[Freesurfer] Hippocampal subfields segmentation

[yunus soleymani]

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Hello Freesurfer users,
I was wondering if there is any Freesurfer code available for performing 
hippocampal subfield segmentation on multiple subjects simultaneously in 
parallel. I already have the code for analyzing a single subject, but I'm 
interested in analyzing hundreds of subjects at once.
Thank you very much.
Best regards,Yunus
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Re: [Freesurfer] Hippocampal subfields

[Erik O'Hanlon]

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Hi Eugenio,

Thanks so much for you reply. I will do that so. Just by way understanding the 
outputs I have , so the extract script only pulls the HBT automatically, and 
you need to simply add these together for the FS60 measures ? You can't modify 
the extract tool to read the FS60 data automatically?

Thanks again for your help. I will follow your instructions.

Best regards

Erik






From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, Juan 
E. 
Sent: Monday 30 August 2021 11:05
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampal subfields

Oh, now I understand.

Yeah you can add the head, body and tail segments of each subfield to get 6.0 
type of measurements ;-)

Cheers,

/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://secure-web.cisco.com/1knFRpDOFuoCvGaipHjXiJ2cPhPsiPMOeHi81MNBHC1pYD-xRCQzIgqWb6hExpRNqTqerIYAq3W6EUbKPQIYN6loykvYK69agvpqiJpixFB0HZxJ3tLZE5VfSe-gO2GqcRvGhQHCfYZw4IhoipbJUOi9v0tL5ajYH_Hv7r1WXRikWcSkenidoPo0bU8j8yPC21LqHlMB6c51XU6vq9XyKWHpExMjlIdUrOvuDxTOVyvXXGX6Z6Vom55EXxKNHs5XA4SgCapcbUOZufvnpzZ1tIw/http%3A%2F%2Fwww.jeiglesias.com

On Aug 28, 2021, at 08:20, Erik O'Hanlon 
mailto:ohanl...@tcd.ie>> wrote:


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Hi Eugenio

So I ran the new Amygdala and hippocampus tool on my longitudinal data and from 
that I got the three output files as described on the wiki( the FS60, HBT and 
the CA) which these mgz files are in the long mri directories for each subject.

This all looks fine. The issue is that I want to look at the FS 60 version of 
the subfields and export these rather than the HBT versions. When I use the 
script to extract all the measures to a file, it works fine and I have the 
amygdala volumes but for the hippocampus, I get the HBT versions. How do you 
get the extract script to output the FS60 subfield measures?
Is it possible? If not can I simply add the HBT sections for each subfield to 
equate to the FS 60 measures?


Thanks for your prompt reply. Much appreciated

Erik






From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Iglesias Gonzalez, Juan E. 
mailto:jiglesiasgonza...@mgh.harvard.edu>>
Sent: Friday 27 August 2021 22:02
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Hippocampal subfields

Dear Erik
I’m not sure I understand. What does your output file look like?
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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On Aug 27, 2021, at 16:14, Erik O'Hanlon 
mailto:ohanl...@tcd.ie>> wrote:

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Dear FS experts,



I've run a lognitudinal hippocampal and amygdala analysis. I jave managed to 
extract the amygdala and the head body tail subfields bui I'm wondering how to 
extract the regular FS60 volume measures? I have the three versions (FS60, HBT 
and CA mgz files in my long mri directories but I just keep getting the HBT 
volumes.

I tried


quantifyHAsubregions.sh hippoSf T1.long Outputfilename

and that gives me the HBT measures

What command do I use to pull out the FS60 subfield measures from my long mri 
directories?

Thanks for any help.

Erik
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Re: [Freesurfer] Hippocampal subfields

[Iglesias Gonzalez, Juan E.]

Oh, now I understand.

Yeah you can add the head, body and tail segments of each subfield to get 6.0 
type of measurements ;-)

Cheers,

/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com

On Aug 28, 2021, at 08:20, Erik O'Hanlon 
mailto:ohanl...@tcd.ie>> wrote:


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Hi Eugenio

So I ran the new Amygdala and hippocampus tool on my longitudinal data and from 
that I got the three output files as described on the wiki( the FS60, HBT and 
the CA) which these mgz files are in the long mri directories for each subject.

This all looks fine. The issue is that I want to look at the FS 60 version of 
the subfields and export these rather than the HBT versions. When I use the 
script to extract all the measures to a file, it works fine and I have the 
amygdala volumes but for the hippocampus, I get the HBT versions. How do you 
get the extract script to output the FS60 subfield measures?
Is it possible? If not can I simply add the HBT sections for each subfield to 
equate to the FS 60 measures?


Thanks for your prompt reply. Much appreciated

Erik






From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Iglesias Gonzalez, Juan E. 
mailto:jiglesiasgonza...@mgh.harvard.edu>>
Sent: Friday 27 August 2021 22:02
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Hippocampal subfields

Dear Erik
I’m not sure I understand. What does your output file look like?
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
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On Aug 27, 2021, at 16:14, Erik O'Hanlon 
mailto:ohanl...@tcd.ie>> wrote:

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Dear FS experts,



I've run a lognitudinal hippocampal and amygdala analysis. I jave managed to 
extract the amygdala and the head body tail subfields bui I'm wondering how to 
extract the regular FS60 volume measures? I have the three versions (FS60, HBT 
and CA mgz files in my long mri directories but I just keep getting the HBT 
volumes.

I tried


quantifyHAsubregions.sh hippoSf T1.long Outputfilename

and that gives me the HBT measures

What command do I use to pull out the FS60 subfield measures from my long mri 
directories?

Thanks for any help.

Erik
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Re: [Freesurfer] Hippocampal subfields

[Erik O'Hanlon]

External Email - Use Caution

Hi Eugenio

So I ran the new Amygdala and hippocampus tool on my longitudinal data and from 
that I got the three output files as described on the wiki( the FS60, HBT and 
the CA) which these mgz files are in the long mri directories for each subject.

This all looks fine. The issue is that I want to look at the FS 60 version of 
the subfields and export these rather than the HBT versions. When I use the 
script to extract all the measures to a file, it works fine and I have the 
amygdala volumes but for the hippocampus, I get the HBT versions. How do you 
get the extract script to output the FS60 subfield measures?
Is it possible? If not can I simply add the HBT sections for each subfield to 
equate to the FS 60 measures?


