Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

help
by whblqh＠mail.ustc.edu.cn 07 Aug '07

07 Aug '07

Hello, I setup FC6 system, and download freesurfer-Linux-centos4-stable-pub-v3.0.4-full.tar.gz. Now FS is installed on my computer, tkmedit work successfully. however, tksurfer work abnormally, its interface cann't display.I think it may be problem of nvidia driver . curr ently I cann' t find tksurfer related to FC6,would you like help me? Wang Hai-bao

1 0

dev version of mri_glmfit for intel macs
by Catherine Hartley 06 Aug '07

06 Aug '07

Hi, I'm getting a bus error when I run mri_glmfit on my Intel Mac. When I had this problem before, I got a development version of mri_glmfit which solved the problem. Unfortunately I've reinstalled a newer version of Freesurfer since then and overwrote that binary file and it's no longer on the public distribution server. If someone could repost the latest version of mri_glmfit for Intel Macs (10.4.9), that would be great. The same problem is described here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg04632.html Thanks, Cate

2 1

determining sizes of clusters at given CWP cutoff
by Robert Levy 06 Aug '07

06 Aug '07

Hi, I was trying to figure out if there is any way to determine the exact size at which clusters becomes significant given a specified significance, and it appeared from the mc-corrected overlay that in this overlay the clusters do not continously change in size but appear discretely at a given threshold and are the same size at higher thresholds in an all-or-nother sort of way. I take this to mean that because the monte carlo simulation was performed at a given threshold, the clusters at that threshold size are corrected for mutiple comparisons based on the probability distribution of the chance data (though I don't know the details). Because it is done in this way, it seems I would either have to run several monte carlo simulations, at successively higher minimum thresholds, in order to arrive at the critical cutoff sizes for significance. This is impractical, so I guess my question is, does the way in which the monte carlo simulations are done preclude the possibility of getting the cluster sizes at which they will have a certain CWP value, or is there some way of doing this? Thanks, 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

2 1

Thickness standard deviation map
by Burmicz, Ryszarda 06 Aug '07

06 Aug '07

Hi Freesurfers, I have tried looking this up on the list, but I don't understand exactly what to do in this scenario: I have a group of subjects (all controls). I want to create a surface map of the standard deviations of the thickness values (i.e. to show how the thicknesses vary across subjects). I am not sure what is the easiest way to go about this - can I: 1) simply convert the ?h.thickness files to .asc and calculate the deviations at each vertex (I am under the impression that this is not correct as they need to be registered to a common surface first), then convert back to .thickness and load into tksurfer 2) use mris_preproc then mris_glmfit? I don't necessarily want to calculate any stats, but I wouldn't mind a pretty picture :) If I have 4 groups of 10 subjects each, so if I churn these all through glm_fit will I be able to access separate thickness files for each group? And how can I map standard deviations for each group in this scenario? Many thanks, Rysia

2 1

editing labels
by Sarah J Greene 06 Aug '07

06 Aug '07

Hi all, I just wanted to ask about editing labels in tksurfer. I have converted my annot files to labels using mri_annotation2label, and now have all of the labels in the label directory. However when I edit the labels, and then save them using save selected label (highlighting the label and choosing the correct label in the correct hemisphere), nothing is saved when I pull up the image again. I have tried to convert the labels to annot files using mris_label2annot, but this isn't working either. I'm not sure what I am doing incorrectly. Thanks, sarah

2 1

mris_anatomical_stats question
by Morgan Hough 06 Aug '07

06 Aug '07

I am reporting thickness values from subjects native space constrained by mask labels using mris_anatomical_stats. I am currently getting the average of the unsmoothed estimates. I would like to be able to get smoothed values but the usage reports the smoothing option as -nsmooth <#> where the # is the # of smoothing iterations. If we are using 10mm FWHM smoothing for the group results can I estimate the number of smoothing iterations to obtain something equivalent? Would it be easier to use mri_surf2surf and create a smoothed thickness file for each subject? Thanks again. Cheers, -Morgan

1 0

Banks of the superior temporal sulcus question
by Morgan Hough 06 Aug '07

06 Aug '07

I was just wondering why the banks of the superior temporal sulcus was made into its own label on the Desikan template. Does this correspond (roughly) to a particular functional area. I didn't see anything in the paper about why it was chosen. Is it just easy to define given sulcal/gyral boundaries? Thanks in advance. Cheers, -Morgan

2 3

possible bug found in mri_surfcluster
by Robert Levy 06 Aug '07

06 Aug '07

Hello, I found a possible bug in mri_surfcluster, but it may be linked specifically to average7 and no other srcsubjects (but I haven't checked that). When I run mri_surfcluster with cluster simulation data, the size is reported at a seemingly arbitrary number, based on the fact that the #of vertices does not change. And the mgh output in null (a blank surface is displayed). However when I run mri_surfcluster with cluster simulation data, but specify srcsubject, it works correctly. This seems like a bug, because I think when surfcluster runs csd files it reads the srcsubject from the csd files, and no other srcsubject should be compatible with the data, therefore it must know the srcsubject in both usages, but in one case it works and the other it doesn't. Thanks, Rob * surflcluster with threshold of 1.3* # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs 1 -2.217 145639 *413.11* -6.4 38.4 5.0 *418* 2 -1.836 29811 141.08 -11.9 53.2 19.0 178 3 -1.532 16680 111.99 -11.1 19.1 22.6 178 4 -1.400 83520 17.42 -3.2 11.4 17.5 23 *surfcluster using csd files* # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs 1 -2.217 145639 *275.40* -6.4 38.4 5.0 0.01190 0.01050 0.01330 *418* 2 -1.836 29811 94.06 -11.9 53.2 19.0 0.50970 0.50330 0.51610 178 3 -1.532 16680 74.66 -11.1 19.1 22.6 0.64580 0.63970 0.65190 178 4 -1.400 83520 11.61 -3.2 11.4 17.5 0.97920 0.97740 0.98100 23 *Apparently this is the right way to do it: with csd files, but specify srcsubj average7:* # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs 1 -2.217 145639 *413.11* -6.4 38.4 5.0 0.00010 0.00000 0.00020 *418* 2 -1.836 29811 141.08 -11.9 53.2 19.0 0.27000 0.26430 0.27570 178 3 -1.532 16680 111.99 -11.1 19.1 22.6 0.40500 0.39870 0.41130 178 4 -1.400 83520 17.42 -3.2 11.4 17.5 0.96970 0.96750 0.97190 23 ------- freesurfer-Linux-centos4_x86_64-dev-20070802 -------- 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 # PWD: /space/ventzl/1/users/SUBJECTS_DIR mri_surfcluster \ --src lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh \ --csd ASevASc_8s_p05_z_lhMCSIM01-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM02-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM03-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM04-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM05-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM06-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM07-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM08-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM09-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM10-BwGroupError5.csd \ --sum lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_lh.sum \ --ocp lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_lh.mgh \ # overlay shows no clusters (tried at 0.5 as well in case it is a binary map) tksurfer average7 lh inflated -overlay lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_lh.mgh mri_surfcluster \ --really-use-average7 \ --src lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh \ --csd ASevASc_8s_p05_z_lhMCSIM01-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM02-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM03-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM04-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM05-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM06-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM07-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM08-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM09-BwGroupError5.csd \ --csd ASevASc_8s_p05_z_lhMCSIM10-BwGroupError5.csd \ --sum lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_lh.sum \ --ocp lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_lh.mgh \ --srcsubj average7 # overlay does show the clusters tksurfer average7 lh inflated -overlay lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_lh.mgh -- 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

2 1

questions
by Paul Aparicio 06 Aug '07

06 Aug '07

Hello All, I have 2 questions I hope someone can help me with. 1) Is it possible to plot on a surface a set of arbitrary points in the coordinate frame of an anatomical volume? In other words if I have a set of x,y, and z points (not voxel indices: e.g. sub-voxel coordinates) can I plot them onto a surface? 2) Is there a way to view the slice lines in a volume and a surface? Can I see the anatomical location of the boundaries of the functional slices on the surface representation? Thanks paul

3 2

optseq2 question about fixing null intervals
by Denis R 06 Aug '07

06 Aug '07

Hello, We're designing a task that has two pairs of events (4 events total). Each pair of events has a pair of allowable null intervals associated with it. Is it possible to use optseq2 to create such a paradigm? Is it appropriate to use optseq2 in this case at all given these constraints?

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