Freesurfer March 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

recon-all error
by Susan Ruiz 23 Mar '12

23 Mar '12

Hello all, I have been using FS5.0 and just started using 5.1. I tried running a recon with the new version with two of my subjects, and in both cases I got the same error message: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUN CTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = 7003.6 tol 0.000010 This error did not stop the rest of the recon from running for quite some time after the error, however, it ultimately exited with errors. I searched the mail archive and found reference to this error message, but I couldn't identify how it was resolved/what the cause of it might be. Any suggestions as to what might be causing this? Thanks, ~Sue * * ** *** ***** ******** ************* Susan M. M. Ruiz, Ph.D. Boston University School of Medicine Laboratory for Neuropsychology VA Boston Healthcare System smosher(a)bu.edu * * ** *** ***** ******** *************

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Checkout release and stable branch
by Nicolas Rannou 23 Mar '12

23 Mar '12

Hi all, I followed the instructions on the wiki but it seems impossible to checkout the stable and release branches? [toor@linux:x86_64-Linux]...or/cvsroot/test$>cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P -r stable5 stable cvs server: cannot find module `stable' - ignored cvs [checkout aborted]: cannot expand modules Did their name changed? Is there a good way with cvs to list the available branches? ('cvs ls' not woking) Thanks, Nicolas

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Jacobian Questions
by Jeff Sadino 22 Mar '12

22 Mar '12

Hello, Since the jacobian files contain only positive numbers, is there any way to make a distinction between a brain area that needs to be stretched bigger to fit the template versus a brain area that needs to be squished smaller? fsaverage is comprised of 40 subjects, but I wonder if the jacobian is most accurate only for my subjects that have the same age as the fsaverage mean? If so, then the younger subjects would need to be squished and the older subjects would need to be stretched. But since the jacobian is always positive, then on a scatterplot of jacobian versus age, this would look like a hump centered on the fsaverage mean age. Am I on the right track with this? Thank you, Jeff

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QDEC with cluster-wise p=.1
by Jeff Sadino 22 Mar '12

22 Mar '12

Hello FreeSurfers, I want to do several cluster-wise corrections at a p value of .1, preferably in QDEC. To create the new "template cluster", I am using this command: mri_mcsim --o test --base mc-z --surf fsaverage lh --nreps 10000 --fwhm 10 Is there a way that I can tell mri_mcsim to do a threshold of 1.00 (p=.1) and only the "abs" sign? Thank you, Jeff Sadino

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make_average_subject failure
by Klein, Holger 22 Mar '12

22 Mar '12

Dear Freesurfers, Command line: make_average_subject --out average --subjects ... (n=60) . . . . . Applying LTAtransformInterp (resample_type 1) writing to /Volumes/Macintosh/freesurfer/Kontrollen//average/tmp/make_average_vol-tmp-15056/orig-A2/WE.mgh... ERROR: failure writing /Volumes/Macintosh/freesurfer/Kontrollen//average/tmp/make_average_vol-tmp-15056/orig-A2/WE.mgh /Volumes/Macintosh/freesurfer/Kontrollen ERROR: mri_convert failed. ERROR: make_average_volume Surface averaging was done without any problem, but the volume averaging .... Any clue what's wrong? Thanks in advance Holger

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Spot Opened in Boston FreeSurfer course
by Allison Stevens Player 22 Mar '12

22 Mar '12

Hi everyone, We had a last minute drop-out from our Boston FreeSurfer course which takes place April 2nd through the 4th. If anyone is interested in taking this spot, please let me know. Details about the course content, the registration fee, and other logistics can be found here: http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription Allison

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Future of freesurfer
by Nicolas Rannou 22 Mar '12

22 Mar '12

Hi all, I'm currently compiling/installing freesurfer on mac osx lion, ubuntu 12.04 (will be relased soon) and lots of packages which are required by freesurfer appear to be outdated. Is there any step-by-step installation/compilation tutorial somewhere in the web? Therefore I have a couple of questions: Do you plan to update the default libraries to newer versions sometimes soon? (I'm not sure for how long building against old packages will build viable?) Shouldn't freesurfer links against the current release of each library? Regarding the build system, do you consider switching to cmake? It would make easier to maintain, keep up to date and deploy freesurfer over mac and linux? Best, Nicolas

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Displaying results from qdec on a single subject
by Emily Rogalski 22 Mar '12

22 Mar '12

Hi All, Is it possible to resample a .sig file from a group thickness analysis in qdec so that the results could be displayed on a single subject's anatomy rather than the fsaverage anatomy in tksurfer? Thanks, Emily -- Emily J Rogalski, PhD Assistant Research Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogalski(a)gmail.com

2 1

editing pial surface
by Richter, Julia 22 Mar '12

22 Mar '12

Hi freesurfer experts, I am trying to correct the pial surfaces of my data. I was able to remove voxels with the right button of my mouse, but unfortunately, it didn't work out to add voxels. Can somebody please help me with that? Do I need a middle button on the mouse for it? Attached you may find a slice of the brain data. The red line (indicating the pial surface) and green line (indicating the grey matter/white matter boundary) cross, which should not happen in my opinion. Is there any possibility to change the lines so that they don't cross anymore? Cheers, Julia

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mkheadsurf and smseghead
by Will Woods 22 Mar '12

22 Mar '12

Hi, In my previous lab, which I no longer have access to, we ran mkheadsurf as part of postprocessing, and it generated smseghead files. The latest version of Freesurfer which I recently downloaded (with mkheadsurf version v 1.8 2011/03/02 20:16:39 nicks Exp) does not generate these files - and moreover the smheadsurf environment variable (which defaults to 'smseghead') in the mkheadsurf script does not appear to be used for anything in that script. Have I forgotten to do something in the earlier processing stages, or have things changed? Will

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Freesurfer March 2012