Re: [Freesurfer] One sample t-test in Qdec
Hello again, Thanks for your quick response. In addition to my previous question, I would also like to learn what the default analysis in Qdec is actually doing. For example, as I said previously, I have only one patient and a group of control participants. In that case, in my data table I'm giving a discrete group factor (patient, control) and the volume values of brain areas I'm interested in (several continuous factors). Then, I'm choosing group as my Selected factor (under Subject exclusions). When I say 'analyze', what the default analysis of Qdec is actually doing? Which statistics exactly? Since I have only one patient, is it computing the patient's mean as 0? Thanks in advance, Buse. -- Hi Buse, I think this is a two-sample t-test where the 2nd sample is your individual. You should be able to this in qdec doug -- 2014-03-05 14:52 GMT+02:00 Buse Merve Ürgen buseur...@gmail.com: Hello, I would like to learn whether we can conduct one-sample t-test using Qdec. I'm working on a single-case study, and I want to compare a single subject's data with a group of controls (to see how this specific subject is different from the group) in terms of volume, thickness and meancurvature. As far as I know, we can do the analysis in Terminal, but I would like to see have the brain figure output (cluster by cluster) in Qdec for one sample t-test as well. Is it possible? Thanks in advance, Buse. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] tkmedit edit voxel tcl script
This topic has been discussed previously without a conclusive answer. After some www inquests I realized that it is easily possible to process nii-images using spm functions for matlab. The functions for loading and saving images are: V = spm_vol(angio_corrected_marked); [Y, XYZ] = spm_read_vols(V); spm_write_vol(V,Y); After the images are loaded they can be processed using matlab functionality. Thus, tcl scripting for those purposes is not necessary. On Fri, 7 Mar 2014 16:37:33 -0500 (EST) Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Pfannmoe, I don't believe it is possible to edit a voxel via tcl scripts. If so the command would be listed on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditReference/TkMeditScripting -Louis On Wed, 5 Mar 2014, Joerg Pfannmoeller wrote: Hello, if I have selected a voxel in a volume with tkmedit with a tcl script, how can I set the voxel value to 0. Sincerely yours pfannmoe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] hypothalamus?
Hi all, I'm looking to create a mask for the hypothalamus on individual subjects. I've had a good look at the literature, and at the moment, am I right in thinking the automatic segmentation in Freesurfer doesn't currently include the hypothalamus? thanks in advance Ella ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] hypothalamus?
Ella, My understanding is the same. I've made my own ROI by hand drawing on the average subject and using various commands to map onto individual subjects. If you're doing resting analysis then you can check your general whole brain correlation results against the literature to see if your ROI performs well. It's not perfect, but it can give decent results. Cheers, Paul Sent from my iPhone On Mar 18, 2014, at 7:13 AM, Ella ellahin...@hotmail.com wrote: Hi all, I'm looking to create a mask for the hypothalamus on individual subjects. I've had a good look at the literature, and at the moment, am I right in thinking the automatic segmentation in Freesurfer doesn't currently include the hypothalamus? thanks in advance Ella ___ Freesurfer mailing list Freesurfer@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@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.
Re: [Freesurfer] Problem about Surface-based Registration
Hi Yufeng perhaps we should take a step back - what are you trying to achieve? cheers Bruce On Tue, 18 Mar 2014, yufeng huang wrote: Dear Bruce, I am a new user of freesurfer. I just followed the process on the webside(https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) to do the surface-based registration. However I do not to know what to do next after I get the lh.sphere.reg.newtemplate1 of each subjects. So could you please send me some papers about what to do next or some instruction about it. I am confuse about what you mentioned(2. You can check the results by mapping the curvature of the subjects into the commmon space and seeing if they align (I think mri_surf2surf can be used for this). So if I can check the result by using tksurfer, However I do not know if the tksurfer will use the lh.sphere.reg.newtemplate1 instead of lh.sphere.reg. I am sorry that I can not find more information about the surface-based registration. I do not know how to check if the subject has already align to each other properly or not. Thank you very much for you help! Please help me ASAP. Yours Yufeng 2014-03-17 8:38 GMT-04:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: 1. Not if all you want to do is surface registration. If you want to do surface and volume you will need to do both. 2. You can check the results by mapping the curvature of the subjects into the commmon space and seeing if they align (I think mri_surf2surf can be used for this). 3. No, as recon-all won't use anything from your new coordinate system. It will only be useful for group analyses cheers Bruce On Sun, 16 Mar 2014, yufeng huang wrote: I followed the process of creating a registration templatefromscratch(GW)(https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemp late s) to do the surface-based registration. My question are as followed: 1 I want to know if I need to use the mri_cvs_registrater to replace mri_register. 2 I check the result and find it produce the lh.sphere.reg.newtemplate1 and rh.sphere.reg.newtemplate1 in each subjects's surf folder. I want to know how to check the result by using the new file. 3 Should I need to re-run recon-all after the mri_register for every subjects? Thanks very much for your help! 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@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.
Re: [Freesurfer] hypothalamus?
Hi Ella yes, it does not cheers Bruce On Tue, 18 Mar 2014, Ella wrote: Hi all, I'm looking to create a mask for the hypothalamus on individual subjects. I've had a good look at the literature, and at the moment, am I right in thinking the automatic segmentation in Freesurfer doesn't currently include the hypothalamus? thanks in advance Ella ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] hypothalamus?
Hi Ella, There are a number of options: You can draw manual segmentations on individual subjects, though the time and cost required for this labor-intensive process of manual tracing has become prohibitive. Paul's suggestion would be a better one, maybe one of our protocols described in e.g. http://www.ncbi.nlm.nih.gov/pubmed/21733239 could be of use to you? In case of drawing on the fsaverage, I would add the suggestion to draw at least two times to see if you're segmentation is reliable (compare your two (or more) ROIs and check for overlap and non-overlapping parts, for non-overlap decide whether those voxels should be in- or excluded). Subsequently, you map your segmentation to individual subjects and check for correct registration. Another approach would be to use the ROI from the Wake Forest University PickAtlas. You can map this to FS-space, and follow similar procedures to map to native space. Though I must note that this ROI is not perfect. All depends on your research question of course, how detailed do you want your ROI to be. Best of luck, Cédric P.C.M.P. Koolschijn (Cédric), PhD Dutch Autism ADHD Research Center Brain and Cognition The Netherlands E p.c.m.p.koolsch...@uva.nlmailto:p.c.m.p.koolsch...@uva.nl W http://www.dutcharc.nlhttp://www.dutcharc.nl// On 3/18/14 1:04 PM, Paul Beach pabea...@gmail.commailto:pabea...@gmail.com wrote: Ella, My understanding is the same. I've made my own ROI by hand drawing on the average subject and using various commands to map onto individual subjects. If you're doing resting analysis then you can check your general whole brain correlation results against the literature to see if your ROI performs well. It's not perfect, but it can give decent results. Cheers, Paul Sent from my iPhone On Mar 18, 2014, at 7:13 AM, Ella ellahin...@hotmail.commailto:ellahin...@hotmail.com wrote: Hi all, I'm looking to create a mask for the hypothalamus on individual subjects. I've had a good look at the literature, and at the moment, am I right in thinking the automatic segmentation in Freesurfer doesn't currently include the hypothalamus? thanks in advance Ella ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@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@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.