Thanks for your prompt reply. Much appreciated

Erik






From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, Juan 
E. 
Sent: Friday 27 August 2021 22:02
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampal subfields

Dear Erik
I’m not sure I understand. What does your output file look like?
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://secure-web.cisco.com/1lOExJeky8AFqkFfrzJ79hMnVWS5jkY1XvPoEM7_fiDyZiO2NCivnLmj1kLuPRm2w88EDcWDJFNg74iZ5sXiGABC3n_oKlQ0uGC_9nPN9HjPWymVUYBrBeTboJSI7XzVHe1kg37ir15P16T7suVpnbFAkPhobCBTQwqWnq4d9hmBt5I1ybk3_w9_yFktbjWWuVl6uJ_6k6IUCsPgYNWjI5LqC-dobHYl3W_y6GhIsiANkJk6bKdBmRwDZDkB7o8lLevPO3On0jPYRQRhL13Rhgg/http%3A%2F%2Fwww.jeiglesias.com

On Aug 27, 2021, at 16:14, Erik O'Hanlon 
mailto:ohanl...@tcd.ie>> wrote:

External Email - Use Caution

External Email - Use Caution

Dear FS experts,



I've run a lognitudinal hippocampal and amygdala analysis. I jave managed to 
extract the amygdala and the head body tail subfields bui I'm wondering how to 
extract the regular FS60 volume measures? I have the three versions (FS60, HBT 
and CA mgz files in my long mri directories but I just keep getting the HBT 
volumes.

I tried


quantifyHAsubregions.sh hippoSf T1.long Outputfilename

and that gives me the HBT measures

What command do I use to pull out the FS60 subfield measures from my long mri 
directories?

Thanks for any help.

Erik
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Re: [Freesurfer] Hippocampal subfields

[Iglesias Gonzalez, Juan E.]

Dear Erik
I’m not sure I understand. What does your output file look like?
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com

On Aug 27, 2021, at 16:14, Erik O'Hanlon 
mailto:ohanl...@tcd.ie>> wrote:

External Email - Use Caution

External Email - Use Caution

Dear FS experts,



I've run a lognitudinal hippocampal and amygdala analysis. I jave managed to 
extract the amygdala and the head body tail subfields bui I'm wondering how to 
extract the regular FS60 volume measures? I have the three versions (FS60, HBT 
and CA mgz files in my long mri directories but I just keep getting the HBT 
volumes.

I tried


quantifyHAsubregions.sh hippoSf T1.long Outputfilename

and that gives me the HBT measures

What command do I use to pull out the FS60 subfield measures from my long mri 
directories?

Thanks for any help.

Erik
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[Freesurfer] Hippocampal subfields

[Erik O'Hanlon]

External Email - Use Caution

Dear FS experts,




I've run a lognitudinal hippocampal and amygdala analysis. I jave managed to 
extract the amygdala and the head body tail subfields bui I'm wondering how to 
extract the regular FS60 volume measures? I have the three versions (FS60, HBT 
and CA mgz files in my long mri directories but I just keep getting the HBT 
volumes.


I tried


quantifyHAsubregions.sh hippoSf T1.long Outputfilename

and that gives me the HBT measures


What command do I use to pull out the FS60 subfield measures from my long mri 
directories?


Thanks for any help.


Erik
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Re: [Freesurfer] Hippocampal Subfields/ASEG

[Panayiota Ventura]

External Email - Use Caution

Hi Philipp,

Thank you very much! This was very helpful!

Best,

Yiota

On Mon, Jun 21, 2021 at 3:38 PM Saemann, Philipp 
wrote:

> External Email - Use Caution
>
> Hello Yiota,
>
>
> the whole hippocampus value is a sum of all subregions except for the
> hippocampal fissure - best try to reproduce this in an example.
>
>
> The recon-all pipeline also delivers a total hippocampal volume, but it is
> an entity/result of its own and produced independently of
>
> the subfield segmentation. It indirectly also contains areas that in the
> subfield segmentation would go to the fissure.
>
>
> There is several papers out that compared the two, generally the subfield
> based sum value is considered more reliable.
>
>
> Best,
>
> Philipp
>
>
> --
> *Von:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Panayiota Ventura <
> panayiota.vent...@gmail.com>
> *Gesendet:* Montag, 21. Juni 2021 21:27
> *An:* freesurfer@nmr.mgh.harvard.edu
> *Betreff:* [Freesurfer] Hippocampal Subfields/ASEG
>
>
> External Email - Use Caution
>
> Hello,
>
> I have a couple of questions concerning the hippocampal subfield
> extractions as well as the hippocampus extraction included in ASEG. I have
> looked around and tried to find as much information as possible about the
> two but I can't seem to find a clear answer. I'm hoping someone can help me
> out with this.
>
> 1. In the hippocampal subfields extraction, one of the labels is called
> "whole hippocampus". I would like to know what exactly is meant by that? In
> other words, what hippocampal regions are included in this "whole
> hippocampus" label?
>
> 2. The ASEG atlas also includes a hippocampus extraction. However this
> value is different from that of the hippocampal subfield extraction. What
> hippocampal regions are being included in this hippocampal extraction.
>
> 3. Which of the two would be a better estimate of hippocampal volume?
>
> Thank you for your time and help!
>
> Kind regards,
>
> Yiota Ventura
>
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Re: [Freesurfer] Hippocampal Subfields/ASEG

[Saemann, Philipp]

External Email - Use Caution

Hello Yiota,


the whole hippocampus value is a sum of all subregions except for the 
hippocampal fissure - best try to reproduce this in an example.


The recon-all pipeline also delivers a total hippocampal volume, but it is an 
entity/result of its own and produced independently of

the subfield segmentation. It indirectly also contains areas that in the 
subfield segmentation would go to the fissure.


There is several papers out that compared the two, generally the subfield based 
sum value is considered more reliable.


Best,

Philipp



Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Panayiota Ventura 

Gesendet: Montag, 21. Juni 2021 21:27
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Hippocampal Subfields/ASEG


External Email - Use Caution

Hello,

I have a couple of questions concerning the hippocampal subfield extractions as 
well as the hippocampus extraction included in ASEG. I have looked around and 
tried to find as much information as possible about the two but I can't seem to 
find a clear answer. I'm hoping someone can help me out with this.

1. In the hippocampal subfields extraction, one of the labels is called "whole 
hippocampus". I would like to know what exactly is meant by that? In other 
words, what hippocampal regions are included in this "whole hippocampus" label?

2. The ASEG atlas also includes a hippocampus extraction. However this value is 
different from that of the hippocampal subfield extraction. What hippocampal 
regions are being included in this hippocampal extraction.

3. Which of the two would be a better estimate of hippocampal volume?

Thank you for your time and help!

Kind regards,

Yiota Ventura

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[Freesurfer] Hippocampal Subfields/ASEG

[Panayiota Ventura]

External Email - Use Caution

Hello,

I have a couple of questions concerning the hippocampal subfield
extractions as well as the hippocampus extraction included in ASEG. I have
looked around and tried to find as much information as possible about the
two but I can't seem to find a clear answer. I'm hoping someone can help me
out with this.

1. In the hippocampal subfields extraction, one of the labels is called
"whole hippocampus". I would like to know what exactly is meant by that? In
other words, what hippocampal regions are included in this "whole
hippocampus" label?

2. The ASEG atlas also includes a hippocampus extraction. However this
value is different from that of the hippocampal subfield extraction. What
hippocampal regions are being included in this hippocampal extraction.

3. Which of the two would be a better estimate of hippocampal volume?

Thank you for your time and help!

Kind regards,

Yiota Ventura
___
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Re: [Freesurfer] Hippocampal Subfields error "no such file or directory"/"dyld library not loaded"

[Chester Kang]

External Email - Use Caution

Hi Eugenio,

Yes, Matlab runtime had already been installed.

