Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

Re: [Freesurfer] Files
by Douglas N Greve 30 Oct '12

30 Oct '12

can you send the fsgd file and command line? On 10/30/2012 06:42 PM, Ryan wrote: > Doug, > Also, I tried running this analysis but got the error below. This > makes me think it's because of all of the 1's and -1's in my FSGD > file, should I just have a factor called "Training" with a "yes" or a > "no" for each subject? > > ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 > Possible problem with experimental design: > Check for duplicate entries and/or lack of range of > continuous variables within a class. > > > On Tue, Oct 30, 2012 at 5:57 PM, Ryan <wmcgarry(a)gmu.edu > <mailto:wmcgarry@gmu.edu>> wrote: > > Doug, > So if I wanted to test if there were effects of training > compared to the control condition, and I had 4 subjects (2 per > group), would the format for my two files shown below be correct? > Thanks. > > > FSGD file: > GroupDescriptorFile 1 > Class Subject1 > Class Subject2 > Class Subject3 > Class Subject4 > Variables TP1-vs-TP2.Group1TrainTP1-vs-TP2.Group2Control > Input 1-2_recon Subject11 0 > Input 1-3_recon Subject11 0 > Input 2-2_recon Subject21 0 > Input 2-3_recon Subject21 0 > Input 3-1_recon Subject3 0-1 > Input 3-2_recon Subject3 0-1 > Input 4-1_recon Subject4 0-1 > Input 4-2_recon Subject40-1 > > > Mtx file: > 0 0 0 0 1 0 > 0 0 0 0 0 -1 > > Additional Mtx file examining cortical thinning or thickening in > the training group: > 0 0 0 0 1 0 > > > On Tue, Oct 30, 2012 at 4:44 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > See http://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova > This is for a single group. For two groups with 3 time points. > In your case, you only have 2 time points (so no TP1-vs-TP3 > variable). To account for the 2nd group, create two variables: > TP1-vs-TP2.Group1 and TP1-vs-TP2.Group2. If a subject is in > Group1, then set the Group2 variable to 0. > doug > > > On 10/30/2012 04:38 PM, Maren Strenziok wrote: > > If you don't agree with our matrix and contrasts, can you > please send us a matrix example for a 2x2 within and > between subjects ANOVA model and contrasts to get the > interaction effect? > Maren > > On Oct 30, 2012, at 4:22 PM, Douglas N > Greve<greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Ryan, I don't understand your model. This does not > look like a standard repeated measures ANOVA. Is it > supposed to be equivalent? > doug > > On 10/30/2012 02:07 PM, Ryan wrote: > > Doug, > Just so our study is understandable, subjects > completed a 6 week period of training or no > training (i.e. the control condition) with a scan > at the beginning and end of the period. Thus, I > entered the pre and post-scans for training and > control subjects in the input files. The names for > all the subjects are kept in an ordered list, > referenced by the other two files I describe below. > In the Xg.dat file, the first column has a +1 > for each control subject's pre-scan and a -1 for > each control subject's post-scan. The second > column has a +1 for each training subject's > pre-scan and a -1 for each training subject's > post-scan. The remaining columns each pertain to a > specific subject's two scans, with 1's showing > FreeSurfer which two scans are being compared pre > to post. > In the mtx file, the -1 references the first > column in Xg.dat (control subjects) and the +1 > references the second column in Xg.dat (training > subjects). The remaining 0's refer to the other > subjects or columns in Xg.dat. > So in order to determine whether there's > thickening or thinning in the controls and > training subjects, would I still need to use an > additional analysis with the contrasts [1 0 0 > ....] and [0 1 0 ....]? Thank you. > > > On Tue, Oct 30, 2012 at 11:28 AM, Douglas N > Greve<greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Hi Ryan, I'm a little lost here. Can you > resend your X and > contrast matrices and explain what each column is? > doug > > > On 10/26/2012 03:45 PM, Ryan wrote: > > Doug, > Actually my input is not the difference > map, but the > separate time points (it's timepoint 2 > weighted with -1 and > timepoint 1 weighted with 1, described in > the matrix file I > sent you). So in order to determine > whether there's thickening > or thinning in the controls and training > subjects, would I > still need to use the additional contrasts > [1 0 0 ....] and [0 > 1 0 ....]? Thank you. > > On Thu, Oct 25, 2012 at 3:48 PM, Douglas N > Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > And the input is already > TimePoint2-TimePoint1? If so, > then you > will need two more contrasts: [1 0 0 > ....] and [0 1 0 > ....]