[Freesurfer] Fixed-Effects Analysis carried out by mri_glmfit

Hi Freesurfers, I am working with fsfast, and interested in doing a 2nd-level fixed effects analysis over a number of subjects. However, the volumes I'm using aren't in a standard freesurfer space (native, talraich, etc.). They are nx1x1 volumes containing results from n ROIs. While I got fi

Re: [Freesurfer] Fixed-Effects Analysis carried out by mri_glmfit

Thanks Doug, I had forgotten that my roadblock was actually in isxconcat_sess, not mri_glmfit. This worked out great. Following this up, how would you recommend calculating the fixed-effects significance of a complex (within subject) contrast with mri_glmfit? For simple contrasts, I have been

Re: [Freesurfer] Fixed-Effects Analysis carried out by mri_glmfit

oug > > > On 11/25/2013 01:35 PM, Clark Fisher wrote: >> Thanks Doug, >> >> I had forgotten that my roadblock was actually in isxconcat_sess, not >> mri_glmfit. This worked out great. >> >> Following this up, how would you recommend calculating th

Re: [Freesurfer] Fixed-Effects Analysis carried out by mri_glmfit

, and it would not take into account the covariance in the measurements from a single subject. Another approach would be to do separate tests for each condition at the group level, then do a type of conjunction analysis to implement the OR. Let me know if you want to pursue that approach. doug

Re: [Freesurfer] Fixed-Effects Analysis carried out by mri_glmfit

ccount the covariance in the measurements from a single subject. Another approach would be to do separate tests for each condition at the group level, then do a type of conjunction analysis to implement the OR. Let me know if you want to pursue that approach. doug On 11/26/13 4:02 PM, Clark Fis

Re: [Freesurfer] Fixed-Effects Analysis carried out by mri_glmfit

Hi Doug (and other Freesurfers), Hope you had a pleasant Thanksgiving. My thread last left off before everyone left for the holidays. I just wanted to re-raise this question, as it's still a pressing one for me. Thanks, Clark On Nov 27, 2013, at 11:06 AM, Clark Fisher mailto

Re: [Freesurfer] Fixed-Effects Analysis carried out by mri_glmfit

e contrast you are interested in. Does that > make sense? > doug > > > On 12/02/2013 12:27 PM, Clark Fisher wrote: >> Hi Doug (and other Freesurfers), >> >> Hope you had a pleasant Thanksgiving. My thread last left off before >> everyone left for the holida

[Freesurfer] Concatenating Transforms

Hi everyone, What is the best way to concatenate transforms (register.dat files, .lta files, etc.)? I'm interested in registering functional data to a structural in another session using a functional to in-session anatomical registration combined with a in-session anatomical to out-of-session

Re: [Freesurfer] Concatenating Transforms

Hi Doug, I do plan to manually align the functionals to the structural as a final step, but our epi scans look different enough from our T1s that I want to use this as a starting point. Also, combining transforms is something I've wanted to be able to do a few times now as I explore different

[Freesurfer] FDR Correction of NHP Surface Data

Hi Freesurfers, I have another monkey-specific question. I'd like to output FDR-corrected signficance surface maps for my monkey data, or at least FDR-threshold the maps. It seems like mri_surfcluster might be one way to go about this however: 1) I don't have any .xfm files for my monk

Re: [Freesurfer] FDR Correction of NHP Surface Data

Ok, maybe I'm making this question too intricate. Here's the short version: How can I FDR correct painted surface significance maps when I have no talraich .xfm file and no cortical segmentation? Thanks again, Clark Hi Freesurfers, I have another monkey-specific question. I'd like to output

Re: [Freesurfer] FDR Correction of NHP Surface Data

configure overlay interface. > > cheers > Bruce > On Tue, 28 Aug 2012, Clark Fisher wrote: > >> Ok, maybe I'm making this question too intricate. Here's the short version: >> How can I FDR correct painted surface significance maps when I have no >> talr

Re: [Freesurfer] FDR Correction of NHP Surface Data

ore than I trust my own. -Clark On Aug 28, 2012, at 2:34 PM, Sebastian Moeller wrote: > Hi Clark, > > > On Aug 28, 2012, at 11:15 AM, Clark Fisher wrote: > >> Hi Bruce, >> >> Thanks. I actually have used this function of tksurfer, but am looking for >&g

Re: [Freesurfer] FDR Correction of NHP Surface Data

uster. Best, Michael On Wed, Aug 29, 2012 at 2:08 PM, Clark Fisher mailto:cfis...@mail.rockefeller.edu>> wrote: Hi Sebastian, I think you are right, both about tksurfer thresholding and the correct interpretation of FDR. As you point out though, there is some value in having maps that s

Re: [Freesurfer] FDR Correction of NHP Surface Data

ait for Doug to get back. Can you repost at the end of next > week? > Bruce > > > On Thu, 30 Aug 2012, Clark Fisher wrote: > >> Thanks Michael, I'll look into Nipy's FDR tools. I actually started this >> thread asking for help getting mri_surfcluster runn

Re: [Freesurfer] FDR Correction of NHP Surface Data

Per Bruce's suggestion, I'm reposting this now. A synopsis: I'm looking for a way to correct painted statistical maps for multiple comparisons using Freesurfer's tools, without having segmentation or any .xfm files. Thanks, Clark On Aug 23, 2012, at 10:09 AM, Clark

[Freesurfer] Phase Encoding Direction and epidewarp.fsl

Hi everyone, I recently switched the phase encoding direction of the functional sequence I've been using from F >> H to R >> L and ran into a problem with epidewarp.fsl (in version 4). The unwarping was still happening along the F >> H axis in the new images where phase encoding was R >> L.

