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30131 discussions

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

2 3

glmfit question
by Robert Levy 05 Jul '07

05 Jul '07

Hello, This is probably a quick question. It seems to take a long time to generate monte carlo simulation data in mri_glmfit. Is it a bad idea to break the iterations into however many available seychelles nodes I can use? Is that equivalent to running the total number of iterations serially? Thanks, Rob fpolli(a)nmr.mgh.harvard.edu wrote: > hi rob, see below for the answers to some of your questions. > > >> Hi Dara and Frida, >> >> The analysis is running. There is one part of Frida's example that I >> will need to emulate once this is done, but if what I have is correct, >> then the part that takes the most time will be done when I come in to >> work on Thursday 7/5. >> >> Frida, >> sometime when you have a moment free, could you look over the commands >> I'm running and tell me if there is anything glaringly (or subtly) >> wrong? I have tried my best to run it in a way that is consistent with >> how you did it, but I think there could be things wrong, because I dont >> 100% understand everything about what these commands are doing, but >> getting there. There's nothing in these commands that looks like >> nonsense to me, but for example, I don't know if the smoothing value of >> 13.488420 is the same in our case. >> > > to find this parameter, you want to open a file that's called > mri_glmfit_log or something like that. it is created in the third step. > however, it usually gives you a value b/w 12.5 and 14.5 and using one > vs.the other does not create a huge diffrence. however, try to find the > file i'm talking about, open it up, and you'll see. > > I'm using a threshold of .01, and I > >> don't know if that would cause any parameters other than the threshold >> to need to change. >> > you should use whatever parameter you want your data displayed at. no that > doesn't change anything else. > > I also don't know why simulation data is generated > >> twice and then both input into the contrast, >> > only b/c it takes a long time to generate 10K simulations, so we broke it > up into 2 x 5K. you can also use 1 x 10 k. > but I'm following that > >> aspect of your example verbatim at least for now, in the commands that >> are now running. Also a default glmfit setting is to use dods (diff >> order diff slope). >> > dods is DEF. the one you want to use. it stands for different offset > different slope - you don't want to assume that both groups have the same > slope to their data. > > Is that what we should be using? There is also a > >> doss (same slope) option. Ally, she is one of the RAs who I talked with >> yesterday about this, mentioned that dods is more unpredictable than doss. >> >> Thanks for your help, >> Rob >> >> > good luck, f > >> #!/usr/local/bin/bash >> >> ################## >> # levy 7/3/07 # >> ################## >> >> # Katy ran intergroupavg-sess on 9/20/05 >> # Last week we used FDR to correct for multiple comparisons on the >> results of the above contrast between groups, >> # but the resulting threshold was too conservative. >> # So now I am running the analysis with a cluster-based threshold using >> a Monte Carlo simulation >> # (simulate a null hypothesis with randomnes, and use it to generate a >> meaningful threshold to judge the results with) >> # In terms of the freesurfer implementation, this is a different process >> and does not build on the results of previous commands. >> >> # so we start from the beginning >> # note: rerunning these 2 lines probably unnecessary, but mris_preproc >> was having problems I thought were due to faulty stxgrinder output >> # This problem led Doug to discover bugs in mris_preproc and also >> mkcontrast-sess, which he then fixed >> # As a result, I re-ran the following 2 commands, which didn't take very >> long anyhow. >> >> mkcontrast-sess -analysis EMerror -contrast ASvfix_6 -a 2 -c 0 >> -setwdelay -sumdelays >> stxgrinder-sess -a EMerror -c ASvfix_6 -sf Subject_Lists/bw-group-error-5 >> >> # resample onto average7 >> # ( use version from doug's home directory with bugs corrected... ) >> >> /space/greve/1/users/greve/freesurfer/bin/mris_preproc --fsgd >> fsgd_and_contrast_files/BwGroupError5.fsgd --target average7 --hemi lh >> --sf Subject_Lists/bw-group-error-5 --a EMerror --c ASvfix_6 --out >> lh.ASvfix_8s_BwGroupError5.fsfast.mgh | tee -a >> logs/mris_preproc_BwGroupError5_ASvfix_8s_lh.log >> /space/greve/1/users/greve/freesurfer/bin/mris_preproc --fsgd >> fsgd_and_contrast_files/BwGroupError5.fsgd --target average7 --hemi rh >> --sf Subject_Lists/bw-group-error-5 --a EMerror --c ASvfix_6 --out >> rh.ASvfix_8s_BwGroupError5.fsfast.mgh | tee -a >> logs/mris_preproc_BwGroupError5_ASvfix_8s_rh.log >> >> >> mkdir lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/ >> mkdir rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/ >> >> # lh >> 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 --surf average7 lh --C >> fsgd_and_contrast_files/BwGroupError5.mat --sim mc-full 5000 2 >> BwGroupError5_ASvfix_8s_lhMCSIM1 --fwhm 13.488420 | tee -a >> logs/glmfit_lh_MCSIM1.log >> 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 --surf average7 lh --C >> fsgd_and_contrast_files/BwGroupError5.mat --sim mc-full 5000 2 >> BwGroupError5_ASvfix_8s_lhMCSIM2 --fwhm 13.488420 | tee -a >> logs/glmfit_lh_MCSIM2.log >> mri_surfcluster --src >> lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh --csd >> BwGroupError5_ASvfix_8s_lhMCSIM1-BwGroupError5.csd --csd >> BwGroupError5_ASvfix_8s_lhMCSIM2-BwGroupError5.csd --sum >> lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM.sum >> --ocp >> lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM.mgh >> --thmax infinity | tee -a >> logs/surfcluster_lh_BwGroupError5_AsvFix_mcsim.log >> # rh >> 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 5000 2 >> BwGroupError5_ASvfix_8s_rhMCSIM1 --fwhm 13.488420 | tee -a >> logs/glmfit_rh_MCSIM1.log >> 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 5000 2 >> BwGroupError5_ASvfix_8s_rhMCSIM2 --fwhm 13.488420 | tee -a >> logs/glmfit_rh_MCSIM2.log >> mri_surfcluster --src >> rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh --csd >> BwGroupError5_ASvfix_8s_rhMCSIM1-BwGroupError5.csd --csd >> BwGroupError5_ASvfix_8s_rhMCSIM2-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 | tee -a >> logs/surfcluster_rh_BwGroupError5_AsvFix_mcsim.log >> >> # getting the correct map to display >> >> # ( not yet done ) >> # >> # here is Frida's example >> # >> # mri_surfcluster --src >> lh.ASevASc_6s_BwGroup3b.fsfast.glmdir/BwGroupError3b_NvSZ_contrast/sig.mgh >> --o >> lh.ASevASc_6s_BwGroup3b.fsfast.glmdir/BwGroupError3b_NvSZ_contrast/sig.clusterMCSIM_o.mgh >> --hemi lh --srcsubj average7 --thmin 1.3 >> # mri_surfcluster --src >> lh.ASevASc_6s_BwGroup3b.fsfast.glmdir/BwGroupError3b_NvSZ_contrast/sig.mgh >> --csd BwGroup3b_ASevASc_6s_lh_MCSIM1-BwGroupError3b_NvSZ_contrast.csd >> --csd BwGroup3b_ASevASc_6s_lh_MCSIM2-BwGroupError3b_NvSZ_contrast.csd >> --thmax infinity --cwsig >> lh.ASevASc_6s_BwGroup3b.fsfast.glmdir/BwGroupError3b_NvSZ_contrast/sig.clusterMCSIM_cwsig.mgh >> >> # mri_mask -T 1.3 >> lh.ASevASc_6s_BwGroup3b.fsfast.glmdir/BwGroupError3b_NvSZ_contrast/sig.clusterMCSIM_o.mgh >> lh.ASevASc_6s_BwGroup3b.fsfast.glmdir/BwGroupError3b_NvSZ_contrast/sig.clusterMCSIM_cwsig.mgh >> lh.ASevASc_6s_BwGroup3b.fsfast.glmdir/BwGroupError3b_NvSZ_contrast/sig.clusterMCSIM_ocwsig.mgh >> >> -- >> >> 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 >> >> >> >> > > > -- 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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another mri_vol2surf question
by Morgan Hough 05 Jul '07

