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30084 discussions

Group Thickness Maps/Looking at outputs from mri_preproc
by Bramen, Jennifer E. 28 Oct '08

28 Oct '08

Dear Freesurfer List I want to look at the average thickness maps for each of my groups, not just the statistical maps displayed by qdec. I think I found a tool that can do this. I used mri_preproc and a list of subjects instead of a single subject, and now have the output. I do not know to view this output though (<group descriptor>_thickness_fsavg.mgh). Can someone explain what this output is and how I can use it? The other alternative is make_average_surface for each of my groups. Is that what I need to be doing? It takes a ong time to run, so I was hoping there was another way to go. Thank you Best regards, Jennifer Bramen, Ph.D. Postdoc David Geffen School of Medicine at UCLA Developmental Cognitive Neuroimaging 635 Charles Young Drive South Los Angeles, CA 90095-7332 Phone: (310)267-5116 Fax: (310)206-5518 Email: jbramen(a)mednet.ucla.edu Campus Mail Code 176919 IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

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FI and sulc -- how are they related?
by Rudolph Pienaar 28 Oct '08

28 Oct '08

> Dear Rudolph Pienaar, > could you please tell me if the Folding index and the sulc are in a way > correlated? > thank you Hi David - This question does not really have a simple yes or no answer, mostly because each measures different features. These features are both derived from the topology of the surface, but are not directly related. The 'sulc' measurement is the distance that a specific vertex is away from a hypothetical "mid-surface" that exists between the gyri and the sulci. This surface is chosen so that the "mean" of all the displacements is zero. The 'sulc' gives a indication then of linear *distance* and displacements: how "deep" and how "high" are the folds, but doesn't say much about how "sharply" folded they are, or in what manner are they folded (like cylinders, like spheres, etc). The FI is a *curvature* (not distance) measure. It uses the k1 and k2 principal curvatures at each vertex to calculate a value according to (per Van Essen/Drury 1997): FI_i = fabs(k1) * (fabs(k1) - fabs(k2)); Conceptually the FI tries to give a measure of how (relatively) tightly or sharply folded a gyrus is in a cylindrical sense. The more cylindrical a gyrus is, the more the FI increases along its length. For regions with spherical or saddle folding, k1 = k2 and the FI is zero. So it tells us more about how much like cylinders the folds are, but tell us nothing about how "deep" the folds extend. Essentially, the 'sulc' and the FI are related of course by the topology of the surface but they each measure conceptually different things. It is not possible to determine 'sulc' from the FI or vice versa. -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

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qdec patch
by Juranek, Jenifer 28 Oct '08

28 Oct '08

Nick, Just in case you're taking a head count, I would benefit from a patch for qdec which reads ?h.pial_lgi files as mentioned in response to Martin's posting yesterday. Cheers, Jenifer

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(no subject)
by david felps 28 Oct '08

28 Oct '08

Dear Rudolph Pienaar, could you please tell me if the Folding index and the sulc are in a way correlated? thank you _________________________________________________________________ Hotmail to go! Hol' Dir Hotmail aufs Handy! http://windowslivemobile.msn.com/BrowserServiceHotmail.aspx?lang=de-de

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cortical thickness
by Al-Radaideh Ali 28 Oct '08

28 Oct '08

Dear FreeSurfer Experts, I was trying to run freesurfer on one of my MPRAGEs that was acquired on 7T scanner with isotropic resolution of 0.5mm. I have got two different errors below. Could you please suggest something for me? ************************************************************************ > > #@# Talairach Failure Detection Tue Sep 9 16:02:41 BST 2008 > > /data_local/ali/freesurfer/subjects/MPRAGE/MS_PC/mri > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0090, pval=0.0000 < threshold=0.0050) > > Linux morgana 2.6.11.4-21.11-smp #1 SMP Thu Feb 2 20:54:26 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux > > recon-all exited with ERRORS at Tue Oct 10 16:12:41 BST 2008 *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=208 y=168 z=180 r=51 first estimation of the main basin volume: 562273 voxels mean intensity too low ! Modification of the image: intensity*0.50 first estimation of the COG coord: x=208 y=168 z=179 r=51 first estimation of the main basin volume: 559292 voxels mean intensity too low ! Modification of the image: intensity*3.72 first estimation of the COG coord: x=208 y=168 z=180 r=51 first estimation of the main basin volume: 569632 voxels mri_watershed Error: Interpolation problem in the white matter curve analysis Linux morgana 2.6.11.4-21.11-smp #1 SMP Thu Feb 2 20:54:26 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Oct 14 18:44:05 BST 2008 Many thanks in advance Ali This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

3 2

Making Binary Masks
by James Porter 27 Oct '08

27 Oct '08

Hello- Can somebody point me towards the best way to make a thresholded binary mask out of a sig.mgh file that comes out of qdec/mri_glmfit? I'd like to take the sig.mgh file and use all values above threshold as a mask for another mri_glmfit analysis. I'm used to functional data in FSL, and could do this lickety-split with fslmaths or fslroi. Does FreeSurfer have a similar set of utilities to be used in manipulating .mgh files? I've tried to run thresholding within tksurfer, then "Save Overlay As" but that doesn't cut off the sub-threshold values. I'm sure I could draw on the surface to trace my supra-threshold areas and create a mask that way, but I'd prefer to just do it mathematically if possible. Thanks! -- --------- Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota

1 0

Qdec questions
by Martin Kavec 27 Oct '08

27 Oct '08

Hello all, I have started with a group analysis using qdec and have some questions: 1. loading fsaverage into tkmedit along with rh.white and lh.white surprised me that the pial surfaces do not run under the skull, as I see it on a single subject but copy the white matter. It is also correct, but it looks a bit odd. I suppose that this is a result of averaged out WM, but my concern is whether it can anyhow affect the analysis 2. I am interested in group analysis of LGI. I do not see however ?h.pial_lgi in fsaverage. Also when I run qdec, lgi is not among the parameters available for testing. I could backup say the thickness files and than rename my lgi results as thickness, but if there is a more straightforward solution I would like to avoid this trouble 3. Since lgi is for each vertex calculated over a certain diameter, thus has inherent smoothing. Therefore I would tend to use 0 smoothing in GLM. What do you think about this idea? Thanks, Martin

2 2

Qdec, group analysis, and p-values
by Judith Segall 27 Oct '08

27 Oct '08

Hi all. I have a few group analysis questions: 1. After running QDEC I find several significant regions that have a p-value associated with them. (This is obtained by clicking on the most significant vertex) However, if I change the threshold from the default to 1.3, 2, 3, to show all vertices with p<.05 then the p-value associated with the significant regions stays this same as it was during the default display. The threshold bar appears to only have affect on the visualization not on finding significant regions. So, is there a default p-value that is in qdec to find signicant regions? 2. How would one go about reporting these regions in a manuscript? Would they be called uncorrected at blank with a value of blank? 3. I thought that mri_glmfit, which is what QDEC does, is essentially an F-test. If so, where is the F value? 4. After running a full monte-carlo simulation I have many regions close to 0.99 and therefore are not significant. However, they were significant enough to be generated on the simulation table. How would one go about reporting these clusters in a manuscript? 5. Are the CWP values, from the simulations, p-values? Any help or input from anyone would be greatly appreciated. Thanks, Judith

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prenatal - cortical thickness
by asaf achiron 27 Oct '08

27 Oct '08

dear support , we are currently interesting in measuring cortical thickness and voulume in prenatals. do you think it can be done in freesurfer? thank you Asaf

2 1

automating tkmedit
by Jared Price 25 Oct '08

25 Oct '08

Hi everybody, I had a quick question I was hoping someone could help me out with. I am trying to automate a few aspects of tkmedit but am running into some trouble in creating a shell script that can control it. Under normal circumstances, for example, the first line would be something like #!/bin/tcsh to tell the program to interpret commands through tcsh. However, I can't seem to get my scripts to recognize free surfer commands. For example if I have a line in the script like LoadSegmentationVolume volume:0 .... I get an error telling me that the command is not recognized. Does anyone know how to get scripts to correctly interpret tkmedit commands? Sorry if this is a novice question but I am just getting my feet wet in the whole scripting business. Thanks -Jared

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