What's your command line? Looks like you might be putting a slash (/) as the first character to your glmdir. You will not have permissions to create this directory.

doug

Chindhuri Selvadurai wrote:

I am actually getting an error message when I type my mri_glmfit command:

ERROR: fio_pushd: /group_analysis/volume/m1/mstmct_v_base/type_v_rest ERROR: must specify input y file

I did specify a y file and I do not know what fio_pushd is.

...

This is controlled by the $FSF_OUTPUT_FORMAT. By default this is compressed nifti (nii.gz). Both nii and nii.gz store the same information. The nii.gz is compressed, so you save some space.

doug

Chindhuri Selvadurai wrote:

...

Hi freesurfers,

I am trying to run an analysis right now, however, after using isxconcat, I am only finding ces.nii.gz files in the output directory and no .nii files.

output dir: /cluster/manoach/milton/subjects/group_analysis/volume/m1 subjects_dir: /cluster/manoach/milton/subjects

command: mri_glmfit --y /group_analysis/volume/m1/mstmct_v_base/type_v_rest/ces.nii.gz --glmdir group_analysis/volume/m1/ --osgm

Not sure why this is the case.. any help would be appreciated! Thanks! _______________________________________________ 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

Best,

Chindhuri Selvadurai

Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307