Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30059 discussions

Re: [Freesurfer] Subject does not have a bstampfile
by fsbuild 04 Mar '24

04 Mar '24

External Email - Use Caution   Let me add that it will not work to use shared mount point from the Windows filesystem as you list below, /mnt/c/Users/GCM/Desktop/subjects/NowakG/mri - for your SUBJECTS_DIR when running a recon-all command.  The command will fail because the Windows file system does not support soft-links.   Any SUBJECTS_DIR used for recon-all needs to be inside the Linux OS image running freesurfer.  You could however copy the files from that mount point to create another SUBJECTS_DIR somewhere inside your Linux image, e.g., under your home directory in linux. .... in your linux terminal window ... $ cd$ mkdir subjects$ export SUBJECTS_DIR=$HOME/subjects$ cd $SUBJECTS_DIR$ cp -p -f -R /mnt/c/Users/GCM/Desktop/subjects/NowakG . - R. On Jan 8, 2024, at 16:10, Huang, Yujing <YHUANG43(a)mgh.harvard.edu> wrote:You need to specify the input files to process. Here is the wiki page for recon-all -  https://secure-web.cisco.com/1hqVY7QioPnD85rxOcGMUcCuynnW47DWZwkPX0Z-CZpPZhsuOE3Dqq56yZOR48pnqlARbSGSU1uJNTssTzOLeJZDej-4B4APtXHQmIDTAeNiz6injsGyGghBE4szgzC-CIvlktYVKAeIFD9vBNBZGTgRtRAfcxOZTJJXzk0kPtE9fSY8vo9o05Q8Lf5La4t7Av6IvB6hkO3ZqlfaDGIxlZfRhNJC0f5oWDNXpfp8nYykG-egLh8zOuhOsHSbWCac7UKV67GamZPc5FS5KwH3vo_4_Omj5v0dIRxZ5O4d9WtJGN0f3IkrLaqnXHmnqhmI4YmYtNQmp-0UBF38a-xfw4w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-allBest,Yujing-----Original Message-----From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Joanna KidonSent: Monday, January 8, 2024 3:33 PMTo: freesurfer(a)nmr.mgh.harvard.eduSubject: [Freesurfer] Subject does not have a bstampfile       External Email - Use Caution        Hello FreeSurfer Developers,I'm attempting to compute Segmentation of hippocampal subfields and nuclei of the amygdala (cross-sectional and longitudinal), as described on the https://secure-web.cisco.com/1JRIAQtmLphlXIykU3RsSWy2GeEv_y0Em3hHjyX02njKQR… I get the following error when I run the recon-all -all -s command:Subject does not have a bstampfile, copying /usr/local/freesurfer/7.3.2/build-stamp.txtSubject FS Version: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version DoneINFO: SUBJECTS_DIR is /mnt/c/Users/GCM/Desktop/subjects Actual FREESURFER_HOME /usr/local/freesurfer/7.3.2 Linux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 521:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux#--------------------------------------------#@# MotionCor Sun Jan  7 20:48:46 CET 2024ERROR: no run data found in/mnt/c/Users/GCM/Desktop/subjects/NowakG/mri. Make sure to have a volume called 001.mgz in /mnt/c/Users/GCM/Desktop/subjects/NowakG/mri/orig.If you have a second run of data call it 002.mgz, etc.See also: http://secure-web.cisco.com/1YoN1A69KdRcMav_4NI9T7PYgKG5FAtbmkvQ7vxtAUykGwu… LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 521:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s NowakG exited with ERRORS at Sun Jan  7 20:48:46 CET 2024I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the scripts/recon-all.log in case it's of any use.Best regards,Joanna------------------------------------------------------------------------------------dr n.med., specjalista fizyki medycznej, neurobiolog Przewodnicząca Sekcji Diagnostyki Obrazowej Polskiego Towarzystwa Fizyki Medycznej Zakład Kardiologii Inwazyjnej i Elektrokardiologii, III Katedra Kardiologii Śląski Uniwersytet Medyczny w Katowicach Kierownik Działu Fizyki Medycznej, Koordynator ds. Ochrony Radiologicznej Z-ca Kierownika Zakładu Diagnostyki Obrazowej Górnośląskie Centrum Medycznego im. prof. L. Gieca SUM w KatowicachPhD, specialist in medical physics, neurobiologist Chairwoman of the Diagnostic Imaging Section of the Polish Society of Medical Physics Department of Invasive Cardiology and Electrocardiology, 3rd Department of Cardiology, Medical University of Silesia in Katowice Head of the Medical Physics Department, Coordinator for Radiological Protection, Deputy Head of the Department of Diagnostic Imaging Leszek Giec Upper-Silesian Medical Centre of the Medical University of Silesia in Katowice_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Longitudinal Freesurfer in the presence of large tissue defects
by Philip P 04 Mar '24

