Hi Aura,

1. What do you mean by “loading Matlab 8.2”? It should be Matlab 8.4 (2014b).

2. “Some still did”: what error did you get?

- Also, I’m confused by what you wrote, that subfields worked but hippocampal module didn’t (aren’t they the same thing?)

- Finally: can you please send us a screenshot of one of those abruptly cut hippocampi, so I better understand what might be going on?

Cheers,

/Eugenio

-- 

Juan Eugenio Iglesias

ERC Senior Research Fellow

Translational Imaging Group

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Hurtado, Aura Maria" <AHURTADO@mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, 21 March 2018 at 22:24
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampal Subfields Module, output error

Hi, 

I am attempting to use the longitudinal pipeline of the "hippocampal subfields and nuclei of amygdala”, but keep getting a flawed output. 

My dataset consists of images from a longitudinal study with some dropouts. First, I ran the reconall longitudinal pipeline in fs60 for all subjects. I got no errors. Then, I tried 

1. Running the longitudinal pipeline of the hippocampal module, loading Matlab 8.2 to run 

segmentHA_T1_long.sh SUBJ1_basetemplate

segmentHA_T1_long.sh SUBJ2_basetemplate

etc

I got an error in most of these jobs (mostly for templates of subjects with multiple visits) that read

"ERROR: MatlabObjectArray(0x7fd7ce84cea0): Trying to access non-existing object (25)

Error in kvlGetOptimizer (line 11)

Error in SegmentSubfieldsT1Longitudinal (line 1155)”

2. I then tried running the cross sectional pipeline for each one of the timepoints in subjects already processed by the reconall longitudinal pipeline (i. e. segmentations in the  .long. directories) 

segmentHA_T1.sh SUBJ1_timepoint1.long.SUBJ1_basetemplate

segmentHA_T1.sh SUBJ1_timepoint2.long.SUBJ1_basetemplate

segmentHA_T1.sh SUBJ2_timepoint1.long.SUBJ2_basetemplate

segmentHA_T1.sh SUBJ3_timepoint1.long.SUBJ3_basetemplate

etc

Most of them ran without errors, but some still did.

3. I then tried to run the cross sectional hippocampal module for all subjects/timepoints without using the reconall longitudinal pipeline 

segmentHA_T1.sh SUBJ1_timepoint1

segmentHA_T1.sh SUBJ1_timepoint2

segmentHA_T1.sh SUBJ2_timepoint1

segmentHA_T1.sh SUBJ3_timepoint1

etc

They were processed without errors. But when inspecting the processing log, there was a message that appeared 4 times in the file

"WARNING: Registration did not converge in 5 steps! 

*          Problem might be ill posed. 

*          Please inspect output manually!

………

……..

…...

Everything done!

It took 766.0135 seconds “

With manual inspection, subfield segmentations output by fs60 seemed fine in all the directories of the reconall cross sectional and longitudinal outputs (hippoSfLabels-T1). For the Hippocampal Module outputs (hippoAmygLabels-T1), the hippocampus was abbruptly cut, sometimes laterally, sometimes dorsally. This was the case for all three analyses. 

I wonder what is the problem and what I can do to fix it so I can successfully run the longitudinal pipeline of the "hippocampal subfields and nuclei of amygdala”

Thanks for your help!

Aura M.