[Freesurfer] RFX using custom registration to common space?

Hello Freesurfers, Is there any way to run random effects analysis using mri_glmfit with registration to MNI152 instead of MNI309? Also, is there a way to use a nonlinear warp instead of an affine transformation (for example by using "applywarp" from FSL) to bring data to a common space for rando

[Freesurfer] extracting segmented images with exact values for GM-WM-VL-CSF

Sorry, that's of course directed to FREESURFER users and developers, and maybe there is a possibility to extract such images cerebellum-stripped? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listin

[Freesurfer] extracting segmented images with exact values for GM-WM-VL-CSF

Dear FSL users and developers, Please, forgive me for such questions - I am asking because I'm really stuck with it... Would you be so kind to explain me how can I extract segmented image with values for GM-WM-VL(ventricular)-CSF of 150-250-50-10? Purpose: preparation for the high-dimensional

[Freesurfer] isxconcat-sess question..

Hi, Is there a way to use" isxconcat-sess" to average monkey fMRI data? i.e. I have two groups of monkeys (say, test and control groups) and I want to do group analysis on their data.. Regards, krishna ___ Freesurfer mailing list Freesurfer@

Re: [Freesurfer] From scanner to freesurfer

Hi Knut, yes, if you point it at one file in each series (with a -i) it will figure out the whole series and load it. If you use multiple -i switches it will load multiple series and motion correct and average them. cheers Bruce On Wed, 23 Mar 2011, Knut J Bjuland wrote: > Hi > > I am now im

[Freesurfer] From scanner to freesurfer

Hi I am now imported my first dicom files into freesurfer. I have followed the protocol as described in the tutorial. I have some questions. Does recon-all -i /path/to/subject's/mprage.dcm -i /second/mprage/if/you/had/one -all -s subj001 import all dicoms if you pint it to hte first i

Re: [Freesurfer] single subject versus a group map in qdec

We have dono something like this in Cortical thickness reduction of normal appearing cortex in patients with polymicrogyria cheers, PPJ

[Freesurfer] BBR References

Again along the same lines, if you've used BBR (bournday-based registration), please send me references. thanks again, doug Douglas N Greve wrote: > Along the same lines, if you have used FSFAST in a paper (task or > retinotopy) please send me your references. > thanks > doug > > > > Martin Reut

[Freesurfer] other interactions

Dear Doug, In the case of a 3x2 design the post hoc contrast for evaluating the interaction effect would be as follows: D1Male D1Female D2Male D2Female D3Male D3Female ANOVA to test the effect of diagnosis (D1, D2, D3) only for males [ 1 0 -1 0 0 0]/2 [ 1 0 0 0 -1 0]/2 ANOVA to t

[Freesurfer] FW: interacciones

Dear Doug, I would like to be sure that I've understood the rules for the following contrast in a 2x2x2 design with diagnosis (D1, D2), gender (Male, Female) and handedness (Left, Right) as discrete factors. D1MaleLeft D1MaleRight D1FemaleLeft D1FemaleRight D2MaleLeft D2MaleRight D2FemaleLeft

[Freesurfer] single subject versus a group map in qdec

Using q dec we have run a single patient versus a group of healthy control subjects (n=20ish) and found significant differences even after FDR correction. Could you describe the process qdec uses to compute these differences? Is it legitimate to report these single subject maps? Practically this i

[Freesurfer] FSFAST References

Along the same lines, if you have used FSFAST in a paper (task or retinotopy) please send me your references. thanks doug Martin Reuter wrote: > Hi everyone, > > we are preparing a list of papers that make use of the unbiased > longitudinal stream in FreeSurfer (in version 4.4 and up). This hel

[Freesurfer] Longitudinal FS References

Hi everyone, we are preparing a list of papers that make use of the unbiased longitudinal stream in FreeSurfer (in version 4.4 and up). This helps us to keep track of impact and application fields (and it helps you to advertise your research on our Wiki :-) Please sent me your references (if possi

Re: [Freesurfer] changing tksurfer window font size...

Hi Gonzalo, I'm not sure you can. Krish might know Bruce On Wed, 23 Mar 2011, Gonzalo Rojas Costa wrote: > Hi: > > How can I change the font size used in the tksurfer dialogs ?... such > as "Configure Overlay Display" dialog ?... Because I changed the font > size in Ubuntu GNOME, but it didn't

Re: [Freesurfer] autorecon1 memory error

your best option is to include the flag -no-gcut at the end of recon-all, which will bypass usage of mri_gcut. you should inspect your brainmask.mgz upon completing the -atuorecon1 stage though. n. On Wed, 2011-03-23 at 11:26 -0500, Paige Scalf wrote: > Hello, > > I'm getting the memory alloca

[Freesurfer] changing tksurfer window font size...

Hi: How can I change the font size used in the tksurfer dialogs ?... such as "Configure Overlay Display" dialog ?... Because I changed the font size in Ubuntu GNOME, but it didn't changed the font size used in tksurfer... I asking that because in the "Configure Overlay Display" didn't a

Re: [Freesurfer] [Fressurfer] fMRI and anatomical T1

There is a tutorial on this on our wiki. Basically, you need to run reg-feat2anat to get a registration file, then run tksurfer passing it the registration file and the stat volume as the overlay. doug leonardo kay wrote: > Hi all > > Can anyone help me overlaying fMRI activations from fsl on

[Freesurfer] [Fressurfer] fMRI and anatomical T1

Hi all Can anyone help me overlaying fMRI activations from fsl on a anatomical T1 volume in freesurfer. Is there any previous format conversion to do before? Thanks in advance best regards, -- Leo Kay. ___ Freesurfer mailing list Freesurfer@nmr.mgh.ha

[Freesurfer] changing tksurfer window font size...

Hi: How can I change the font size used in the tksurfer dialogs ?... such as "Configure Overlay Display" dialog ?... Because I changed the font size in Ubuntu GNOME, but it didn't changed the font size used in tksurfer... Sincerely, Gonzalo Rojas Costa

[Freesurfer] recon-all errors

Dear freesurfer users, I had some problems with 3 images of different patients running the recon-all comand. With one of them, I received the following message: ERROR: vbmAMIPP.nii exists but is not readable With the others two there were no error messages, but both stopped at the same point: