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: [cid:0CDB6186-1903-4AD2-AE6C-261FBC2A8F2C@piaguest.partners.org] 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...)

[cid:6F3B0870-51B4-43A7-BC65-67217B1A00FE@piaguest.partners.org] 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

[cid:CE691785-1220-4743-9855-3753D7F7E7BC@piaguest.partners.org] 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.ukmailto: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 http://www.jeiglesias.comhttp://www.jeiglesias.com/ http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Hurtado, Aura Maria" <AHURTADO@mgh.harvard.edumailto:AHURTADO@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, 21 March 2018 at 22:24 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto: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.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Thanks, Eugenio. We used the stable 6 version for reconall: reconall -all back in 06 13 2017, this is the build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-v6-20170215-dc3d7a6 reconall -long back in 02 27 2018, this is the build-stamp.txt: freesurfer-Linux-centos7_x86_64-stable-v6-20161229-80ac5eb

I did use a development version for the hippocampal analyses on 02/28, 03/01 and 03/02. I can’t find any specific references to those…

Aura M.

On Mar 23, 2018, at 5:43 AM, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> wrote:

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.comhttp://www.jeiglesias.com/ http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Hurtado, Aura Maria" <AHURTADO@mgh.harvard.edumailto:AHURTADO@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, 23 March 2018 at 05:28 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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: <image001.png> 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...)

<image002.png> 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

<image003.png> 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.ukmailto: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 http://www.jeiglesias.comhttp://www.jeiglesias.com/ http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Hurtado, Aura Maria" <AHURTADO@mgh.harvard.edumailto:AHURTADO@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, 21 March 2018 at 22:24 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto: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.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer