Hi Clara,
more likely there is a problem with your sever (e.g. disk IO problems).
The label intersection works like this:
For each subject it copies the of the first time point to rh.cortex.label
to the base directory as:
rh.long.cortex.label
it then intersect the label with the one from the next time point and overwrites the rh.long.cortex.label.
(you can find the two commands in your email below). Try running them manually on the server. Also look at each output to check if it was corrupted.
Best, Martin
On 05/26/2017 04:08 PM, Clara Kühn wrote:
Hi everyone,
it seems the error isn't hemisphere specific after all. It shows up on 1 subject in the left hemisphere, too (just later in the subject list). Weirdly the subjects that produce the error on the right hemisphere are different one than those producing the error when working on the left hemisphere.
I've also narrowed the problem down to server-vs-local hard drive. We have a server at work that I work on that emulates a hard drive which is where the error occurs. When I tried running the same command again on my local hard drive it worked fine.
Is there some bug in the program that has problems when running it remotely?
Cheers, Clara
----- Weitergeleitete Mail ----- Von: "ckuehn" ckuehn@cbs.mpg.de An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 24. Mai 2017 19:00:51 Betreff: [Freesurfer] error in long_mris_slopes
Dear Freesurfer experts,
I'm running into some problems when running the long_mris_slopes command (longitudinal 2 stage model) to get the rate of change for thickness and area for each hemisphere.
This is the command I ran:
for i in thickness area ; do for j in rh ; do
long_mris_slopes --qdec $SUBJECTS_DIR/qdec/39kids-covariates-MT2-1.dat --meas ${i} --hemi ${j} --do-rate --do-stack --do-label --time years --qcache 81kids_template --sd $SUBJECTS_DIR donedone
For the left hemisphere everything works fine but for the right hemisphere it stops working at my second subject and I get the following error:
ERROR -6 : mris_label_calc intersect did not work?
This is the terminal output for said subject: Subject-Template: BJ4K.base
INFO: 2 TPs in BJ4K.base , mean age: 0.041095
=============================================================================== SUBJECT BJ4K.base Intersecting Within-Subject Cortex Label
cp /data/p_npsy001_neurotrain/kids_data/39kids-sem-con-3goodscans/semcon-3goodscans2-1/BJ4K_1.long.BJ4K.base/label/rh.cortex.label /data/p_npsy001_neurotrain/kids_data/39kids-sem-con-3goodscans/semcon-3goodscans2-1/BJ4K.base/label/rh.long.cortex.label
mris_label_calc intersect /data/p_npsy001_neurotrain/kids_data/39kids-sem-con-3goodscans/semcon-3goodscans2-1/BJ4K_2.long.BJ4K.base/label/rh.cortex.label /data/p_npsy001_neurotrain/kids_data/39kids-sem-con-3goodscans/semcon-3goodscans2-1/BJ4K.base/label/rh.long.cortex.label /data/p_npsy001_neurotrain/kids_data/39kids-sem-con-3goodscans/semcon-3goodscans2-1/BJ4K.base/label/rh.long.cortex.label
mris_label_calc: malloc.c:2392: sysmalloc: Assertion `(old_top == initial_top (av) && old_size == 0) || ((unsigned long) (old_size) >= MINSIZE && prev_inuse (old_top) && ((unsigned long) old_end & (pagesize - 1)) == 0)' failed. ERROR -6 : mris_label_calc intersect did not work?
I've googled a bit and suggestions were a memory problem but I don't think that's the case if it is hemisphere specific and the first subject in the list works fine...
I've also attached the input file.
What could be the problem and how can I fix it? Cheers Clara