Copying initial description of checks/troubleshooting already done so far,
"...
> Things that have been checked/tried or troubleshooting attempted:
>  - SIP protection is disabled (csrutil status shows "disabled")
>  - Checked that there are files and correct permissions in the "lib/gcc/lib"
> and the "MCRv84" folders
>  - tried to unset DYLD_LIBRARY_PATH (in the SetUpFreeSurfer.sh)
>  - checked the DYLD_LIBRARY_PATH value and run a step directly (both with ""
> empty value and the values below)
..."

Hope to that helps!


Regards,
Chester


--

Message: 4
Date: Fri, 11 Jun 2021 11:43:21 +
From: "Iglesias Gonzalez, Juan E." 
Subject: Re: [Freesurfer] Hippocampal Subfields error "no such file or
directory"/"dyld library not loaded"
To: Freesurfer support list 
Message-ID: 
Content-Type: text/plain; charset="us-ascii"

Thanks, Chester, that looks good. Am I safely assuming that the Matlab runtime 
has been installed?
Cheers,
/Eugenio

> On 10 Jun 2021, at 21:31, Chester Kang  wrote:
>
>External Email - Use Caution
>
> Hi Eugenio,
>
> The command that was run is segmentHA_T1.sh.
>
> I've rerun and copy-n-pasted the entire session below.
>
> "...
>
> chesterk@selma:~$ source SetUpFreeSurfer_mac.sh
>  freesurfer-darwin-macOS-7.1.0-20200511-813297b 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /Applications/freesurfer_v7.1.0
> FSFAST_HOME   /Applications/freesurfer_v7.1.0/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /Users/chesterk/subjects
> MNI_DIR   /Applications/freesurfer_v7.1.0/mni
> FSL_DIR   /usr/local/fsl_v6.0.4
> chesterk@selma:~$ cd subjects
> chesterk@selma:~/subjects$ segmentHA_T1.sh 1001126copy
> #
> #@# Hippocampal Subfields processing (T1) left Fri 11 Jun 2021 11:25:12
> AEST
> --
> Setting up environment variables
> ---
> DYLD_LIBRARY_PATH is
> .:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/free
> surfer_v7.1.0/MCRv84//bin/maci64:/Applications/freesurfer_v7.1.0/MCRv84//sy
> s/os/maci64:/Applications/freesurfer_v7.1.0/lib/gcc/lib:/Applications/frees
> urfer_v7.1.0/lib/gcc/lib:/Applications/freesurfer_v7.1.0/lib/gcc/lib
> /Applications/freesurfer_v7.1.0/bin/run_segmentSubjectT1_autoEstimateAlveus
> ML.sh: line 33:
> /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1_autoEstimateAlveusML.a
> pp/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or
> directory
> Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: Tue
> Dec 19 10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64
>
>
> T1 hippocampal subfields exited with ERRORS at Fri 11 Jun 2021 11:25:12
> AEST
>
>
> For more details, see the log file
> /Users/chesterk/subjects/1001126copy/scripts/hippocampal-subfields-T1.log
>
>
> chesterk@selma:~/subjects$ more
> 1001126copy/scripts/hippocampal-subfields-T1.log
> --
> USER chesterk
> HOST selma.nnf.unimelb.edu.au
> PROCESSID 37954
> PROCESSOR x86_64
> OS Darwin
> ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1
> Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: Tue
> Dec 19 10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64
> --
>
> freesurfer-darwin-macOS-7.1.0-20200511-813297b
>
> setenv SUBJECTS_DIR /Users/chesterk/subjects
> cd /Users/chesterk/subjects
> /Applications/freesurfer_v7.1.0/bin/segmentHA_T1.sh 1001126copy
>
>
> #
> #@# Hippocampal Subfields processing (T1) left Fri 11 Jun 2021 11:25:12
> AEST
> --
> Setting up environment variables
> ---
> DYLD_LIBRARY_PATH is
> .:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/free
> surfer_v7.1.0/MCRv84//bin/maci64:/Applications/freesurfer_v7.1.0/MCRv84//sy
> s/os/maci64:/Applications/freesurfer_v7.1.0/lib/gcc/lib:/Applications/frees
> urfer_v7.1.0/lib/gcc/lib:/Applications/freesurfer_v7.1.0/lib/gcc/lib
> /Applications/freesurfer_v7.1.0/bin/run_segmentSubjectT1_autoEstimateAlveus
> ML.sh: line 33:
> /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1_autoEstimateAlveusML.a
> pp/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or
> directory
> Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: Tue
> Dec 19 10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64
>

Re: [Freesurfer] Hippocampal Subfields error "no such file or directory"/"dyld library not loaded"

[Iglesias Gonzalez, Juan E.]

2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>> .mgh.harvard.edu
>> or, via email, send a message with subject or body 'help' to
>>  freesurfer-requ...@nmr.mgh.harvard.edu
>> 
>> You can reach the person managing the list at
>>  freesurfer-ow...@nmr.mgh.harvard.edu
>> 
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Freesurfer digest..."
>> 
>> 
>> Today's Topics:
>> 
>>  1. Re: Hippocampal Subfields error "no such file or
>> directory"/"dyld library not loaded" (Iglesias Gonzalez, Juan E.)
>>  2. Ill-Conditioned/Badly Scaled Matrix Error (Lurie, Lucy)
>>  3. LGI FS 7.1 (Del Re, Elisabetta)
>>  4. mri_glmfit with pvr (std...@virgilio.it)
>>  5. Re: FW:  WM or Pial edits to correct surfaces (Fischl, Bruce)
>> 
>> 
>> --
>> 
>> Message: 1
>> Date: Wed, 9 Jun 2021 12:24:19 +
>> From: "Iglesias Gonzalez, Juan E." 
>> Subject: Re: [Freesurfer] Hippocampal Subfields error "no such file or
>>  directory"/"dyld library not loaded"
>> To: Freesurfer support list 
>> Message-ID: <8419d11c-c916-4249-9983-557a25229...@mgh.harvard.edu>
>> Content-Type: text/plain; charset="us-ascii"
>> 
>> Dear Chester,
>> What command did you exactly run? There seems to be a mix of T1 and
>> T1+additionalMRI segmentation commands in there.
>> Cheers,
>> /Eugenio
>> 
>> Juan Eugenio Iglesias
>> Senior research fellow
>> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>> http://secure-web.cisco.com/1qi_706jGqyyM3M3yDYUokzl_m0IkJHWaqcVYgXiltKvmf2sZt9X-pyYSQmncbstu3rICy2Z7fHggRXk-aKCs7Fr-HTjpj0zQ6tCKLBMJ8qQlxpHWzL3Pl8OR-xTpN-F23znGzhgWE7K9yMHxIKC4JDu_uhiU4UqXswGp7DW6ImpICnIp2rAN9sjKc2johSTK9aRjCmaxJgCb5oKn4sJyy6IbRQBmyVceflyPgKIXagCBaIcBUNYGwHkmdx9RCUleJuy7MjerHcAPxmXS2QZAAA/http%3A%2F%2Fwww.jeiglesias.com
>> s.com 
>> 
>>> On Jun 9, 2021, at 00:23, Chester Kang  wrote:
>>> 
>>>   External Email - Use Caution
>>> 
>>> Hello FreeSurfer Developers,
>>> 
>>> I am trying to run subfield segmentation of the hippocampus using
>>> Freesurfer v7.1.0. Recon-all has been previously run on all subjects,
>>> however with a different version of Freesurfer (v5.3.0).
>>> 
>>> Getting the error(s): "No such file or directory" and on further
>>> investigation "dyld: Library not loaded: @rpath/libmwlaunchermain.dylib"
>>> 
>>> I've searched the archive but could not find a solution.
>>> 
>>> Could someone please help?
>>> 
>>> Below are details of the system and unsuccessful troubleshooting
>>> attempts.
>>> 
>>> Regards,
>>> Chester
>>> 
>>> 
>>> FreeSurfer version: 7.1.0
>>> Platform: Mac OS 10.13.3
>>> hippocampal-subfields-T1.log is below:
>>> 
>>> Things that have been checked/tried or troubleshooting attempted:
>>> - SIP protection is disabled (csrutil status shows "disabled")
>>> - Checked that there are files and correct permissions in the
>>> "lib/gcc/lib" and the "MCRv84" folders
>>> - tried to unset DYLD_LIBRARY_PATH (in the SetUpFreeSurfer.sh)
>>> - checked the DYLD_LIBRARY_PATH value and run a step directly (both
>>> with "" empty value and the values below)
>>> 
>>> $ echo $DYLD_LIBRARY_PATH
>>> 
>>> 
>>> .:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/fr
>>> eesurfer_v7.1.0/MCRv84//sys/os/maci64:/Applications/freesurfer_v7.1.0/lib
>>> /gcc/lib
>>> 
>>> $ 
>>> /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveus
>>> ML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML
>>> 
>>> 
>>> /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveus
>>> ML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML
>>> dyld: Library not loaded: @rpath/libmwlaunchermain.dylib
>>> Referenced from:
>>> /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveus
>>> ML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML
>>> Reason: image not found
>>> Abort trap: 6
>>> 
>>> 
>>> 
>>> === hippocampal-subfields-T1.log ===
>>> 
>>> 
>>> "...
>>> --
>>&

Re: [Freesurfer] Hippocampal Subfields error "no such file or directory"/"dyld library not loaded"

[Chester Kang]

edits to correct surfaces (Fischl, Bruce)
>
>
>--------------
>
>Message: 1
>Date: Wed, 9 Jun 2021 12:24:19 +
>From: "Iglesias Gonzalez, Juan E." 
>Subject: Re: [Freesurfer] Hippocampal Subfields error "no such file or
>   directory"/"dyld library not loaded"
>To: Freesurfer support list 
>Message-ID: <8419d11c-c916-4249-9983-557a25229...@mgh.harvard.edu>
>Content-Type: text/plain; charset="us-ascii"
>
>Dear Chester,
>What command did you exactly run? There seems to be a mix of T1 and
>T1+additionalMRI segmentation commands in there.
>Cheers,
>/Eugenio
>
>Juan Eugenio Iglesias
>Senior research fellow
>CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>http://secure-web.cisco.com/1qi_706jGqyyM3M3yDYUokzl_m0IkJHWaqcVYgXiltKvmf2sZt9X-pyYSQmncbstu3rICy2Z7fHggRXk-aKCs7Fr-HTjpj0zQ6tCKLBMJ8qQlxpHWzL3Pl8OR-xTpN-F23znGzhgWE7K9yMHxIKC4JDu_uhiU4UqXswGp7DW6ImpICnIp2rAN9sjKc2johSTK9aRjCmaxJgCb5oKn4sJyy6IbRQBmyVceflyPgKIXagCBaIcBUNYGwHkmdx9RCUleJuy7MjerHcAPxmXS2QZAAA/http%3A%2F%2Fwww.jeiglesias.com
>s.com 
>
>> On Jun 9, 2021, at 00:23, Chester Kang  wrote:
>> 
>>External Email - Use Caution
>> 
>> Hello FreeSurfer Developers,
>> 
>> I am trying to run subfield segmentation of the hippocampus using
>>Freesurfer v7.1.0. Recon-all has been previously run on all subjects,
>>however with a different version of Freesurfer (v5.3.0).
>> 
>> Getting the error(s): "No such file or directory" and on further
>>investigation "dyld: Library not loaded: @rpath/libmwlaunchermain.dylib"
>> 
>> I've searched the archive but could not find a solution.
>> 
>> Could someone please help?
>> 
>> Below are details of the system and unsuccessful troubleshooting
>>attempts.
>> 
>> Regards,
>> Chester
>> 
>> 
>> FreeSurfer version: 7.1.0
>> Platform: Mac OS 10.13.3
>> hippocampal-subfields-T1.log is below:
>> 
>> Things that have been checked/tried or troubleshooting attempted:
>> - SIP protection is disabled (csrutil status shows "disabled")
>> - Checked that there are files and correct permissions in the
>>"lib/gcc/lib" and the "MCRv84" folders
>> - tried to unset DYLD_LIBRARY_PATH (in the SetUpFreeSurfer.sh)
>> - checked the DYLD_LIBRARY_PATH value and run a step directly (both
>>with "" empty value and the values below)
>> 
>> $ echo $DYLD_LIBRARY_PATH
>> 
>> 
>>.:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/fr
>>eesurfer_v7.1.0/MCRv84//sys/os/maci64:/Applications/freesurfer_v7.1.0/lib
>>/gcc/lib
>> 
>> $ 
>>/Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveus
>>ML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML
>> 
>> 
>>/Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveus
>>ML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML
>> dyld: Library not loaded: @rpath/libmwlaunchermain.dylib
>>  Referenced from:
>>/Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveus
>>ML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML
>>  Reason: image not found
>> Abort trap: 6
>> 
>> 
>> 
>> === hippocampal-subfields-T1.log ===
>> 
>> 
>> "...
>> --
>> USER chester
>> HOST selma.nnf.unimelb.edu.au
>> PROCESSID 17656 
>> PROCESSOR x86_64
>> OS Darwin
>> ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1
>> Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0:
>>Tue Dec 19 10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64
>> --
>> 
>> freesurfer-darwin-macOS-7.1.0-20200511-813297b
>> 
>> setenv SUBJECTS_DIR /data/netapp02/work/chester/global_pass_all
>> cd /data/netapp02/work/chester/global_pass_all
>> /Applications/freesurfer_v7.1.0/bin/segmentHA_T1.sh 1002310
>> 
>> #
>> #@# Hippocampal Subfields processing (T1) left Tue  8 Jun 2021 15:25:15
>>AEST
>> --
>> Setting up environment variables
>> ---
>> DYLD_LIBRARY_PATH is
>>.:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/fr
>>eesurfer_v7.1.0/MCRv84//bin/maci64:/Applications/freesurfer_v7.1.0/MCRv84
>>//sys/os/maci64:/Applications/freesurfer_v7.1.0/lib/gcc/lib
>> 
>>/Applications/freesurfer_v7.1.0/bin/run_segmentSubjectT1_autoEstimateAlve
>

Re: [Freesurfer] Hippocampal Subfields error "no such file or directory"/"dyld library not loaded"

[Iglesias Gonzalez, Juan E.]

Dear Chester,
What command did you exactly run? There seems to be a mix of T1 and 
T1+additionalMRI segmentation commands in there.
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com 

> On Jun 9, 2021, at 00:23, Chester Kang  wrote:
> 
>External Email - Use Caution
> 
> Hello FreeSurfer Developers,
> 
> I am trying to run subfield segmentation of the hippocampus using Freesurfer 
> v7.1.0. Recon-all has been previously run on all subjects, however with a 
> different version of Freesurfer (v5.3.0). 
> 
> Getting the error(s): "No such file or directory" and on further 
> investigation "dyld: Library not loaded: @rpath/libmwlaunchermain.dylib"
> 
> I've searched the archive but could not find a solution.  
> 
> Could someone please help?
> 
> Below are details of the system and unsuccessful troubleshooting attempts.
> 
> Regards,
> Chester
> 
> 
> FreeSurfer version: 7.1.0
> Platform: Mac OS 10.13.3
> hippocampal-subfields-T1.log is below:
> 
> Things that have been checked/tried or troubleshooting attempted:
> - SIP protection is disabled (csrutil status shows "disabled")
> - Checked that there are files and correct permissions in the "lib/gcc/lib" 
> and the "MCRv84" folders
> - tried to unset DYLD_LIBRARY_PATH (in the SetUpFreeSurfer.sh)
> - checked the DYLD_LIBRARY_PATH value and run a step directly (both with "" 
> empty value and the values below)
> 
> $ echo $DYLD_LIBRARY_PATH
> 
> .:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/freesurfer_v7.1.0/MCRv84//sys/os/maci64:/Applications/freesurfer_v7.1.0/lib/gcc/lib
> 
> $ 
> /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML
> 
> /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML
>  
> dyld: Library not loaded: @rpath/libmwlaunchermain.dylib
>  Referenced from: 
> /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML
>  Reason: image not found
> Abort trap: 6
> 
> 
> 
> === hippocampal-subfields-T1.log ===
> 
> 
> "...
> --
> USER chester
> HOST selma.nnf.unimelb.edu.au
> PROCESSID 17656 
> PROCESSOR x86_64
> OS Darwin
> ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 
> Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: Tue Dec 
> 19 10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64
> --
> 
> freesurfer-darwin-macOS-7.1.0-20200511-813297b
> 
> setenv SUBJECTS_DIR /data/netapp02/work/chester/global_pass_all
> cd /data/netapp02/work/chester/global_pass_all
> /Applications/freesurfer_v7.1.0/bin/segmentHA_T1.sh 1002310
> 
> #
> #@# Hippocampal Subfields processing (T1) left Tue  8 Jun 2021 15:25:15 AEST
> --
> Setting up environment variables
> ---
> DYLD_LIBRARY_PATH is 
> .:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/freesurfer_v7.1.0/MCRv84//bin/maci64:/Applications/freesurfer_v7.1.0/MCRv84//sys/os/maci64:/Applications/freesurfer_v7.1.0/lib/gcc/lib
> /Applications/freesurfer_v7.1.0/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
>  line 33: 
> /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML:
>  No such file or directory
> Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: Tue Dec 
> 19 10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64
> 
> T1 hippocampal subfields exited with ERRORS at Tue  8 Jun 2021 15:25:16 AEST
> 
> ..."
> 
> 
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
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[Freesurfer] Hippocampal Subfields error "no such file or directory"/"dyld library not loaded"

[Chester Kang]

External Email - Use Caution

Hello FreeSurfer Developers,

I am trying to run subfield segmentation of the hippocampus using Freesurfer 
v7.1.0. Recon-all has been previously run on all subjects, however with a 
different version of Freesurfer (v5.3.0). 

Getting the error(s): "No such file or directory" and on further investigation 
"dyld: Library not loaded: @rpath/libmwlaunchermain.dylib"

I've searched the archive but could not find a solution.  

Could someone please help?

Below are details of the system and unsuccessful troubleshooting attempts.

Regards,
Chester


FreeSurfer version: 7.1.0
Platform: Mac OS 10.13.3
hippocampal-subfields-T1.log is below:

Things that have been checked/tried or troubleshooting attempted:
 - SIP protection is disabled (csrutil status shows "disabled")
 - Checked that there are files and correct permissions in the "lib/gcc/lib" 
and the "MCRv84" folders
 - tried to unset DYLD_LIBRARY_PATH (in the SetUpFreeSurfer.sh)
 - checked the DYLD_LIBRARY_PATH value and run a step directly (both with "" 
empty value and the values below)

$ echo $DYLD_LIBRARY_PATH

.:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/freesurfer_v7.1.0/MCRv84//sys/os/maci64:/Applications/freesurfer_v7.1.0/lib/gcc/lib

$ 
/Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML

/Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML
 
dyld: Library not loaded: @rpath/libmwlaunchermain.dylib
  Referenced from: 
/Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML
  Reason: image not found
Abort trap: 6



=== hippocampal-subfields-T1.log ===


"...
--
USER chester
HOST selma.nnf.unimelb.edu.au
PROCESSID 17656 
PROCESSOR x86_64
OS Darwin
ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 
Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: Tue Dec 19 
10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64
--
 
freesurfer-darwin-macOS-7.1.0-20200511-813297b
 
setenv SUBJECTS_DIR /data/netapp02/work/chester/global_pass_all
cd /data/netapp02/work/chester/global_pass_all
/Applications/freesurfer_v7.1.0/bin/segmentHA_T1.sh 1002310

#
#@# Hippocampal Subfields processing (T1) left Tue  8 Jun 2021 15:25:15 AEST
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is 
.:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/freesurfer_v7.1.0/MCRv84//bin/maci64:/Applications/freesurfer_v7.1.0/MCRv84//sys/os/maci64:/Applications/freesurfer_v7.1.0/lib/gcc/lib
/Applications/freesurfer_v7.1.0/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
 line 33: 
/Applications/freesurfer_v7.1.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML:
 No such file or directory
Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: Tue Dec 19 
10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64

T1 hippocampal subfields exited with ERRORS at Tue  8 Jun 2021 15:25:16 AEST

..."




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Re: [Freesurfer] Hippocampal Subfields

[Jindal, Saurabh]

External Email - Use Caution

Do we have an editing criteria for hippocampal inclusion/exclusion error in 
recon_all and in subfields?

Best,
Saurabh

From: Jindal, Saurabh 
Sent: Thursday, April 22, 2021 2:03 PM
To: Freesurfer support list 
Subject: Re: Hippocampal Subfields

Okay, Thank you very much Philipp.


Best,
Saurabh


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Saemann, Philipp 

Sent: Thursday, April 22, 2021 2:01 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Hippocampal Subfields


* External Email - Caution *

External Email - Use Caution

Hi Saurabh,


you have to run (and QC) recon-all before,


Best,

Philipp



Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Jindal, Saurabh 

Gesendet: Donnerstag, 22. April 2021 20:55
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Hippocampal Subfields


External Email - Use Caution

Hi experts,

I am focusing on hippocampus for my work using subfield analysis on freesurfer 
7.1. Is there is way to run the container only for subfields or do we have to 
run recon_all on the subject first always? Thanks.

Saurabh
Postdoc Research Fellow





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immediately notify the sender via telephone or return mail.


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Re: [Freesurfer] Hippocampal Subfields

[Jindal, Saurabh]

External Email - Use Caution

Okay, Thank you very much Philipp.


Best,
Saurabh


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Saemann, Philipp 

Sent: Thursday, April 22, 2021 2:01 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Hippocampal Subfields


* External Email - Caution *

External Email - Use Caution

Hi Saurabh,


you have to run (and QC) recon-all before,


Best,

Philipp



Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Jindal, Saurabh 

Gesendet: Donnerstag, 22. April 2021 20:55
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Hippocampal Subfields


External Email - Use Caution

Hi experts,

I am focusing on hippocampus for my work using subfield analysis on freesurfer 
7.1. Is there is way to run the container only for subfields or do we have to 
run recon_all on the subject first always? Thanks.

Saurabh
Postdoc Research Fellow





The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.


The materials in this message are private and may contain Protected Healthcare 
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intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
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Re: [Freesurfer] Hippocampal Subfields

[Saemann, Philipp]

External Email - Use Caution

Hi Saurabh,


you have to run (and QC) recon-all before,


Best,

Philipp



Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Jindal, Saurabh 

Gesendet: Donnerstag, 22. April 2021 20:55
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Hippocampal Subfields


External Email - Use Caution

Hi experts,

I am focusing on hippocampus for my work using subfield analysis on freesurfer 
7.1. Is there is way to run the container only for subfields or do we have to 
run recon_all on the subject first always? Thanks.

Saurabh
Postdoc Research Fellow


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
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[Freesurfer] Hippocampal Subfields

[Jindal, Saurabh]

External Email - Use Caution

Hi experts,

I am focusing on hippocampus for my work using subfield analysis on freesurfer 
7.1. Is there is way to run the container only for subfields or do we have to 
run recon_all on the subject first always? Thanks.

Saurabh
Postdoc Research Fellow


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
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Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

[Hoopes, Andrew]

Matt (cc’d) has recently posted a similar error on the last. Unfortunately, 
these mac MCR errors are difficult to debug. You could wait for the python 
subfield port to get released, but that might be a few months down the line. If 
you want to get things running immediately, one thing to try is to download the 
7.1 docker container from https://hub.docker.com/r/freesurfer/freesurfer and 
run FS through that. That should fix any system-specific problems.

Best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ramtilak Gattu 

Date: Thursday, March 25, 2021 at 7:20 PM
To: fsbuild , freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

External Email - Use Caution

External Email - Use Caution
Hi 'E' / 'R',

I even tried changing the resolution to 1.0 with no success ruling put memory 
issues.

Just wondering if its time to give up and wait for your python build to 
successfully finish the job in mac. I wonder if any other user with a similar 
MacBook pro configuration as mine
Hardware Overview:

  Model Name: MacBook Pro
  Model Identifier: MacBookPro16,1
  Processor Name: 6-Core Intel Core i7
  Processor Speed: 2.6 GHz
  Number of Processors: 1
  Total Number of Cores: 6
  L2 Cache (per Core): 256 KB
  L3 Cache: 12 MB
  Hyper-Threading Technology: Enabled
  Memory: 16 GB
  System Firmware Version: 1554.80.3.0.0 (iBridge: 18.16.14347.0.0,0)
  Serial Number (system): C02DPB3BMD6M
  Hardware UUID: D313516B-A3B9-500F-9303-EB0F4D4946A4
  Provisioning UDID: D313516B-A3B9-500F-9303-EB0F4D4946A4
  Activation Lock Status: Enabled

had successfully finished the processing or encountered the same issue and 
later fixed it to successfully run the segmentation. Is there a way to bypass 
that step and run the program till the end?

I think some Compatability issues with 'MCR' holding back the processing at 
that stage.

Again, thanks a lot for all your help in this regards.

Regards
Tilak

From: Ramtilak Gattu 
Sent: Wednesday, March 24, 2021 8:32 PM
To: fsbuild ; freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

First let me thank you 'R' and 'E' for being so patient and working with me to 
resolve this issue.

As suggested by 'R' I monitored the activity monitored but unfortunately, the 
memory pressure graph remained green throughout the process. When the program 
was running memory usage jumped from 6.25gb to 7.85 gb.

As suggeted by 'E" I even tried to run the code by changing the parameters in 
the code for


set RESOLUTION="0.".

by:

set RESOLUTION="0.5";

still, the error persists.

It works fine on my Linux centos system(8gb ram) but fails on both the macs. 
surprisingly, it's the same exact error.

Does running the routine after installing full matlab instead of just mcr8.4 
would help? just a thought.

Thanks

Regards
Tilak


From: fsbuild 
Sent: Wednesday, March 24, 2021 5:09 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Ramtilak Gattu 
Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

I don’t see anything in your output showing say code 01 with Bus Error.  But 
code 01 could indicate a memory issue, e.g., not enough RAM.

You could bring up the Activity Monitor program and click on the memory tab to 
profile memory during the command run.  But the "memory pressure" graph does 
not go back very far in time, so you would need to be able to see it close to 
the time the command exits. See  
https://www.lifewire.com/use-activity-monitor-to-track-mac-memory-usage-2260880

- R.


On Mar 24, 2021, at 04:26, Ramtilak Gattu  wrote:

External Email - Use Caution
External Email - Use Caution
Yes it says enabled.

[tilak:~] tilak% csrutil status
System Integrity Protection status: enabled.

Thanks

Regards,
Tilak

From: fsbuild mailto:fsbu...@contbay.com>>
Sent: Wednesday, March 24, 2021 4:22 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: Ramtilak Gattu mailto:rg...@med.wayne.edu>>
Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

Maybe you could let us know if the system integrity protection feature is 
turned on the Mac (which is the default).  The following command will report if 
it is enabled or disabled, e.g., when enabled,

$ csrutil status
System Integrity Protection status: enabled.
- R.

On Mar 24, 2021, at 01:48, Ramtilak Gattu  wrote:

External Email - Use Caution
External Email - Use Caution
Hi,

Earlier I didnt have a full matlab verion but I installed mcr by running 
"fs_install_mcr R2014b" as suggested in FSwiki.

I updated java to version "1.8.0_281" (Java(TM) SE Runtime Environment (b

Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

[Iglesias Gonzalez, Juan E.]

Thank you both! On Linux, 8GB is insufficient, and 16GB is normally 
sufficient; I wonder if the requirements are a bit higher on MAC?

