Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

what is inflating to sphere rms error?
by chenchunhuichina 19 Mar '14

19 Mar '14

Dear Freesurfers, I am new to freesurfer and I am afraid of doing something wrong, so I am writing to ask is this error indicating something wrong with my data? Any help is appreciated. below are detials of my question. Thank you! I used freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 with this command fsl_sub -N cch recon-all -i ${i} -s FSsub${i:3:5} -all I checked the O file from fsl_sub and it said at the end "recon-all -s FSsub12534 finished without error at Thu Jan 23 15:44:35 CST 2014 done" Seems it's OK then checked the e file from fsl_sub (standard_in) 2: Error: comparison in expression Seems this is a problem of fsl_sub, According to https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-May/023961.html I guess I can ignore it? Then I checked the recon-all.log file and find a lot of "error", Someone asked this question and got the answer "We see this mysterious message sometimes...usually things are fine". So when and why get there errors and does they always fine? https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-October/020810.h… the "rms radial error" and "distance error " are below or see my attached log file. $ grep -n error FSsub12534/scripts/recon-all.log 2931:inflating to sphere (rms error < 2.00) 2932:000: dt: 0.0000, rms radial error=176.789, avgs=0 2933:005/300: dt: 0.9000, rms radial error=176.532, avgs=0 2934:010/300: dt: 0.9000, rms radial error=175.978, avgs=0 2935:015/300: dt: 0.9000, rms radial error=175.253, avgs=0 2936:020/300: dt: 0.9000, rms radial error=174.426, avgs=0 2937:025/300: dt: 0.9000, rms radial error=173.543, avgs=0 2938:030/300: dt: 0.9000, rms radial error=172.627, avgs=0 2939:035/300: dt: 0.9000, rms radial error=171.693, avgs=0 2940:040/300: dt: 0.9000, rms radial error=170.750, avgs=0 2941:045/300: dt: 0.9000, rms radial error=169.806, avgs=0 2942:050/300: dt: 0.9000, rms radial error=168.861, avgs=0 2943:055/300: dt: 0.9000, rms radial error=167.919, avgs=0 2944:060/300: dt: 0.9000, rms radial error=166.980, avgs=0 2945:065/300: dt: 0.9000, rms radial error=166.045, avgs=0 2946:070/300: dt: 0.9000, rms radial error=165.114, avgs=0 2947:075/300: dt: 0.9000, rms radial error=164.188, avgs=0 2948:080/300: dt: 0.9000, rms radial error=163.267, avgs=0 2949:085/300: dt: 0.9000, rms radial error=162.351, avgs=0 2950:090/300: dt: 0.9000, rms radial error=161.439, avgs=0 2951:095/300: dt: 0.9000, rms radial error=160.532, avgs=0 2952:100/300: dt: 0.9000, rms radial error=159.629, avgs=0 2953:105/300: dt: 0.9000, rms radial error=158.732, avgs=0 2954:110/300: dt: 0.9000, rms radial error=157.839, avgs=0 2955:115/300: dt: 0.9000, rms radial error=156.951, avgs=0 2956:120/300: dt: 0.9000, rms radial error=156.068, avgs=0 2957:125/300: dt: 0.9000, rms radial error=155.189, avgs=0 2958:130/300: dt: 0.9000, rms radial error=154.316, avgs=0 2959:135/300: dt: 0.9000, rms radial error=153.447, avgs=0 2960:140/300: dt: 0.9000, rms radial error=152.583, avgs=0 2961:145/300: dt: 0.9000, rms radial error=151.723, avgs=0 2962:150/300: dt: 0.9000, rms radial error=150.868, avgs=0 2963:155/300: dt: 0.9000, rms radial error=150.018, avgs=0 2964:160/300: dt: 0.9000, rms radial error=149.173, avgs=0 2965:165/300: dt: 0.9000, rms radial error=148.332, avgs=0 2966:170/300: dt: 0.9000, rms radial error=147.496, avgs=0 2967:175/300: dt: 0.9000, rms radial error=146.665, avgs=0 2968:180/300: dt: 0.9000, rms radial error=145.838, avgs=0 2969:185/300: dt: 0.9000, rms radial error=145.015, avgs=0 2970:190/300: dt: 0.9000, rms radial error=144.198, avgs=0 2971:195/300: dt: 0.9000, rms radial error=143.384, avgs=0 2972:200/300: dt: 0.9000, rms radial error=142.576, avgs=0 2973:205/300: dt: 0.9000, rms radial error=141.771, avgs=0 2974:210/300: dt: 0.9000, rms radial error=140.971, avgs=0 2975:215/300: dt: 0.9000, rms radial error=140.176, avgs=0 2976:220/300: dt: 0.9000, rms radial error=139.385, avgs=0 2977:225/300: dt: 0.9000, rms radial error=138.598, avgs=0 2978:230/300: dt: 0.9000, rms radial error=137.816, avgs=0 2979:235/300: dt: 0.9000, rms radial error=137.039, avgs=0 2980:240/300: dt: 0.9000, rms radial error=136.265, avgs=0 2981:245/300: dt: 0.9000, rms radial error=135.496, avgs=0 2982:250/300: dt: 0.9000, rms radial error=134.731, avgs=0 2983:255/300: dt: 0.9000, rms radial error=133.971, avgs=0 2984:260/300: dt: 0.9000, rms radial error=133.215, avgs=0 2985:265/300: dt: 0.9000, rms radial error=132.463, avgs=0 2986:270/300: dt: 0.9000, rms radial