Freesurfer

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30132 discussions

Freesurfer coordinate problem
by xiaoning wu 26 Mar '12

26 Mar '12

Hi all, Recently I have a problem about coordinate of freesurfer. I have reprocessed the MRI data to get the cortical thickness and then I want to get the indexes, coordinate and cortical thickness of a region of interest(ROI). I have use the Surfstat toolbox of matlab to process the data.Now I want to use the function SurfStatROI ( function maskROI = SurfStatROI( centre, radius, surf ) ) to get the ROI, however, I have known the MNI coordinates (x,y,z) only .I want to convert this MNI coordinates to the freesurfer coordinates which can be used by SurfStatROI.center. That is ,if I use the function SurfStatReadSurf to read surf files (surf=SurfStatReadSurf(..)) to get the variable surf, then I can get surf.coord(:,index) by a index. How can the surf.coord() corresponding to the MNI coordinate systems or Talairach systems. I have seen the website of Freesurfer coordinate systems ( http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems) but I can not solve my problem. Looking forward to your help sincerely. Your sincerely! Xiaoning Wu Mar 20,2012

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question about Cluster-wise Correction for Multiple Comparisions
by ZhiLiangLong 26 Mar '12

26 Mar '12

Hi all: I'm performing the group analysis on my own data using command line on FS5.1.0 and i'm a little confused about the Clusterwise Correction for Multiple Comparisions. the command is as follows: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 10000 4 mc-z.negative \ --sim-sign neg --cwpvalthresh 0.05\ --overwrite In this command, does the vertex-wise threshold (here, '4') mean that the vertex whose p value is lower than 0.0001 can be considered to used for the Correction for Multiple Comparisions ? likewise, does the sign (here,'neg') mean that only negtive vertexs can be considered? Is there a criterion which vertex-wise threshold and sign i should choose? Hope you can give me some suggestions !

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question about FSGD file
by ZhiLiangLong 26 Mar '12

26 Mar '12

Hi, FS experts: I'm scanning freesurfer pages about FSGD files here: http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V and i'm interested in one contrast file(the example of Contrast 5 right-left.intercept.mtx). The original FSGD file is list as follows: GroupDescriptorFile 1 Title OSGM Class MaleRight Class MaleLeft Class FemaleRight Class FemaleLeft Variables Age Input subject1 MaleRight 30 Input subject2 MaleLeft 40 Input subject3 FemaleRight 50 Input subject4 FemaleLeft 60 The contrast file is : 0.5 -0.5 0.5 -0.5 0 0 0 0, meaning to exame the difference between Righties and Lefties regressing out the effects of gender and age. Now i consider gender as the covariate variable ('1' represents the Male and '2' represents the Female), and i setup a new FSGD file: GroupDescriptorFile 2 Title OSGM Class Right Class Left Variables Age gender Input subject1 Right 30 1 Input subject2 Left 40 2 I also want to exame the difference as suggested above, and I setup the new contrast file as :1 -1 0 0 0 0. My question is that : are the new FSGD and contrast files correct to exame the difference as suggested by original FSGD and contrast files?

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make_average_subject
by sonya kaur 26 Mar '12

26 Mar '12

Dear all, I'm getting an error with the make_average_subject command on freesurfer. The error is vm_allocate (size=262144) failed (error code 3). According to the freesurfer helpdesk, it seems to be a problem with creating an "average" aseg. Is there any solution for this that you know of? Thank you in advance! -- 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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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 * * ** *** ***** ******** *************

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