Re: [Freesurfer] Restrict QDEC analysis to a region
Tanks doug, Is it ok like this: mri_glmfit-sim --glmdir qdec/Untitled --cache 1.3 neg ? Best regards, Amirhossein Manzouri On Mon, Mar 17, 2014 at 8:25 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: you will have to run the correction for multiple comparisons with mri_glmfit-sim (ie, you can't do it in qdec). doug On 03/17/2014 02:03 PM, amirhossein manzouri wrote: Yes. Basically I want to see the effect of restricting the brain area on the group comparison clusters from Monte Carlo Simulation (threshold 1.3). As you mentioned before from mdi_glmfit I just get a masked version of whole brain analysis. How can I do the correction for multiple comparison with Monte Carlo (threshold 1.3) command based? Best regards, Amirhossein Manzouri On Mon, Mar 17, 2014 at 6:52 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I don't know what you mean. Can you elaborate? doug On 03/17/2014 01:19 PM, amirhossein manzouri wrote: Can I also use mri_surfcluster as it is in qdec since I want to compare the whole brain and masked brain results? Best regards, Amirhossein Manzouri On Fri, Mar 14, 2014 at 4:49 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: you are doing it the right way. There is no difference in the uncorrected analysis. There will be a difference when you correct for multiple comparisons doug On 03/14/2014 11:15 AM, amirhossein manzouri wrote: Dear Experts, I have read the previous posts in the list regarding restricted ROI analysis. So I generated my label from tksurfer and used that for group difference analysis by adding --label to mri_glmfit, but the result (sig.mgh) seems just a masked version of the analysis including whole brain ( no difference in significance! ). I expected to see a different pattern of significance by limiting the region. Would you please advise if I am doing this in a right way? Best regards, Amirhossein Manzouri -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
Re: [Freesurfer] Restrict QDEC analysis to a region
yes On 3/18/14 9:14 AM, amirhossein manzouri wrote: Tanks doug, Is it ok like this: mri_glmfit-sim --glmdir qdec/Untitled --cache 1.3 neg ? Best regards, Amirhossein Manzouri On Mon, Mar 17, 2014 at 8:25 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: you will have to run the correction for multiple comparisons with mri_glmfit-sim (ie, you can't do it in qdec). doug On 03/17/2014 02:03 PM, amirhossein manzouri wrote: Yes. Basically I want to see the effect of restricting the brain area on the group comparison clusters from Monte Carlo Simulation (threshold 1.3). As you mentioned before from mdi_glmfit I just get a masked version of whole brain analysis. How can I do the correction for multiple comparison with Monte Carlo (threshold 1.3) command based? Best regards, Amirhossein Manzouri On Mon, Mar 17, 2014 at 6:52 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I don't know what you mean. Can you elaborate? doug On 03/17/2014 01:19 PM, amirhossein manzouri wrote: Can I also use mri_surfcluster as it is in qdec since I want to compare the whole brain and masked brain results? Best regards, Amirhossein Manzouri On Fri, Mar 14, 2014 at 4:49 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: you are doing it the right way. There is no difference in the uncorrected analysis. There will be a difference when you correct for multiple comparisons doug On 03/14/2014 11:15 AM, amirhossein manzouri wrote: Dear Experts, I have read the previous posts in the list regarding restricted ROI analysis. So I generated my label from tksurfer and used that for group difference analysis by adding --label to mri_glmfit, but the result (sig.mgh) seems just a masked version of the analysis including whole brain ( no difference in significance! ). I expected to see a different pattern of significance by limiting the region. Would you please advise if I am doing this in a right way? Best regards, Amirhossein Manzouri -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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
Re: [Freesurfer] fMRI contrasts in Freesurfer