error=131.715, avgs=0 2987:275/300: dt: 0.9000, rms radial error=130.972, avgs=0 2988:280/300: dt: 0.9000, rms radial error=130.232, avgs=0 2989:285/300: dt: 0.9000, rms radial error=129.497, avgs=0 2990:290/300: dt: 0.9000, rms radial error=128.766, avgs=0 2991:295/300: dt: 0.9000, rms radial error=128.039, avgs=0 2992:300/300: dt: 0.9000, rms radial error=127.316, avgs=0 3017:distance error %100000.00 3572:pass 1: epoch 1 of 3 starting distance error %19.12 3573:pass 1: epoch 2 of 3 starting distance error %19.11 3575:starting distance error %19.02 3577:final distance error %19.05 4618:inflating to sphere (rms error < 2.00) 4619:000: dt: 0.0000, rms radial error=176.609, avgs=0 4620:005/300: dt: 0.9000, rms radial error=176.351, avgs=0 4621:010/300: dt: 0.9000, rms radial error=175.799, avgs=0 4622:015/300: dt: 0.9000, rms radial error=175.074, avgs=0 4623:020/300: dt: 0.9000, rms radial error=174.248, avgs=0 4624:025/300: dt: 0.9000, rms radial error=173.365, avgs=0 4625:030/300: dt: 0.9000, rms radial error=172.450, avgs=0 4626:035/300: dt: 0.9000, rms radial error=171.518, avgs=0 4627:040/300: dt: 0.9000, rms radial error=170.578, avgs=0 4628:045/300: dt: 0.9000, rms radial error=169.635, avgs=0 4629:050/300: dt: 0.9000, rms radial error=168.695, avgs=0 4630:055/300: dt: 0.9000, rms radial error=167.757, avgs=0 4631:060/300: dt: 0.9000, rms radial error=166.822, avgs=0 4632:065/300: dt: 0.9000, rms radial error=165.892, avgs=0 4633:070/300: dt: 0.9000, rms radial error=164.966, avgs=0 4634:075/300: dt: 0.9000, rms radial error=164.044, avgs=0 4635:080/300: dt: 0.9000, rms radial error=163.127, avgs=0 4636:085/300: dt: 0.9000, rms radial error=162.215, avgs=0 4637:090/300: dt: 0.9000, rms radial error=161.307, avgs=0 4638:095/300: dt: 0.9000, rms radial error=160.405, avgs=0 4639:100/300: dt: 0.9000, rms radial error=159.507, avgs=0 4640:105/300: dt: 0.9000, rms radial error=158.613, avgs=0 4641:110/300: dt: 0.9000, rms radial error=157.725, avgs=0 4642:115/300: dt: 0.9000, rms radial error=156.841, avgs=0 4643:120/300: dt: 0.9000, rms radial error=155.961, avgs=0 4644:125/300: dt: 0.9000, rms radial error=155.086, avgs=0 4645:130/300: dt: 0.9000, rms radial error=154.217, avgs=0 4646:135/300: dt: 0.9000, rms radial error=153.351, avgs=0 4647:140/300: dt: 0.9000, rms radial error=152.490, avgs=0 4648:145/300: dt: 0.9000, rms radial error=151.634, avgs=0 4649:150/300: dt: 0.9000, rms radial error=150.783, avgs=0 4650:155/300: dt: 0.9000, rms radial error=149.936, avgs=0 4651:160/300: dt: 0.9000, rms radial error=149.094, avgs=0 4652:165/300: dt: 0.9000, rms radial error=148.256, avgs=0 4653:170/300: dt: 0.9000, rms radial error=147.423, avgs=0 4654:175/300: dt: 0.9000, rms radial error=146.594, avgs=0 4655:180/300: dt: 0.9000, rms radial error=145.770, avgs=0 4656:185/300: dt: 0.9000, rms radial error=144.950, avgs=0 4657:190/300: dt: 0.9000, rms radial error=144.135, avgs=0 4658:195/300: dt: 0.9000, rms radial error=143.324, avgs=0 4659:200/300: dt: 0.9000, rms radial error=142.517, avgs=0 4660:205/300: dt: 0.9000, rms radial error=141.715, avgs=0 4661:210/300: dt: 0.9000, rms radial error=140.918, avgs=0 4662:215/300: dt: 0.9000, rms radial error=140.125, avgs=0 4663:220/300: dt: 0.9000, rms radial error=139.336, avgs=0 4664:225/300: dt: 0.9000, rms radial error=138.552, avgs=0 4665:230/300: dt: 0.9000, rms radial error=137.771, avgs=0 4666:235/300: dt: 0.9000, rms radial error=136.995, avgs=0 4667:240/300: dt: 0.9000, rms radial error=136.223, avgs=0 4668:245/300: dt: 0.9000, rms radial error=135.455, avgs=0 4669:250/300: dt: 0.9000, rms radial error=134.692, avgs=0 4670:255/300: dt: 0.9000, rms radial error=133.933, avgs=0 4671:260/300: dt: 0.9000, rms radial error=133.178, avgs=0 4672:265/300: dt: 0.9000, rms radial error=132.427, avgs=0 4673:270/300: dt: 0.9000, rms radial error=131.680, avgs=0 4674:275/300: dt: 0.9000, rms radial error=130.938, avgs=0 4675:280/300: dt: 0.9000, rms radial error=130.200, avgs=0 4676:285/300: dt: 0.9000, rms radial error=129.466, avgs=0 4677:290/300: dt: 0.9000, rms radial error=128.736, avgs=0 4678:295/300: dt: 0.9000, rms radial error=128.011, avgs=0 4679:300/300: dt: 0.9000, rms radial error=127.289, avgs=0 4704:distance error %100000.00 5218:pass 1: epoch 1 of 3 starting distance error %19.52 5219:pass 1: epoch 2 of 3 starting distance error %19.45 5221:starting distance error %19.40 5223:final distance error %19.42 9439:recon-all -s FSsub12534 finished without error at Thu Jan 23 15:44:35 CST 2014 2014-03-19 Chunhui Chen _________________ State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875

