On Thu, Dec 15, 2016 at 9:15 PM, Clare Kelly <[log in to unmask]> wrote:

Hello wise ones,

I am having a hard time getting a 3-level group analysis to run. I am on a shared server using SLURM.
I have set up a fixed-effects analysis with 19 subjects (3 lower level directories each, with 12 copes per dir). The analysis runs up to the point of the stats in cope1.feat and then, as far as I can tell, this odd thing happens where the stats directory (which did exist) gets replaced by a file containing the number 36.

Could it be that for some weird reason, the following line of the script is actually replacing the stats directory with the dof file:
/bin/rm -f stats/zem* stats/zols* stats/mask* ; /bin/mv dof stats

Does that make sense? The full error is below. We did have an fsl_sub problem earlier which I thought was sorted but could it be that again> Would love your ideas on how to fix this one! Boo to missing the OHBM deadline!

Thank you!
Clare

Progress Report / Log
Started at Thu Dec 15 17:38:12 GMT 2016<p>
<pre>

cp -r ../.files .files
couldn't change working directory to "/projects/pi-kellyc58/HPC_16_00936/anderson_ADHD/groups/fixed_effects_18subs_20161215.gfeat/cope1.feat/stats": no such file or directory
    while executing
"if { [ catch {

for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
    switch -- [ lindex $argv $argindex ] {

        -I {
            incr arginde..."
    (file "/home/support/tcin/apps/fsl/5.0.9/bin/feat" line 309)
Error encountered while running in main feat script, halting.
couldn't change working directory to "/projects/pi-kellyc58/HPC_16_00936/anderson_ADHD/groups/fixed_effects_18subs_20161215.gfeat/cope1.feat/stats": no such file or directory
</pre><hr>Higher-level stats<br><pre>

cat ../design.lcon | awk '{ print  }' > design.lcon

/home/support/tcin/apps/fsl/5.0.9/bin/fslsplit mask tmpmask -z

/home/support/tcin/apps/fsl/5.0.9/bin/fslsplit filtered_func_data tmpcope -z

/home/support/tcin/apps/fsl/5.0.9/bin/fslsplit var_filtered_func_data tmpvarcope -z

/home/support/tcin/apps/fsl/5.0.9/bin/fslsplit tdof_filtered_func_data tmptdof -z
/home/support/tcin/apps/fsl/5.0.9/bin/flameo --cope=tmpcope0000 --vc=tmpvarcope0000 --dvc=tmptdof0000 --mask=tmpmask0000 --ld=stats0000 --dm=design.mat --cs=design.grp --tc=design.con  --runmode=fe

/bin/rm -f stats/zem* stats/zols* stats/mask* ; /bin/mv dof stats
</pre><hr>Post-stats<br><pre>