Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

about issues with "recon-all"
by Abel Lei 06 Sep '14

06 Sep '14

Hi FreeSurfers, I’m a very beginner to both the Linux OS and the FreeSurfer program. After finally setting up the FreeSurfer, I was trying to do recon-all for my trial subject. But when I ran the “recon-all” command, it returned with a long error message indicating many commands not found. The message is copied and pasted below. I also attached the recon-all.log and recon-all.error in this email, which (probably) contains two failed attempts of the same command. Please let me know if you need any other info from me. I appreciate your help and time greatly! Thank you so much! Chia-Ming (Abel) Lei PhD Student/Graduate Student Researcher Language and Brain Lab (LABlab) & Adult Language Lab Department of Communication Sciences and Disorders School of Health and Rehabilitation Science University of Pittsburgh -----below is the long~ error message------ chiaming-PORTEGE-R835:~> recon-all -all -s mike_dickeySubject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot Actual FREESURFER_HOME /home/chia-ming/Desktop/freesurfer -rw-rw-r-- 1 chia-ming chia-ming 2119 Sep 6 01:34 /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/scripts/recon-all.log Linux chiaming-PORTEGE-R835 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux mri_motion_correct.fsl: Command not found. talairach_avi: Command not found. tkregister2_cmdl: Command not found. nu_correct: Command not found. mri_make_uchar: Command not found. mri_normalize: Command not found. mri_watershed: Command not found. mri_gcut: Command not found. mri_segment: Command not found. mri_label2label: Command not found. mri_em_register: Command not found. mri_ca_normalize: Command not found. mri_ca_register: Command not found. mri_ca_label: Command not found. mri_pretess: Command not found. mri_fill: Command not found. mri_tessellate: Command not found. mri_concatenate_lta: Command not found. mri_normalize_tp2: Command not found. mris_smooth: Command not found. mris_inflate: Command not found. mris_curvature: Command not found. mris_sphere: Command not found. mris_fix_topology: Command not found. mris_topo_fixer: Command not found. mris_ca_label: Command not found. mris_euler_number: Command not found. mris_make_surfaces: Command not found. mris_register: Command not found. mris_volmask: Command not found. mris_anatomical_stats: Command not found. mrisp_paint: Command not found. mris_curvature_stats: Command not found. mris_calc: Command not found. mri_robust_register: Command not found. mri_robust_template: Command not found. mri_and: Command not found. mri_or: Command not found. mri_fuse_segmentations: Command not found. mri_segstats: Command not found. cp: cannot stat 'Desktop/freesurfer/bin/recon-all': No such file or directory #-------------------------------------------- #@# MotionCor Sat Sep 6 01:40:13 EDT 2014 ERROR: no run data found in /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/mri. Make sure to have a volume called 001.mgz in /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux chiaming-PORTEGE-R835 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s mike_dickey exited with ERRORS at Sat Sep 6 01:40:13 EDT 2014 For more details, see the log file /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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LGI Topological Defect
by Tara Miskovich 06 Sep '14

06 Sep '14

Hi all, I am getting an error that seems common for people running LGI where it crashes due to a topological defect. I have run mris_euler_number and everything looks fine. Plus, I went through each slice and made sure the surfaces looked good. Any advice on any other steps I can take? I have already tried rerunning recon-all. Thank you! Tara

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Re: [Freesurfer] tracula: bvec-error
by Robby De Pauw 05 Sep '14

05 Sep '14

Hi Anastasia, I’m using this version of tracula. trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp I’ve attached the log-file you requested. Robby De Pauw, dra. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent Robby.DePauw(a)Ugent.be

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Nframes greater than 1...
by Gonzalo Rojas Costa 05 Sep '14

05 Sep '14

Hi: I have an mprage image with nframes = 2... how can I convert it to use it in freesurfer ?... Sincerely, Gonzalo Rojas Costa -------------------------------- Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Re: [Freesurfer] trac-all -prep error field map error
by Eileen Moore 05 Sep '14

05 Sep '14

Hi - I still have not been able to apply the field map correction within tracula. Tracula does not appear to recognize the format of my field maps in either dicom or nifti formats. However, as a work around I first did the field map correction outside tracula (using our wrapper script for epidewarp). Next I used this field map corrected image as the input diffusion image for tracula and set dob0 = 0 in my dmrirc file (so as to skip tracula's field map correction). This appears to be working. Eileen. > > ------------------------------ > > Message: 5 > Date: Wed, 27 Aug 2014 13:51:06 -0700 > From: Eileen Moore <eimoore(a)mail.sdsu.edu> > Subject: Re: [Freesurfer] trac-all -prep error field map error > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CA++dajQo_2EF= > LvUFCKbs+_061v7dcTFC5T11PN0K4G9d-CuAw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Anastasia, I'm not sure how I can give tracula the phase difference maps, > can you provide an example? > > As a reminder, I've run a wrapper script around epidewarp which takes our > dicom images and converts them into a phase difference map (it is based on > the script that was authored by Doug Greve for the fBIRN consortium). > > In the tutorial dmrirc example I see only the 'set b0mlist' and 'set > b0plist' options, and am unsure where I could give it the phase difference > map. > > I've also tried converting the dicom magnitude and phase maps to nifti > format and inputting these into the dmrirc file but I am still getting an > error. (See attached log file). > > Thanks, > Eileen. > > > > > ------------------------------ > > > > Message: 10 > > Date: Thu, 17 Jul 2014 04:14:16 -0400 (EDT) > > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] trac-all -prep error field map error > > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > > Message-ID: <alpine.LRH.2.03.1407170411110.12767(a)nmr.mgh.harvard.edu> > > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > > > > Hi Eileen - All image formats that mri_convert (and thus any freesurfer > > program) can read will do, you don't need dicom. Try giving trac-all the > > phase difference maps you have and let's see what happens. > > > > Best, > > a.y > > > > On Wed, 16 Jul 2014, Eileen Moore wrote: > > > > > Hi Anastasia, > > > > > > OK - our imaging physicists had developed a wrapper script around > > epidewarp > > > which takes our dicom images and converts them into the phase > difference > > map > > > (it is based on the script that was authored by Doug Greve for the > fBIRN > > > consortium). It looks like the tracula script requires dicom images. Is > > > there a way for me to do epidewarp manually and then follow through > with > > the > > > remaining steps using trac-all? > > > > > > Thanks, > > > Eileen. > > > > > > > > > Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT) > > > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > > Subject: Re: [Freesurfer] trac-all -prep error field map error > > > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > > > Message-ID: > > > <alpine.LRH.2.03.1407141119560.23459(a)nmr.mgh.harvard.edu> > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > > Hi Eileen - That step is run with the program epidewarp.fsl, > > > which you can > > > run on the command line to see the available options. The input > > > phase map > > > volume is expected to have either 2 frames (2 separate phase > > > maps) or 1 > > > frame (the difference phase map). This error from trac-all means > > > that it > > > found that your input phase map has something other than 1 or 2 > > > frames, so > > > it doesn't know how to handle it. > > > > > > Hope this helps, > > > a.y > > > > > > On Sat, 12 Jul 2014, Eileen Moore wrote: > > > > > > > Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. > > > I'm tyring to > > > > run tracula on some? images acquired from a GE scanner. I am > > > running into > > > > problems when I try to perform the registration-based > > > B0-inhomogeneity > > > > compensation, getting an error in the terminal output: "ERROR: > > > Unrecognized > > > > format of phase map". However, trac-all -prep runs fine when I > > > skip the > > > > B0-inhomogeneity compensation step. Is there something else I > > > need to do to > > > > use field map correction? > > > > > > > > I've attached the trac-all.log and a copy of the terminal > > > output. > > > > > > > > Thanks, > > > > Eileen. > > > > > > > > > > > > > > > > > > > > > > > > > > > >

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Re: [Freesurfer] longitudinal QDEC help
by Martin Reuter 05 Sep '14

05 Sep '14

Hi Taylor, You can do the glmfit osgm on whatever you like (rate, percentchange pc1, or symm. percent change spc). I recommend SPC. The 2stage model page shows an example of glmfit with osgm flag and explains how to stack your data first. Best Martin Sent via my smartphone, please excuse brevity. <div>-------- Original message --------</div><div>From: Taylor North <taylornorth189(a)hotmail.ca> </div><div>Date:09/04/2014 11:14 PM (GMT-05:00) </div><div>To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> </div><div>Subject: Re: [Freesurfer] longitudinal QDEC help </div><div> </div>Hi Martin Yes I that definitely clears things up, thanks very much for the help. As for the QCAHCE we did use the long_mris_slopes described in the tutorial you linked in your email. Just to confirm I believe I should be using the mri_glmfit -osgm model for my one sample group mean analysis and then when I want to compare against my continuous/dependent variables I should be using QDEC? Also it looks like mri_glmfit -osgm calculates % change, so should I be analyzing % change, not symmetrized percent change on my QDEC analysis as well, even though it say symmetrized percent change is the more robust result? Thanks again for your help Taylor From: mreuter(a)nmr.mgh.harvard.edu Date: Thu, 4 Sep 2014 22:44:16 -0400 To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] longitudinal QDEC help Hi Taylor, first, in your description you mention 'base and 6 month'. Better call it 'baseline' or 'first and second time points at 0 and 6 months' in order to not confuse the first time point with the 'base' = within-subject template created as the second step. I think you did not confuse it, but just want to make sure. From your description it is not clear how you computed the symmetrized percent change. You say you ran QCACHE, but how? Did you use long_mris_slopes as described here: http://freesurfer.net/fswiki/LongitudinalTwoStageModel http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial That step computes slopes for each subject and (instead of having 2 thickness maps) reduces the information to a single map (here the symmetrized percent change is simply: 100 * tp2-tp1/(0.5*(tp1+tp2)) ) . These maps are stored in the base directories (one for each subject and of corse each hemisphere that you run). Now to your questions: 1) I think a 'one sample group mean' analysis is not possible in QDEC. For that you have to use mri_glmfit -osgm …. I wish we had this functionality and I'll see how hard it would be to implement it in future versions of QDEC (this came up frequently and it should not be too hard). 2) a) the longitudinal qdec table use the cross id's in the fsid column for simplicity. When it is used in many programs (e.g. long_mris_slopes, long_stats_slopes and other scripts with the long-qdec option) the scripts knows that it is a longitudinal qdec table (because of the existing fsid-base column) and internally use the longitudinal directories for processing. The cross sectional directories are never used. b) as mentioned above, the results from the first stage analysis (creation of the within subject slopes and percent changes) are stored in the base directories. They are used in this step and found there. (and you are right, the recon-all results from the base should not be analyzed directly, but here the data that is used is derived from the longitudinal directories and just placed in the base so that it can be found for each subject). Hope that explains it. Best, Martin On Sep 4, 2014, at 9:33 PM, Taylor North <taylornorth189(a)hotmail.ca> wrote: Hello, I am having some troubles using QDEC to analyze the cortical thickness changes in my group study and I was hoping someone may be able to give me a hand. The steps I have done are as follows: I am working on a study looking at 40 subjects scanned at two time points (base and 6 months after). I have followed all the steps for longitudinal processing for each subject (cross,base, and longitudinals) and made edits where they were necessary to the base. I then entered all 40 subjects into a QDEC table as follows fsid fsid-base time gender age crosstpN1 base1 0 female 20 crosstpN2 base1 6 female 20 .......... continues for rest of the subjects then I ran the QCHACHE on the data, made a Qdecrc. file in the subject DIR, and then transformed the longitudinal QDEC table into a QDEC table which looks like: fsid time gender age Base1 3 female 20 .......... continues for the rest of the subjects. I then followed the QDEC steps outlined In the group tutorial. (import cross sectional table, generate stats data table, import aseg volume, set longitudinal dependent variables and pick continuous variable. 1) the first problem I am having is that when I go to process the longitudinal group results through QDEC it makes me pick a continuous variable when I just want to analyze the dependent variable The symmetrized percent change. So I have tried picking different continuous variables ( such as age or importing rhcortex volume etc...) with choosing symmetrized percent change as the dependent variable. No matter what continuous variable I pick the question: ``does the average symmetrized percent change differ from zero"? always comes up, the problem is depending on what continuous variable I pick the results change. Is there a way to just look at the longitudinal thickness changes across a group alone, because I first want to look at the atrophy across the whole group over 6 months and then compare the differences in atrophy against the diagnosed and non diagnosed group. 2) another thing I don't quite understand is it seems like the longitudinal qdec tables are made with the cross of the subjects under fsid, but why wouldn't you use the longitudinals under the fsid for the longitudinal table instead? Also it seems like in the cross sectional qdec table the base is the subject being analyzed under fsid, which also doesn't make sense to me because in the tutorial it says base should not be used directly for analysis. thanks for the help! Taylor _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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longitudinal QDEC help
by Taylor North 04 Sep '14

04 Sep '14

Hello, I am having some troubles using QDEC to analyze the cortical thickness changes in my group study and I was hoping someone may be able to give me a hand. The steps I have done are as follows: I am working on a study looking at 40 subjects scanned at two time points (base and 6 months after). I have followed all the steps for longitudinal processing for each subject (cross,base, and longitudinals) and made edits where they were necessary to the base. I then entered all 40 subjects into a QDEC table as follows fsid fsid-base time gender age crosstpN1 base1 0 female 20 crosstpN2 base1 6 female 20 .......... continues for rest of the subjects then I ran the QCHACHE on the data, made a Qdecrc. file in the subject DIR, and then transformed the longitudinal QDEC table into a QDEC table which looks like: fsid time gender age Base1 3 female 20 .......... continues for the rest of the subjects. I then followed the QDEC steps outlined In the group tutorial. (import cross sectional table, generate stats data table, import aseg volume, set longitudinal dependent variables and pick continuous variable. 1) the first problem I am having is that when I go to process the longitudinal group results through QDEC it makes me pick a continuous variable when I just want to analyze the dependent variable The symmetrized percent change. So I have tried picking different continuous variables ( such as age or importing rhcortex volume etc...) with choosing symmetrized percent change as the dependent variable. No matter what continuous variable I pick the question: ``does the average symmetrized percent change differ from zero"? always comes up, the problem is depending on what continuous variable I pick the results change. Is there a way to just look at the longitudinal thickness changes across a group alone, because I first want to look at the atrophy across the whole group over 6 months and then compare the differences in atrophy against the diagnosed and non diagnosed group. 2) another thing I don't quite understand is it seems like the longitudinal qdec tables are made with the cross of the subjects under fsid, but why wouldn't you use the longitudinals under the fsid for the longitudinal table instead? Also it seems like in the cross sectional qdec table the base is the subject being analyzed under fsid, which also doesn't make sense to me because in the tutorial it says base should not be used directly for analysis. thanks for the help! Taylor

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recon-all input
by Xinfa Shi 04 Sep '14

04 Sep '14

Hello, Now I have a subject data,including 156 dicom images(MR0001~MR0156),amd they were converted into a .nii.gz file(eg.CON_T1_01.nii.gz) .I am wondering whether they are the same : recon-all -i MR00001.dcm -s con01 -all recon-all -i CON_T1_01.nii.gz -s con01 -all Many Regards. Xin-Fa Shi.

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invalid=96777 in recon-all
by Pom Sailasuta 04 Sep '14

04 Sep '14

Hello, I am using FreeSurfer version 5.3.0 in 64bit desktop, I got these errors at the begining of recon-all but the reconstruction is not stop, keep on going with lots of invalid=96777. **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.849, neg=0, invalid=96777 0001: dt=129.472000, rms=0.789 (7.080%), neg=0, invalid=96777 0002: dt=295.936000, rms=0.765 (3.083%), neg=0, invalid=96777 0003: dt=129.472000, rms=0.759 (0.766%), neg=0, invalid=96777 0004: dt=517.888000, rms=0.749 (1.353%), neg=0, invalid=96777 0005: dt=92.480000, rms=0.744 (0.567%), neg=0, invalid=96777 0006: dt=369.920000, rms=0.740 (0.600%), neg=0, invalid=96777 0007: dt=73.984000, rms=0.738 (0.229%), neg=0, invalid=96777 0008: dt=73.984000, rms=0.737 (0.148%), neg=0, invalid=96777 0009: dt=73.984000, rms=0.735 (0.250%), neg=0, invalid=96777 0010: dt=73.984000, rms=0.733 (0.313%), neg=0, invalid=96777 0011: dt=73.984000, rms=0.730 (0.371%), neg=0, invalid=96777 0012: dt=73.984000, rms=0.727 (0.408%), neg=0, invalid=96777 0013: dt=73.984000, rms=0.724 (0.430%), neg=0, invalid=96777 0014: dt=73.984000, rms=0.721 (0.450%), neg=0, invalid=96777 0015: dt=73.984000, rms=0.718 (0.450%), neg=0, invalid=96777 0016: dt=73.984000, rms=0.714 (0.455%), neg=0, invalid=96777 0017: dt=73.984000, rms=0.711 (0.442%), neg=0, invalid=96777 0018: dt=73.984000, rms=0.708 (0.424%), neg=0, invalid=96777 0019: dt=73.984000, rms=0.705 (0.403%), neg=0, invalid=96777 0020: dt=73.984000, rms=0.703 (0.388%), neg=0, invalid=96777 0021: dt=73.984000, rms=0.700 (0.347%), neg=0, invalid=96777 0022: dt=73.984000, rms=0.698 (0.329%), neg=0, invalid=96777 thanks for the comments. Pom -- Pom

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Re: [Freesurfer] problems with tracula pre-processing (bvecs)
by Michele Cavallari 04 Sep '14

04 Sep '14

Hi Barbara, thanks for your reply. I checked the dwi series on a viewer and it looks fine: I have 1960 dicoms, corresponding to 56 slices x 35 directions specified in the bval/bvec. Also, I was able to obtain the FA and MD maps through fsl using the very same dicoms and bval/bvec. Any suggestion? Thanks On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp <bakk.hbg(a)googlemail.com> wrote: Dear Michele, I cannot find anything wrong with your bvec and bval files. Seeing as you had an errormessage related to the dwi (the one about the dwi_frame.nii.gz): Did you check that your dwi data have the same amount of volumes as entries in bvec and bval? Good luck, Barbara On 28/08/2014 22:47, Michele Cavallari wrote: Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries The original bvals and bvecs files seem to have the same numbers of entries to me. But the bvecs file produced by the processing - both the bvecs.norot and the bvecs files in the dmri folder - don't have all the information of the vectors. I am enclosing a zip folder with attachments: 1) original bvecs and bvals files organized in rows and columns 2) bvecs and bvals files generated by tracula 3) error logs Let me know if you need any other information. Thanks in advance for your help. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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