04 Mar '24

External Email - Use Caution Dear Freesurfer Developers, I am currently running the Longitudinal Pipeline on a cohort with significant portions of brain tissue removed. The obtained base templates overall look reasonable, however, when overlaying the transformed session T1ws and flicking between them, there still are noticeable residual differences. This is not surprising, given the inevitable brain shift after tissue removal, which rigid registration cannot account for. In my search for a non-linear base template option I came across the "Longitudinal FreeSurfer with non-linear subject-specific template improves sensitivity to cortical thinning” ISMRM abstract (https://secure-web.cisco.com/1me4RY0enlek75e3PAqIseSGOO7tfF84eBwPlWXYndHKO5…) as well as related code on Github (https://secure-web.cisco.com/10WRpCPnvc4D9H2TOaZHsTUn0u7cWtVKoReU9EtexFnzvs…) I was wondering whether you could provide insights into what you think the best strategy for obtaining reliable longitudinal cortical thickness measurements in such a dataset. Do you have a feel for whether the Longitudinal Freesurfer processing stream still provides benefits over Cross-Sectional analysis in the presence of large defects? Would you recommend giving the above-mentioned non-linear implementation a shot or were there other reasons the feature has not been implemented yet in the official version? Thanks already in advance! Best Philip

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control points do not help with pial and white matter edits to frontal areas with atrophy
by Lydia Chung 03 Mar '24

03 Mar '24

External Email - Use Caution Hi Freesurfer Team, I have a pt with significant atrophy in the right orbitofrontal/rostral middle frontal area (see screenshots below). I have added several control points but this has not been successful, as there is not much white matter in that area to begin with. Do you have recommendations for dealing with this type of issue? Do you typically leave as is or discard the subject entirely? Thanks for your help, Lydia [image: image.png] [image: image.png] [image: image.png] [image: image.png] -- Lydia Wu-Chung, M.A. Doctoral candidate BMED Lab Department of Psychological Sciences Rice University 6500 Main St - MS201 Houston, TX 77030 Lab Phone: 713-348-8126 Email: lydia.wu(a)rice.edu <lw50(a)rice.edu> *Confidentiality Text:* The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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Re: [Freesurfer] Freesurfer white matter overestimated
by Douglas N. Greve 03 Mar '24

03 Mar '24

Can you include an image with and without the surfaces? Make sure to include slices where you think the white surface extends too far. On 2/28/2024 9:13 AM, Luisa Klahn wrote: > > External Email - Use Caution > > Dear Douglas, > Please find the nu.mgz screenshot attached. > Best, > Luisa > > > ------------------------------------------------------------------------ > *Von:* Luisa Klahn <luisa.klahn(a)gu.se> > *Gesendet:* Montag, 26. Februar 2024 08:53 > *An:* dgreve(a)mgh.harvard.edu <dgreve(a)mgh.harvard.edu> > *Betreff:* Re: [Freesurfer] Freesurfer white matter overestimated > Dear Douglas, > Please find attached the pictures for the following issue: > I am processing structural data from a 3T scanner using Freesurfer > version 7.3.2. For some subjects, the grey matter looks very thin, and > the white matter looks overestimated. I'll attach screenshots of the > brainmask, wm mask, and T1 including wm and pial surface lines. > I have tried to set control points into the wm but this did not change > the results. > Does anyone have an idea? Would it be possible to change the intensity > settings in the recon-all command? > > Thanks for helping! > Best, > Luisa

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Is the slice delay of each slice needed for slice time correction with preprocess-sess?
by Maria Hakonen 03 Mar '24

03 Mar '24

External Email - Use Caution Dear all, Have I understood correctly that the slice delay of each slice is not needed when performing slice time correction with preprocess-sess? I am processing an open OASIS fMRI dataset. The dataset has fMRI data in nifti format and JSON files that contain information about the data. In the instructions they say: "Slice timing is included in the JSON when available. Some original DICOM files did not have slice timing info. When slice timing information is unavailable use the ratio TR/#slices." The data is collected with a Siemens scanner. If the slice timing is available it seems to be interleaved: "SliceTiming": [ 1.1025, 0, 1.165, 0.059999999999999998, 1.2250000000000001, 0.1225, 1.2875000000000001, 0.1825, 1.3474999999999999, 0.245, 1.4099999999999999, 0.30499999999999999, 1.47, 0.36749999999999999, 1.5325, 0.42749999999999999, 1.595, 0.48999999999999999, 1.655, 0.55000000000000004, 1.7175, Could I just run slice time correction with the siemens option? Best regards, Maria

2 1

Vertex / voxel lesion symptom mapping
by Martin Juneja 03 Mar '24

03 Mar '24

External Email - Use Caution Greetings FreeSurfer community, I was just wondering if it's possible to perform vertex/voxel lesion symptom mapping (VLSM) using FreeSurfer? In other words, I would like to assess the impact of lesion topography (of course, heterogenous locations across patients) on neurocognitive function in brain tumor patients. I would greatly appreciate any help/response. Thanks!

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Samseg (cross-sectional, longitudinal, MS lesions)
by Krzysztof Barć 01 Mar '24

01 Mar '24

External Email - Use Caution Good morning, 1) For the Samseg protocol, are only T1 and FLAIR sequences required (no MPRAGE scans required)? 2) What does the numerical output of the Samseg calculation look like? Best regards, Krzysztof Barć

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Re: [Freesurfer] Freesurfer Digest, Vol 240, Issue 19
by Li, Shasha,MD,MS,PhD 29 Feb '24

29 Feb '24

??????? ______________________ Shasha Li MD, PhD Assistant Professor, Martinos Center/Radiology (She/her/hers) Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 T 617-642-0449 massgeneral.org ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Thursday, February 29, 2024 5:00:01 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 240, Issue 19 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Support Request NextBrain (Sorby-Adams, Annabel) 2. Re: Longitudinal Freesurfer in the presence of large tissue defects (Philip P) 3. mri_synthseg fails with current model files (was Re: Support Request NextBrain) (fsbuild) 4. Re: [ext] Re: mris_convert reading surf.gii files? (Westin, Karin) 5. Re: [ext] Re: mris_convert reading surf.gii files? (Huang, Yujing) 6. Re: [ext] Re: mris_convert reading surf.gii files? (Westin, Karin) 7. Re: Creating a custom registration template with FreeSurfer template (Huang, Yujing) 8. Re: [ext] Re: mris_convert reading surf.gii files? (Huang, Yujing) 9. Re: [ext] Re: mris_convert reading surf.gii files? (Westin, Karin) 10. Re: [ext] Re: mris_convert reading surf.gii files? (Huang, Yujing) ---------------------------------------------------------------------- Message: 1 Date: Thu, 29 Feb 2024 01:11:25 +0000 From: "Sorby-Adams, Annabel" <ASORBY-ADAMS(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Support Request NextBrain To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Cc: fsbuild <fsbuild(a)contbay.com> Message-ID: <CF02DF80-4A65-4780-85A0-26F4D30B59B4(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Helen, I managed to run mri_synthseg on my M2 Mac by coping over the model file to the 7.3.2 version of freesurfer, and installing the tensorflow workaround previously posted on the forum for apple silicon machines. I have not been able to get it to work on the 7.4 or most recent dev versions unfortunately. The work around for 7.3.2 isn?t ideal, but does the trick. Freesurfer gurus may have more insight though! Annabel On 28 Feb 2024, at 20:03, Friedrich, Helen <hfriedrich(a)bwh.harvard.edu> wrote: ? Hi R, Thanks for your quick response. We actually did that initially and it did not work unfortunately. Could you provide me with segmentations for a certain scan? Or do you see any other possibility to make it work? Best, Helen ______________________ Helen Friedrich, B.Sc. Doctoral Student Netstim Laboratory Center for Brain Circuit Therapeutics Department of Neurology Harvard Medical School Brigham and Women?s Hospital 75 Francis St, Boston MA 02115 brighamandwomens.org <Outlook-rrf3zs4o.png> ________________________________ Von: fsbuild <fsbuild(a)contbay.com> Gesendet: Mittwoch, 28. Februar 2024 17:20 An: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Cc: Friedrich, Helen <hfriedrich(a)bwh.harvard.edu> Betreff: Re: [Freesurfer] Support Request NextBrain External Email - Use Caution The mri_synthseg script and python in the freesurfer disrtibution you are running are not entirely compatible with the arm64 M1, M2, M3 processors in silicon Macs. You could try installing and running the development build of Freesurfer for the silicon Mac via the link below. (After download, right click on the .pkg installer, and select open with default, then follow the prompts). https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-macOS… We would be interested to know if you run into such issues with the above development build. Please keep in mind a development build can be unstable and has not been tested like an actual release. Your numerical result may differ with the development build compared to the previous build/release. - R. On Feb 28, 2024, at 14:25, Friedrich, Helen <hfriedrich(a)bwh.harvard.edu> wrote: Dear Support Team, I'm reaching out for assistance with setting up NextBrain - mri_synthseg. Unfortunately, I could not make it work. There seems to be an issue with the np.float128-section. This error keeps showing up: <image.png> I have also tried to delete np.float128 from the script (as per suggestion from my colleague). However, the same error showed up. I'm working on a macOS M1. I would be very grateful for your assistance. Best, Helen ______________________ Helen Friedrich, B.Sc. Doctoral Student Netstim Laboratory Center for Brain Circuit Therapeutics Department of Neurology Harvard Medical School Brigham and Women?s Hospital 75 Francis St, Boston MA 02115 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be brighamandwomens.org<http://secure-web.cisco.com/17q0ctEVbQ3PCi9RlB5rYtmqkWfH8bL_7IwtwRdv14OcX42…> <Outlook-jaw0jfh4.png> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://secure-web.cisco.com/1rtWoOggy348yAexwX2GFQkliC-8Cc9lypKqh3QJHEwErL…> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Creating a custom registration template with FreeSurfer template
by Asuka Toyofuku 29 Feb '24

29 Feb '24

External Email - Use Caution Dear Freesurfer experts, I have issues with creating a custom registration template. (I'm following this instruction: https://secure-web.cisco.com/1_qfYxT5WNAR-lGRNh895Kl4pqE513hIRdGqZt0w-oDRR8… ) According to the instructions, we need to 1) Create an average subject (Creates $SUBJECTS_DIR/newtemplate) 2) Register each subject to the new template (do for both lh and rh), resulting in lh.sphere.reg.newtemplate and rh.sphere.reg.newtemplate 3) Get thickness values in the newtemplate space for GLM analysis 4) Create another average template based on the previous one: (Creates $SUBJECTS_DIR/newnewtemplate) I'm stuck with the 3) command. Instruction suggests: mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s subj3 ... and this is my code: for d in Teen* do mris_preproc --surfreg sphere.reg.teenheart_average_template --s $d --hemi lh --out lh.surfreg.teenheart_average_template.thickness --meas thickness done ( I specified hemi and output because, without it, I got ERROR: no source hemi specified) My command led to an error saying: ERROR: format for lh.surfreg.teenheart_average_template.thickness not recognized So my questions are: a) what does it mean that "format for lh.surfreg.average_template.thickness not recognised"? Any ideas on how to fix this? b) Does this mris_preproc --surfreg command produce different smoothing mgh files? (e.g., fwhm10, fwhm15, fwhm20...?) Because standard mris_preproc before GLM analysis(https://secure-web.cisco.com/1lH2n5girv1pSO3WmL3I9nDeL07oFU0ViiAmz… are done with previously qcashed data (e.g., need thickness.fwhm10.fsaverage to run mris_preproc), but at this point, I don't have any of these thickness files with different smoothing levels. c ) If this mris_preproc --surfreg command does not generate a set of thickness maps in **newtemplate space** at different smoothing levels, what kind of command should I run? Any input is appreciated! Best regards, Asuka

