[Freesurfer] Questions aobut using monte carlo sim in Qdec
Hi, I have some questions about using monte carlo sim in qdec: First of all, I just want to verify it's ok to use the simulation with a whole-brain analysis and not just an ROI analysis. Second, I'm a bit confused about how to calculate the p-threshold for my max clusters. Looking here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary tells me how to calculate the p-value of my clusters, but according to the page, max = -log(base10) (pvalue). The example given is the 13th cluster where max = -5.981, and the stated p value is p .006. I can't figure out how you came up with this p-value, can you please clarify your calculations? Finally, in qdec when I change my threshold from say 1.3 (.05) to 2.0 (.01) I notice the CW Pvalue threshold doesn't change in the terminal output, and remains at .05. Can you please explain this? What exactly am I changing when I change the threshold in qdec? Thank you in advance for your assistance, Ashley -- Ashley A. Shurick Ph.D. Candidate Department of Psychology Stanford University ___ 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] Combining scans with different scanning parameters
Hi Bruce (and others), We can balance the numbers to allow the same number in each configuration. But just to clarify, are you saying we should do, for example, 10 patient scan 1, 10 patient scan 2, 10 patient scan 3, and 10 HC scan 1, 10 HC scan 2, 10 HC scan 3, to perfectly balance everything out? Or do we just need to have X patient and X HC in scan 1, Y patient and Y HC with scan 2, and Z patient and Z HC with scanning parameter 3? Thank you for your assistance. Ashley On Tue, Mar 11, 2014 at 5:22 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Ashley that is probably trouble unless your groups are perfectly balanced across the datasets (that is, the same # in each group were scanned on each configuration). cheers Bruce On Tue, 11 Mar 2014, Ashley Shurick wrote: Hi, I'm interested in comparing CT differences between 2 different groups, and in order to increase my sample size I'm contemplating combining 3 datasets with different scanning parameters. Some scans were collected with a 3T1 with fmri head coil, while others were collected with a 3T2 magnet with 8 channel head coil. The scans also differ in FOV (25.6 vs 22cm) and resolution. Thank you in advance for your support. Ashley -- Ashley A. ShurickPh.D. Candidate Department of Psychology Stanford University 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. -- Ashley A. Shurick Ph.D. Candidate Department of Psychology Stanford University ___ 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] Combining scans with different scanning parameters
Hi, I'm interested in comparing CT differences between 2 different groups, and in order to increase my sample size I'm contemplating combining 3 datasets with different scanning parameters. Some scans were collected with a 3T1 with fmri head coil, while others were collected with a 3T2 magnet with 8 channel head coil. The scans also differ in FOV (25.6 vs 22cm) and resolution. Thank you in advance for your support. Ashley -- Ashley A. Shurick Ph.D. Candidate Department of Psychology Stanford University ___ 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] Fwd: Qdec Questions
Great - and this would be true for all models? For example, in the attached graph, I'm looking at a region representing increased cortical thickness for one group compared to the other (orange blob, Q: Does the average thickness differ between HC and SAD? nuisance factor: mean thickness). From this plot it appears that SAD HC, but based on your answer to the previous question I would think this region should represent HC SAD. Can you please explain this? Thank you! On Wed, Oct 30, 2013 at 7:33 AM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: In your case you have HC listed first, so red/yellow means HCSAD, blue means SADHC doug On 10/29/2013 11:03 PM, Ashley Shurick wrote: Hi Doug, Apologies, but I have a rather easy follow-up question that I can't figure out: How do you interpret the effect in each significant region? A previous post suggests using ctrl + left mouse click on a blob and examining the plot of the data. However, for the model I am looking at (Does the thickness-ERQ correlation differ between HC and SAD?) I still can't determine if cortical thinning represents HCSAD or SADHC. I'm attaching a representative plot here. Thank you, Ashley On Tue, Oct 29, 2013 at 10:25 AM, Ashley Shurick ashley.shur...@gmail.com mailto:ashley.shurick@gmail.**comashley.shur...