Freesurfer

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30076 discussions

between group contrast using glmfit
by Robert Levy 09 Jul '07

09 Jul '07

Hello, I ran a group contrast in an ROI, correcting for multiple comparisons using the cluster size threshold method. It seems to have worked, however the one element that I don't understand as well is the basic between group contrast using an fsgd file, so I'm wondering if my commands really do what I want them to do. Is the below a correct usage to accomplish that? (apologies again for average7, it is because the data is relatively old.) The output looks very similar to the results of the contrast using intergroup_avg so that is promising. The main thing I'm uncertain about is how the fsgd file specifes that the two classes are to be contrasted. Thanks, Rob # perform the actual contrast mri_glmfit \ --really-use-average7 \ --y rh.ASvfix_8s_BwGroupError5.fsfast.mgh \ --fsgd fsgd_and_contrast_files/BwGroupError5.fsgd \ --glmdir rh.ASvfix_8s_BwGroupError5.fsfast.glmdir \ --pca \ --surf average7 rh \ --C fsgd_and_contrast_files/BwGroupError5.mat \ --label average7/label/dACC_rACC_final-rh.label \ --fwhm 13.488420 Contents of matfile: [levy@vantz fsgd_and_contrast_files]$ cat BwGroupError5.mat +1 -1 Contents of fsgd file: [levy@vantz fsgd_and_contrast_files]$ cat BwGroupError5.fsgd GroupDescriptorFile 1 Title HCvASD Class Normals Class ASD Input mano001 Normals Input mano002 Normals Input mano004 Normals Input mano005 Normals Input mano007 Normals Input mano008 Normals Input mano009 Normals Input mano010 Normals Input mano011 Normals Input mano012 Normals Input mano013 Normals Input mano014 Normals Input mano016 Normals Input mano025 Normals Input manoA02 ASD Input manoA03 ASD Input manoA04 ASD Input manoA05 ASD Input manoA07 ASD Input manoA08 ASD Input manoA09 ASD Input manoA10 ASD Input manoA11 ASD Input manoA13 ASD And just for the sake of completenes, here is a sample of what I ran after that: # monte carlo simulation data mri_glmfit --really-use-average7 \ --y rh.ASvfix_8s_BwGroupError5.fsfast.mgh \ --fsgd fsgd_and_contrast_files/BwGroupError5.fsgd \ --glmdir rh.ASvfix_8s_BwGroupError5.fsfast.glmdir \ --surf average7 rh \ --C fsgd_and_contrast_files/BwGroupError5.mat \ --sim mc-full 1000 2 BwGroupError5_ASvfix_8s_rhMCSIM01 \ --fwhm 13.488420 \ --label average7/label/dACC_rACC_final-rh.label ( x10 ) # apply simulation data to show significant clusters mri_surfcluster \ --src rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh \ --csd BwGroupError5_ASvfix_8s_rhMCSIM01-BwGroupError5.csd \ --csd BwGroupError5_ASvfix_8s_rhMCSIM02-BwGroupError5.csd \ --csd BwGroupError5_ASvfix_8s_rhMCSIM03-BwGroupError5.csd \ --csd BwGroupError5_ASvfix_8s_rhMCSIM04-BwGroupError5.csd \ --csd BwGroupError5_ASvfix_8s_rhMCSIM05-BwGroupError5.csd \ --csd BwGroupError5_ASvfix_8s_rhMCSIM06-BwGroupError5.csd \ --csd BwGroupError5_ASvfix_8s_rhMCSIM07-BwGroupError5.csd \ --csd BwGroupError5_ASvfix_8s_rhMCSIM08-BwGroupError5.csd \ --csd BwGroupError5_ASvfix_8s_rhMCSIM09-BwGroupError5.csd \ --csd BwGroupError5_ASvfix_8s_rhMCSIM10-BwGroupError5.csd \ --sum rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM.sum \ --ocp rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM.mgh \ --thmax infinity -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2656 Charlestown, MA 02129 email: levy(a)nmr.mgh.harvard.edu phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

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Retinotopic mapping: fMRI analysis help?
by McLean John (NHS Greater Glasgow & Clyde) 09 Jul '07

