Freesurfer June 2007

freesurfer@nmr.mgh.harvard.edu

59 participants
82 discussions

Matlab and Freesurfer
by Robert Baldwin 09 Mar '08

09 Mar '08

Hello- I am new to Freesurfer and Matlab. I have Matlab 7.4.0 installed on an Intel Mac. I just installed Freesurfer. Now when I start Matlab I get the following warnings: Warning: Name is nonexistent or not a directory: /matlab. In path at 110 In startup at 4 In matlabrc at 255 Warning: Name is non existent or not a directory: /toolbox. In path at 110 In startup at 11 In Matlabrc at 255 I have tried adding the freesurfer folder to these files to the path for matlab, but the error still occurs. Any suggestions on how to get this error to quit? Thanks! -Robert

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measurement of cortical thickness
by T. Song 01 Aug '07

01 Aug '07

Hi All: I am trying to measure the cortical thickness of specific ROI. I got a ROI, and are able to save it to a label file. Should I use mris_thickness to measure the thickness? If so, how do I get the thickness file, using mri_label2vol? Thanks in advance! Tao

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calculation of total cortical gray matter volume
by Michael Harms 24 Jul '07

24 Jul '07

Hello FS-list, Could you please confirm the recommended current approach for calculating the total cortical gray matter volume. Based on the following Wiki page http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats? action=highlight&value=mris_volume I presume that the recommended calculation (illustrated using tcsh syntax) is: @ total_cort_gm_vol = `mris_volume ?h.pial` - `mris_volume ?h.white` My only hesitation is that I noticed the resulting value doesn't quite match the value of "total gray matter volume" that is output by mris_anatomical_stats. Is this because mris_anatomical_stats uses a older approach that is no longer considered quite as accurate? thanks, Mike Harms

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Segmentation
by Gallo, Antonio (NIH/NINDS) [F] 19 Jul '07

19 Jul '07

Hi All, Upon reviewing subortical segmentations I see that often a mismatch exists between what appears on the wm.mgz and the color-coded segmented maps. Precisely - as an example - in the attached figure you can see that in the case of left insula WM, part of the tissue was classified as GM (in brown) in the color-coded segmented map and as WM in the wm.mgz. Contrariwise, the right temporal-parietal GM cortex part of the tissue is classified as WM (in green) the color-coded segmented map and as non-WM in the wm.mgz. The latter occurs in many regions of the brain without a clear anatomical pattern. I was wondering if this is just a display issue or it rather reflects some mismatch in actual tissue classification with consequential errors in the generated values of thickness and volumes as well? If so, is there any way I can correct for this? Thank you in advance, 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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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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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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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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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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Freesurfer June 2007