. The > first tells you if controls are > thinning (blue) or thickening > (red), the 2nd tells you if the > training is doing the same. > doug > > > On 10/25/2012 03:34 PM, Ryan wrote: > > Doug, > Yes, it's a longitudinal study > since we MRI > participants > pre-training and post-training. > > On Thu, Oct 25, 2012 at 2:37 PM, > Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > I'm not sure I understand. Is > this a longitudinal > study? > > > On 10/25/2012 01:26 PM, Ryan > wrote: > > Doug, > Also, how can I tell if > it's thickening or > thinning if > red/blue corresponds to > the group? Thanks for > the help. > > ---------- Forwarded > message ---------- > From: *Douglas N Greve* > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>>> > Date: Thu, Oct 25, 2012 at > 12:20 PM > Subject: Re: Files > To: Ryan<wmcgarry(a)gmu.edu > <mailto:wmcgarry@gmu.edu> > <mailto:wmcgarry@gmu.edu > <mailto:wmcgarry@gmu.edu>> > <mailto:wmcgarry@gmu.edu <mailto:wmcgarry@gmu.edu> > <mailto:wmcgarry@gmu.edu <mailto:wmcgarry@gmu.edu>>> > <mailto:wmcgarry@gmu.edu > <mailto:wmcgarry@gmu.edu><mailto:wmcgarry@gmu.edu > <mailto:wmcgarry@gmu.edu>> > <mailto:wmcgarry@gmu.edu > <mailto:wmcgarry@gmu.edu><mailto:wmcgarry@gmu.edu > <mailto:wmcgarry@gmu.edu>>>> > <mailto:wmcgarry@gmu.edu > <mailto:wmcgarry@gmu.edu><mailto:wmcgarry@gmu.edu > <mailto:wmcgarry@gmu.edu>> > <mailto:wmcgarry@gmu.edu > <mailto:wmcgarry@gmu.edu><mailto:wmcgarry@gmu.edu > <mailto:wmcgarry@gmu.edu>>> > <mailto:wmcgarry@gmu.edu > <mailto:wmcgarry@gmu.edu><mailto:wmcgarry@gmu.edu > <mailto:wmcgarry@gmu.edu>> > <mailto:wmcgarry@gmu.edu > <mailto:wmcgarry@gmu.edu><mailto:wmcgarry@gmu.edu > <mailto:wmcgarry@gmu.edu>>>>>> > > > That contrast will compute > training-controls. > In the maps, > red/yellow will mean > training>controls, blue/cyan > otherwise > > doug > > > > On 10/25/2012 12:47 AM, > Ryan wrote: > > Doug, > Here are the Xg.dat > (where the first > column is for > controls and > the second column is > for training > subjects) and > mtx files, I > didn't use the FSGD > design. Please let me > know if > this is > sufficient for you to > answer my question, > thank > you very much. > > -- -Ryan > > > -- Douglas N. > Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>> > Phone Number: 617-724-2358 > <tel:617-724-2358><tel:617-724-2358 > <tel:617-724-2358>> > <tel:617-724-2358 > <tel:617-724-2358><tel:617-724-2358 > <tel:617-724-2358>>> > <tel:617-724-2358 > <tel:617-724-2358><tel:617-724-2358 > <tel:617-724-2358>> <tel:617-724-2358 > <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > <tel:617-724-2358 > <tel:617-724-2358><tel:617-724-2358 > <tel:617-724-2358>> <tel:617-724-2358 > <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>> > <tel:617-724-2358 > <tel:617-724-2358><tel:617-724-2358 > <tel:617-724-2358>> > <tel:617-724-2358 > <tel:617-724-2358><tel:617-724-2358 > <tel:617-724-2358>>>>> > Fax: 617-726-7422 > <tel:617-726-7422><tel:617-726-7422 > <tel:617-726-7422>> > <tel:617-726-7422 > <tel:617-726-7422><tel:617-726-7422 > <tel:617-726-7422>>> <tel:617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 > <tel:617-726-7422><tel:617-726-7422 > <tel:617-726-7422>>>> <tel:617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 > <tel:617-726-7422><tel:617-726-7422 > <tel:617-726-7422>>> > > <tel:617-726-7422 > <tel:617-726-7422><tel:617-726-7422 > <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>>>> > > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > 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. > > > > > -- -Ryan > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > Phone Number: 617-724-2358 > <tel:617-724-2358><tel:617-724-2358 > <tel:617-724-2358>> > <tel:617-724-2358 > <tel:617-724-2358><tel:617-724-2358 > <tel:617-724-2358>>> > <tel:617-724-2358 > <tel:617-724-2358><tel:617-724-2358 > <tel:617-724-2358>> <tel:617-724-2358 > <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > Fax: 617-726-7422 > <tel:617-726-7422><tel:617-726-7422 > <tel:617-726-7422>> > <tel:617-726-7422 > <tel:617-726-7422><tel:617-726-7422 > <tel:617-726-7422>>> <tel:617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 > <tel:617-726-7422><tel:617-726-7422 > <tel:617-726-7422>>>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > -- -Ryan > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 > <tel:617-724-2358><tel:617-724-2358 > <tel:617-724-2358>> > <tel:617-724-2358 > <tel:617-724-2358><tel:617-724-2358 > <tel:617-724-2358>>> > Fax: 617-726-7422 > <tel:617-726-7422><tel:617-726-7422 > <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > -- -Ryan > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 > <tel:617-724-2358><tel:617-724-2358 > <tel:617-724-2358>> > Fax: 617-726-7422 > <tel:617-726-7422><tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > -- > -Ryan > > -- > 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: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > -- > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > -- > -Ryan > > > > > -- > -Ryan -- 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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error: 'fast_contrastmtx' undefined near line 25 column 21
by Garlinghouse, Matthew 30 Oct '12

30 Oct '12

Dear Doug, Sorry to bother you with this. When I type "which fast_contrastmtx" after starting Octave from the command line, it simply clears to the next line - no output. I also looked at the fast_contrastmtx.m file and noted that line 25 (as are the first 30 some lines) appear to be commented out by %, for documentation purposes. I did note, however, that the word fast_contrastmtx.m is listed on line 25. Also, I ran the same command on a machine with Matlab and Octave. The Matlab command continues to run well, and after setting up the Octave paths, Octave continues to give me the same error. Best, Matthew ____________________________________________________________________________ Hi Matthew, I'm not sure what the issue could be. If you start octave from the command line and type "which fast_contrastmtx" does it say it is not found? doug ____________________________________________________________________________ On 10/29/12 12:38 PM, Garlinghouse, Matthew wrote: > > Dear Surfers, > > I was running mkcontrast-sess with Matlab and having good success. > Then wanted to try Octave for ease of use on a cluster I have access > to, and after browsing the listserv set the following: > > export FS_USE_OCTAVE=1 > > export FS_OCTAVE_LIB=/usr/lib64/octave > > export FS_OCTAVE_BIN=/usr/bin/octave > > However when I run mkcontrast-sess now (on the cluster and a VB ubuntu > machine, both without Matlab), it runs through launching Octave and > then errors out as noted below. I'm new to using Octave and wasn't > sure what else I might need to set up for it to run properly? Any > thoughts would be much appreciated. > > Best Regards, > > Matthew > > *brain@neurodebian:/usr/local/freesurfer/subjects$ mkcontrast-sess > -analysis test.08.lh -contrast faces_gt_objects -a 2 -c 3* > > ** > > *INFO: Found 3 Non-Null Conditions* > > *INFO: Found 1 Delays* > > *Condition Weights: 0 1.00000000000000000000 -1.00000000000000000000* > > *mkcontrast -anadir test.08.lh -wcond 0 1.00000000000000000000 > -1.00000000000000000000 -sumconds -o test.08.lh/faces_gt_objects.mat > -wdelay 1 -octave* > > * $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $* > > *cmtxfile test.08.lh/faces_gt_objects.mat* > > *nconds 3, wcond 0 1.00000000000000000000 -1.00000000000000000000* > > *ndelays 1, wdelay 1* > > *ndelays 1, wpsa * > > *sumconds 1* > > *sumdelays 0* > > *nircorr 0* > > *TER 0.050000* > > *rdelta * > > *rtau * > > *GNU Octave, version 3.2.4* > > *Copyright (C) 2009 John W. Eaton and others.* > > *This is free software; see the source code for copying conditions.* > > *There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or* > > *FITNESS FOR A PARTICULAR PURPOSE. For details, type `warranty'.* > > ** > > *Octave was configured for "i486-pc-linux-gnu".* > > ** > > *Additional information about Octave is available at > http://www.octave.org.* > > ** > > *Please contribute if you find this software useful.* > > *For more information, visit http://www.octave.org/help-wanted.html* > > ** > > *Report bugs to <bug(a)octave.org<mailto:bug@octave.org>> (but first, please read* > > *http://www.octave.org/bugs.html to learn how to write a helpful report).* > > ** > > *For information about changes from previous versions, type `news'.* > > ** > > *error: `fast_contrastmtx' undefined near line 25 column 21* ________________________________ The Nebraska Medical Center E-mail Confidentiality Disclaimer The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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Re: [Freesurfer] Files
by Douglas N Greve 30 Oct '12

30 Oct '12

And the input is already TimePoint2-TimePoint1? If so, then you will need two more contrasts: [1 0 0 ....] and [0 1 0 ....]. The first tells you if controls are thinning (blue) or thickening (red), the 2nd tells you if the training is doing the same. doug On 10/25/2012 03:34 PM, Ryan wrote: > Doug, > Yes, it's a longitudinal study since we MRI participants > pre-training and post-training. > > On Thu, Oct 25, 2012 at 2:37 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > I'm not sure I understand. Is this a longitudinal study? > > > On 10/25/2012 01:26 PM, Ryan wrote: > > Doug, > Also, how can I tell if it's thickening or thinning if > red/blue corresponds to the group? Thanks for the help. > > ---------- Forwarded message ---------- > From: *Douglas N Greve* <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > Date: Thu, Oct 25, 2012 at 12:20 PM > Subject: Re: Files > To: Ryan <wmcgarry(a)gmu.edu <mailto:wmcgarry@gmu.edu> > <mailto:wmcgarry@gmu.edu <mailto:wmcgarry@gmu.edu>>> > > > That contrast will compute training-controls. In the maps, > red/yellow will mean training>controls, blue/cyan otherwise > > doug > > > > On 10/25/2012 12:47 AM, Ryan wrote: > > Doug, > Here are the Xg.dat (where the first column is for > controls and > the second column is for training subjects) and mtx files, I > didn't use the FSGD design. Please let me know if this is > sufficient for you to answer my question, thank you very much. > > -- -Ryan > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > 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. > > > > > -- > -Ryan > > > -- > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > -- > -Ryan -- 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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recon-all finished with ERRORs
by Christine Smith 30 Oct '12

30 Oct '12

Hello, After successfully running a subject through freesurfer (recon-all -make all) several times as I fixed some pial and white matter edits, I now get the message that recon-all finished with errors. Inspection of the recon-all.log doesn't reveal any error messages to me in any particular step. What should I be looking for to track down the reason that errors were generated? I already examined the talairach transform and that looks great. I loaded the pial and white matter surfaces and they look fine. The segmentation aparc+aseg looks great too. Thanks, Christine -- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego

2 1

average lobar thickness
by Khalid Hamandi 30 Oct '12

30 Oct '12

Dear FSers I am looking for help in determining the average thickness for each lobe, frontal, temporal, parietal, occipital and cingulate by merging Desikan atlas ROI values. I have had a look at the parcellation wiki http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation and see the basic principles, i think.... I believe i could extract labels from each subject using mri_annotation2label, multiply the number of vertices per ROI by the average ROI thickness from asegstats and sum the lobar ROIs (no of vertices x av thickness), then divide by the total number of vertices in that lobe. I have 82 subjects. If mris_anatomical_stats is the way to go then i'm having trouble following the command line options. Is there an 'easy' way to do this, are there Freesurf command tools that help? or does someone already have a script they are willing to share? I'm using Freesurf version 4.4.0. so don't have --lobesStrict if that was going to be on offer. many thanks Khalid

2 1

fieldsign-sess problem in retinotopy
by Zhou, Wei 30 Oct '12

30 Oct '12

Dear freesurfers, I am trying retinotopy analysis in freesurfer. For "fieldsign-sess", I encounter the following problem when I type "fieldsign-sess -a rtopy.self.lh -occip -s SUBJ01" or "fieldsign-sess -a rtopy.self.lh -occip -sf sessid": /media/users/zhouw4/testf/retinotopy/SUBJ01/log/fieldsign-sess.log subject: Undefined variable. my structure of retinotopy fold is : retinotopy |--sessid |--SUBJ01 |--subjectname |--bold |--001 |--f.nii |--rtopy.par I really appreciate it if you could give me some idea about that problem. Thanks a lot in advance. Best Wei Zhou Medical Physics Ph.D. Student Diagnostic Imaging Track cgxzwwd(a)gmail.com<mailto:cgxzwwd@gmail.com> zhouw4(a)livemail.uthscsa.edu<mailto:zhouw4@livemail.uthscsa.edu>

