Re: [Freesurfer] mri_surfcluster CWP values

Yep. That would explain it. Thanks! - Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota Doug Greve wrote: The values in the mgh file should be -log10(abs(CWP)). Would that explain the discrepancy? James N Porter wrote: Hello-

[Freesurfer] qdec regression coeffs

Hello All- When viewing the scalar overlays in qdec, how do I tell which coefficient is being displayed when I select "Regression Coefficients" from the menu? Having more than one regressor, I would expect more than one overlay of coefficients. Am I missing something very elementary? -- ---

[Freesurfer] mri_surfcluster CWP values

Hello- When I look at the CWP results of mri_surfcluster in the sig.cluster.sum versus the resultant sig.cluster.mgh, the results are different. Specifically, all clusters negatively correlated with my independent variable display a value in tksurfer of -1+CWP, and clusters that are positivel

[Freesurfer] Re: qdec error...

Hi Nick- I've run into the same problem recently and am looking at piping my FreeSurfer data out to another stats program. There is all sorts of info on the list about sending FS data out to Matlab, but are there any tips for getting it into a format that SPM will agree with? My other option is t

[Freesurfer] qdec vertex selection

Howdy- I am working in qdec and having a problem selecting vertices. I can move the cross-hairs by entering a vertex number in the "Jump to vertex number" box, but I can't actually just click on the brain to get the vertex where I want it. Also, the ctrl-click function to pull up the scatterp

Re: [Freesurfer] Problem make_average_subject

Sorry to say but, just like for Juergen, the same error pops up for make_average_volume when run by itself or within the new make_average_subject scripts. - Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota James N. Porter w

Re: [Freesurfer] Problem make_average_subject

7;ve put new versions of make_average_subject  make_average_surface  make_average_volume here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve Copy them into $FREESURFER_HOME/bin (make backups:), and give it a try. doug James N. Porter wrote:

Re: [Freesurfer] Problem make_average_subject

.mgh.harvard.edu/transfer/outgoing/flat/greve Copy them into $FREESURFER_HOME/bin (make backups:), and give it a try. doug James N. Porter wrote:  So, I believe I have isolated the problem. The failure happens during the mri_concat phase of make_average_volumes

Re: [Freesurfer] Problem make_average_subject

at I can modify that would allow the programs to reach out and use the swap space? Thanks, Jim - Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota James N. Porter wrote: Juergen--Have you had successful resolution to this problem?

Re: Re: [Freesurfer] Problem make_average_subject

Juergen--Have you had successful resolution to this problem? Nick--I'm attempting to average 175 subjects, but make_average_volume returns the same error as Juergen reports.     > Allocing output     > MRIalloc(256,256,256): could not allocate 262144 bytes for 15547th slice I'm running frees

Re: [Freesurfer] Surfaces, asegs, aparcs, Subcortical Structures

ick On Mon, 2007-12-10 at 13:32 -0600, James N. Porter wrote: Hello Bruce- From the wiki, I gather that I would rerun recon-all from -finalsurfs onward, as that is the step that calls make_final_surfaces. In order to insert the fix_mtl flag I'll have to run that section via a sepa

Re: [Freesurfer] Surfaces, asegs, aparcs, Subcortical Structures

he surfaces instead of the aseg, as we find it to be more accurate than the voxel-based techniques. cheers, Bruce On Tue, 27 Nov 2007, James N. Porter wrote: Hello FreeSurfer Folks- I've seen several threads in the archives discussing the expected inaccuracies in the pial, white, a

Re: [Freesurfer] Re: qdec Table Loading Error

(subject) will not be found. I will try to improve the qdec code to automatically handle files like this (ie 'Mac' text files). Nick On Tue, 2007-12-04 at 22:10 -0600, James N. Porter wrote: Actually, scratch that. I had a hunch that I should change my header from "subj&

[Freesurfer] Re: qdec Table Loading Error

& Psychopathology Research University of Minnesota James N. Porter wrote: Hello- I'm getting a rather nondescript message of "Error loading the data table" when I try to load my qdec.table.dat into the qdec GUI. I've tried using Excel, OpenOffice Calc, OpenOffice Wordp

[Freesurfer] qdec Table Loading Error

Hello- I'm getting a rather nondescript message of "Error loading the data table" when I try to load my qdec.table.dat into the qdec GUI. I've tried using Excel, OpenOffice Calc, OpenOffice Wordprocessor, and Kate to save my table as a tab-delimited text file. Nothing works. Any suggestions o

[Freesurfer] Surfaces, asegs, aparcs, Subcortical Structures

Hello FreeSurfer Folks- I've seen several threads in the archives discussing the expected inaccuracies in the pial, white, and orig surfaces running through subcortical structures. However, I've been unable to ascertain exactly how much and what kind of inaccuracy is acceptable. It makes sense

[Freesurfer] Segmentation Probability Values

Hello FreeSurfers- At any point in the recon-all processing stream does a voxel by voxel map of segmentation probability values get generated? If not, are that at all obtainable through post-processing methods? -- Jim Porter Graduate Student Clinical Science & Psychopathology Research Univers

[Freesurfer] Skull Stripping Corrections

Hello- I've been working through the Skull Stripping checking/corrections tutorial and have a question. So far, I have found no problems akin to the tutorial, where skull is left behind or brain parts are missing. However, I do see remnants of eyeballs/eye sockets, arteries, and dura/pia/meni

Re: [Freesurfer] Turn Off Verbose Output

Doug- It's not really a 'problem' per se, I'm just writing analysis scripts and I only want my terminal to display things that I write, like "Registering subject X" instead of flying through the ras-to-vox tables and such. It's just a visual aesthetic display issue for me. The cat advice wor