[Freesurfer] structure volume

Hi, After running dti_recon and recon_all, I noticed that they produce different volumes of structures for the same brain. Just trying to understand why that is? best, AJ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mg

Re: [Freesurfer] refeventdur in mkanalysis-sess

Hi Maryam, yes, I admit, that is a confusing option. The "events" that the help refers to only apply to task events (not the fixation). In your case, you would just set it to 16 sec. doug On 9/8/11 10:55 PM, Maryam Vaziri Pashkam wrote: Hi, I am making an analysis in freesurfer 5.1 using mka

[Freesurfer] refeventdur in mkanalysis-sess

Hi, I am making an analysis in freesurfer 5.1 using mkanalysis-sess and I am a bit confused about the flag refeventdur. In the help it is said that it should be set to the event duration if the events have similar durations. I have four conditions that last for 16 second each in a block design par

Re: [Freesurfer] FS-FAST modeling question

I think this is known bug in version 4.5 in which stored t-stats are simply the square of the p-value map. Hope it helps, Pablo On Thu, Sep 8, 2011 at 3:37 PM, Douglas N Greve wrote: > So, which version did you find that ces/sqrt(cesvar) did not equal t? > doug > > > Ben Deen wrote: > > Hi Doug,

Re: [Freesurfer] FS-FAST modeling question

4.5, but only for my results, not others from my lab. On Thu, Sep 8, 2011 at 3:37 PM, Douglas N Greve wrote: > So, which version did you find that ces/sqrt(cesvar) did not equal t? > doug > > > Ben Deen wrote: >> >> Hi Doug, >> >> Thanks for your response.  The comments below all regard question

Re: [Freesurfer] FS-FAST modeling question

So, which version did you find that ces/sqrt(cesvar) did not equal t? doug Ben Deen wrote: > Hi Doug, > > Thanks for your response. The comments below all regard question #2, > is this is the only one that still concerns me. > > I actually was using the nowhiten flag in the last analysis I > des

Re: [Freesurfer] FS-FAST modeling question

Hi Doug, Thanks for your response. The comments below all regard question #2, is this is the only one that still concerns me. I actually was using the nowhiten flag in the last analysis I described, which was run in version 4.5. From looking at the ces, cesvar, and t images in the contrast dire

Re: [Freesurfer] FS-FAST modeling question

Ben Deen wrote: > Hi, > > I have an update to this query. I tried using mkanalysis-sess instead > of the ".new" version, and now I do seem to be able to get rid of > intensity normalization and prewhitening (or at least, adding these > flags now has an effect on betas/t-stats, and in the expecte

Re: [Freesurfer] mri_convert: orientation issue

I have no idea. That's pretty old code that we are not really maintaining anymore. Why are you using analyze? doug Mohana Ramaratnam wrote: > Hello, > > I am using mri_convert to convert dicom image into analyze format using: > > mri_convert -i PATH_TO_DICOM_HERE --out_type analyze -o analyze.im

[Freesurfer] mri_convert: orientation issue

Hello, I am using mri_convert to convert dicom image into analyze format using: mri_convert -i PATH_TO_DICOM_HERE --out_type analyze -o analyze.img The problem is: The hdr.hist.orient in the output file is set to 0, but the pixels in the analyze image are saggital. Does anybody have any sugg

Re: [Freesurfer] Tracula - Bedpostx - missing output

Hi Judit - Hard to tell what could've gone wrong but you can try running the postprocessing yourself as follows: bedpostx_postproc.sh /path/to/subject/dmri Hope this helps, a.y On Thu, 8 Sep 2011, Judit Haasz wrote: > Hi, > > I am running bedpostx within Freesurfer Tracula with default

[Freesurfer] Tracula - Bedpostx - missing output

Hi, I am running bedpostx within Freesurfer Tracula with default settings. I got the following error message: Queuing post processing stage [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_post: unexpected operator [: 486: x: unexpected operator [: 486: -le: a