Hi Nick, I finally got a chance to use the sequence of command that you had provided below. In continuation of this thread:
a) The output of using the command mentioned in reply 2) below is an MGH file (and not faces/vertices combination)? How is it possible to get a smoothed surface that i can load as an overlay in tksurfer? I would ultimately like to average all the smoothed lgi mappings as one single surface per hemisphere. Is this possible in freesurfer? In any case, although my pial_lgi surfaces look ok, i do not see anything in the .fwhmxx.fsaverage.mgh files, when i load them using tkmedit. what can be going wrong? I used fwhm = 15.
b) Are there known issues with migrating the data set processed partiallty at one mount point, to some different location? Due to lack of space, i had to do some recon-all processing in one directory, and then copied the tree to a different location for subsequent steps. I get tksurfer errors "surfer: not in "scripts" dir ==> using cwd for session root", followed by, what i think, a read attempt of the corresponding T1.mgz file. No window is drawn. I googled with the error string, and it seems there was a similar error under discussion, which had to do with moving files and absolute paths. I was not able to understand the fix, though, and hence i wanted to confirm with the list what exactly has to be done in this situation.
Thanks, sid.
On Fri, Dec 5, 2008 at 10:42 AM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
Sid,
- when recon-all is finished on a subject, there are a number of stats
found in the <subj>/stats directory. for the additional ones you want, you can use mris_anatomical_stats. see 'mris_anatomical_stats --help'. ex. mris_anatomical_stats -a aparc -t lgi subjid lh see also 'aparcstats2table' to group a collection of subjects.
- you can use the -qcache option of recon-all (normally used to
generate files used by the qdec app) to handle the resampling of data to a common surface (fsaverage). example:
recon-all -s subj -qcache -measure lgi -fwhm 0 -hemi lh
will create subj/surf/lh.lgi.fwhm0.fsaverage.mgh
where fwhm is the amount of smoothing (0mm in this case means no smoothing). then, once you have this file for every subject, to get a mean, you can use: mri_concat --i subj1/surf/lh.lgi.fwhm0.fsaverage.mgh \ subj2/surf/lh.lgi.fwhm0.fsaverage.mgh \ subj3/surf/lh.lgi.fwhm0.fsaverage.mgh ... \ --mean \ --o mygroup.lh.lgi.fwhm0.mean.fsaverage.mgh
- there is no way to change the colors in the tkmedit/tksurfer colormap
(other than the color options available). people change the thresholds to get the nice pictures.
Nick
On Thu, 2008-12-04 at 19:50 -0800, Siddharth Srivastava wrote:
Hi everyone, while the machine is busy crunching through our data set, i would like to prepare myself from the next step of the analysis, which is a region-wise analysis of the computed metrics by the freesurfer pipeline. Being a complete novice in the use of this software, i would like to know how do i go about doing the following:
- With the parcellations already available in freesurfer, i would
like to extract metrics (curvature, lgi, thickness) etc. for each label, and process them outside freesurfer (matlab, since i am more used to it). Is it possible to do this within freesurfer or without, i.e read these values on the pial/white matter/inflated surfaces, ans also extract ones corresponding to a particular label? 2) How do i go about generating a group average of the various maps that freesurfer generates (curvature/thickness/lgi) ? As i understand, the analysis is done entirely in the subject space. Can i apply a transformation to the generated surfaces for averaging? Or does it require a re- processing after registering/reslicing all the data to a common space? 3) I am still struggling with a proper colormap, which can bring out the structure in out data. I see very nice renderings in various publications, of data generated with freesurfer. Is it possible to tweak the colormap to get such a rendering?
Thanking you all in anticipation, sid. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer