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, 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.
Sid,
1) 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.
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:
- 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
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
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 nicks@nmr.mgh.harvard.edu wrote: Sid,
1) 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. 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, > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 nicks@nmr.mgh.harvard.eduwrote:
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 nicks@nmr.mgh.harvard.edu wrote: Sid,
1) 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. 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, > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 nicks@nmr.mgh.harvard.edu 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 > <nicks@nmr.mgh.harvard.edu> wrote: > Sid, > > 1) 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. > > 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, > > 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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi all, I am trying to understand the --surf flag in the mri_glmfit command, and the 2 parameters that follow it. The tutorial mentions --surf average lh . 1) what should "average" contain? should it point to the average of the population, of fsaverage, or is it just a flag? 2) lh: is this just the specification of the hemisphere to be processed or should it point to a valid set of files.
If i am doing a group analysis of a measure (say, thickness), and i have smoothed thickness maps registered to a population specific template in a subdir, how should i specify --surf and subsequebt parameters?
Further, i also get an error saying --C command not found (for the contrast vector). why is this happenning?
best regards, sid.
On Sun, Dec 28, 2008 at 12:24 PM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
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 nicks@nmr.mgh.harvard.edu 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 > <nicks@nmr.mgh.harvard.edu> wrote: > Sid, > > 1) 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. > > 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, > > 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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Siddharth Srivastava wrote:
Hi all, I am trying to understand the --surf flag in the mri_glmfit command, and the 2 parameters that follow it. The tutorial mentions --surf average lh .
- what should "average" contain? should it point to the average of
the population, of fsaverage, or is it just a flag?
This is the name of the average subject as created by make_average_subject. If you did not make an average subject, then use fsaverage.
- lh: is this just the specification of the hemisphere to be processed
or should it point to a valid set of files.
Just the hemisphere
If i am doing a group analysis of a measure (say, thickness), and i have smoothed thickness maps registered to a population specific template in a subdir, how should i specify --surf and subsequebt parameters?
The input is specified with with --y. The --surf just tells glmfit that it is a surface so that it can compute the FWHM appropriately.
Further, i also get an error saying --C command not found (for the contrast vector). why is this happenning?
Can't say without the cmd line, but I'm guessing you have a rouge space in your script
best regards, sid.
On Sun, Dec 28, 2008 at 12:24 PM, Nick Schmansky <nicks@nmr.mgh.harvard.edu mailto:nicks@nmr.mgh.harvard.edu> wrote:
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 > <nicks@nmr.mgh.harvard.edu <mailto:nicks@nmr.mgh.harvard.edu>> 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 > > <nicks@nmr.mgh.harvard.edu <mailto:nicks@nmr.mgh.harvard.edu>> wrote: > > Sid, > > > > 1) 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. > > > > 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, > > > 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I want to ask a related question: We study group differences between patients and controls, and correlations of symptoms and thickness in patients only. We would like to display (and extract) the common regions between two analyses in ONE figure. Which template can we use? We created two sets of ROIs in Qdec: one set is defined using an averge from all subjects; the other set is defined using an average of patients only. The ROI.labels from one set can not be loaded correctly on the average tamplate of the other set. The problem remains even if we convert both sets of ROI.labels to individual spaces. can we use fsaverage for both analyses?
thanks,
Xin Wang
________________________________
From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Mon 1/5/2009 2:23 PM To: Siddharth Srivastava Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] questions about region-wise analysis data
Siddharth Srivastava wrote:
Hi all, I am trying to understand the --surf flag in the mri_glmfit command, and the 2 parameters that follow it. The tutorial mentions --surf average lh . 1) what should "average" contain? should it point to the average of the population, of fsaverage, or is it just a flag?
This is the name of the average subject as created by make_average_subject. If you did not make an average subject, then use fsaverage.
2) lh: is this just the specification of the hemisphere to be processed or should it point to a valid set of files.
Just the hemisphere
If i am doing a group analysis of a measure (say, thickness), and i have smoothed thickness maps registered to a population specific template in a subdir, how should i specify --surf and subsequebt parameters?
The input is specified with with --y. The --surf just tells glmfit that it is a surface so that it can compute the FWHM appropriately.
Further, i also get an error saying --C command not found (for the contrast vector). why is this happenning?
Can't say without the cmd line, but I'm guessing you have a rouge space in your script
best regards, sid. On Sun, Dec 28, 2008 at 12:24 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
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 > nicks@nmr.mgh.harvard.edu 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 > > nicks@nmr.mgh.harvard.edu wrote: > > Sid, > > > > 1) 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. > > > > 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, > > > 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 > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
________________________________
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
hmmm, you should be able to display any of the average RIOs on any of the surfaces as they should all have the topology of ic7. What exactly fails?
On Mon, 5 Jan 2009, Wang, Xin wrote:
I want to ask a related question: We study group differences between patients and controls, and correlations of symptoms and thickness in patients only. We would like to display (and extract) the common regions between two analyses in ONE figure. Which template can we use? We created two sets of ROIs in Qdec: one set is defined using an averge from all subjects; the other set is defined using an average of patients only. The ROI.labels from one set can not be loaded correctly on the average tamplate of the other set. The problem remains even if we convert both sets of ROI.labels to individual spaces. can we use fsaverage for both analyses?
thanks,
Xin Wang
From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Mon 1/5/2009 2:23 PM To: Siddharth Srivastava Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] questions about region-wise analysis data
Siddharth Srivastava wrote:
Hi all, I am trying to understand the --surf flag in the mri_glmfit command, and the 2 parameters that follow it. The tutorial mentions --surf average lh .
- what should "average" contain? should it point to the average of
the population, of fsaverage, or is it just a flag?
This is the name of the average subject as created by make_average_subject. If you did not make an average subject, then use fsaverage.
- lh: is this just the specification of the hemisphere to be processed
or should it point to a valid set of files.
Just the hemisphere
If i am doing a group analysis of a measure (say, thickness), and i have smoothed thickness maps registered to a population specific template in a subdir, how should i specify --surf and subsequebt parameters?
The input is specified with with --y. The --surf just tells glmfit that it is a surface so that it can compute the FWHM appropriately.
Further, i also get an error saying --C command not found (for the contrast vector). why is this happenning?
Can't say without the cmd line, but I'm guessing you have a rouge space in your script
best regards, sid.
On Sun, Dec 28, 2008 at 12:24 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
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 > <nicks@nmr.mgh.harvard.edu> 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 > > <nicks@nmr.mgh.harvard.edu> wrote: > > Sid, > > > > 1) 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. > > > > 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, > > > 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 > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you, Dr. Fischl. A set of ROIs can be displayed on the average template of the other set of ROIs. The location is about right, but the XYZ coordinates of the ROI seems different from that on the its own average template. This raise another question: we assumed that the average subjects of different groups of subjects are different. Otherwise, why to create an average subject for each analysis? what are the differences in using an average subject for a analysis and using fsaverage for all analyses?
Thanks,
Xin
________________________________
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Mon 1/5/2009 3:51 PM To: Wang, Xin Cc: Doug Greve; Freesurfer Mailing List Subject: RE: [Freesurfer] questions about region-wise analysis data
hmmm, you should be able to display any of the average RIOs on any of the surfaces as they should all have the topology of ic7. What exactly fails?
On Mon, 5 Jan 2009, Wang, Xin wrote:
I want to ask a related question: We study group differences between patients and controls, and correlations of symptoms and thickness in patients only. We would like to display (and extract) the common regions between two analyses in ONE figure. Which template can we use? We created two sets of ROIs in Qdec: one set is defined using an averge from all subjects; the other set is defined using an average of patients only. The ROI.labels from one set can not be loaded correctly on the average tamplate of the other set. The problem remains even if we convert both sets of ROI.labels to individual spaces. can we use fsaverage for both analyses?
thanks,
Xin Wang
From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Mon 1/5/2009 2:23 PM To: Siddharth Srivastava Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] questions about region-wise analysis data
Siddharth Srivastava wrote:
Hi all, I am trying to understand the --surf flag in the mri_glmfit command, and the 2 parameters that follow it. The tutorial mentions --surf average lh . 1) what should "average" contain? should it point to the average of the population, of fsaverage, or is it just a flag?This is the name of the average subject as created by make_average_subject. If you did not make an average subject, then use fsaverage.
2) lh: is this just the specification of the hemisphere to be processed or should it point to a valid set of files.Just the hemisphere
If i am doing a group analysis of a measure (say, thickness), and i have smoothed thickness maps registered to a population specific template in a subdir, how should i specify --surf and subsequebt parameters?The input is specified with with --y. The --surf just tells glmfit that it is a surface so that it can compute the FWHM appropriately.
Further, i also get an error saying --C command not found (for the contrast vector). why is this happenning?Can't say without the cmd line, but I'm guessing you have a rouge space in your script
best regards, sid. On Sun, Dec 28, 2008 at 12:24 PM, Nick Schmansky <nicks@nmr.mgh.harvard.edu> wrote: 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 > <nicks@nmr.mgh.harvard.edu> 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 > > <nicks@nmr.mgh.harvard.edu> wrote: > > Sid, > > > > 1) 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. > > > > 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, > > > 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 > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
the average subject isn't all that different from group to group since we explicitly normalize out the majority of the differences. Nevertheless, displaying on the average of your study instead of fsaverage gives a better idea of the localization accuracy.
The XYZ will be different since they are the average talairach of the vertices that map to that surface location. I don't think this should have any effect though if you are displaying it on the surface. Does it?
cheers, Bruce
On Mon, 5 Jan 2009, Wang, Xin wrote:
Thank you, Dr. Fischl. A set of ROIs can be displayed on the average
template of the other set of ROIs. The location is about right, but the XYZ coordinates of the ROI seems different from that on the its own average template.
This raise another question: we assumed that the average subjects of
different groups of subjects are different. Otherwise, why to create an average subject for each analysis? what are the differences in using an average subject for a analysis and using fsaverage for all analyses? >
Thanks,
Xin
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Mon 1/5/2009 3:51 PM To: Wang, Xin Cc: Doug Greve; Freesurfer Mailing List Subject: RE: [Freesurfer] questions about region-wise analysis data
hmmm, you should be able to display any of the average RIOs on any of the surfaces as they should all have the topology of ic7. What exactly fails?
On Mon, 5 Jan 2009, Wang, Xin wrote:
I want to ask a related question: We study group differences between patients and controls, and correlations of symptoms and thickness in patients only. We would like to display (and extract) the common regions between two analyses in ONE figure. Which template can we use? We created two sets of ROIs in Qdec: one set is defined using an averge from all subjects; the other set is defined using an average of patients only. The ROI.labels from one set can not be loaded correctly on the average tamplate of the other set. The problem remains even if we convert both sets of ROI.labels to individual spaces. can we use fsaverage for both analyses?
thanks,
Xin Wang
From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Mon 1/5/2009 2:23 PM To: Siddharth Srivastava Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] questions about region-wise analysis data
Siddharth Srivastava wrote:
Hi all, I am trying to understand the --surf flag in the mri_glmfit command, and the 2 parameters that follow it. The tutorial mentions --surf average lh . 1) what should "average" contain? should it point to the average of the population, of fsaverage, or is it just a flag?This is the name of the average subject as created by make_average_subject. If you did not make an average subject, then use fsaverage.
2) lh: is this just the specification of the hemisphere to be processed or should it point to a valid set of files.Just the hemisphere
If i am doing a group analysis of a measure (say, thickness), and i have smoothed thickness maps registered to a population specific template in a subdir, how should i specify --surf and subsequebt parameters?The input is specified with with --y. The --surf just tells glmfit that it is a surface so that it can compute the FWHM appropriately.
Further, i also get an error saying --C command not found (for the contrast vector). why is this happenning?Can't say without the cmd line, but I'm guessing you have a rouge space in your script
best regards, sid. On Sun, Dec 28, 2008 at 12:24 PM, Nick Schmansky <nicks@nmr.mgh.harvard.edu> wrote: 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 > <nicks@nmr.mgh.harvard.edu> 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 > > <nicks@nmr.mgh.harvard.edu> wrote: > > Sid, > > > > 1) 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. > > > > 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, > > > 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 > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
an addition question: it is plausible to load multiple sets of ROIs created by different analyses on one subject thickness map after converted all of them back to the individual space. This approach may be more accurate than loading ROIs in the average template. But It doesn't work in our experience. I would like to know what is the problem of this approach.
Thank you in advance,
Xin
________________________________
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Mon 1/5/2009 3:51 PM To: Wang, Xin Cc: Doug Greve; Freesurfer Mailing List Subject: RE: [Freesurfer] questions about region-wise analysis data
hmmm, you should be able to display any of the average RIOs on any of the surfaces as they should all have the topology of ic7. What exactly fails?
