[Freesurfer] summing across FIR timepoints

[Ellen Lau]

Hi,

We ran a first-level FIR analysis on our functional data with selxavg3-sess, 
which outputs a single ces.nii file for each subject containing the contrast 
images for all timepoints. Now we would like to create an image representing 
the sum of a subset of these images in a time-window of interest (e.g. 
contrast4s + contrast6s + contrast8s) and then bring this single 4-8s contrast 
for each subject forward to the second-level (presumably by concatenating these 
summed 4-8s images into a single file that mri_glmfit will accept). Could 
someone advise us on the best way to do these two steps? 

thanks,
Ellen
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[Freesurfer] mri_convert with flash - FS 4.5.0 vs 5.0

[Ellen Lau]

Hi,

We're having trouble using mri_convert as wrapped within mne_flash_bem to
create the bem surfaces from our FLASH volumes. The script runs but the
inner_skull and outer_skull surfaces that it outputs seem to be rotated,
for example if we display the surfaces on the T1 coronal, we see what
looks like the sagittal inner_skull surface.

I'm guessing this is some kind of registration problem. I noticed that we
are getting a warning at one point in the process when the flash is being
registered with the MPRAGE, which I've pasted below.

I am wondering if this might have something to do with the switch to
version 5.0.0. For this dataset, we ran the reconstruction and all the
subsequent processing on v5.0.0. However, I have gotten the exact same
error (rotated inner and outer skull surfaces) when I accidentally ran
mne_flash_bem in v5.0 with a previous dataset that was reconstructed in
v4.5.0. When I re-ran mne_flash_bem in v4.5.0 the surfaces came out
correctly for the previous dataset. But I was reluctant to try this with
my new dataset since ideally we'd like to be able to switch completely
over to v5.0.0.

Thanks,
Ellen

---
[kerryave:test] (nmr-std-env) which mri_convert
/usr/local/freesurfer/stable5/bin/mri_convert

setenv SUBJECTS_DIR /cluster/kuperberg/SemPrMM/MRI/structurals/subjects/


selected output from mne_flash_bem containing the warning:

/autofs/cluster/kuperberg/SemPrMM/MRI/structurals/subjects/ya1/mri/flash/parameter_maps
mri_convert ./fsl_rigid_register.7595/outvol.fsl_rigid_register.nii
flash5_reg.mgz
mri_convert ./fsl_rigid_register.7595/outvol.fsl_rigid_register.nii
flash5_reg.mgz
$Id: mri_convert.c,v 1.166.2.4 2010/09/20 17:29:33 nicks Exp $
reading from ./fsl_rigid_register.7595/outvol.fsl_rigid_register.nii...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 5.63785e-17)
j_ras = (0, 3.67872e-08, -1)
k_ras = (0, 1, -1.5134e-08)
writing to flash5_reg.mgz...
/autofs/cluster/kuperberg/SemPrMM/MRI/structurals/subjects/ya1/mri/flash/parameter_maps
mri_copy_params flash5_reg.mgz flash5.mgz flash5_reg.mgz
WARNING: volume sizes are different
in_vol : 256, 256, 256
  temp_vol : 256, 256, 176
Cleaning up


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