Could you please try the following?

  1.  Edit $FREESURFER_HOME/bin/segmentHA_T1.sh (might require sudo)
  2.  Replace the line:
set RESOLUTION="0.";
by:
set RESOLUTION="0.5";
  3.  Rerunning the code, and see if it runs to completion?
Cheers,
/E


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From:  on behalf of Ramtilak Gattu 

Reply-To: Freesurfer support list 
Date: Tuesday, March 23, 2021 at 17:46
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal Subfields Segmentation Violation-error


External Email - Use Caution

External Email - Use Caution
Hi,

I am also encountering the same issue as WON JONG CHWA on my macbook pro (16gb 
ram) and I even tried the same on imac (8gb ram). I ran recon-all successfully 
on both systems. Here are my system details


Hardware Overview:



  Model Name: MacBook Pro

  Model Identifier: MacBookPro16,1

  Processor Name: 6-Core Intel Core i7

  Processor Speed: 2.6 GHz

  Number of Processors: 1

  Total Number of Cores: 6

  L2 Cache (per Core): 256 KB

  L3 Cache: 12 MB

  Hyper-Threading Technology: Enabled

  Memory: 16 GB

  System Firmware Version: 1554.80.3.0.0 (iBridge: 18.16.14347.0.0,0)

  Serial Number (system): C02DPB3BMD6M

  Hardware UUID: D313516B-A3B9-500F-9303-EB0F4D4946A4

  Provisioning UDID: D313516B-A3B9-500F-9303-EB0F4D4946A4

  Activation Lock Status: Enabled



Here is the log for segmentation violation error
***
Fitting mesh to image data took 742.9022 seconds
Transforming points
Transforming points
Wrote image to file image.mgz
Constructing image-to-world transform from header information (asmr1.mgz)
Constructing image-to-world transform from header information 
(/Users/tilak/Desktop/Work/CNS_cases/Hipps/AD/tmp/hippoSF_T1_v21_left/imageDump.mgz)
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
Caught unexpected exception of unknown type.


   Segmentation violation detected at Tue Mar 23 15:53:07 2021


Configuration:
  Crash Decoding : Disabled
  Current Visual : Quartz
  Default Encoding   : ISO-8859-1
  MATLAB Architecture: maci64
  MATLAB Root: /Applications/freesurfer/7.1.1/MCRv84
  MATLAB Version : 8.4.0.150421 (R2014b)
  Operating System   : Darwin 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 
00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64
  Processor ID   : x86 Family 6 Model 158 Stepping 10, GenuineIntel
  Software OpenGL: 0
  Virtual Machine: Java 1.7.0_55-b13 with Oracle Corporation Java 
HotSpot(TM) 64-Bit Server VM mixed mode
  Window System  : Quartz

Fault Count: 1


Abnormal termination:
Segmentation violation

Register State (from fault):
  RAX = 0003  RBX = 000102cde080
  RCX = 7ff4ce00  RDX = 7624c180
  RSP = 7ff4ce00  RBP = 7fff2041595e
  RSI = 7000  RDI = 7fff204171f9

   R8 = 660333a0   R9 = 7624c180
  R10 = 7fff20410002  R11 = 7ff4ce05b4e0
  R12 = 7624c498  R13 = 
  R14 = 00010e5fbd9b  R15 = 0060

  RIP = 7624c498  RFL = 7624c1e0

   CS = 00010e49227b   FS = 7624c1c0   GS = 0001

Stack Trace (from fault):
[  0] 0x0001048a9e64 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+0052
[  1] 0x0001048ada2a 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 
_ZN2fl4test17terminate_handledEv+0906
[  2] 0x0001048ad477 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 
_ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+0119
[  3] 0x000107e39b7a 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 
_Z32mnRunPathDependentInitializationv+3146
[  4] 0x000107e39e58 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 
_Z32mnRunPathDependentInitializationv+3880
[  5] 0x000107e37733 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 
mnFatalSignalHandler+0275
[  6] 0x7fff20630d7d   
/usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+0029
[  7] 0x   
+
[  8] 0x00010e49227b 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01782395
 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00010667
[  9] 0x00010e3eba17 
/Applications/free

Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

[Ramtilak Gattu]

External Email - Use Caution

Yes it says enabled.


[tilak:~] tilak% csrutil status

System Integrity Protection status: enabled.

Thanks

Regards,
Tilak

From: fsbuild 
Sent: Wednesday, March 24, 2021 4:22 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Ramtilak Gattu 
Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

Maybe you could let us know if the system integrity protection feature is 
turned on the Mac (which is the default).  The following command will report if 
it is enabled or disabled, e.g., when enabled,

$ csrutil status
System Integrity Protection status: enabled.

- R.
On Mar 24, 2021, at 01:48, Ramtilak Gattu  wrote:

External Email - Use Caution
External Email - Use Caution
Hi,

Earlier I didnt have a full matlab verion but I installed mcr by running 
"fs_install_mcr R2014b" as suggested in FSwiki.

I updated java to version "1.8.0_281" (Java(TM) SE Runtime Environment (build 
1.8.0_281-b09) Java HotSpot(TM) 64-Bit Server VM (build 25.281-b09, mixed mode) 
and reinstalled or overwritten mcrv8.4 by running the same command again 
"fs_install_mcr R2014b" but still it ended after running for a whileand exited 
with errors again. But this time it says "Bus error detected instead of 
segmentation violation error.

Bus error detected at Wed Mar 24 00:59:58 2021


Configuration:
  Crash Decoding : Disabled
  Current Visual : Quartz
  Default Encoding   : ISO-8859-1
  MATLAB Architecture: maci64
  MATLAB Root: /Applications/freesurfer/7.1.1/MCRv84
  MATLAB Version : 8.4.0.150421 (R2014b)
  Operating System   : Darwin 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 
00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64
  Processor ID   : x86 Family 6 Model 158 Stepping 10, GenuineIntel
  Software OpenGL: 0
  Virtual Machine: Java 1.7.0_55-b13 with Oracle Corporation Java 
HotSpot(TM) 64-Bit Server VM mixed mode
  Window System  : Quartz

Fault Count: 1


Abnormal termination:
Bus error

Register State (from fault):
  RAX = 0003  RBX = 00010145d080
  RCX = 7fdc9c70  RDX = 7959f180
  RSP = 7fdc9c70  RBP = 7fff2027d95e
  RSI = 7000  RDI = 7fff2027f1f9

   R8 = 70c054b0   R9 = 7959f180
  R10 = 7fff20270002  R11 = 7fdc9c7429e0
  R12 = 7959f498  R13 = 
  R14 = 00010f061d9b  R15 = 0060

