher in one hemisphere than another, potentially seriously affecting the ADNI results. The actual error for a particular scan depends upon a variety of physical factors and the specific software version the site used for that scan reconstruction. *Technical details of the problem:* The problem is in the Siemens OSEM reconstruction, where the ordered subsets of the PET and CT data sets used by the EM algorithm are not correctly matched between emission (PET) and transmission (CT) data. In other words, the emission projections are being attenuation corrected with the wrong CT projections. The artifact appears as an asymmetry in the image that does not really exist. If the subject is low in the field-of-view, an image left > image right asymmetry occurs (mostly in posterior regions). If the subject is high in the FOV, the opposite occurs, but more in the frontal regions. The magnitude of the artifacts depends upon many factors, including physical factors and the particular software version and software parameters being used. These are summarized as follows. Physical factors: If the object being imaged is cylindrical and perfectly centered in the field-of-view, there is no artifact. As the object becomes more elliptical (such as a head), and as the object is located further from the center of the scanner’s FOV, the magnitude of the asymmetry increases. This error was not seen in the phantom studies that were done at the start of ADNI since the Hoffman phantom is cylindrical, and each site scanned the phantom very near to the center of the FOV. Software version/parameter factors: The error is both software version and OSEM parameter dependent. The error is less noticeable for software versions 3.x and more noticeable in the newer software releases, 4.x. (see below for explanation). The ADNI protocol specifies 4 iterations and 16 subsets with reconstruction into a 168x168 grid using “TRIM=2”. In OSEM reconstruction, the number of projections has to be divisible by the number of subsets so that the number of projections per subset is constant. The number of angular projections for the !BioGraph !HiRez is 336. This is divisible by 16 (336/16=21 projections per subset). HOWEVER, a feature of Siemens software used to speed up reconstruction is to interpolate the number of rays per projection and the number of projections to the output image grid size. Thus, if the 336 projections are interpolated to 168 projections prior to reconstruction, 16 subsets cannot be used (168/16=10.5, and you can’t have half a projection). The older software either forced the user to select 14 subsets (168/14=12), or actually used 14 subsets even when 16 subsets was selected. When the version 4.x software was released, the option for 14 subsets disappeared, and when the user selects 16 subsets the software rounds this UP, not DOWN to the nearest number of acceptable subsets, which happens to be 21 (168/21=8). Thus, even though the software says 16 subsets, 21 are being used with version 4.x software. This has two effects. The minor one is that the images are noisier than before since 50% more total sub-iterations are being used (4 x 21, instead of 4x14), but more importantly, the error due to the mismatch of PET and CT projections for attenuation correction has become considerably more pronounced with 21 subsets than 14 subjects, due to the particulars of the actual software bug in Siemens code. ---+++++ Current Advice (May 8, 2007): All !BioGraph !HiRez PET scans need to be interpreted with caution. While the majority of artifact-induced asymmetries are probably only a few percent or less, in some cases these will be greater. If during longitudinal analysis, one finds a change in the degree of asymmetry between scans, this finding in particular should be questioned. Final conclusions should wait until the re-reconstructions are uploaded to LONI. One can make an educated guess about the magnitude of the artifact for a given scan by considering the above information (i.e. version 3 vs. version 4, location within the FOV), but also by looking at the raw images to see whether the asymmetries are seen in the scalp. While scalp uptake of FDG may also be asymmetric, the artifact will be more apparent in regions farther from the center of the object (such as scalp). Hence, in many of the ADNI !BioGraph !HiRez images, one can see a noticeable scalp asymmetry. In my review of all !BioGraph !HiRez scans, most subjects are scanned a little below the center of the field-of-view, and hence in many images one scan see an image left (brain right) posterior increase in scalp activity. ---+++++ Plan: When the software patch is available and re-reconstructions are performed by the sites, and uploaded to LONI, we will provide the updates here concerning the availability of these re-processed !BioGraph !HiRez scans. -- Main.BobKoeppe - 08 May 2007 ---++++++ Topic permissions * Set ALLOWTOPICCHANGE = Main.AdniGroup -- Main.KarenCrawford - 07 May 2007 --- --- ---
