Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

question about Correction for Multiple Comparison
by ZhiLiangLong 26 Mar '12

26 Mar '12

Hi all: A few days ago, i have asked about some questions about Correction for Multiple Comparison. But i'm still confused about it. The version of FS is 5.1.0. when i performed Correction for Multiple Comparison using command line with 'mris_glmfit-sim', it usually took many hours to complete. However, when i performed this in qdec, it only took a few seconds. Moreover, i couldn't find command with ''mris_glmfit-sim' in the terminal except for the 'mri_surfcluster' command. I wander whether the 'mri_surfcluster' command can be used for the Correction for Multiple Comparison? Any suggestions will be appreciated. Thank you!

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Watershed gca atlas
by Vincent 24 Mar '12

24 Mar '12

I noticed in this skull strip tutorial<http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix> that sometimes when adjusting the watershed threshold the -no-wsgcaatlas option is used. I understand that it means that the atlas, which is used to assist in detecting physical features while stripping the skull, is not used during this step. Why wouldn't you want to use it? -- Vincent

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fitting a priori ROI masks to freesurfer
by sonya kaur 24 Mar '12

24 Mar '12

Dear all, I have an a priori ROI mask previously created in AFNI for functional data. My hypothesis requires me to derive cortical thickness values for the same ROIs. How would I obtain the values using these ROIs from freesurfer? The mask was generated in Talairach space and are surface level ROIs. I tried using mris_anatomical_stats but it didn't seem to work (possibly because the masks weren't created using freesurfer/weren't saved in .label files). How would I proceed? I realize this is probably pretty simple but I'm new to freesurfer and really appreciate any guidance. -- Sonya Kaur Clinical Psychology Graduate Student Department of Psychology The University of Texas, Austin 1 University Station, A8000 Austin, TX 78712 SEA 4.110E <sonya_kaur(a)mail.utexas.edu> sonya_kaur(a)mail.utexas.edu

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Fwd: Skull strip failure
by Vincent 23 Mar '12

23 Mar '12

Hi, I've uploaded my subject to the FTP server. The file is called AL.zip. I'm really enjoying using freesurfer and I'm excited to hear what you think about this subject. Thanks so much for the help. -- Vincent On Thursday, March 22, 2012 at 8:25 AM, Louis Nicholas Vinke wrote: Hi Vincent, Yep, that'll work or the web file drop, whichever you prefer. https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html -Louis On Thu, 22 Mar 2012, Vincent wrote: Hi Louis, Thank you very much! I'm eager to upload something but I am stuck working another job until later today. I'll have to wait until then because I've never uploaded something to your servers and I'll have to figure out the best way to go about it. I believe I should upload to ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Thanks again. -- Vincent On Thursday, March 22, 2012 at 7:42 AM, Louis Nicholas Vinke wrote: Hi Vincent, Let me know when you upload this case, I think I may be able to help. -Louis On Wed, 21 Mar 2012, Vincent wrote: Hi, I have an image that is completing the skull strip with a lot of skull remaining and it is have a large effect on the surfaces. I've tried lowering the watershed threshold as low as 5 and I've tried adding the -gcut option, but the low threshold by itself does not eliminate the skull and gcut not only fails to remove the skull but it removes cerebellum as well. There is so much skull left that I am hesitant to try manual edits, but I don't know any other options. Are there any? By the way, this brain is from an older individual with pretty substantial atrophy. --Vincent 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.

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Cutting closed line for flat map
by Greg Burgess 23 Mar '12

23 Mar '12

I'm trying to cut the medial wall as described in Step 2 on http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch . However, each time I click "Cut Closed Line", I get a jumble of lines that go all over the cortex and medial wall, rather than a clean circle around the medial wall. I've tried putting cut points so close that they're nearly on top of each other, but it still doesn't help. Does anyone have an idea why this won't cut right? Thanks, --Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology Email: burgessg(a)pcg.wustl.edu

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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 * * ** *** ***** ******** *************

2 1

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

2 1

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

1 0

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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