[Freesurfer] average cortical thickness measure?
Hi, in response to the average thickness measure (see below). In ?h.aparc.stats, I see a variable ThickAvg, is that it? And then to get the average thickness across the *entire* cortex, I average across the couple of dozen regions that it provides? Thanks! Maria > > >Message: 7 >Date: Fri, 11 Dec 2015 13:49:23 -0500 >From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] average cortical thickness measure? >To: freesurfer@nmr.mgh.harvard.edu >Message-ID: <566b1ab3.9090...@nmr.mgh.harvard.edu> >Content-Type: text/plain; charset=windows-1252; format=flowed > >In ?h.aparc.stats, you'll find a line like > ># Measure Cortex, MeanThickness, Mean Thickness, 2.40617, mm > >You'll have to get the value for each hemi and compute the mean > > >On 12/11/2015 01:38 PM, Maria Kharitonova wrote: >> I know that the aseg atlas provides a number of voume measures >> (e.g. EstimatedTotalIntraCranialVol, TotalGrayVol), but is there a >> variable for an average cortical thickness? I?d like to see if >> thickness in some of the regions is associated with a variable of >> interest over and above an overall main effect, so would like to >> control for the average thickness, but can?t figure out a good way to >> do that. >> >> Thanks! >> Maria >> >> ? >> Maria Kharitonova, PhD >> Research Assistant Professor >> Department of Medical Social Sciences >> Northwestern University Feinberg School of Medicine >> 625 N. Michigan Ave, Suite 2700 >> Chicago, IL 60611 >> Phone: (312) 503-6503 >> Email: maria.khariton...@northwestern.edu >> <mailto:maria.khariton...@northwestern.edu> >> >> >> >> ___ >> 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] average cortical thickness measure?
I know that the aseg atlas provides a number of voume measures (e.g. EstimatedTotalIntraCranialVol, TotalGrayVol), but is there a variable for an average cortical thickness? I'd like to see if thickness in some of the regions is associated with a variable of interest over and above an overall main effect, so would like to control for the average thickness, but can't figure out a good way to do that. Thanks! Maria - Maria Kharitonova, PhD Research Assistant Professor Department of Medical Social Sciences Northwestern University Feinberg School of Medicine 625 N. Michigan Ave, Suite 2700 Chicago, IL 60611 Phone: (312) 503-6503 Email: maria.khariton...@northwestern.edu<mailto:maria.khariton...@northwestern.edu> ___ 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] error with asegstats2table
Hi all, I'm trying to extract aseg and aparc stats. Aparc worked fine, but when I'm trying to extract aseg stats, I get the following warnings, then error: Parsing the .stats files WARN: 3696 nmeasures = 66, expecting 55 WARN: 4455 nmeasures = 66, expecting 55 Building the table.. ERROR: All stat files should have the same segmentations If one or more stats file have different segs from others, use --common-segs or --all-segs flag depending on the need. If I use the -all-segs flag like it suggests, I end up with 0s in the following variables: BrainSegVol BrainSegVolNotVent BrainSegVolNotVentSurf SupraTentorialVolNotVent SupraTentorialVolNotVentVox MaskVol BrainSegVol-to-eTIV MaskVol-to-eTIV lhSurfaceHoles rhSurfaceHoles SurfaceHoles EstimatedTotalIntraCranialVol I've run this command before and never ran into this issue. Do you have any ideas for how to extract the necessary volume information without errors? Thanks, Maria -- Maria Kharitonova, PhD Research Assistant Professor Department of Medical Social Sciences Northwestern University Feinberg School of Medicine 625 N. Michigan Ave, Suite 2700 Chicago, IL 60611 Phone: (312) 503-6503 Email: maria.khariton...@northwestern.edu ___ 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] qdec question: discrepancy in sig. clusters
Hello, I have another newbie question. I'm running qdec, trying to compare cortical thickness in children with and without ADHD. However, I'm seeing a discrepancy between the clusters that are significant according to the terminal (after applying the Monte-Carlo simulation with default parameters; output below) and the ones that pop up when I hit Find clusters and goto Max. For example, I'm seeing 4 regions in the terminal: medialorbitalfrontal, inferiorparietal, caudalmiddlefrontal, and precentral. However, when I hit Find clusters and goto Max, I only see the Frontalpole. Using mri_surfcluster to extrat thickness measures only extracts it for the frontalpole, and not for the 4 ROIs listed in the terminal. I would like to be able to extract stats on those 4 that are listed in the terminal, if possible. Can you please help me reconcile the 2 types of output? Thanks! *** terminal output: # Input /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/FS_5.3_final/qdec/dx_age_icv_nuis_lh/rh-Diff-CONTROL-ADHD-Cor-thickness-age/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi rh # surface white # annot aparc # SUBJECTS_DIR /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/FS_5.3_final # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Signabs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold0 mm^2 # CSD thresh 2.00 # CSD nreps1 # CSD simtype null-z # CSD contrast NA # CSD confint 90.00 # Overall max 4.75828 at vertex 134555 # Overall min -2.56762 at vertex 93241 # NClusters 4 # Total Cortical Surface Area 65020.8 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZCWPCWPLow CWPHi NVtxs Annot 14.758 134555 1015.59 8.7 58.2 -5.8 0.00010 0.0 0.00020 1292 medialorbitofrontal 23.968 135840466.91 40.0 -66.8 25.9 0.01790 0.01620 0.01960 750 inferiorparietal 33.954 115431497.60 29.3 21.4 39.9 0.01150 0.01010 0.01290 900 caudalmiddlefrontal 43.242 133890439.44 49.4 -5.1 22.0 0.02520 0.02320 0.02720 932 precentral Simulation complete. ___ 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 -- confused by glm output for custom ROIs
