The km.hb.tac.nii.gz is not a volume. It is a single voxel of data stored in nii format. This format is needed to input to mri_glmfit. Try loading it in matlab, eg,

hb = fast_vol2mat( MRIread('km.hb.tac.nii.gz')); plot(hb)

if that is all 0s then it will surely cause mrtm1 to fail.

doug

On 01/07/2016 11:40 PM, Jonathan DuBois wrote:

Hi Freesurfer developers,

I’m trying to perform BP analysis with mri_glmfit —mrtm1. I ran mri_gtmpvc without PVC, which finished without error. However, the km.hb.tac.nii.gz appears empty when I open it with fslview or tkmedit, although this may be due to the nature of the file (I’m not sure what it is supposed to show). The km.ref.tac.dat and km.hb.tac.dat are normal. Please let me know what you think.

The command and error: mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o mrtm1 --no-est-fwhm --nii.gz Segmentation fault (core dumped)

Where time.dat is a text file with the time (in seconds) of each frame: 0 30 60 90 120 150 180 240 300 360 420 540 660 780 900 1020 1140 1260 1380 1620 1860 2100 2400 2700 3000 3300

I’m using the linux version 6 beta downloaded on Oct. 30th freesurfer-Linux-centos4_x86_64-dev-20151030

Best, Jonathan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer