[Freesurfer] Error message of Ubuntu 13.04 and Centos4 & Centos6

Dear Freesurfer experts, I installed FS Centos4-64(and also tried Centos6) on Ubuntu 13.04. I followed the commands in tutorial and got error message, listed as follows. (Nevertheless, FS can read in volume and surface from GUI.) Another question is, which one of Centos4 or Centos6 is more sui

Re: [Freesurfer] Make an average activation map of 2 scans

Hi Alex, You may use mri_concat with --mean flag, or alternatively use fslmaths to compute the average. Maybe Doug or Bruce or others have better ideas. Hth, Shantanu On Fri, August 23, 2013 2:56 pm, Alexandra Tanner wrote: > Hi Freesurfers, > > Does anyone know how to make an average activation

Re: [Freesurfer] Make an average activation map of 2 scans

Hi Alex, you're almost there. When you run your "group" analysis with mri_glmfit, perform a fixed effects analysis, something like mri_glmfit --y ces.nii.gz --yffxvar ces.var.nii.gz --ffxdofdat ../ffxdof.dat ... doug On 08/23/2013 02:56 PM, Alexandra Tanner wrote: > Hi Freesurfers, > > Does a

[Freesurfer] Make an average activation map of 2 scans

Hi Freesurfers, Does anyone know how to make an average activation map of two subjects without running a group analysis? I have 15 subjects that each have a pre and a post scan (30 scans total) and we would like to combine the pre and post bold runs for each subject to generate an averaged AllvFix

Re: [Freesurfer] ribbon.mgz, -1) : could not open file ERROR

For now I only need brainmask.mgz and wmparc.mgz, so Yes. In case I need other files in the future (i.e. mri_segstats) I plan to run all processing again. Thanks a lot! Pedro Rosa On 23 Aug 2013, at 11:36 AM, Douglas N Greve wrote: > > Are all the files you need there? If not, what is missing

Re: [Freesurfer] Otto: unsupported slice timing pattern 5

Can you send a *single* dicom file to me? No need to copy the list On 08/22/2013 04:30 PM, Otto Muzik wrote: > Hi, > > I am trying to convert a SIEMENS T1-weighted volume to the mgz > format (via mri_convert) but I am getting constantly the error message > > unsupported slice timing pattern 5 in

Re: [Freesurfer] ribbon.mgz, -1) : could not open file ERROR

Are all the files you need there? If not, what is missing? On 08/22/2013 07:41 PM, Pedro Rosa wrote: > Hi, > Thank you. It seems to be working. The command returns, however, that there > is nothing to be done in all three autorecons individually. What should that > mean, considering the erro

Re: [Freesurfer] FW: FW: Contrast and F-test

The values in the interaction column are probably much larger than the values in the other columns (thus they are "badly scaled"). You can divide them by a number to bring their scale down to that of the other columns without changing the p-values. Version 5.x does this automatically. On 0

Re: [Freesurfer] entorhinal ex vivo > stats 2 table?

Hi Simon, I just created a little script (attached) which will do what you want. You may want to create two scripts out of it, one to compute the individual stats, then another to run asegstats2table. You will need to supply the subjectlist Note that even though it uses mri_segstats and asegs

Re: [Freesurfer] FW: FW: Contrast and F-test

I am using version 4.5, as all the old analyses were also done with this version. What do you mean with rescale? THanks Heidi Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve [gr...@nmr.mgh.harvar

Re: [Freesurfer] FW: FW: Contrast and F-test

what version of FS are you using? It may be that you just need to rescale that column (if the scale is much more than the other columns) On 08/23/2013 11:12 AM, Jacobs H (NP) wrote: > Hi again! > > I am trying to run these contrasts but FreeSurfer tells me that "ERROR: > matrix is ill-condition

Re: [Freesurfer] FW: FW: Contrast and F-test

Hi again! I am trying to run these contrasts but FreeSurfer tells me that "ERROR: matrix is ill-conditioned or badly scaled, condno = 101380 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class." Could this be due to t

Re: [Freesurfer] TBSS doubts

Hi Anupa this should probably go to the FSL list. cheers Bruce On Fri, 23 Aug 2013, Anupa AV wrote: > Dear All, > I was trying to do TBSS analysis. But I encountered with some problems.I > attached a ppt which shows raw DWI, FA map generated using FDT FSL toolbox > and the TBSS results. > If yo

[Freesurfer] entorhinal ex vivo > stats 2 table?

Dear all, Sorry if this has been covered previously (I've not been able to find a solution in the archives). Is there a script that automatically puts your sample of entorhinal ex vivo labels into a table for each value (volume, thickness etc), something like asegstats2table or aparcstats2tabl