Re: [Freesurfer] questions about region-wise analysis data
Sid, The .mgh files, in the case of the commands you ran, store surface data corresponding to the 'fsaverage' subject. So you would first load the inflated surface for fsaverage (tksurfer fsaverage lh inflated), then you would use the Load Overlay menu option to load the .mgh file(s) you created. You probably will have to adjust the color thresholds (View- >Configure->Overlay). For the lgi data, you can use: recon-all -s subj -qcache -measure pial_lgi which will sample the subjects lgi data to the fsaverage surface, at which point you could average that (although typically a statistical analysis is performed on the set of subjects sampled to fsaverage, see out group analysis slides and tutorial pages). You should be able to move subject data around to other directories without any problems. Does tksurfer really halt after that 'not in scripts dir' message? That is a common message and not an error. Can you open tksurfer for the sample bert subject? Nick On Sat, 2008-12-27 at 19:14 -0800, Siddharth Srivastava wrote: > 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 > wrote: > Sid, > > 1) when recon-all is finished on a subject, there are a number > of stats > found in the /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. > > 2) 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 > > 3) 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: > > > > 1) With the parcellations already available in freesurfer, i > would > > like to > > extract metrics (curvature, lgi, thickness) etc. for > each label, >
Re: [Freesurfer] questions about region-wise analysis data
Hi Nick, Thanks, It was my mistake. It works exactly as you say. I still have to look at qdec documentation, but could i ask if it is possible to perform the group analysis in a batch mode, without the GUI, i.e ? regarding the movement of data, the first time i did it, i got a screen full of memory addresses and corresponding routines, followed by a crash ( exit from wish, back to shell). I am not able to replicate it, seems to work now. Also, is it possible to register everything to a different surface, other that fsaverage.. for example to one of the subjects? Can this be located outside the relative paths reachable via $SUBJECTS_DIR ? In fact, can fsaverage be located outside? For the processing i did, i had to copy the fsaverage as one of the subjects, so that it can be located within the current context of $SUBJECTS_DIR . Thanks again, for the timely help. sid. On Sun, Dec 28, 2008 at 9:17 AM, Nick Schmansky wrote: > Sid, > > The .mgh files, in the case of the commands you ran, store surface data > corresponding to the 'fsaverage' subject. So you would first load the > inflated surface for fsaverage (tksurfer fsaverage lh inflated), then > you would use the Load Overlay menu option to load the .mgh file(s) you > created. You probably will have to adjust the color thresholds (View- > >Configure->Overlay). For the lgi data, you can use: > > recon-all -s subj -qcache -measure pial_lgi > > which will sample the subjects lgi data to the fsaverage surface, at > which point you could average that (although typically a statistical > analysis is performed on the set of subjects sampled to fsaverage, see > out group analysis slides and tutorial pages). > > You should be able to move subject data around to other directories > without any problems. Does tksurfer really halt after that 'not in > scripts dir' message? That is a common message and not an error. Can > you open tksurfer for the sample bert subject? > > Nick > > > > On Sat, 2008-12-27 at 19:14 -0800, Siddharth Srivastava wrote: > > 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 > > wrote: > > Sid, > > > > 1) when recon-all is finished on a subject, there are a number > > of stats > > found in the /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. > > > > 2) 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 > > > > 3) there is no way to
Re: [Freesurfer] questions about region-wise analysis data
Sid, A group analysis can be performed from the command-line using mri_glmfit directly. See this tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis You can use a different average subject, other than fsaverage, although it doesnt improve an analysis to use a subject from your group. Also, you can create a symlink from $FREESURFER_HOME/subjects/fsaverage to your SUBJECTS_DIRS, to spare having to copy the data. Nick On Sun, 2008-12-28 at 12:01 -0800, Siddharth Srivastava wrote: > Hi Nick, > Thanks, It was my mistake. It works exactly as you say. > I still have to look at qdec documentation, but could i ask if it is > possible to perform the group analysis in a batch mode, without > the GUI, i.e ? > > regarding the movement of data, the first time i did it, i got a > screen full > of memory addresses and corresponding routines, followed by a crash ( > exit from wish, back to shell). I am not able to replicate it, seems > to work > now. > > Also, is it possible to register everything to a different surface, > other > that fsaverage.. for example to one of the subjects? Can this be > located > outside the relative paths reachable via $SUBJECTS_DIR ? In fact, can > fsaverage be located outside? For the processing i did, i had to copy > the fsaverage as one of the subjects, so that it can be located > within > the current context of $SUBJECTS_DIR . > > Thanks again, for the timely help. > sid. > > > On Sun, Dec 28, 2008 at 9:17 AM, Nick Schmansky > wrote: > Sid, > > The .mgh files, in the case of the commands you ran, store > surface data > corresponding to the 'fsaverage' subject. So you would first > load the > inflated surface for fsaverage (tksurfer fsaverage lh > inflated), then > you would use the Load Overlay menu option to load the .mgh > file(s) you > created. You probably will have to adjust the color > thresholds (View- > >Configure->Overlay). For the lgi data, you can use: > > recon-all -s subj -qcache -measure pial_lgi > > which will sample the subjects lgi data to the fsaverage > surface, at > which point you could average that (although typically a > statistical > analysis is performed on the set of subjects sampled to > fsaverage, see > out group analysis slides and tutorial pages). > > You should be able to move subject data around to other > directories > without any problems. Does tksurfer really halt after that > 'not in > scripts dir' message? That is a common message and not an > error. Can > you open tksurfer for the sample bert subject? > > Nick > > > > > On Sat, 2008-12-27 at 19:14 -0800, Siddharth Srivastava wrote: > > 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 > >
