Freesurfer

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30080 discussions

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.

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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

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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

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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

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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

1 0

optseq psdwin
by Linh Dang 24 Oct '08

24 Oct '08

Hi, I have 2 questions. 1) How do I calculate psd min, max, and dpsd. Is there a formula for calculating these values? I have 4 kinds of stimuli, stim duration = 3s, stim repetition = 25, TR =2 so: optseq2 --ntp 180 --tr 2 --psdwin [?] --ev A 3 25 --ev B 3 25 --ev C 3 25 --ev D 3 25 --o 4types --tsearch 10 --nkeep 4 What should my psd min, max, and dpsd be? 2) My task is history-dependent. I would like to control the probabilities that stimulus B follows A, C follows A, A follows D... Is there a way for me to do that with optseq? Thank you so much for your help. Cheers, Linh

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Re: [Freesurfer] convert multiple Analyze to single 4D nifti
by Kara Dyckman 24 Oct '08

24 Oct '08

I'm not sure. When I just tried it, it converted to .nii.gz. Maybe it has to do with the version of fsl being used? I'm posting this to the freesurfer listserv to see if anyone else has ideas. Xu Cui wrote: > Thanks Kara. I tried fslmerge on my images and the result is a single > .img / .hdr pair, not a nii or nii.gz file. Do you have any clue? > The reason to convert to nii is that fsfast seems to require nii file. > > Thanks, > Xu > > On Thu, Oct 23, 2008 at 2:20 PM, Kara Dyckman > <kara(a)nmr.mgh.harvard.edu <mailto:kara@nmr.mgh.harvard.edu>> wrote: > > If I remember correctly, you can use the fslmerge command to merge > all the .hdr files into one nifti file. > > Try this in the directory where your analyze files are: > fslmerge -t outputname *.hdr > > outputname is whatever you want to call your new nifti file > > The result will be outputname.nii.gz > > Hope that helps! > Kara > > > Xu Cui wrote: > > Does anybody know how to convert a series of Analyze files > into a single nii file? Each analyze file is a single 3D > volume at a time point; the nii file would be 4d. > > Thanks, > Xu > > -- > ---------------------------------------------------------------- > Xu Cui > Department of Psychiatry and Behavioral Sciences > Stanford University > ---------------------------------------------------------------- > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > Kara A. Dyckman, Ph.D. > Postdoctoral Fellow, Manoach Lab > Psychiatric Neuroimaging > Massachusetts General Hospital > Charlestown Navy Yard > 149 13th St. > Charlestown, MA 02129 > email: kara(a)nmr.mgh.harvard.edu <mailto:kara@nmr.mgh.harvard.edu> > phone: 617-724-4604 > fax: 617-726-4078 > > http://nmr.mgh.harvard.edu/manoachlab > > > > > -- > ---------------------------------------------------------------- > Xu Cui > Department of Psychiatry and Behavioral Sciences > Stanford University > ---------------------------------------------------------------- -- Kara A. Dyckman, Ph.D. Postdoctoral Fellow, Manoach Lab Psychiatric Neuroimaging Massachusetts General Hospital Charlestown Navy Yard 149 13th St. Charlestown, MA 02129 email: kara(a)nmr.mgh.harvard.edu phone: 617-724-4604 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

3 2

deflate compression support
by lan lin 24 Oct '08

24 Oct '08

I'm trying to make a monkey template using mris_make_template. So far, every time I run the mris_make_template, I get this error: monkey.tif: Deflate compression support is not configured. TiffWrite: TIFFWriteScanline returned error

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subcortical masks
by Martin Ystad 24 Oct '08

24 Oct '08

Hi, I'd like to create binary masks in the nifti-format from each of the subcortical segmentations in freesurfer, separately (one for hippocampus, one for thalamus, and so forth..). Is there any way to do this automatically from the command line? Thanks, Martin Ystad Ph.D. candidate, University of Bergen

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