[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 maili

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

Sorry I meant to ask if the weight for the baseline/fixation is set to -1 (not 0). Thanks,Leila On Tuesday, May 31, 2016 1:44 PM, Leila Reddy wrote: 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

[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 Free

Re: [Freesurfer] convert from MNI152 to native space

seem to be there anymore. Thanks, Leila On Wednesday, June 15, 2016 11:55 AM, Leila Reddy 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 convert this mas

Re: [Freesurfer] convert from MNI152 to native space

n't figure 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 wrote: Hi, I have a binary mask from the WFU_Pickatlas. I thi

[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 mach

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 stuck.

Re: [Freesurfer] Dev builds not found

Thanks! It's working now! On Sunday, September 18, 2016 10:34 PM, Leila Reddy 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 folder? I totally chang

[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 firs

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 para.pa

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

Hi Doug, Here it is. cheers, Leila From: Douglas N Greve To: Leila Reddy Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Tuesday, October 1, 2013 5:53 PM Subject: Re: Question about preproc-sess -no-subcort-mask Hmmm, not sure what to say. CA

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

Hi Doug, Now that I know that I wasn't inadvertently making a stupid mistake in my analysis, and I also know how to get around the problem, I don't really need to solve it anymore. Thanks for your time. Leila From: Douglas N Greve To: Leila

[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 I

[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 wan

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 info

[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] 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 the

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] 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 log

Re: [Freesurfer] selxavg error

litude profiles 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 To: Leila Reddy Cc: freesurfer@nmr.mgh.harvard.edu Sent: Fri, M

[Freesurfer] Error with mc-sess

Hi, I recently installed freesurfer, AFNI etc but am having problems with mc-sess. The script runs and gets to the stage in each run where it calls up matlab, enters the MRIwrite command but then gives the message below. It then hangs. >> >> >> >> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pc

[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 wor

[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 fo

[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 fs