OK, thanks! Francesco On 17 March 2014 17:50, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Francesco, please remember to post to the list. Thanks! The baseline is a regressor with all ones, so it is measured throughout the scan, not just during the rests. This makes the other regression coefficients relative to baseline. doug On 03/17/2014 01:05 PM, Francesco Puccettone wrote: thank you Doug, I am just still not sure about comparing to the baseline vs comparing between conditions; since the baseline it's not one of the predictors, how is it exactly used to define the contrasts and influence the regression coefficients? And is it the case that the baseline is taken as the average of all non-stimulus (rest) periods in the scan, i.e. the zero periods in the block-design boxcar diagram? Thank you again, --Francesco On 17 March 2014 15:33, Douglas N Greve gr...@nmr.mgh.harvard.edumailto: gr...@nmr.mgh.harvard.edu wrote: On 03/15/2014 06:35 PM, Francesco Puccettone wrote: Dear Freesurfer community: I have some (perhaps silly, but I think fundamental) questions about contrasts in functional analyses: 1. When wanting to see what regions are activated by exposure to a certain stimulus (blocked-design), what is the exact stats that is happening voxel-wise: (i) correlation between the time series of the HRF-convoluted BOLD and that of the behavioural stimulus that was used, or (ii) t-test between the BOLD signal during the stimulus and the BOLD signal during a resting baseline If ii) is the answer, then is baseline taken as an average of all non-stimulus (rest) periods in the scan, i.e. the zero periods in the block-design boxcar diagram? Neither. A GLM is set up with regressors for you conditions and nuisance variables. The GLM is fit to the time course to compute a regression coefficient for each regressor. This is a multivariate operation and does not reduce to a simple correlation. For a task regressor, the regression coefficient indicates the amplitude of the HRF. This amplitude is tested with a t-test 2. When wanting, on the other hand, to see what regions are active in condition A but not in condition B (so a comparison this time), is it the case that i) is no longer a choice and a t-test always has to be used between condition A and condition B? If so, is the stimulus-vs-baseline situation from the previous question just a special case of this, where condition B = (passive) baseline? This would be a conjunction analysis that does not reduce to a simple contrast. 3. Is it the case that a contrast probing the difference between two groups is using independent samples t-tests, whereas one probing the within-subject difference between two time-points is using paired-samples t-tests? Between groups is independent two-sample. Within subject uses a GLM and does not reduce to a simple paired formula (but that is basically the right way to think about it) doug Thank you for your help:-) --Francesco ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs:
Re: [Freesurfer] One sample t-test in Qdec
It is constructing a GLM with design matrix with 2 columns and N rows where each row is a subject. The row of your patient gets 1 0 and the rows for the other subjects gets 0 1. When you set up a contrast with [1 -1], you are comparing the value of the subject against the mean of the others. doug On 3/18/14 4:02 AM, Buse Merve Ürgen wrote: Hello again, Thanks for your quick response. In addition to my previous question, I would also like to learn what the default analysis in Qdec is actually doing. For example, as I said previously, I have only one patient and a group of control participants. In that case, in my data table I'm giving a discrete group factor (patient, control) and the volume values of brain areas I'm interested in (several continuous factors). Then, I'm choosing group as my Selected factor (under Subject exclusions). When I say 'analyze', what the default analysis of Qdec is actually doing? Which statistics exactly? Since I have only one patient, is it computing the patient's mean as 0? Thanks in advance, Buse. -- Hi Buse, I think this is a two-sample t-test where the 2nd sample is your individual. You should be able to this in qdec doug -- 2014-03-05 14:52 GMT+02:00 Buse Merve Ürgen buseur...@gmail.com mailto:buseur...@gmail.com: Hello, I would like to learn whether we can conduct one-sample t-test using Qdec. I'm working on a single-case study, and I want to compare a single subject's data with a group of controls (to see how this specific subject is different from the group) in terms of volume, thickness and meancurvature. As far as I know, we can do the analysis in Terminal, but I would like to see have the brain figure output (cluster by cluster) in Qdec for one sample t-test as well. Is it possible? Thanks in advance, Buse. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Segmentation fault:11 with mris_anatomical_stats
Can you verify that the label does actually have label points in it? Just open it in a text editor or cat it to a terminal. If it does have points, send it to me. Also let me know which version of FS you are running. doug On 3/17/14 5:35 PM, Rupa Sabbineni wrote: muen223-105-dhcp:subjects rupasabbineni$ mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh limiting computations to label /Volumes/DISK/Software/freesurfer/subjects/qdec/Results/new.label. computing statistics for each annotation in aparc.a2009s.annot. outputting results to outSUB1_lhVOL2... reading volume /Volumes/DISK/Software/freesurfer/subjects/SUB1/mri/wm.mgz... reading input surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... reading input pial surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.pial... reading input white surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Segmentation fault: 11 On Mon, Mar 17, 2014 at 11:54 AM, Rupa Sabbineni asabbin...@mrn.org mailto:asabbin...@mrn.org wrote: Good morning! I was trying to run the mris_anatomical_stats command and for some subjects I keep getting Segmentation fault:11 error. Some of the posts in the archive suggested that I run the recon-all command since it usually means that subjects surfaces are out of sync SO I RERAN RECON_ALL(which created the stats). Then I reran the mris_anatomical_stats command and got the segmentation fault again. The command im using is mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh A little background on the new.label. We got the label by doing a regression in qdec at FDR 0.05 which created cluster and peak cluster label. Can anyone please provide me some insight on how to trouble shoot this problem? Thank you! Rupa -- Rupa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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] Mapping parcellation ROIs to the surface
Dear FreeSurfer experts, I am trying to find the surface ROIs for (volumetric) parcellation ROIs, as mentioned in: Frye, RE et al. 2010. Surface Area Accounts for the Relation of Gray Matter Volume to Reading-Related Skills and History of Dyslexia. Cerebral Cortex 20:2625-2635. I have run all subjects through the recon-all stream, and now want to project the inferior frontal, fusiform, angular, and supramarginal gyri to the surfaces. I've been able to find these ROIs in: subject/label/aparc.annot.a2009s.ctab: 25 G_pariet_inf-Angular20 60 2200 and subject/label/aparc.annot.ctab 07 fusiform180 220 1400 31 supramarginal80 160 200 18 parsopercularis220 180 140 0 20 parstriangularis220 60 20 0 For the above, I'm assuming this means that in the relevant volume files (aparc.a2009s.+aseg.mgz aparc+aseg.mgz), the voxels with intensities as labelled correspond to to the gyri. How do I project these regions to the subject surfaces? I assume I must use 'mri_vol2surf', but there are so many options I'm not sure what to use. I'd very much appreciate some input! Thanks in advance, Danielle -- Danielle Sliva, MA Data Coordinator Boston Children's Hospital Division of Developmental Medicine Laboratories of Cognitive Neuroscience, Gaab Lab Fetal-Neonatal Neuroimaging Developmental Science Center 1 Autumn St, AU640 Boston, MA 02215 tel: (857) 218-5210 fax: (617) 730-0518 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Mapping parcellation ROIs to the surface
These already exist on the surface in the form of annotation, so you can view them with something like tksurfer subject lh inflated -annot aparc.annot there are also stat summaries in the stats folder doug On 03/18/2014 10:10 AM, Danielle Sliva wrote: Dear FreeSurfer experts, I am trying to find the surface ROIs for (volumetric) parcellation ROIs, as mentioned in: Frye, RE et al. 2010. Surface Area Accounts for the Relation of Gray Matter Volume to Reading-Related Skills and History of Dyslexia. Cerebral Cortex 20:2625-2635. I have run all subjects through the recon-all stream, and now want to project the inferior frontal, fusiform, angular, and supramarginal gyri to the surfaces. I've been able to find these ROIs in: subject/label/aparc.annot.a2009s.ctab: 25 G_pariet_inf-Angular20 60 2200 and subject/label/aparc.annot.ctab 07 fusiform180 220 1400 31 supramarginal80 160 200 18 parsopercularis220 180 140 0 20 parstriangularis220 60 20 0 For the above, I'm assuming this means that in the relevant volume files (aparc.a2009s.+aseg.mgz aparc+aseg.mgz), the voxels with intensities as labelled correspond to to the gyri. How do I project these regions to the subject surfaces? I assume I must use 'mri_vol2surf', but there are so many options I'm not sure what to use. I'd very much appreciate some input! Thanks in advance, Danielle -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] FW: bug in surface-based area and volume, and use of total brain volume as a covariate
Hi all, just two quick questions: to what FS version is this related? And what is wrong to do if one does not have the fix? Using what stats/procedures? Thanks, Andreia Quoting Douglas N Greve gr...@nmr.mgh.harvard.edu: why would one control for total brain volume in doing vertex-based analyses when the vertex-based measures are computed in standard space? The vertex-based measures are computed in individual space, not standard space doug On 03/17/2014 05:12 PM, Narly Golestani wrote: Dear Doug, Many thanks for your answers. 3. The bug was related to how the measures were converted to standard space - I?d like to therefore confirm that when doing surface/vertex-based analyses, it is not necessary to use total brain volume as a covariate (whereas it is for ROI-based analyses). This question has nothing to do with the bug. People generally use ICV or total brain volume when exploring cortical volume or surface area, but it is inappropriate for thicknss studies doug Regarding the last point (which indeed has nothing to do with the bug, sorry for having given the impression that I thought that it did), why would one control for total brain volume in doing vertex-based analyses when the vertex-based measures are computed in standard space? I realize that this has to be done for ROI analyses since these measures are in native space. Thanks again, and best, Narly. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] TRACULA preprocessing error, FreeSurfer 5.2.0
Dear Anastasia, Hello, many thanks for your quick reply, sorry for the delay. I have switched to 3-column format and that does indeed get the process a little further, so many thanks for that. Unfortunately however I get this new error during the trac-all -bedp stage: An exception has been thrown ERROR: Could not open image /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/data_slice_ Trace:read_volume4DROI. I saw that similar errors had been identified in the past, but I wasn't really clear from the dialogue what the cause was or how to correct. Could you explain, please? I have tried to run bedpostx directly as previously advised, it seems to be running at present. IF it is successful, can I just always do this instead and then continue with trac-all -path? Or do I need to use trac-all -bedp specifically? Many thanks in advance, Best wishes, Colm. Colm McGinnity King's College London -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: 11 March 2014 00:39 To: McGinnity, Colm Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA preprocessing error, FreeSurfer 5.2.0 Hi Colm - Note that the information in the tutorial (particularly the part where gradient tables can be formatted in 3 rows or 3 columns) pertains to the latest tracula update: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates You're using an older version that only supports the 3-column format. I have no idea if this is what's causing the error without looking at your trac-all.log, but this would be a first guess. a.y On Mon, 10 Mar 2014, McGinnity, Colm wrote: Dear Experts, I am very new to TRACULA, I apologise for what is probably a silly question. I’ve got the following error on running trac-all –prep (FreeSurfer 5.2.0): awk: cmd. line:1: fatal: cannot open file `0' for reading (No such file or directory) mri_concat --i /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz --mean --o /home/k1193186/ FreeSurfer/TRACULA/ROLAND03A/dmri/lowb.nii.gz niiRead(): error opening file /home/k1193186/ FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz Can anyone tell me what this means and how to fix this, please? I’m guessing I’ve set up my configuration wrong or have the files in the wrong place? Many thanks! Best wishes, Colm. King's College London 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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] selxavg3-sess error
Hi, When I run selxavg3-sess, I face this error: ERROR: cannot find volume matching /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg ERROR: loading nonpar reg /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg -- ERROR: fast_selxavg3() failed\n I repeated the preproc-sess from scratch and it worked fine, finished without any problem and I still get the same error. I even check the registration in this run and it fine. Now I am wondering why do I see this error for this subjects (and why I don't see it for the other subjects)? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] TRACULA preprocessing error, FreeSurfer 5.2.0
Hi Colm - Yes, it's fine to run bedpostx directly, with the path to the dmri directory as its argument. Since you're using 5.2, note that although there were no issues with tracula in that version, it is not advisable to use freesurfer recons produced with 5.2. There was a bug in that version, which is why 5.3 was released shortly after 5.2: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes Hope this helps, a.y On Tue, 18 Mar 2014, McGinnity, Colm wrote: Dear Anastasia, Hello, many thanks for your quick reply, sorry for the delay. I have switched to 3-column format and that does indeed get the process a little further, so many thanks for that. Unfortunately however I get this new error during the trac-all -bedp stage: An exception