Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

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.

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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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Re: [Freesurfer] questions on optseq2
by peng 01 Jul '07

01 Jul '07

Thank you for your advice, Daniel. I think you may suggest the latter way I mentioned in your first piece of advice. I have two conditions with equal trials:for target(t),32*2(t15&t25); for standard(s),8*8(s11-14,21-24). Maybe my expression in the first email was not clear enough. I don't care the activation of the individual stimuli within certain conditions. I just need to balance them to make sure "I don't care" is reasonable. Now I am going to use the seqence generated by the first piece of code. But when evaluate it with seqefficiency, I would merge stimuli within conditions together. Then I would run more runs than needed, but not as much as consider the stimuli separately. Then I would be sure the two conditions were well randomized. The stimuli within condition were also reasonablely randomized. I am not sure whether I correctly understand your second piece of advice. But I can't change the ratio because I have to combine the fMRI data with a finished EEG experiment with the same paradigm. On 6/29/07, Daniel G. Wakeman <dwakeman(a)nmr.mgh.harvard.edu> wrote: > Hi Peng, > > I'm sure Doug and others will have very valuable advice, but why not just > keep the number of trials in the two conditions equal and separate out the > individual stimuli in the actual events (dividing to keep the number of > events per condition equal). That way you can keep your power and if you > want to do the other analysis later you can take a look at that. You > could of course, also fiddle with the ratios, so you use 1/2 (bottom most) > the time instead of 1/4. I'm not sure if all of this makes sense, but > according to this I believe the command would look like the one below > (Note! I kept the ratio of trials to null the same as in your examples). > > optseq2 --ntp 160 --tr 2 --psdwin 0 14 --ev s11 2 32 --ev s12 2 32 --ev 21 > 2 8 --ev s22 2 8 --ev s23 2 8 --ev s24 2 8 --ev s25 2 8 --ev s26 2 8 --ev > s27 2 8 --ev s28 2 8 > > optseq2 --ntp 160 --tr 2 --psdwin 0 14 --ev s11 2 16 --ev s12 2 16 --ev 21 > 2 12 --ev s22 2 12 --ev s23 2 12 --ev s24 2 12 --ev s25 2 12 --ev s26 2 12 > --ev s27 2 12 --ev s28 2 12 > > Dan > > > hi list, > > > > I have two conditions, one contain 2 stimuli and the other 8. The > > difference between stimuli within certain condition is vey small, and > > could be omitted in further analysis if they're treated equal. Now I > > have two choice: > > optseq2 --ntp 160 --tr 2 --psdwin 0 14 / > > --ev s11 2 8 --ev s12 2 8 --ev s13 2 8 --ev s14 2 8 / > > --ev t15 2 32 / > > --ev s21 2 8 --ev s22 2 8 --ev s23 2 8 --ev s24 2 8 / > > --ev t25 2 32 / > > --nkeep 6 --o pl1 --nsearch 10000 > > or > > optseq2 --ntp 160 --tr 2 --psdwin 0 14 / > > --ev s 2 64 --ev t 2 64 / > > --nkeep 6 --o pl2 --nsearch 10000 > > Obviously, the first one would need more test runs, which in fact was > > nearly 2 hours for the subjects . And the second one need only 1/4 > > time, but is risky. I am afraid it would induce difference between > > stimuli within condition. > > Do you have any suggestions on it? > > Thanks a lot. > > > > Peng > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > >

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make_average_subject
by Lars M. Rimol 01 Jul '07

01 Jul '07

Hi Bruce, Oh yes, I see that now! And the problem is that FS looks for the FSGDF under SUBJECTS_DIR//space/emc1/3/data/TOP/Analysis_lmr/, but SUBJECTS_DIR and Analysis_lmr are both in the same directory, i.e. /space/emc1/3/data/TOP. I thought that by giving the full path to the FSGDF I had taken care of that: make_average_subject --fsgd /space/emc1/3/data/TOP/Analysis_lmr/TOPtest.fsgdf --out /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest Is there a way around that, or do I have to put the FSGDF inside the SUBJECTS_DIR? The reason I would like to keep them separate is that lab techs are doing scan workups inside the SUBJECTS_DIR, and I don't want to create new directories and files inside there all the time. I guess this is a general question, is it possible to run make_average_subject, mris_preproc and surf2surf and get the FSGDF from a dir that is not a subdirectory of the subjectsdir, and also write the output to that dir? It seems if you give the full path, FS assumes that it should be added to the path of the subjects dir. Thank you! Lars Hi Lars, it looks like no input subjects are defined. Bruce On Wed, 27 Jun 2007, Lars M. Rimol wrote: > Hi, > Trying to run make_average_subject but getting an error message. Any idea > what may be wrong? > > Thank you! > Lars M. Rimol > > > > make_average_surface --fsgd > /space/emc1/3/data/TOP/Analysis_lmr/TOPtest.fsgdf --out > /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest > $Id: make_average_surface,v 1.27.2.2 2006/06/09 15:46:28 nicks Exp $ > Wed Jun 27 18:06:43 PDT 2007 > /space/emc1/3/data/TOP/Analysis_lmr > setenv SUBJECTS_DIR /space/emc1/3/data/TOP/Containers > output sdir is /space/emc1/3/data/TOP/Containers > uid=7266(lmr) gid=7266(lmr) groups=7266(lmr),7450(topproj) > context=user_u:system_r:unconfined_t > ==================== > make_average_surface > ==================== > input subjects: > output subject: /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest > mri_add_xform_to_header -c auto -- yours, LMR

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questions on optseq2
by peng 29 Jun '07

29 Jun '07

hi list, I have two conditions, one contain 2 stimuli and the other 8. The difference between stimuli within certain condition is vey small, and could be omitted in further analysis if they're treated equal. Now I have two choice: optseq2 --ntp 160 --tr 2 --psdwin 0 14 / --ev s11 2 8 --ev s12 2 8 --ev s13 2 8 --ev s14 2 8 / --ev t15 2 32 / --ev s21 2 8 --ev s22 2 8 --ev s23 2 8 --ev s24 2 8 / --ev t25 2 32 / --nkeep 6 --o pl1 --nsearch 10000 or optseq2 --ntp 160 --tr 2 --psdwin 0 14 / --ev s 2 64 --ev t 2 64 / --nkeep 6 --o pl2 --nsearch 10000 Obviously, the first one would need more test runs, which in fact was nearly 2 hours for the subjects . And the second one need only 1/4 time, but is risky. I am afraid it would induce difference between stimuli within condition. Do you have any suggestions on it? Thanks a lot. Peng

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[Freesurfer] 3D volume generation, ROI selection, subvolume analysis
by Greg Soltis 28 Jun '07

28 Jun '07

Good morning, We have been working on Slicer and have been able to read in our stack of images. I can view them at the desired cross-sections by moving the three planes at will. But now we would like to be able to generate a 3D volume (in this case a rectangular prism) that contains all of these images in the stack. Once this is assembled, we are interested in being able to have Slicer/Free Surfer select ROI's or do so ourselves and be able to analyze these subvolumes from within the prism itself. Before I delve to deeply into FreeSurfer, I just wanted to make sure that it was capable of providing these capabilities and that Slicer cannot do them on its own. Are there any resources that I could access to aid me that are not accessible through the main FreeSurfer site: http://surfer.nmr.mgh.hardvard.edu/fswiki ? Could you give me a few quick pointers to get me started? Thanks a lot. Greg _________________________________________________________________ Picture this share your photos and you could win big! http://www.GETREALPhotoContest.com?ocid=TXT_TAGHM&loc=us

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Problems with surface topologies
by jorge luis 28 Jun '07

28 Jun '07

Hello all I have the freesurfer automatic hippocampus segmentation for some subjects. It seems that the segmentation is not bad. I have produced the binary masks (after labels generation in tksurfer)with the following command: mri_label2vol --label label/lefthipoca.label --temp mri/orig.mgz --o lefthipoca.img I have loaded the lefthipoca.img mask in matlab and used the standard matlab isosurface algorithm to triangulate the contours of the binary mask. The problem is that the resulting surface although no topological defects and no boundaries does not have spherical topology (euler number<2). Is it a consequence of imperfections in the freesurfer segmentation? How can I correct it? I have seen that with litter volumetric smoothing of the mask I get surfaces with spherical topology after the triangulation, but the structure volume is remarkable increased after the smoothing. Any tip is welcome In advance Thank you Jorge ____________________________________________________________________________________ ¡Descubre una nueva forma de obtener respuestas a tus preguntas! Entra en Yahoo! Respuestas. http://es.answers.yahoo.com/info/welcome

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