05 Jul '07

Hi there, Hopefully a quick question. I was wondering what the del represents in the mri_vol2surf option --projfrac-avg? --projfrac-avg min max del If I use 0 and 1 for min and max, what should del be to average across all the voxels between the two surfaces? Thanks in advance. Cheers, -Morgan

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data conversion
by Chuan.Chih.Yang＠rwth-aachen.de 05 Jul '07

05 Jul '07

Dear list, I have a question about dicom sorting and the coversion to nifti. That is, I used Osirix to sort dicom images into separate runs, and then use mri_convert to convert them from dicom to nifti, which works well for anatomical scans, but not for the functional ones. I have no clue what is lost in the funcitonal runs after sorting with Osirix. So I tried with Dimon (afni) to sort, and 3DAFNItoNIFTI to convert, but the problem is, the functional and anatomical runs are all in the same folder,and Dimon seems to be a bit problematic with this,(Dimon searches for images that all have the same volume definitions,and since in one folder there are many different z-offset images) Any suggestions will be helpful. cheers, Jackie

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retinotopy question
by Lars Kuchinke 04 Jul '07

04 Jul '07

Hi all, I used a retinotopy paradigm with two horizontal and vertical wedges located at the meridians (flickering at 8Hz, switching every 20 seconds) do you think that this paradigm does fit into fsfastretinotopy analysis? I'm not sure if it makes a difference compared to rotating edges... Any suggestions? Thanks, Lars -- Lars Kuchinke, PhD Freie Universität Berlin Allgemeine Psychologie Habelschwerdter Allee 45 14195 Berlin kuchinke(a)zedat.fu-berlin.de www.fu-berlin.de/allgpsy Tel: 030 838 55776

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Error making a surface
by Richard Frye 03 Jul '07

03 Jul '07

When I have tried to create a surface from a specific subject, freesurfer recon-all existed with ERRORS (log file attached) The first run suggested the use of wsatlas. Even with this, the watershed algorithm did not think the segmentation was correct. I have had others try to process this data on a Mac, but it appears to hang the computer. The T1 surfaces look ok -- 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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