Freesurfer September 2011

freesurfer@nmr.mgh.harvard.edu

119 participants
181 discussions

ICV differences from version 5.0 to 5.1
by Koller, Jonathan 16 Sep '11

16 Sep '11

Hi, We have noticed differences in Talairach registration (and therefore ICV estimates) in some of our subjects from version 5.0 to version 5.1. Please see the attached document. There are 4 subjects, each row represents the same subject, same input images, same recon-all options (-all) between versions. The bottom of the second page has a table with the ICV values for these subjects across versions. Have there been any changes to the Talairach registration step from 5.0 to 5.1 that would account for these differences? Thanks, Jon

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mri_surf2vol
by Peter Savadjiev 16 Sep '11

16 Sep '11

Hi, I am trying to convert the "curv" surfaces to a volume, using the mri_surf2vol command in the following manner: cd subjects/subjid mri_surf2vol --surf curv --hemi lh --template ./mri/orig.mgz --outvol /tmp/curv.mgz --surfval ./surf/lh.curv --fillribbon --volregidentity subjid I get the following output: gdiagno = -1 Using identity matrix for registration Cannot find orig.mgz, trying orig/COR files instead... mri_read(): couldn't determine type of file subjects/subjid/mri/orig mri_surf2vol ERROR: reading subjects/subjid/mri/orig header Could you please tell me what is wrong with the command? In particular, the file orig.mgz does exist at the specified path, so I don't understand why "cannot find orig.mgz"? The file can be visualized without problems, so the file is not corrupted. Thank you

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Colours for significant clusters
by Antonella Kis 16 Sep '11

16 Sep '11

Hi, Based on Group Analysis tutorial by loading the cluster annotation in tksurfer you can visualize all clusters, regardless of significance. Then changing the label mode to "Outline" by hitting the outline button and loading the cluster p-value overlay I can see all the significant clusters coloured in blue and having a different colour for the outline. I wonder if there is a way so I can make all the significant clusters blue without having any outline. If I change the outline mod the clusters will show different colours (the same as the outline colour). Thank you. Antonella

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distance scale bar on tksurfer
by Yang Liu 16 Sep '11

16 Sep '11

Hi, I want to get a distance scale bar on tksurfer's window. I can get a very dark bar on the black background, but I can't see any text around it. I guess it is because the text is also black, which is buried under the black background. Is there a way to change the text color? Thanks, Yang

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Brain volume covariate problem in QDEC
by Adam David Felton 16 Sep '11

16 Sep '11

Hello, I am using Qdec to analyze thickness (etc) using various IVs (e.g., Verbal IQ) while controlling for cortical grey matter volume (or ICV) as a nuisance factor. With the exception of the IV Sex, every time I run the analysis it goes into an endless loop, sporadically stating that the "Matrix is Ill-conditioned". It doesn't work with discrete or continuous variables. It also happens for the other DVs, like Sulc. Has anyone ran into this problem before? I couldn't find it on the listserv archives. Thank you for your help, Adam

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Errors in Cortical Parcellation
by Omer Tal 16 Sep '11

16 Sep '11

Hey there, I was excited to find out that Freesurfer has two atlases built in which do cortical parcellation as I am trying to do analysis on the precentral gyrus ROI only. However, when creating a mask showing the pre-central gyrus parcellation, I noticed that in the middle of the gyrus the algorithm fails and skips to the next gyrus over (the post-central gyrus). I added an image showing the failed parecellation (not sure if it shows up). Is there any solution around this? Is there where I can change parcellation options to maybe help better restrict the automatic algorithm? Or is there an easy way to redirect/train the algorithm? Thank you very much for any advice and your time, Omer Tal, M.S. UCSD Center for Functional MRI

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Differences in nu.mgz between v5.0.0 and v5.1.0
by Ed Gronenschild 16 Sep '11

16 Sep '11

Hi, I noticed a difference in the file nu.mgz between FreeSurfer version v5.0.0 and v5.1.0 (running on Mac OSX10.6). It looks as if nu.mgz in v5.1.0 is an intensity scaled-down version of nu.mgz in v5.0.0. The release notes tell that a bug is fixed in mri_nu_correct.mni, I don't know if that may cause this difference. Cheers, Ed

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manual editting problem
by Jing Ming 15 Sep '11

