[Freesurfer] error with fast_selxavg3

Hi, I am running into an error with fast_selxavg3 (NaN values in XtX). Other have people reported similar problems on the mailing list and I've tried implementing some of the suggestions (namely, using -nowhiten and checking that all events exist in my paradigm file), but I can't get rid of

Re: [Freesurfer] error with fast_selxavg3

Hi Doug, Thanks for your reply. Yes, it does work with a longer -refeventdur. In fact, I had tried that yesterday before posting my original message but I'd forgotten to make the corresponding changes to the 3rd column of the paradigm file and so kept getting the error message. The shortest I

[Freesurfer] Question about preproc-sess -no-subcort-mask

Hi, I would like to verify (as a sanity check and to make sure that I'm on the right track in my analysis) that preproc-sess runs with -no-subcort-mask by default in freesurfer-Darwin-lion-stable-pub-v5.2.0, but with -no-subcort-mask turned off by default in stablev5.3.0 on snowleopard. I

Re: [Freesurfer] Question about preproc-sess -no-subcort-mask

Hi again, Sorry, I didn't list all the commands I have been using: preproc-sess -s $subj -fsd bold -sliceorder odd -surface fsaverage lhrh -mni305 -fwhm 3 -per-run -force (and with -no-subcort-mask in v5.3.0 on snowleopard) mkanalysis-sess -fsd bold -stc odd -mni305 2 -fwhm 3 -paradigm

Re: [Freesurfer] Question about preproc-sess -no-subcort-mask

Hi Doug, Here it is. cheers, Leila From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Leila Reddy le...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, October 1, 2013 5:53 PM Subject: Re: Question about preproc

Re: [Freesurfer] Question about preproc-sess -no-subcort-mask

To: Leila Reddy le...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, October 1, 2013 6:57 PM Subject: Re: Question about preproc-sess -no-subcort-mask I have to say that I'm stumped. Do you really need to resolve this question? doug On 10/01/2013

[Freesurfer] Question about freesurfer coordinates

Hi, I've been trying to understand the FScoordinates powerpoint and I would like to ask a few questions (these questions might simply be about mri_convert, depending on where my confusion is...). 1) I think the orig.mgz volume is in the CRS space. Now, looking at slide 8 in the powerpoint, if

[Freesurfer] help with save_nifti

Hi, I am trying to save a nifti file using save_nifti. I'm running into a strange problem that I describe below. I have a nifti file (subj_mask.nii) created by a colleague using Nibabel (http://nipy.sourceforge.net/nibabel/). This volume is in the MNI305 space. Step1: In a first step I

Re: [Freesurfer] help with save_nifti

Hi Doug, Thanks for your reply. I have the problem even if I use MRIread and MRIwrite. But I have done a little more digging following your suggestions. Basically, there are differences in the output of mri_vol2surf (that I should have spotted earlier), as well as differences in the header

[Freesurfer] Download problem wih freesurfer-Darwin-lion-stable-pub-v5.2.0.dmg

Hi, I'm trying to install the latest Mac OSX 64bit FreeSurfer version but when I click on the download link I get an error: 550 Failed to change directory. I can't find a file with this filename in ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/ either. Is this version not yet available

[Freesurfer] selxavg error

Hi, I'm running into an error with selxavg ('Input to SVD must not contain NaN or Inf') that has been posted before on the mailing list but I couldn't find a solution to it. The command was selxavg-sess -sf sessid -df sessdir -analysis loc-sm3. The output of the log file is: selxavg-sess

Re: [Freesurfer] selxavg error

look pretty similar for all subjects. Could this be a divide by zero error somewhere in selxavg? And is there some way around it? Thanks in advance, Leila From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Leila Reddy le...@yahoo.com Cc: freesurfer

[Freesurfer] Error with selxavg-sess

Hi, I encountered an error with selxavg-sess -sf sessid -df sessdir -analysis loc-sm3. Looking through the archives I found that others had errors with selxavg-sess but the errors don't seem to be exactly the same as mine. Please let me know if you have any suggestions on how to get this to

[Freesurfer] orientation problem when converting from SPM .nii format to bshort

Hi, I am trying to convert SPM5 .nii files into bshort and I used the following command: mri_concat fkoch-0007*.nii --o bold/007/fspm_000.bshort The command seems to work in that I have a bunch of bshort files in my bold/007 directory but when I try to view the slices (using sliceview-sess

[Freesurfer] inorm-sess error

Hi, I'm trying to get around the problems from my previous post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07669.html I am now trying to use mri_convert to convert from nifti to bshort using the following command: mri_convert -i rfkoch-0021-00144-000144-00.nii -it nii -o

[Freesurfer] convert from MNI152 to native space

Hi, I have a binary mask from the WFU_Pickatlas. I think this mask in in the MNI152 space (when I load_nifti in Matlab I get dimensions of [91 109 91]. I would like to convert this mask into the native space of each subject. I tried the following command but the results do not look right in

[Freesurfer] Question about selxavg3-sess -no-con-ok

Hi,I was just wondering what exactly the -no-con-ok option does in selxavg3-sess. Is it the same as setting the weights for all conditions to 1 and give the baseline/fixation (i.e., 0s in the para files) a weight of 0? Thanks, Leila ___ Freesurfer

Re: [Freesurfer] convert from MNI152 to native space

out if the problem had been solved. The version of mni152reg I am using is$Id: mni152reg,v 1.9 2014/07/07 18:59:08 greve Exp $ on Mac OS 10.8. Thanks,Leila On Wednesday, June 15, 2016 11:55 AM, Leila Reddy <le...@yahoo.com> wrote: Hi, I have a binary mask from the WFU_Pickat

Re: [Freesurfer] convert from MNI152 to native space

to be there anymore. Thanks, Leila On Wednesday, June 15, 2016 11:55 AM, Leila Reddy <le...@yahoo.com> wrote: Hi, I have a binary mask from the WFU_Pickatlas. I think this mask in in the MNI152 space (when I load_nifti in Matlab I get dimensions of [91 109 91]. I would like to c

[Freesurfer] Dev builds not found

Hi,I get an error with mri_nu_correct.mni. I've seen on the FS wiki that this is because I have a new version of perl and that I should download the development version. However, I cannot access this page ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ (nothing happens on a linux

Re: [Freesurfer] Dev builds not found

Hi Bruce,Thanks for your reply. Does anyone on the list have access to the tar file of the latest dev build that they could put on some other site or in a public Dropbox folder? I totally changed my system and don't have a working version of Freesurfer/FS-FAST anymore and am pretty much

Re: [Freesurfer] Dev builds not found

Thanks! It's working now! On Sunday, September 18, 2016 10:34 PM, Leila Reddy <le...@yahoo.com> wrote: Hi Bruce,Thanks for your reply. Does anyone on the list have access to the tar file of the latest dev build that they could put on some other site or in a public Dropbox fol