@gmail.com wrote: Thank you! On Tue, Oct 29, 2013 at 10:19 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: On 10/29/2013 01:10 PM, Ashley Shurick wrote: Hi all, I'm running analyses in Qdec and want to verify a few things: 1. When comparing two groups (HC vs patients) I am including mean cortical thickness as a covariate, using the following equation: bh.thickness = (lh.thickness*lh.surfarea + rh.thickness*rh.surfarea) / (lh.surfarea + rh.surfarea) Is this the best way to calculate global mean thickness? Yes 2. I want to regress out any effects of age, therefore I need to demean the ages for my groups as a whole, and not perform this calculation on each group separately, correct? Yes, in which case the test of the difference between groups will be done at an age equal to the mean of the ages. 3. I'm including questionnaires as a covariate of interest - do I need to demean these values as well? When you do a test on a continuous covariate, that test will be unaffected by demeaning of the covariate. Demeaning will affect the difference between groups if you use a separate covariate for each group. If you have a single covariate across groups, demeaning will have no effect. doug Thank you in advance for your help! Ashley -- Ashley A. Shurick Ph.D. Candidate Department of Psychology Stanford University __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurfer 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.**edugr...@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Qdec Questions
Hi all, I'm running analyses in Qdec and want to verify a few things: 1. When comparing two groups (HC vs patients) I am including mean cortical thickness as a covariate, using the following equation: bh.thickness = (lh.thickness*lh.surfarea + rh.thickness*rh.surfarea) / (lh.surfarea + rh.surfarea) Is this the best way to calculate global mean thickness? 2. I want to regress out any effects of age, therefore I need to demean the ages for my groups as a whole, and not perform this calculation on each group separately, correct? 3. I'm including questionnaires as a covariate of interest - do I need to demean these values as well? Thank you in advance for your help! Ashley -- Ashley A. Shurick Ph.D. Candidate Department of Psychology Stanford University ___ 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] libjpeg.so.62
Hi all, My RA's are having similar issues running Freeview on Ubuntu (I've read others are having the same issue). They get the following error when trying to call freeview: freeview.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory We ran apt-get install libjpeg62 to install missing libraries, and when that didn't fix the issue we tried Nick's fix below just in case it might work. Unfortunately we are still getting the error. Any ideas about what's going on? Thank you in advance for your assistance! On Tue, Feb 26, 2013 at 7:47 AM, Nick Schmansky ni...@nmr.mgh.harvard.eduwrote: Chikku, I am guessing that you are using Ubuntu. To fix this problem: cd /usr/lib sudo ln -s libjpeg.so.8 libjpeg.so.62 in other words, link whatever libjpeg is already installed to the name libjpeg.so.62. Nick Hi I am getting an error while using qdec. It says error while loading shared libraries ,libjpeg.so.62 cannot open shared object file No such file or directory I ran reconall with out any problem. Any idea, tx chikku ___ 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. -- Ashley A. Shurick Graduate Student, Psychology Stanford University ___ 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] Adding low-res T2 and PD images in the recon-all stream - any advantages?
Hi all, I have a similar question: My T2 scans are similar to Nicola's - approximately .86 x .86 x 4.5mm. However, about 60/168 subjects don't have T2 scans. Would you recommend including the T2's for the subjects who have them, or excluding the T2 scans altogether? Thank you in advance for your help! On Wed, Feb 27, 2013 at 5:44 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Nicola the T2 might in 5.2, but it is pretty thick slices so might hurt more than it helps. Not sure, but you can try it out cheers Bruce On Wed, 27 Feb 2013, Nicola Toschi wrote: Hello List, on out 3T scanner, in addition to MPRAGE images (1 mm^3), we usually acquire T2 and PD images - however they are at 1x1x5 mm resolution. Would you recommend passing these (T2+PD) to the recon-all stream anyway - would they add value/accuracy to the segmentation/parcellation (or would they possibly decrease accuracy)? Thanks in advance, Nicola ___ 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. -- Ashley A. Shurick Graduate Student, Psychology Stanford University ___ 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.