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Fwd: questions to qdec
by Daniel Klein 30 Oct '12

30 Oct '12

-----Ursprüngliche Mitteilung----- Von: Daniel Klein <dolphinede(a)aol.com> An: freesurfer-owner <freesurfer-owner(a)nmr.mgh.harvard.edu> Verschickt: So, 28 Okt 2012 11:58 am Betreff: questions to qdec Dear FreeSurfer experts, i want to test the effect of age square (in contrast to age) on cortical thickness in qdec. How can I do that? Am I right, that there is no possibility in qdec to use the per regressor-option to analyse the effects of cortical thickness on lGI vertex-wise? Many thanks Daniel

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Re: [Freesurfer] average measure of cortical thickness
by Daniel Ferreira 30 Oct '12

30 Oct '12

So, as a measure of whole brain cortical thickness average is it better to "Mean Thickness" from aparc.stats file? > > > 2012/10/30 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > >> Hi Daniel >> >> the parcellations are not uniform in size, and therefore the average of >> them will not be the same as averaging over the cortex. >> >> cheers >> Bruce >> >> On Tue, 30 Oct 2012, Daniel Ferreira wrote: >> >> Hi, >>> I was wondering what should I use as an average of cortical thickness for >>> the whole cortex. >>> >>> The aparc.stats output gives a value of "Mean Thickness" for each >>> hemisphere. But this value does not coincide with the one I get if I >>> average >>> the 34 variables from aparc.stats. Do you know why? >>> >>> thanks so much in advance >>> >>> Daniel >>> >>> >>> >> >> 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<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

Re: [Freesurfer] Talairach Failure Detection
by Daniel Ferreira 30 Oct '12

30 Oct '12

Thanks Nick very much for your suggestion. Unfortunately it did not fix the error. I run the mri_nu_correct command trying several -n values (1, 5, 20), then I -talairach, but the output is always the same. Talairach finish but when I check it the brain and standars are slided down to the bottom of the window. See a new output attached. What can be happening here? Any idea to fix it? thanks Daniel > > > > 2012/10/17 Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> > >> Daniel, >> >> See this page which i just created which describes a workaround to a >> problem some people are having with the Talairach stage in the v5.1 >> release: >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1 >> >> Nick >> >> >> On Wed, 2012-10-17 at 08:24 +0200, Daniel Ferreira wrote: >> > Dear experts, >> > >> > Please, I'm getting the Talairach Failure Detection problem in one of >> > my subjects (message enclosed below). >> > >> > >> > I tried to follow the tutorial to fix a bad Talairach with: >> > >> > >> > 1) tkregister2 --mgz -s <id> --fstal --> not green lines appear, I >> > attach a screenshot. Both the standard and my MRI are slided down to >> > the bottom of the window. See also attached tkmedit file. >> > >> > >> > 2) Anyway, I tried also -notal-check to see if something changed in >> > spite Talairach failed, but it fails also (off course). >> > >> > >> > 3) I used -use-mritotal but I still get the same. However, this time >> > processing finishes without errors, but my MRI is still at the bottom >> > of the window and output cut all what is between middle temporal >> > regions and neck. >> > >> > >> > Please, any idea? >> > >> > >> > Thanks a lot >> > >> > >> > Daniel >> > >> > >> > >> > #@# Talairach Failure Detection Wed Oct 10 09:08:27 CEST 2012 >> > /home/daniel/FreeSurfer/subjects/N001511_d2/mri >> > >> > talairach_afd -T 0.005 -xfm transforms/talairach.xfm >> > >> > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >> > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) >> > Manual Talairach alignment may be necessary, or >> > include the -notal-check flag to skip this test, >> > making sure the -notal-check flag follows -all >> > or -autorecon1 in the command string. >> > See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach >> > Linux siv 2.6.32-33-generic #72-Ubuntu SMP Fri Jul 29 21:07:13 UTC >> > 2011 x86_64 GNU/Linux >> > >> > recon-all -s N001511_d2 exited with ERRORS at Wed Oct 10 09:08:27 CEST >> > 2012 >> > >> > To report a problem, see >> > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > >> > >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)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. >> > >

3 8

average measure of cortical thickness
by Daniel Ferreira 30 Oct '12

30 Oct '12

Hi, I was wondering what should I use as an average of cortical thickness for the whole cortex. The aparc.stats output gives a value of "Mean Thickness" for each hemisphere. But this value does not coincide with the one I get if I average the 34 variables from aparc.stats. Do you know why? thanks so much in advance Daniel

2 1

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