All,

I'm encountering an error when I run selxavg3-sess and I am not sure how to get around the problem, or what it means.

I am running the following command, which has worked with the data for the other participants in my study.

selxavg3-sess -s c43 -d . -analysis Flanker_nResp -overwrite

Several minutes in I am getting the following error...

GLS Beta Pass run 1 t= 0.0 Loaded /ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/006/flanker_nResp.par as a par3 file. run 2 t= 5.7 Loaded /ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/007/flanker_nResp.par as a par3 file. run 3 t=11.3 Loaded /ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/008/flanker_nResp.par as a par3 file. run 4 t=17.1 Loaded /ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/009/flanker_nResp.par as a par3 file. run 5 t=22.7 Loaded /ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/010/flanker_nResp.par as a par3 file. GLS Residual Pass /users/aholmes/.bashrc: line 229: SetUpFreeSurfer.sh: No such file or directory run 1 t= 0.0 Loaded /ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/006/flanker_nResp.par as a par3 file. ??? Error using ==> fclose Invalid file identifier. Use fopen to generate a valid file identifier.

Error in ==> save_nifti at 162 fclose(fp);

Error in ==> MRIwrite at 145 err = save_nifti(hdr,fspec);

Error in ==> fast_selxavg3 at 634 MRIwrite(rrunmri,fname);

...

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ERROR: fast_selxavg3() failed\n

Does anyone know what might be going on and/or how I can correct the problem?

Thanks, Avram

Jurgen,

To create thickness difference maps, follow the instructions on this page:

http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility

In your case, you would skip step 1, since the recon-all -long will create the .lta transform (from tp1 to tp2) already (look for it in the tp2subj/mri/transform dir). You can use this .lta file to transform the T1.mgz image in tkmedit, so that they are in the same stereotactic space, for viewing.

If you are not doing a group analysis, then you only need to run step 2, mri_thickness_diff, which creates the overlay file. Note that smoothing is not done (as was the case in the thickness repeatability study from which these steps originate).

You would do mri_surf2surf if doing a group analysis, per the instructions.

Nick

On Mon, 2009-02-16 at 18:42 +0100, J=?ISO-8859-1?B?/A==?=rgen H=? ISO-8859-1?B?5A==?=nggi wrote:

Dear FS experts

I had run recon-all -long on two time points and would like to subtract the cortical thickness maps of the two time points.

Do the two ?h.thickness maps of the different time points are already in the same space so that they can be directly subtracted in MATLAB?

Or

Do I have to use mri_surf2surf to register them before I can subtract them?

Do you recommend smoothing the thickness maps?

When looking at T1.mgz with the overlaying aseg the images of the two time points are not in the same stereotactic space: hence, I would like to known whether this is also the case for the thickness maps.

Sorry for reposting this question

Thanks Regards Jürgen

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