has been thrown ERROR: Could not open image /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/data_slice_ Trace:read_volume4DROI. I saw that similar errors had been identified in the past, but I wasn't really clear from the dialogue what the cause was or how to correct. Could you explain, please? I have tried to run bedpostx directly as previously advised, it seems to be running at present. IF it is successful, can I just always do this instead and then continue with trac-all -path? Or do I need to use trac-all -bedp specifically? Many thanks in advance, Best wishes, Colm. Colm McGinnity King's College London -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: 11 March 2014 00:39 To: McGinnity, Colm Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA preprocessing error, FreeSurfer 5.2.0 Hi Colm - Note that the information in the tutorial (particularly the part where gradient tables can be formatted in 3 rows or 3 columns) pertains to the latest tracula update: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates You're using an older version that only supports the 3-column format. I have no idea if this is what's causing the error without looking at your trac-all.log, but this would be a first guess. a.y On Mon, 10 Mar 2014, McGinnity, Colm wrote: Dear Experts, I am very new to TRACULA, I apologise for what is probably a silly question. I’ve got the following error on running trac-all –prep (FreeSurfer 5.2.0): awk: cmd. line:1: fatal: cannot open file `0' for reading (No such file or directory) mri_concat --i /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz --mean --o /home/k1193186/ FreeSurfer/TRACULA/ROLAND03A/dmri/lowb.nii.gz niiRead(): error opening file /home/k1193186/ FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz Can anyone tell me what this means and how to fix this, please? I’m guessing I’ve set up my configuration wrong or have the files in the wrong place? Many thanks! Best wishes, Colm. King's College London 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@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] Recon process
Hello all, I think this is a fairly simple question, but I could not find an existing answer online. If I close out the terminal window while recon is running, will the process end? I've had the issue in the past where my computer has gone to sleep and the process ends up exiting with error. Also, is it possible to rerun a recon command after a previous failed attempt without being prompted to delete the older files that had already been made? I know that usually if you attempt to rerun a recon command after you have already tried, you're usually prompted to remove the older files. This time around, I wasn't ever prompted to do that but the scripts show that the last time recon-all ran, it completed without error. Thanks very much! ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] FW: bug in surface-based area and volume, and use of total brain volume as a covariate
why would one control for total brain volume in doing vertex-based analyses when the vertex-based measures are computed in standard space? The vertex-based measures are computed in individual space, not standard space doug Many thanks Doug, Best wishes, Narly. ___ Freesurfer mailing list Freesurfer@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] ADC, Radial diffusivity, Axial diffusivity and thresholds
Hello FreeSurfer experts, I have a question regarding DTI analysis. I understand that FA values ranges 0-1, and the values are often thresholded by 0.2. Now I am asked to report ADC, RD, AD values in my ROIs, and wondering what would be the most reasonable way. [1] Do not apply thresholds, just average the values within a ROI. [2] Use some arbitrary thresholds to each of ADC, RD, AD. [3] create a mask that contains voxels of the above-threshold-FAvalues, then, calculate mean within the mask. Any suggestions? Best, Yuko Yotsumoto ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] ADC, Radial diffusivity, Axial diffusivity and thresholds
Hi Yuko - Option 3, using the same FA threshold to create a mask for all measures makes sense. a.y On Wed, 19 Mar 2014, Yuko Yotsumoto wrote: Hello FreeSurfer experts, I have a question regarding DTI analysis. I understand that FA values ranges 0-1, and the values are often thresholded by 0.2. Now I am asked to report ADC, RD, AD values in my ROIs, and wondering what would be the most reasonable way. [1] Do not apply thresholds, just average the values within a ROI. [2] Use some arbitrary thresholds to each of ADC, RD, AD. [3] create a mask that contains voxels of the above-threshold-FAvalues, then, calculate mean within the mask. Any suggestions? Best, Yuko Yotsumoto ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