Hi, I'm sorry for sending a duplicate request, but I am still really confused about the discrepancy between group-level findings in qdec (ROIs that are different across my 2 groups) and lack of a difference on the extracted thickness measures for those same custom ROIs. More info is below. Please let me know if you have any insight about this discrepancy. Thanks in advance! -- Forwarded message -- From: Maria Kharitonova maria.khariton...@colorado.edu Date: Thu, Jul 18, 2013 at 4:32 PM Subject: qdec -- confused by glm output for custom ROIs To: freesurfer freesurfer@nmr.mgh.harvard.edu, Douglas N Greve gr...@nmr.mgh.harvard.edu Hello, I have a question regarding the interpretation qdec's output for the custom ROI's thickness estimates. I ran an analysis comparing cortical thickness in children with and without ADHD (categorical variable), controlling for age and demeaned ICV, using 5.0. After controlling for multiple comparisons with the monte-carlo simulation, there were 2 ROIs in the right hemisphere that were significantly different across groups: a regions near parstriangularis and near medial orbital cortex. I then created custom ROIs for these regions, and extracted thickness estimates for each participant for each of these ROIs. I then decided to do a sanity check of the data -- run a linear regression on these extracted thickness estimates to see if the mean thickness in each region differed as a function of diagnosis (again controlling for age and demeaned ICV). By logic, I should see differences in thickness estimates for these 2 ROIs across the 2 groups, because that's how these ROIs were defined, right? But in reality, there is no difference at all between groups, with p-values around .9! I tried saving the ROIs by both manually tracing and with the mri_surfcluster command -- I get very similar estimates of thickness (correlation coefficients of .9 across 32 subjects). So that's not the cause of error. Both manual and automatic extraction fails to find differences across subjects that I described above. What am I missing? is the original GLM in QDEC that finds differences between groups doings something other than looking for differences in each voxel/region across groups? Thanks in advance for the help! Maria *** Maria Kharitonova, Ph.D. Postdoctoral Research Fellow Laboratories of Cognitive Neuroscience Boston Children's Hospital Division of Developmental Medicine 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.
[Freesurfer] qdec -- confused by glm output for custom ROIs
Hello, I have a question regarding the interpretation qdec's output for the custom ROI's thickness estimates. I ran an analysis comparing cortical thickness in children with and without ADHD (categorical variable), controlling for age and demeaned ICV, using 5.0. After controlling for multiple comparisons with the monte-carlo simulation, there were 2 ROIs in the right hemisphere that were significantly different across groups: a regions near parstriangularis and near medial orbital cortex. I then created custom ROIs for these regions, and extracted thickness estimates for each participant for each of these ROIs. I then decided to do a sanity check of the data -- run a linear regression on these extracted thickness estimates to see if the mean thickness in each region differed as a function of diagnosis (again controlling for age and demeaned ICV). By logic, I should see differences in thickness estimates for these 2 ROIs across the 2 groups, because that's how these ROIs were defined, right? But in reality, there is no difference at all between groups, with p-values around .9! I tried saving the ROIs by both manually tracing and with the mri_surfcluster command -- I get very similar estimates of thickness (correlation coefficients of .9 across 32 subjects). So that's not the cause of error. Both manual and automatic extraction fails to find differences across subjects that I described above. What am I missing? is the original GLM in QDEC that finds differences between groups doings something other than looking for differences in each voxel/region across groups? Thanks in advance for the help! Maria *** Maria Kharitonova, Ph.D. Postdoctoral Research Fellow Laboratories of Cognitive Neuroscience Boston Children's Hospital Division of Developmental Medicine 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.
[Freesurfer] qdec differences in FS 5.0 vs 5.3
Hi, I'm learning how to use QDEC and was comparing results that it produces under FresSurfer 5.0 vs 5.3. I know the 5.0 has an option for either DODS or DOSS method of producing a design matrix, while the 5.3 only has DODS. This suggests that results should be identical (or at least similar) across versions if I select DODS. However, I'm getting very different results based on the version I select: complete lack of differences across groups in 5.3 and a predicted pattern of differences in 5.0 using DODS. I'd like to understand where the differences are stemming from -- any ideas? Thanks in advance! Maria *** Maria Kharitonova, Ph.D. Postdoctoral Research Fellow Laboratories of Cognitive Neuroscience Boston Children's Hospital ___ 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] field of value too small, wrap-around
Hello, We have a relatively small FOV in our study because we mostly scan kids. Sometimes we scan adults with the same protocol, though, and after looking through the adults' reconned brains, I've noticed wrap-around on some brains. For one subject it's particularly bad; it affects aparc labels, where the very back of the brain gets labeled as orbitofrontal cortex. Is there a way to remedy this (other than increasing the FOV for subsequent subjects)? E.g. manually relabeling the affected regions? I'm pretty new to FreeSurfer, so I apologize in advance if this questions is naive. Thanks! Maria Kharitonova, Ph.D. Postdoctoral Research Fellow Laboratories of Cognitive Neuroscience Boston Children's Hospital ___ 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.