09 Jul '07

Hi, I am hoping to perform a retinotopic mapping fMRI study. My paradigms consist of a reversing checkerboard annulus which increases and decreases in size and a reversing checkerboard wedge which moves clockwise dor 180 degrees and then anticlockwise. I am struggling to correctly perform the fMRI analysis. I hope to use FSL so that i can then overlay the functional data on the flattened visual cortex using freesurfer. My problem is that i do not know how to correctly model the fMRI data using FSL, i believe i should use a sinusoid model but i am unsure of how to proceed. Would anyone with experience in this area be willing to discuss these issues with me? Thanks for your help, John ********************************************************************** This message may contain confidential and privileged information. If you are not the intended recipient please accept our apologies. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Please inform us that this message has gone astray before deleting it. Thank you for your co-operation. NHSmail is used daily by over 100,000 staff in the NHS. Over a million messages are sent every day by the system. To find out why more and more NHS personnel are switching to this NHS Connecting for Health system please visit www.connectingforhealth.nhs.uk/nhsmail **********************************************************************

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mean thickness of whole cortex
by Wang, Xin 09 Jul '07

09 Jul '07

Hello, Group Could anybody please tell me how to get the mean thickness of whole cortex? I got only the average thickness of each hemisphere with mris_anatomical_stats -a subject/lable/lh.aparc.annot -b subject lh Thank you in advance, Xin Wang

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installing FreeSurfer on Mandrake 10.2
by Narly A Golestani 09 Jul '07

09 Jul '07

Hello, I would like to install FreeSurfer on Mandrake 10.2 (Mandriva), and would like to know which version I should download. The available versions appear to be for: CentOS 4, CentOS 4 x86_64, or Red Hat 9. Also, posts to the archive seem to suggest that Mandrake may not be an optimal platform for Freesurfer, and that it may be necessary to compile tk8.3. Unfortunately I am not a unix expert and do not know exactly how to proceed. I would appreciate any guidance / suggestions. Thanks, Narly.

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mri_convert: Dicom to 4D Niftii
by Gallo, Antonio (NIH/NINDS) [F] 06 Jul '07

06 Jul '07

Hello all Is there an option in mri_convert to create 4D niftii from Dicom diffusion files? Thanks Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 ***********************

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missing transforms/talairach.xfm
by Richard Frye 06 Jul '07

06 Jul '07

For some reason my mris do not have a transforms/talairach.xfm file (created in old version of freesurfer) Is there any way of creating this file without going through the entire freesurfer workflow? Thanks Rich -- Best Wishes, Richard E. Frye, M.D., Ph.D., F.A.A.P. Assistant Professor of Pediatrics and Neurology University of Texas Medical School at Houston 7000 Fannin -- UCT 2478 Houston, TX 77030 Office: 713-500-3245 e-mail: richard.frye(a)gmail.com

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glm_fit segmentation fault
by Robert Levy 06 Jul '07