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

Thanks Doug, Would the proper way to handle this then be to switch the rows and columns before unwarping, then switch them back before the further processing steps? -Clark ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

t; to begin with. What did you use to convert the dicoms to nifti? > doug > > On 11/13/2012 11:59 AM, Clark Fisher wrote: >> Thanks Doug, >> >> Would the proper way to handle this then be to switch the rows and columns >> before unwarping, then switch them back b

[Freesurfer] ROI analysis and whitening in fsfast

Hi everyone, In a previous discussion on this list (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17681.html), Pablo Polosecki was asking the best way to perform hypothesis testing using functional data within an ROI. The final opinion was that it was best to average all of th

Re: [Freesurfer] ROI analysis and whitening in fsfast - Percent activity change

at cesvarpct.nii contains? Thanks again, Clark Hi Clark, On 02/06/2013 05:55 PM, Clark Fisher wrote: > Hi everyone, > > In a previous discussion on this list > (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17681.html), > Pablo Polosecki was asking the best w

Re: [Freesurfer] ROI analysis and whitening in fsfast - Percent activity change

-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20130213> 1). Yes 2) Right, pull the scale outside of the sqrt() doug On 02/13/2013 03:36 PM, Clark Fisher wrote: > Hi Doug, > > Thanks for the help, that seemed to worked great. I have a few > follow up questions abou

Re: [Freesurfer] ROI analysis and whitening in fsfast - Percent activity change

it > > > On 02/14/2013 07:25 AM, Clark Fisher wrote: >> Hi Doug and the list, >> >> I think I still have a problem understanding what cesvar.nii contains. As a >> sanity check, I tried to create 95% confidence intervals around my CES. I >> found that in s

[Freesurfer] register.dat Matrix Conventions

Hello, I was wondering what orientation conventions are used when calculating the affine transformation matrix in register.dat. For an example, I'll use the data from subject 101 of the fsfast tutorial. According to mri_info, the functional volume is in LPS orientation, and the processed anato

Re: [Freesurfer] register.dat Matrix Conventions

k, have you looked at this documentation yet? http://www.freesurfer.net/fswiki/CoordinateSystems?action=AttachFile&do=get&target=fscoordinates.ppt doug Clark Fisher wrote: Hello, I was wondering what orientation conventions are used when calculating the affine transformation matrix in regist

Re: [Freesurfer] register.dat Matrix Conventions

Thanks Sebastian and Doug, that clears everything up. -Clark On Sep 26, 2011, at 11:27 AM, Douglas N Greve wrote: > > > Clark Fisher wrote: >> Hi Doug, >> >> Thanks for pointing me back to that; I had forgotten how much depth it >> goes into! I have 2 rema

[Freesurfer] ribbon.mgz Without aseg.mgz

Hello, I'm working with primate data, and I'm wondering: is there any way to create a ribbon.mgz file from surfaces since I don't have aseg.mgz? I can't seem to run mris_volmask without it, and running reconall -autorecon3 -noaseg did not output ribbon.mgz. Thanks for the help, Clark _

Re: [Freesurfer] ribbon.mgz Without aseg.mgz

ote: > Hi Clark > > I think you can just call mri_ribbon directly using say the orig.mgz as > the input_volume_pref. > > cheers > Bruce > On Mon, 6 Feb 2012, Clark Fisher wrote: > >> Hello, >> >> I'm working with primate data, and I'm

[Freesurfer] niiRead(): unsuported datatype 64

Hi all, I'm trying to use Freesurfer to work with a parameter map saved as a nifti volume by another package (mrVista). However, whenever I try to open it using a Freesurfer tool (tkmedit, mri_info, freeview, etc.) I get the following error : niiRead(): unsuported datatype 64 (with scl_slope

[Freesurfer] mri_convert and --out_orientation (once again)

Hi everyone, I have looked through the mailing list, and read a number of threads on using (or rather not using) mri_convert to change the orientation of a volume, and I have read the mri_convert help, which says about the --in_orientation and --out_orientation flags: "This is only to

Re: [Freesurfer] mri_convert and --out_orientation (once again)

Thanks Doug, In that case, since everything seems to be working as I want it to, I'm going to leave it as-is. Do you think that this is likely to change back to it's intended (pixel data ignoring) function in future versions, or can I continue to use it like this? -Clark __