On Mon, 5 Jan 2009, Wang, Xin wrote:
I want to ask a related question: We study group differences between patients and controls, and correlations of symptoms and thickness in patients only. We would like to display (and extract) the common regions between two analyses in ONE figure. Which template can we use? We created two sets of ROIs in Qdec: one set is defined using an averge from all subjects; the other set is defined using an average of patients only. The ROI.labels from one set can not be loaded correctly on the average tamplate of the other set. The problem remains even if we convert both sets of ROI.labels to individual spaces. can we use fsaverage for both analyses?
thanks,
Xin Wang
From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Mon 1/5/2009 2:23 PM To: Siddharth Srivastava Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] questions about region-wise analysis data
Siddharth Srivastava wrote:
Hi all, I am trying to understand the --surf flag in the mri_glmfit command, and the 2 parameters that follow it. The tutorial mentions --surf average lh . 1) what should "average" contain? should it point to the average of the population, of fsaverage, or is it just a flag?This is the name of the average subject as created by make_average_subject. If you did not make an average subject, then use fsaverage.
2) lh: is this just the specification of the hemisphere to be processed or should it point to a valid set of files.Just the hemisphere
If i am doing a group analysis of a measure (say, thickness), and i have smoothed thickness maps registered to a population specific template in a subdir, how should i specify --surf and subsequebt parameters?The input is specified with with --y. The --surf just tells glmfit that it is a surface so that it can compute the FWHM appropriately.
Further, i also get an error saying --C command not found (for the contrast vector). why is this happenning?Can't say without the cmd line, but I'm guessing you have a rouge space in your script
best regards, sid. On Sun, Dec 28, 2008 at 12:24 PM, Nick Schmansky <nicks@nmr.mgh.harvard.edu> wrote: 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 > <nicks@nmr.mgh.harvard.edu> 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 > > <nicks@nmr.mgh.harvard.edu> wrote: > > Sid, > > > > 1) 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. > > > > 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, > > > 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 > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, that should work using mri_label2label. What doesn't work? On Mon, 5 Jan 2009, Wang, Xin wrote:
an addition question: it is plausible to load multiple sets of ROIs created by different analyses on one subject thickness map after converted all of them back to the individual space. This approach may be more accurate than loading ROIs in the average template. But It doesn't work in our experience. I would like to know what is the problem of this approach.
Thank you in advance,
Xin
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Mon 1/5/2009 3:51 PM To: Wang, Xin Cc: Doug Greve; Freesurfer Mailing List Subject: RE: [Freesurfer] questions about region-wise analysis data
hmmm, you should be able to display any of the average RIOs on any of the surfaces as they should all have the topology of ic7. What exactly fails?
On Mon, 5 Jan 2009, Wang, Xin wrote:
I want to ask a related question: We study group differences between patients and controls, and correlations of symptoms and thickness in patients only. We would like to display (and extract) the common regions between two analyses in ONE figure. Which template can we use? We created two sets of ROIs in Qdec: one set is defined using an averge from all subjects; the other set is defined using an average of patients only. The ROI.labels from one set can not be loaded correctly on the average tamplate of the other set. The problem remains even if we convert both sets of ROI.labels to individual spaces. can we use fsaverage for both analyses?
thanks,
Xin Wang
From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Mon 1/5/2009 2:23 PM To: Siddharth Srivastava Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] questions about region-wise analysis data
Siddharth Srivastava wrote:
Hi all, I am trying to understand the --surf flag in the mri_glmfit command, and the 2 parameters that follow it. The tutorial mentions --surf average lh . 1) what should "average" contain? should it point to the average of the population, of fsaverage, or is it just a flag?This is the name of the average subject as created by make_average_subject. If you did not make an average subject, then use fsaverage.
2) lh: is this just the specification of the hemisphere to be processed or should it point to a valid set of files.Just the hemisphere
If i am doing a group analysis of a measure (say, thickness), and i have smoothed thickness maps registered to a population specific template in a subdir, how should i specify --surf and subsequebt parameters?The input is specified with with --y. The --surf just tells glmfit that it is a surface so that it can compute the FWHM appropriately.
Further, i also get an error saying --C command not found (for the contrast vector). why is this happenning?Can't say without the cmd line, but I'm guessing you have a rouge space in your script
best regards, sid. On Sun, Dec 28, 2008 at 12:24 PM, Nick Schmansky <nicks@nmr.mgh.harvard.edu> wrote: 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 > <nicks@nmr.mgh.harvard.edu> 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 > > <nicks@nmr.mgh.harvard.edu> wrote: > > Sid, > > > > 1) 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. > > > > 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, > > > 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 > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Doug Greve -
Nick Schmansky -
Siddharth Srivastava -
Wang, Xin