06 Jul '07

Hi, I'm getting a segmentation fault when trying to do a group contrast using glmfit. I think it's likely to be the parameters I'm using, because this is this is the first time I've tried to do this. This seems correct, but I don't know for sure. I've included the evironment/command/output info below and below that the contents of my fsgd file. Thanks, Rob [levy@vantz ~]$ cd $SUBJECTS_DIR/ [levy@vantz SUBJECTS_DIR]$ use_dev -------- freesurfer-Linux-centos4_x86_64-dev-20070706 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/dev FSFAST_HOME /usr/local/freesurfer/dev/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /space/ventzl/1/users/SUBJECTS_DIR MNI_DIR /usr/local/freesurfer/dev/mni FSL_DIR /usr/local/freesurfer/dev/fsl [vantz:SUBJECTS_DIR] (nmr-dev-env) mri_glmfit \ ? --really-use-average7 \ ? --y lh.ASvfix_8s_BwGroupError5.fsfast.mgh \ ? --fsgd fsgd_and_contrast_files/BwGroupError5.fsgd \ ? --glmdir lh.ASvfix_8s_BwGroupError5.fsfast.glmdir \ ? --pca \ ? --surf average7 lh \ ? --C fsgd_and_contrast_files/BwGroupError5.mat gdfReadHeader: reading fsgd_and_contrast_files/BwGroupError5.fsgd INFO: demeaning continous variables Continuous Variable Means (all subjects) Class Means of each Continuous Variable 1 Normals 2 ASD INFO: gd2mtx_method is dods INFO: you have selected subject average7 (and REALLY want to use it) instead of fsaverage. So I'm going to turn off fixing of vertex area to maintain compatibility with the pre-stable3 release. Reading source surface /space/ventzl/1/users/SUBJECTS_DIR/average7/surf/lh.whiteNumber of vertices 163842 Number of faces 327680 Total area 63393.164062 AvgVtxArea 0.386916 AvgVtxDist 0.710285 StdVtxDist 0.246011 $Id: mri_glmfit.c,v 1.134 2007/06/24 21:05:52 greve Exp $ cwd /autofs/space/ventzl_001/users/SUBJECTS_DIR cmdline mri_glmfit --really-use-average7 --y lh.ASvfix_8s_BwGroupError5.fsfast.mgh --fsgd fsgd_and_contrast_files/BwGroupError5.fsgd --glmdir lh.ASvfix_8s_BwGroupError5.fsfast.glmdir --pca --surf average7 lh --C fsgd_and_contrast_files/BwGroupError5.mat sysname Linux hostname vantz machine x86_64 user levy FixVertexAreaFlag = 0 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /autofs/space/ventzl_001/users/SUBJECTS_DIR/lh.ASvfix_8s_BwGroupError5.fsfast.mgh logyflag 0 usedti 0 FSGD fsgd_and_contrast_files/BwGroupError5.fsgd glmdir lh.ASvfix_8s_BwGroupError5.fsfast.glmdir DoFFx 0 Creating output directory lh.ASvfix_8s_BwGroupError5.fsfast.glmdir Loading y from /autofs/space/ventzl_001/users/SUBJECTS_DIR/lh.ASvfix_8s_BwGroupError5.fsfast.mgh Matrix condition is 1 Pruning voxels by frame. Found 153159 voxels in mask Saving mask to lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/mask.mgh search space = 59259.7 DOF = 22 Starting fit and test 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Fit completed in 0.03595 minutes Computing spatial AR1 on surface Residual: ar1mn=0.948094, ar1std=0.034478, gstd=1.538271, fwhm=3.622352 Writing results BwGroupError5 maxvox sig=-4.67846 F=28.9727 at index 14025 0 0 seed=1184295814 Computing PCA (24) Segmentation fault [vantz:SUBJECTS_DIR] (nmr-dev-env) Contents of fsgd file: [levy@vantz ~]$ cat $SUBJECTS_DIR/fsgd_and_contrast_files/BwGroupError5.fsgd GroupDescriptorFile 1 Title HCvASD Class Normals Class ASD Input mano001 Normals Input mano002 Normals Input mano004 Normals Input mano005 Normals Input mano007 Normals Input mano008 Normals Input mano009 Normals Input mano010 Normals Input mano011 Normals Input mano012 Normals Input mano013 Normals Input mano014 Normals Input mano016 Normals Input mano025 Normals Input manoA02 ASD Input manoA03 ASD Input manoA04 ASD Input manoA05 ASD Input manoA07 ASD Input manoA08 ASD Input manoA09 ASD Input manoA10 ASD Input manoA11 ASD Input manoA13 ASD -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2656 Charlestown, MA 02129 email: levy(a)nmr.mgh.harvard.edu phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

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About QDEC
by Mostaf Ghannad 06 Jul '07

06 Jul '07

Hi Doug, I was in Multi Modal course and back home I am asked for qdec demonstration. I have a package without qdec. Do I have to download all 1G package again for it? I know I was not released before the course, what about now? Cheers Mostafa --------------------------------- No need to miss a message. Get email on-the-go with Yahoo! Mail for Mobile. Get started.

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Animal Model
by Mostaf Ghannad 06 Jul '07

06 Jul '07

Hi, anyone using freesurfer for animal models? i am interested in rats and mice templates cheers Mostafa --------------------------------- Need a vacation? Get great deals to amazing places on Yahoo! Travel.

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Reprocessing data, COR-files
by Inge K. Amlien 06 Jul '07

06 Jul '07

Hi, we are about to reprocess quite a few subjects originally done in 2004. I am wondering if I will need to dig up the original dicoms, or if I can convert the COR-files to .mgz. -In the first study we have 2 series converted to orig/001/COR* and orig/002/COR*. -In the second study we have only 1 series, and only the orig/COR-files, (I believe the averaging step has been run somehow). Does Freesurfer (3.05) handle the first steps any different now, or is okay to convert to .mgz and go from there? Thanks, Inge

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