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tksurfer problems
by Joo Tan 19 Mar '14

19 Mar '14

Hello I'm having problems with tksurfer. It crashes whenever I load overlays using File -> Load Overlays. Am not too sure why. Could someone help? I'm using freesurfer 5.1.0 and fsl 5.0.6 on Mac OSX version 10.7.5 Here's what i did bash-3.2$ tksurfer AMP01 rh inflated subject is AMP01 hemi is rh surface is inflated surfer: current subjects dir: /Applications/freesurfer5.1.0/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/Joo/Documents/fMRI/AMMatch/analysis checking for nofix files in 'inflated' Reading image info (/Applications/freesurfer5.1.0/subjects/AMP01) Reading /Applications/freesurfer5.1.0/subjects/AMP01/mri/orig.mgz surfer: Reading header info from /Applications/freesurfer5.1.0/subjects/AMP01/mri/orig.mgz surfer: vertices=134552, faces=269100 surfer: single buffered window surfer: tkoInitWindow(AMP01) surfer: using interface /Applications/freesurfer5.1.0/tktools/tksurfer.tcl Reading /Applications/freesurfer5.1.0/tktools/tkm_common.tcl Reading /Applications/freesurfer5.1.0/tktools/tkm_wrappers.tcl Reading /Applications/freesurfer5.1.0/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer5.1.0/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % HIPS unsupported -- Cheers Joo

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ADC, Radial diffusivity, Axial diffusivity and thresholds
by Yuko Yotsumoto 18 Mar '14

18 Mar '14

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

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Re: [Freesurfer] FW: bug in surface-based area and volume, and use of total brain volume as a covariate
by Narly Golestani 18 Mar '14

18 Mar '14

>> 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.

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Mapping parcellation ROIs to the surface
by Danielle Sliva 18 Mar '14

18 Mar '14

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-Angular 20 60 220 0 and <subject>/label/aparc.annot.ctab 07 fusiform 180 220 140 0 31 supramarginal 80 160 20 0 18 parsopercularis 220 180 140 0 20 parstriangularis 220 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

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One sample t-test in Qdec
by Buse Merve Ürgen 18 Mar '14

18 Mar '14

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.

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Restrict QDEC analysis to a region
by amirhossein manzouri 18 Mar '14

18 Mar '14

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

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Re: [Freesurfer] fMRI contrasts in Freesurfer
by Douglas N Greve 18 Mar '14

18 Mar '14

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 <greve(a)nmr.mgh.harvard.edu > <mailto:greve@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(a)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 > greve(a)nmr.mgh.harvard.edu <mailto:greve@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(a)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 greve(a)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/

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Re: [Freesurfer] hypothalamus?
by Koolschijn, Cédric 18 Mar '14

18 Mar '14

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.Koolschijn(a)uva.nl<mailto:P.C.M.P.Koolschijn@uva.nl> W http://www.dutcharc.nl<http://www.dutcharc.nl/>/ On 3/18/14 1:04 PM, "Paul Beach" <pabeach1(a)gmail.com<mailto:pabeach1@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 <ellahinton(a)hotmail.com<mailto:ellahinton@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(a)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.

1 0

hypothalamus?
by Ella 18 Mar '14

18 Mar '14

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

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