[Freesurfer] fast_selxavg3.m - ERROR: design is ill-conditioned

/bin/selxavg3-sess -s subj008_10block -analysis improv.10blocks.sm05.lh $Id: selxavg3-sess,v 1.60 2011/12/09 20:03:03 greve Exp $ uid=8240(preciado) gid=8240(preciado) groups=8240(preciado),160(fsdev),1071(birn),1107(fddev),1576(tbi) /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast Linux quito

[Freesurfer] mergecontrasts-sess - Comparisons between subjects

Is it possible to do a conjunction analysis between subjects using one contrast? So far I've been able to do comparisons between contrasts within subjects but not between subjects. Thanks, -Ronny ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] FS-FAST - ERROR: mapping surfaces

Thanks Doug, I did make some manual edits to wm.mgz and brainmask.mgz then reran the subject a couple times using: recon-all -autorecon2-wm -subjid subj007 Shouldn't -autorecon2-wm run through -autorecon2 and -autorecon3? Will running 'recon-all -make all -s subj007' do away with my manual edits?

[Freesurfer] FS-FAST - ERROR: mapping surfaces

ast -fsd bold -update $Id: stc-sess,v 1.10 2011/02/24 20:19:03 greve Exp $ quito subj007 - Fri Jun 7 10:50:49 EDT 2013 -rw-rw-r-- 1 preciado birn 379957459 Jun 7 10:00 /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/fmcpr.siemens.nii.gz -rw-rw-r-- 1 preciado b

Re: [Freesurfer] FS-FAST motion correction / register

If anything I was thinking of removing the first two time points, as those are going to get nixed anyway. I was hoping it wouldn't come to that but i f that's the only way... -Ronny > Hi Ronny, the time point used to as the template is hard-coded to be the > middle time point. If this is just the

[Freesurfer] FS-FAST motion correction / register

One of my subjects exhibited motion during the middle time point of one the functional scans. FS-FAST then reads all other time points as having a significant amount of motion because the subject was out of place during the point that is marked as the origin. Is there some way that I can set a diff

Re: [Freesurfer] Problem with aseg - Other segmentations fine

Yes, the white surface is actually pretty good all around. I am actually concerned about how the conditions that created the poor aseg segmentation would impact any subcortical analysis. I am not entirely clear what the impact of this segmentation could be and how (besides a voxel by voxel correcti

Re: [Freesurfer] Underestimated Pial surface - after deleting problematic voxels

has a time/date stamp from the last time I executed recon-all -autorecon-pial... -rw-rw-r-- 1 preciado birn 1416877 Mar 26 22:23 brain.finalsurfs.manedit.mgz -rw-rw-r-- 1 preciado birn16605 Mar 27 09:39 brain.finalsurfs.mgz A more basic question, I am assuming that -autorecon-pial defaul

[Freesurfer] fs-fast processing questions

Hello all, I am starting to run some analysis using fs-fast and I had a few basic questions that I couldn't find answers on the wiki/tutorial. 1) Format of files for mkanalysis-sess -tpexclude tpexclude.dat What is the format of the input file for -tpexclude? Is it simply a single column of intege

Re: [Freesurfer] Permission denied - could not open lh.BA3b.thresh.label

I am thinking that that's possible. Same command with same type of parameters executed successfully before the failure, and now previously failed command is working. I will try it again... Thanks for the input. -Ronny > > Probably a network glitch? I'd try restarting it and seeing if the error >

Re: [Freesurfer] Permission denied - could not open lh.BA3b.thresh.label

It looks like this is the first *thresh.* label that caused the problem. The following command ran and executed properly just before the error message on the log. mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh

[Freesurfer] Permission denied - could not open lh.BA3b.thresh.label

Hello, I ran recon-all and left it running Friday afternoon/evening. When I next checked it this morning, the script had finished with errors. Looks like there was a problem with the file: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label /clus

[Freesurfer] tkregister2 error

Dear list, I'm having problems with the tkregister2 command, I input the following command: tkregister2 --mov ~/Desktop/input/*_d/mri/rawavg.mgz --noedit --s *_d --regheader --reg ~/Desktop/input/*_d/mri/register.dat Where I'm setting the directory of my subjects, and I get the following outp