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30132 discussions

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

3 13

using mri_label2label with full path
by Chris 15 Sep '11

15 Sep '11

I have a tricky situation where we can't use symbolic links ( cifs/smb mounts ) and it doesn't make sense to copy the fsaverage to the SUBJECTS_DIR. The subjects_dir is actually a separate directory for every subject when trying to run things through the connectome toolkit. I've edited my own version of recon-all in attempts of passing full paths to some of the tools if necessary. I'm getting caught in the mri_label2label step, since its using "--srcsubject" and "--srclabel" Passing a full path to "--srcsubject" doesn't work as expected, since its assuming the path of --srcsubject exists inside my SUBJECTS_DIR. If i only pass the default "fsaverage", then that also doesn't work because it doesn't exist inside my SUBJECTS_DIR either. Any suggestions? -Chris [petty@node61 free]$ mri_label2label --srcsubject /usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage --srclabel /usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage/label/lh.BA1.label --trgsubject test20090520_36099 --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage/label/lh.BA1.label srcsubject = /usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage trgsubject = test20090520_36099 trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/BIAC/munin2.dhe.duke.edu/BIAC/TestSuite.01/Analysis/speed_test/20090520_36099/free/ FREESURFER_HOME /usr/local/packages/freesurfer_v5.1.0 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /mnt/BIAC/munin2.dhe.duke.edu/BIAC/TestSuite.01/Analysis/speed_test/20090520_36099/free///usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage/surf/lh.sphere.reg MRISread(/mnt/BIAC/munin2.dhe.duke.edu/BIAC/TestSuite.01/Analysis/speed_tes…: could not open file No such file or directory ERROR: could not read /mnt/BIAC/munin2.dhe.duke.edu/BIAC/TestSuite.01/Analysis/speed_test/20090520_36099/free///usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage/surf/lh.sphere.reg

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FSGD Contrast Setup Question
by Adam Nitenson 15 Sep '11

15 Sep '11

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

2 1

mri_mcsim and mri_glmfit-sim
by MCLAREN, Donald 14 Sep '11

14 Sep '11

I am trying to figure out how to cluster some data on the cortical surface; however, I've run into a few issues: (1) I can't seem to find a description or examples for running mri_mcsim and mri_glmfit-sim won't work because I'm not using FSFAST to create my statistical maps. (2) A previous email suggested that there are stored values that I could lookup, but I can't seem to locate the files anywhere. (3) With respect to the fwhm values used in the simulations, it was suggested that this be matched to the fwhm.dat file output from mri_glmfit; however, since I didn't use mri_glmfit, I don't have fwhm.data file. Should I just use the smoothing used on the surfaces? Any thoughts would be appreciated. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

2 1

Converting a cluster to a ROI without manually drawing
by Nasim Maleki 14 Sep '11

14 Sep '11

Hi all, In qdec, is there a way to convert a cluster to an ROI without manually drawing the ROI? I'm talking about selecting clusters on the mc-z maps. Thanks, Nasim

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