[Freesurfer] FSL and freesurfer: combine runs in volume or on surface?
Dear all, I am trying to figure out how to bring my fMRI data from FSL to the freesurfer surface. The way I understood it from the tutorial 3.0 Surface-based Group Functional Analysis( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat) There are two possibilities of combining multiple runs per subject: - using mris_preproc for each run and having runs as frames in the lh.copex.mhg file - running first gfeat in FSL and registering gfeat copes to fsaverage ( Runs combined in a GFEAT within a Subject), which would result in 1-frame lh.copex.mhg file I wonder if it is possible to say which procedure is better/more sensitive? Should the fmri data be non-smoothed before this step for both above options? Thank you! Cheers, Aga ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Fw: manually specifying design matrix
Hello Sorry for reposting again. Would really appreciate a feedback on the following mail. Thanks in advance for your time Raka - Forwarded Message From: raka maitra rakamai...@yahoo.com To: Douglas N Greve gr...@nmr.mgh.harvard.edu Sent: Fri, January 15, 2010 9:34:02 PM Subject: Re: [Freesurfer] manually specifying design matrix Thank you Doug. I am trying to create a design matrix for repeated measures anova. Lets say subjects A and B have been measured at sitting and standing positions. As the same subjects have been measured at the same positions, hence both the factors i.e subjects and positions are fixed factors. Hence a design matrix exploring the within subject effects of positions would be 1 0 1 0 0 1 1 0 1 0 0 1 0 1 0 1 The first two columns are position and the last two are the subjects. But mri_glmfit does not accept this design and I get the following error message: 'Matrix condition is 1e+08 ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class.' Looking forward to your suggestion Thanks in advance Raka From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: raka maitra rakamai...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu Sent: Thu, January 14, 2010 7:05:28 PM Subject: Re: [Freesurfer] manually specifying design matrix If you specify it manually, you don't specify groups, etc, or pass an fsgd file. You just create your design matrix pass it to mri_glmfit directly with the --X flag. doug raka maitra wrote: Hi all I want to specify a design matrix manually. In the usual pipeline for analysis in freesurfer, one specifies the groups, regressors in the fsgd and then when mri_glmfit is run, it creates the design matrix. For eg if I have two classes with 3 subjects each, in my fsgd, mri_glmfit would create the following design matrix 1 0 1 0 1 0 0 1 0 1 0 1 If I want to specify the above design matrix manually, how and where do I specify the groups, regressors ? Thanks in advance Raka ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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
Re: [Freesurfer] number of vertices per hemisphere using mri_glmfit
In the mri_glmfit.log file, there is a SearchSpace this will be in mm2 for surfaces and mm3 for vols. There will also be a mask.mgh file. You can run mri_segstats on this to give you the number of elements that are == 1. doug Stefan Brauns wrote: Hi there, I am running surface based analysis of cortical thickness using FreeSurfer. Sometimes I constrain the analysis to certain regions of the brain, e.g. only frontal lobes. I would like to find out how many vertices per hemisphere are analysed with the mri_glmfit I am running. Is there a possibility to get these values from any of the log-files? What is the usual number of vertices per hemisphere? Many thanks, Stefan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fw: manually specifying design matrix
It would probably be more like this: 1. 00.5000 1. 0 -0.5000 01.0.5000 01. -0.5000 The 1st col codes subject 1. The 1st row is the 1st measure of subject 1 and the 2nd row is the 2nd measure of subject 1. doug raka maitra wrote: Hello Sorry for reposting again. Would really appreciate a feedback on the following mail. Thanks in advance for your time Raka - Forwarded Message *From:* raka maitra rakamai...@yahoo.com *To:* Douglas N Greve gr...@nmr.mgh.harvard.edu *Sent:* Fri, January 15, 2010 9:34:02 PM *Subject:* Re: [Freesurfer] manually specifying design matrix Thank you Doug. I am trying to create a design matrix for repeated measures anova. Lets say subjects A and B have been measured at sitting and standing positions. As the same subjects have been measured at the same positions, hence both the factors i.e subjects and positions are fixed factors. Hence a design matrix exploring the within subject effects of positions would be 1 0 1 0 0 1 1 0 1 0 0 1 0 1 0 1 The first two columns are position and the last two are the subjects. But mri_glmfit does not accept this design and I get the following error message: 'Matrix condition is 1e+08 ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class.' Looking forward to your suggestion Thanks in advance Raka *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* raka maitra rakamai...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu *Sent:* Thu, January 14, 2010 7:05:28 PM *Subject:* Re: [Freesurfer] manually specifying design matrix If you specify it manually, you don't specify groups, etc, or pass an fsgd file. You just create your design matrix pass it to mri_glmfit directly with the --X flag. doug raka maitra wrote: Hi all I want to specify a design matrix manually. In the usual pipeline for analysis in freesurfer, one specifies the groups, regressors in the fsgd and then when mri_glmfit is run, it creates the design matrix. For eg if I have two classes with 3 subjects each, in my fsgd, mri_glmfit would create the following design matrix 1 0 1 0 1 0 0 1 0 1 0 1 If I want to specify the above design matrix manually, how and where do I specify the groups, regressors ? Thanks in advance Raka ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] a question about rebuild_gca_atlas.csh
Hi, there, In rebuild_gca_atlas.csh, I read something like: # A talairach registration should be generated for this first subject as well, # in order to align the final atlas to the Talairach space. Is this talairach registration file the same as the talairach.xfm under each subject's /mri/transforms/ direcotry? Thanks! Guang _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/196390709/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] a question about rebuild_gca_atlas.csh
yes. be sure to double-check it with tkregister2. On Tue, 2010-01-19 at 12:24 -0600, Guang Zeng wrote: Hi, there, In rebuild_gca_atlas.csh, I read something like: # A talairach registration should be generated for this first subject as well, # in order to align the final atlas to the Talairach space. Is this talairach registration file the same as the talairach.xfm under each subject's /mri/transforms/ direcotry? Thanks! Guang __ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up now. ___ 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
Re: [Freesurfer] number of vertices per hemisphere using mri_glmfit
usually around 140k/hemi. If you make a label and save it as a label file it will have 1 line/vertex On Tue, 19 Jan 2010, Stefan Brauns wrote: Hi there, I am running surface based analysis of cortical thickness using FreeSurfer. Sometimes I constrain the analysis to certain regions of the brain, e.g. only frontal lobes. I would like to find out how many vertices per hemisphere are analysed with the mri_glmfit I am running. Is there a possibility to get these values from any of the log-files? What is the usual number of vertices per hemisphere? Many thanks, Stefan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] number of vertices per hemisphere using mri_glmfit
If you do: $mris_calc overlay stats the first line reported back will be the number of vertices. So, if you want to know how many vertices on the left hemisphere: $mris_calc lh.thickness stats and look at the Size[ XXX ] where XX will be number of vertices. Stefan Brauns wrote: Hi there, I am running surface based analysis of cortical thickness using FreeSurfer. Sometimes I constrain the analysis to certain regions of the brain, e.g. only frontal lobes. I would like to find out how many vertices per hemisphere are analysed with the mri_glmfit I am running. Is there a possibility to get these values from any of the log-files? What is the usual number of vertices per hemisphere? Many thanks, Stefan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FreeSurfer two atalses
Hi, there, Are there any place in FreeSurfer Wiki or journal paper explain why FreeSurfer need to atlases; Subcortical and Surface? Thanks! Guang _ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/196390706/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] brainmask
if one wants to get at the brain only (similar to bet), is brainmask.mgz the best file to use? on some of our data, we are noticing a lot of eyeball. i presume one can use aseg as an alternative. is this more recommended than brainmask.mgz? also, is the total brain volume computation based on aseg or some other file? cheers, satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] brainmask
aparc+aseg.mgz is probably better. See surfer.nmr.mgh.harvard.edu/fswiki/BrainVolume for the answer to your question. Satrajit Ghosh wrote: if one wants to get at the brain only (similar to bet), is brainmask.mgz the best file to use? on some of our data, we are noticing a lot of eyeball. i presume one can use aseg as an alternative. is this more recommended than brainmask.mgz? also, is the total brain volume computation based on aseg or some other file? cheers, satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Vol index to Talairach
Dear experts, I like to find Tarairach and MNI coordinate from volume index (data has been already processed with recon-all) off line using Matlab. Which transform should I use to find it ? Thank you. Hiroyuki ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] WM.mgz corrections in the ventricles Individual Normalization
Hello - I have two questions: 1) I noticed on wm.mgz volumes that were segmented properly, that even when the ventricles were automatically filled in, on some slices they are somewhat patchy (partially filled in with white, with some black/blank voxels). Do these patchy wm fill-ins require manual fill-ins to make them entirely opaque? I went through the tutorial, and it was not clear whether a patchy fill-in required a correction or not. 2) What is the best automated measurement that can be used to normalize an individual's cortical segmentation volumes for between subject comparison? We have been using gray+white volumes (why we need the ventrical volume processing to be consistent) - but not sure if ICV would be better individual normalizer. Thank you for your time - Sherri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