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mri_synthseg fails with current model files (was Re: Support Request NextBrain)
by fsbuild 28 Feb '24

28 Feb '24

External Email - Use Caution I don’t believe the workaround will be supported or provided with future releases intended to run on Silicon Macs.  If there is still an issue with mri_synthseg running with the current model files in the freesurfer dev build, then please let us know the details. - R. On Feb 28, 2024, at 20:11, Sorby-Adams, Annabel <ASORBY-ADAMS(a)mgh.harvard.edu> wrote:Hi Helen,I managed to run mri_synthseg on my M2 Mac by coping over the model file to the 7.3.2 version of freesurfer, and installing the tensorflow workaround previously posted on the forum for apple silicon machines.I have not been able to get it to work on the 7.4 or most recent dev versions unfortunately. The work around for 7.3.2 isn’t ideal, but does the trick. Freesurfer gurus may have more insight though! AnnabelOn 28 Feb 2024, at 20:03, Friedrich, Helen <hfriedrich(a)bwh.harvard.edu> wrote:Hi R,Thanks for your quick response. We actually did that initially and it did not work unfortunately.Could you provide me with segmentations for a certain scan? Or do you see any other possibility to make it work? Best,Helen______________________ Helen Friedrich, B.Sc.Doctoral Student Netstim Laboratory Center for Brain Circuit TherapeuticsDepartment of Neurology Harvard Medical SchoolBrigham and Women’s Hospital 75 Francis St, Boston MA 02115 brighamandwomens.org   <Outlook-rrf3zs4o.png> Von: fsbuild <fsbuild@contbay.com>Gesendet: Mittwoch, 28. Februar 2024 17:20An: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: Friedrich, Helen <hfriedrich@bwh.harvard.edu>Betreff: Re: [Freesurfer] Support Request NextBrain         External Email - Use Caution         The mri_synthseg script and python in the freesurfer disrtibution you are running are not entirely compatible with the arm64 M1, M2, M3 processors in silicon Macs.   You could try installing and running the development build of Freesurfer for the silicon Mac via the link below.  (After download, right click on the .pkg installer, and select open with default, then follow the prompts).https://secure-web.cisco.com/1lFsgk7vtXlatyZGhw2wfTf_WTyioo4BmLzbK… would be interested to know if you run into such issues with the above development build.  Please keep in mind a development build can be unstable and has not been tested like an actual release.  Your numerical result may differ with the development build compared to the previous build/release.- R.On Feb 28, 2024, at 14:25, Friedrich, Helen <hfriedrich(a)bwh.harvard.edu> wrote:Dear Support Team,I'm reaching out for assistance with setting up NextBrain - mri_synthseg. Unfortunately, I could not make it work. There seems to be an issue with the np.float128-section. This error keeps showing up: <image.png>I have also tried to delete np.float128 from the script (as per suggestion from my colleague). However, the same error showed up. I'm working on a macOS M1. I would be very grateful for your assistance. Best, Helen ______________________ Helen Friedrich, B.Sc.Doctoral Student Netstim Laboratory Center for Brain Circuit TherapeuticsDepartment of Neurology Harvard Medical SchoolBrigham and Women’s Hospital 75 Francis St, Boston MA 02115 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be brighamandwomens.org   <Outlook-jaw0jfh4.png> _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1rwDcenDHH042rGVnR9ADpR-TvoThnsOLxqL-W… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<Outlook-rrf3zs4o.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer

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