Thanks, Aura.

What exact version of FreeSurfer are you using? I’m assuming it’s a development version, but from when? The results are indeed weird…

 

-- 

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: Friday, 23 March 2018 at 05:28
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Hippocampal Subfields Module, output error

 

Hi Eugenio, 

 

Thank you for replying so quickly to my lengthy message. I correct some of my statements,

 

1. Matlab 8.4 was used (not 8.2)

2. When I ran the cross-sectional subfield command, I did not get exit errors as I did with the longitudinal command (kvlGetOptimizer). I got output errors and warnings of non convergence in the log file. 

 

-I see your point. I mean the built-in hippocampal module (v10) worked when reconall was run with fs60 (hippoSf). When run independently, the hippocampal module (v21) exited with errors when using segmentHA_T1_long.sh, and the output was off when using segmentHA_T1.sh (this is better seen in pic 3). I hope this clarifies a bit. Please tell me if it doesn’t.

 

These are screenshots of the images output by jobs that exited without processing errors:

Pic 1 is an overlay of:

rh.hippoAmygLabels-T1 and lh.hippoAmygLabels-T1 output by segmentHA_T1_long.sh SUBJ1_timepoint1.long.SUBJ1_basetemplate 

aseg and T1 output by fs60 reconall -long

(I am now noticing these *.long.* directories contain hippoSfVolumes text files, but not hippoSfLabels mgz files...)

 

 

Pic 2 is an overlay of:

rh.hippoAmygLabels-T1 and lh.hippoAmygLabels-T1 output by segmentHA_T1.sh SUBJ1_timepoint1.long.SUBJ1_basetemplate 

aseg and T1 output by fs60 reconall

 

 

 

Pic 3 is an overlay of:

rh.hippoAmygLabels-T1 output by segmentHA_T1.sh SUBJ1_timepoint1 

aseg, T1 and lh.hippoSfLabels-T1.v10 output by fs60 reconall

 

 

 

Thanks again

 

Aura M.

 

 

 

 



On Mar 21, 2018, at 6:33 PM, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk> wrote:

 

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

 

 

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.

 

 

 

 

 

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