15 Sep '11

Hi Surfers: We have been coming across several gray matter regions that are not included within the pial surface (red line) when it should be (e.g., very anterior parts of the temporal lobe). From my understanding of similar posts on the forum, it seems that there isn't a way to add this region to the pial surface so that the missing brain matter is included. We have tried using the clone tool to fill in this region, as per the tutorial and have experimented with this tool using the tutorial data. I followed the steps in the tutorial but could not observe any changes when the middle button was selected. Does anyone have any ideas on how to troubleshoot this issue? Can someone please explain to me why this is not possible? Also how does Freesurfer determine what regions to include within the pial surface? If there is a way that has been developed recently, please enlighten me. -Jing

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Re: [Freesurfer] FSGD Contrast Setup Question
by Douglas N Greve 15 Sep '11

15 Sep '11

Hi Josh, there is not a way that I know of to do the paired analysis if some are missing a scan. A "real" statistician might know of a way theoretically, and I might be able to implement that theory, but I don't know myself. So does that mean you want to do an unpaired test? doug Roffman, Joshua L.,M.D. wrote: > Hi Doug, > Thanks for weighing in. For this study, while most subjects have 2 sets of good > scan data (pre and post treatment), a number have only one set (pre or post). > We're hoping to use all of the data given that it's overall a pretty small > study. Is it possible to run the paired analysis if we are missing pre or post > data for some subjects? > Best, > Josh > > > -----Original Message----- > From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Thu 9/15/2011 4:54 PM > To: Adam Nitenson > Cc: freesurfer(a)nmr.mgh.harvard.edu; Roffman, Joshua L.,M.D. > Subject: Re: [Freesurfer] FSGD Contrast Setup Question > > Hi Adam, you have a "repeated measures" design. In your case, this is > best handled using a paired analysis. You can search for "paired" on the > wiki to get instructions. The easiest way to do this is to run > mris_preproc with the --paired-diff option, then follow the instructions > for the "standard" one or two group analysis (search for "fsgd"). > > doug > > Adam Nitenson wrote: > >> Hi Freesurfers, >> >> I am trying to set up both a 2 Group 1 Covariate and a 4 Group 1 >> Covariate analysis but just want to make sure I'm using the correct >> contrast option. >> >> For the first analyis, the two groups are Drug Pre and Drug Post, >> with folate-serum level as a covaraite. We want to keep the covariate >> under consideration in our analyses, but we really want to look at >> the difference between the Drug Pre and Drug Post activation (so >> folate-serum level is more of a nuisance variable). It seems that the >> first option under the 2G1V Page "Null Hypothesis: is there a >> difference between the group intercepts? Is there a difference >> between groups regressing out the effect of age? 1 -1 0 0" >> reflects this idea best. >> >> For the second analysis, the 4 Groups are Drug Pre, Drug Post, >> Placebo Pre, and Placebo Post, with the same folate-serum level >> covariate. We are intersted in the double subtraction of (Drug Post >> - Drug Pre) MINUS (Placebo Post - Placebo Pre), but again wish to >> covary by folate level. For this it seems like contast 7 on the 4G1V >> page "is there an interaction between gender and handedness >> regressing out the effects of age? 0.5 -0.5 -0.5 0.5 0 0 0 >> 0" is best. >> >> Is this the best way to go about analyzing these two questions? >> >> Thanks, >> >> Adam Nitenson, B.S. >> Brain Genomics Lab >> Massachusetts General Hospital >> nitenson(a)nmr.mgh.harvard.edu >> Phone: 617-643-3215 >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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 Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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GLM or Qdec ?
by Antonella Kis 15 Sep '11

15 Sep '11

Dear FS experts, I finished running the GLM and I wonder what is the best way to further analyse my data in order to see if there is any relation between age (at seizure onset) and cortical thickness for my patients versus control group. 1). Why when I overlay the sig.mgh in tksurfer lh inflated, I get more clusters than the number of clusters obtained from mri_glmfit-sim? 2). What sig.mgh represents? 3) What's the real significance of a cluster (how a cluster is formed)? 4). Why my thickness value in clusters (eg cluster no. 1 which coresponds to the posteriorcingulate) for subject no.1 is different that the thickness value obtained for the same region in the lh.aparc.stats while running recon-all? 5). After running the GLM should I use visualizing and plotting method to further analyse my data and load FSGD file lh.gender_age.glmdir/y.fsgd? 6). Should my ROI's be defined or be the same with my clusters? 7). What is the difference between GLM and Qdec? What method is the best to analyse the relation between age and cortical thickness for my patients versus control group? 8). Why when analysing with Qdec I get more clusters? Are this defining or representing the sig.mgh as in GLM? 9). When using Qdec were I can find as an output of results the number of clusters and the cortical thickness value? Thank you and have a great day! Antonella

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Freesurfer September 2011