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freesurfer@nmr.mgh.harvard.edu

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30076 discussions

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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Question about strange tkmedit behavior
by Camilo Lamus 03 Jul '07

03 Jul '07

Hi Freesurfer help, I am currently going through the workflow following the recommended reconstruction for 4 of my new subjects. I used recon-all scripts fo the stages 1 and 2. Now I am checking if the surfaces are correct with tkmedit. I have found a strange behavior with this viewer. When I run: tkmedit 010748_8 wm.mgz rh.white -aux brainmask.mgz -aux-surface lh.white, It then show the coronal slice 128 and some surfaces are badly position (see attached image bad_slice_128.tif) with zigzag like surfaces. The funny part is that I then surf through the volume, and some images are bad and some a perfect. Then I go back to the coronal slice 128 (see attached image good_slice_128.tif), and the surfaces are then perfect. And after that all the surfaces in the volume are position correctly. He is the summary of my error report: Machine: lacolombiana (in the martinos center) version: source /usr/local/freesurfer/nmr-std-env SUBJECT_DIR /autofs/space/rao_001/users/patrickp/propofol/ which tkmedit: /usr/local/freesurfer/stable/bin//tkmedit Current working directory: /autofs/space/rao_001/users/patrickp/propofol/010748_8 Subject: 010748_8 This same thing happen with my other 3 subjects: 010748_10, 010748_11, 010748_112. Then I run tkmedit in machine rao, and the funny behavior disappeared. Is there anything that you guys can think of that I must modify in my machine to fix this? Thanks, --Camilo ----- End forwarded message -----

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cluster-based threshold on ROI-constrained surface data
by Robert Levy 03 Jul '07

03 Jul '07

Hi, I know that mri_glmfit and mri_surfcluster can be used to threshold activity on the surface using a monte carlo simulation, but I was wondering if it is possible to do this on data that has been constrained by an anatomical label. I think this could be described as the Monte Carlo analog of tksurfer's FDR "marked label only" option. The documentation lists 3 steps for the more general case: 1. Estimation: run the analysis on your data without simulation. Note: at this point you can view your results with FDR thresholding in tksurfer. FDR is often conservative relative to cluster-based thresholding. 2. Simulation: run the simulator with the same parameters as the estimation to get the Cluster Simulation Data (CSD). 3. Clustering: run mri_surfcluster, passing it the CSD from the simulator and the output of the estimation. These programs will print out clusters along with their p-values. Where in this flow, and how, could func2roi be used to limit everything to activity taking place in an ROI? I have a guess, but I think it is at best overcomplicated and worst not possible to do (this way). 1. Run mkcontrast and stxgrinder to generate the significance maps for the contrasts, given the list of subjects. 2. Using mris_preproc, resample the data onto average7 This generates mgh files. 3. Run func2roi to constrain the contrasts, for subject average7, using the ROI labels. I'm not so sure about this step. Can this input be specified to func2roi? Is it possible to do this? The output side of this step is a little more clear than the input. One of the ouputs of func2roi are bfloat files. bfloat: "This is where the hemodynamic averages (as computed by selxavg-sess) averaged within the ROI are stored." 4. Using mri_surf2surf, convert the bfloat files to mgh files. 5. Create a group descriptor file to compare between groups. Is this done manually, or using a specific program? 6. Run mri_glmfit on the mgh files to estimate at a predefined significance level. 7. Run mri_glmfit again on the same files to simulate random null hypothesis data. 8. Run mri_surfcluster to generate clusters at a p-value based on a monte carlo algorithm using the null data vs. 'real' hypothesis data. Thanks in advance, Rob -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2611 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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mkcontrast-sess "ERROR: Flag 1 unrecognized."
by Robert Levy 03 Jul '07

03 Jul '07

Hi, I'm having problems running mkcontrast-sess. More information is shown further down, but the command I ran was: mkcontrast-sess -analysis EMerror -contrast AScvfix_6 -a 2 -c 0 -setwdelay 0 0 0 0 0 0 1 0 0 0 0 0 The error was "ERROR: Flag 1 unrecognized." This is the same syntax I have used before, but it doesn't seem to work. Was there a change in mkcontrast's flags? Something else I don't realize I'm doing wrong? Thanks, Rob [levy@vantz ~]$ cd $SUBJECTS_DIR/ [levy@vantz SUBJECTS_DIR]$ pwd /space/ventzl/1/users/SUBJECTS_DIR [levy@vantz SUBJECTS_DIR]$ use_dev -------- freesurfer-Linux-centos4_x86_64-dev-20070703 -------- 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) echo "0 0 0 0 0 0 1 0 0 0 0 0" | mkcontrast-sess -analysis EMerror -contrast AScvfix_6 -a 2 -c 0 -setwdelay INFO: Found 12 Delays INFO: Found 4 Non-Null Conditions Condition Weights: 0 1.00000000000000000000 0 0 ################################### ### Enter 12 Delay Weights (Return) mkcontrast -anadir EMerror -wcond 0 1.00000000000000000000 0 0 -sumconds -o EMerror/AScvfix_6 1 -wdelay 0 0 0 0 0 0 1 0 0 0 0 0 -setwdelay $Id: mkcontrast,v 1.7 2007/06/13 01:02:48 greve Exp $ ERROR: Flag 1 unrecognized. -anadir EMerror -wcond 0 1.00000000000000000000 0 0 -sumconds -o EMerror/AScvfix_6 1 -wdelay 0 0 0 0 0 0 1 0 0 0 0 0 -setwdelay ERROR running mkcontrast mkcontrast -anadir EMerror -wcond 0 1.00000000000000000000 0 0 -sumconds -o EMerror/AScvfix_6 1 -wdelay 0 0 0 0 0 0 1 0 0 0 0 0 -setwdelay Tue Jul 3 13:22:50 EDT 2007 [vantz:SUBJECTS_DIR] (nmr-dev-env) -- 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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general FreeSurfer GUI question
by Boris Epstein 03 Jul '07

03 Jul '07

Hello everyone, I am just wondering if there is a "central" GUI to the FreeSurfer - some sort of a control utility like one finds in many applications, a utility from which all other functions are called. Thanks. Boris.

2 1

error in WM segmentation?
by Burmicz, Ryszarda 02 Jul '07

02 Jul '07

Hello there, I am testing out various standard SPGR protocols and am having trouble with one in particular in that FS fails to recognise the GM/WM boundary accurately. I have attached some screen dumps of brainmask.mgz, T1.mgz and WM.mgz. The image on the left is much better than the one on the right (although it still requires some correcting, but I have just used it for comparison) - the one on the right has most of the GM classified as WM in fact. Is there some way of adjusting input parameters so as to get around this or do I need to manually edit the WM.mgz? I am getting to grips with the program and am still a little hazy on the background. Thanks, Rysia

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