Hi,
Now it seems to be working with the par file but I am getting this error. Any help will be appreciated. Thanks,
Meryem
Computing compensation for resdual AR1 bias 1 -0.5 -0.473129 (t=0.192235) 2 -0.25 -0.238292 (t=1.09283) 3 0 -0.00411884 (t=1.27811) 4 0.25 0.228971 (t=2.16243) 5 0.5 0.459511 (t=2.33787) AR1 Correction M: 0.00580007 1.07178 Computing contrast matrices OLS Beta Pass run 1 t= 0.0 Global Mean Global In-Mask Mean = ??? Error using ==> mrdivide Matrix dimensions must agree.
Error in ==> fast_selxavg3 at 399 RescaleFactor = flac0.inorm/gmean;
Hi,
I am trying to use selxavg3-sess function and getting this error. Below is the error I get. I actually have this fingertap.par file but freesurfer somehow does not see it. Any help would be appreciated.
Thanks!
Meryem Yucel PMI Lab
Extension format = nii.gz ERROR: opening /autofs/space/moe_002/users/mayucel/PROJECT/Subject20/bold/001/fingertap No such file or directory ??? Output argument "partype" (and maybe others) not assigned during call to "/usr/local/freesurfer/stable5_1_0/fsfast/toolbox/fast_ldpar4.m (fast_ldpar4)".
Error in ==> fast_ldpar4 at 45 par4 = [];
Error in ==> flac_customize at 121 [par partype] = fast_ldpar4(parpath);
Error in ==> fast_selxavg3 at 65 flac0 = flac_customize(flac0);
The mask used to compute the global mean does not have any voxels in it because the field of view is so small. Try running mkbrainmask-sess -s session -nero 1 -fsd bold Then run selxavg again. The above mkbrainmask command tells it to only erode the mask by one voxel (the default in preproc-sess is 3 which is removing all of them).
doug
Meryem Ayse Yucel wrote:
Hi,
Now it seems to be working with the par file but I am getting this error. Any help will be appreciated. Thanks,
Meryem
Computing compensation for resdual AR1 bias 1 -0.5 -0.473129 (t=0.192235) 2 -0.25 -0.238292 (t=1.09283) 3 0 -0.00411884 (t=1.27811) 4 0.25 0.228971 (t=2.16243) 5 0.5 0.459511 (t=2.33787) AR1 Correction M: 0.00580007 1.07178 Computing contrast matrices OLS Beta Pass run 1 t= 0.0 Global Mean Global In-Mask Mean = ??? Error using ==> mrdivide Matrix dimensions must agree.
Error in ==> fast_selxavg3 at 399 RescaleFactor = flac0.inorm/gmean;
Hi,
I am trying to use selxavg3-sess function and getting this error. Below is the error I get. I actually have this fingertap.par file but freesurfer somehow does not see it. Any help would be appreciated.
Thanks!
Meryem Yucel PMI Lab
Extension format = nii.gz ERROR: opening /autofs/space/moe_002/users/mayucel/PROJECT/Subject20/bold/001/fingertap No such file or directory ??? Output argument "partype" (and maybe others) not assigned during call to "/usr/local/freesurfer/stable5_1_0/fsfast/toolbox/fast_ldpar4.m (fast_ldpar4)".
Error in ==> fast_ldpar4 at 45 par4 = [];
Error in ==> flac_customize at 121 [par partype] = fast_ldpar4(parpath);
Error in ==> fast_selxavg3 at 65 flac0 = flac_customize(flac0);
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I tried this. It is still giving the same error. Should I check my mask files?
Thanks.
The mask used to compute the global mean does not have any voxels in it because the field of view is so small. Try running mkbrainmask-sess -s session -nero 1 -fsd bold Then run selxavg again. The above mkbrainmask command tells it to only erode the mask by one voxel (the default in preproc-sess is 3 which is removing all of them).
doug
Meryem Ayse Yucel wrote:
Hi,
Now it seems to be working with the par file but I am getting this error. Any help will be appreciated. Thanks,
Meryem
Computing compensation for resdual AR1 bias 1 -0.5 -0.473129 (t=0.192235) 2 -0.25 -0.238292 (t=1.09283) 3 0 -0.00411884 (t=1.27811) 4 0.25 0.228971 (t=2.16243) 5 0.5 0.459511 (t=2.33787) AR1 Correction M: 0.00580007 1.07178 Computing contrast matrices OLS Beta Pass run 1 t= 0.0 Global Mean Global In-Mask Mean = ??? Error using ==> mrdivide Matrix dimensions must agree.
Error in ==> fast_selxavg3 at 399 RescaleFactor = flac0.inorm/gmean;
Hi,
I am trying to use selxavg3-sess function and getting this error. Below is the error I get. I actually have this fingertap.par file but freesurfer somehow does not see it. Any help would be appreciated.
Thanks!
Meryem Yucel PMI Lab
Extension format = nii.gz ERROR: opening /autofs/space/moe_002/users/mayucel/PROJECT/Subject20/bold/001/fingertap No such file or directory ??? Output argument "partype" (and maybe others) not assigned during call to "/usr/local/freesurfer/stable5_1_0/fsfast/toolbox/fast_ldpar4.m (fast_ldpar4)".
Error in ==> fast_ldpar4 at 45 par4 = [];
Error in ==> flac_customize at 121 [par partype] = fast_ldpar4(parpath);
Error in ==> fast_selxavg3 at 65 flac0 = flac_customize(flac0);
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Sorry, this is a bug. The work-around requires that you: 1. Re-run mkbrainmask-sess without the "-nero 1" 2. cd into the mask directory in each run and run mri_binarize, like this cd /autofs/space/moe_002/users/mayucel/PROJECT/Subject20/bold/001/masks mri_binarize --i brain.nii.gz --o brain.e3.nii.gz --min 0.5 --erode 1 3. Then re-run selxavg3-sess
doug
Meryem Ayse Yucel wrote:
I tried this. It is still giving the same error. Should I check my mask files?
Thanks.
The mask used to compute the global mean does not have any voxels in it because the field of view is so small. Try running mkbrainmask-sess -s session -nero 1 -fsd bold Then run selxavg again. The above mkbrainmask command tells it to only erode the mask by one voxel (the default in preproc-sess is 3 which is removing all of them).
doug
Meryem Ayse Yucel wrote:
Hi,
Now it seems to be working with the par file but I am getting this error. Any help will be appreciated. Thanks,
Meryem
Computing compensation for resdual AR1 bias 1 -0.5 -0.473129 (t=0.192235) 2 -0.25 -0.238292 (t=1.09283) 3 0 -0.00411884 (t=1.27811) 4 0.25 0.228971 (t=2.16243) 5 0.5 0.459511 (t=2.33787) AR1 Correction M: 0.00580007 1.07178 Computing contrast matrices OLS Beta Pass run 1 t= 0.0 Global Mean Global In-Mask Mean = ??? Error using ==> mrdivide Matrix dimensions must agree.
Error in ==> fast_selxavg3 at 399 RescaleFactor = flac0.inorm/gmean;
Hi,
I am trying to use selxavg3-sess function and getting this error. Below is the error I get. I actually have this fingertap.par file but freesurfer somehow does not see it. Any help would be appreciated.
Thanks!
Meryem Yucel PMI Lab
Extension format = nii.gz ERROR: opening /autofs/space/moe_002/users/mayucel/PROJECT/Subject20/bold/001/fingertap No such file or directory ??? Output argument "partype" (and maybe others) not assigned during call to "/usr/local/freesurfer/stable5_1_0/fsfast/toolbox/fast_ldpar4.m (fast_ldpar4)".
Error in ==> fast_ldpar4 at 45 par4 = [];
Error in ==> flac_customize at 121 [par partype] = fast_ldpar4(parpath);
Error in ==> fast_selxavg3 at 65 flac0 = flac_customize(flac0);
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Meryem Ayse Yucel