  RIP = 7959f498  RFL = 7959f1e0

   CS = 00010eef827b   FS = 7959f1c0   GS = 0001

Stack Trace (from fault):
[  0] 0x0001036a0e64 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+0052
[  1] 0x0001036a4a2a 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 
_ZN2fl4test17terminate_handledEv+0906
[  2] 0x0001036a4477 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 
_ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+0119
[  3] 0x00010ec3bb7a 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 
_Z32mnRunPathDependentInitializationv+3146
[  4] 0x00010ec3be58 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 
_Z32mnRunPathDependentInitializationv+3880
[  5] 0x00010ec39733 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 
mnFatalSignalHandler+0275
[  6] 0x7fff20498d7d   
/usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+0029
[  7] 0x   
+
[  8] 0x00010eef827b 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01782395
 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00010667
[  9] 0x00010ee51a17 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01100311
 _Z15inRunFinalizers7opcodesPS_Pi+0119
[ 10] 0x00010eef629d 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01774237
 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+2509
[ 11] 0x00010fc74c55 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_dispatcher.dylib+00400469
 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+0645
[ 12] 0x00010ee9948b 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01393803
 
_Z23inEvalPcodeHeaderToWordP15_memory_contextiPP11mxArray_tagP12_pcodeheaderP6Mfh_mpj+0219
[ 13] 0x00010ee4bf4b 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci6

Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

[fsbuild]

10ee47a62 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01059426
 
_ZN12InterpBridge33EvalCmdWithLocalReturnInDesiredWSERKSbItSt11char_traitsItESaItEEPibbP15inWorkSpace_tag+0066[
 17] 0x00010eda72de 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+00402142
 
_Z51inEvalCmdWithLocalReturnInDesiredWSAndPublishEventsRKSbItSt11char_traitsItESaItEEPibbP15inWorkSpace_tag+0062[
 18] 0x00010f8f593e 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00227646 
_ZNK3iqm18InternalEvalPlugin24inEvalCmdWithLocalReturnERKSbItSt11char_traitsItESaItEEP15inWorkSpace_tag+0094[
 19] 0x00010f8f4df4 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00224756 
_ZN3iqm18InternalEvalPlugin7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+0132[
 20] 0x00010ec10358 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00209752 
_ZN3mcr3mvm27McrSwappingIqmPluginAdapterIN3iqm18InternalEvalPluginEE7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+0600[
 21] 0x00010f8e5418 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00160792 
_ZNK3iqm17DefaultPacketInfo7executeEP15inWorkSpace_tag+0296[ 22] 
0x00010f8d07f1 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00075761 
_ZN3iqm3Iqm15setupIqmFcnPtrsEv+4945[ 23] 0x00010148e005 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+00196613 
_ZN10eventqueue18UserEventQueueImpl5flushEv+1205[ 24] 0x00010fa83a65 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwuix.dylib+00043621 
_Z25isHandleUserEventCallbackPFvPvE+0501[ 25] 0x00010155da45 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01047109 
_Z21svWS_ProcessCallbacksv+00016693[ 26] 0x000101559152 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01028434 
_Z25svWS_ProcessPendingEventsiib+0834[ 27] 0x000101558e5e 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01027678 
_Z25svWS_ProcessPendingEventsiib+0078[ 28] 0x00010ebfa18f 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00119183 
_ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+0095[
 29] 0x00010ebfa49f 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00119967 
_ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+0335[
 30] 0x00010ebe0d1b 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00015643 
_Z26run_init_and_handle_eventsPv+0059[ 31] 0x7fff20454950  
   
/usr/lib/system/libsystem_pthread.dylib+00026960 
_pthread_start+0224[ 32] 0x7fff2045047b
 /usr/lib/system/libsystem_pthread.dylib+9339 
thread_start+0015If this problem is reproducible, please submit a Service 
Request via: 
http://secure-web.cisco.com/1VXNlaPSDpyVyn99uzU-nnvtrM7e9mrXcEfiGMaaVKXFdjYhZDFyLjaVzfXE3m5W4-v_BYIDQCI1YujdbT0EwuX_CuBErnGN-70qx6qpNsr4LA1ZXP9ygc_YZVj9wkpFFIpg-P45dPGyTnp9RwHnY11v-6ntXmbbkupdDvuEb_eh7HFkFmU9-WQifdcGDbvY2yr6Nf9i2Z-WP2NILWKbRVuDO31llfKFIqC_A0dc68Skvd_2Etg5f1Gn3CFaSvaqMRbJdMjUy36sCZB6F9a50Ew/http%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcontact_us%2FA
 technical support engineer might contact you with further information.Thank 
you for your help.** This crash report has been saved to disk as 
/Users/tilak/matlab_crash_dump.2179-1 **MATLAB is exiting because of fatal 
error/Applications/freesurfer/7.1.1/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
 line 33:2179 Killed: 9 
 
/Applications/freesurfer/7.1.1/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
 Amy_Damboise /Users/tilak/Desktop/Work/CNS_cases/Hipps 
0. 
/Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasMesh.gz 
/Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasDump.mgz 
/Applications/freesurfer/7.1.1/average/HippoSF/atlas/compressionLookupTable.txt 
0.05 left L-BFGS v21 '/Applications/freesurfer/7.1..1/bin/fs_run_from_mcr 
/Applications/freesurfer/7.1.1/bin/' 0Darwin tilak.lan 20.3.0 Darwin Kernel 
Version 20.3.0: Thu Jan 21 00:07:06 PST 2021; 
root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64T1 hippocampal subfields exited with 
ERRORS at Wed Mar 24 00:59:59 EDT 2021For more details, see the log file 
/Users/tilak/Desktop/Work/CNS_cases/Hipps/Amy_Damboise/scripts/hippocampal-subfields-T1.logtilak@tilak
 Hipps %  From:fsbuild 
fsbu...@contbay.comSent:Tuesday, March 23, 2021 11:00 
PMTo:freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.eduCc:Ramtilak
 Gattu rg...@med.wayne.eduSubject:Re: [Freesurfer] Hippocampal 
Subfields Segmentation Violation-error[EXTERNAL]I”m wondering if this is 
an issue with the version of Java installed on the machine and Matlab. 
I’ve seen the latest MCR Matlab in

Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

[Ramtilak Gattu]

bbP15inWorkSpace_tag+0066

[ 17] 0x00010eda72de 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+00402142
 
_Z51inEvalCmdWithLocalReturnInDesiredWSAndPublishEventsRKSbItSt11char_traitsItESaItEEPibbP15inWorkSpace_tag+0062

[ 18] 0x00010f8f593e 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00227646 
_ZNK3iqm18InternalEvalPlugin24inEvalCmdWithLocalReturnERKSbItSt11char_traitsItESaItEEP15inWorkSpace_tag+0094

[ 19] 0x00010f8f4df4 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00224756 
_ZN3iqm18InternalEvalPlugin7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+0132

[ 20] 0x00010ec10358 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00209752 
_ZN3mcr3mvm27McrSwappingIqmPluginAdapterIN3iqm18InternalEvalPluginEE7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+0600

[ 21] 0x00010f8e5418 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00160792 
_ZNK3iqm17DefaultPacketInfo7executeEP15inWorkSpace_tag+0296

[ 22] 0x00010f8d07f1 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00075761 
_ZN3iqm3Iqm15setupIqmFcnPtrsEv+4945

[ 23] 0x00010148e005 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+00196613 
_ZN10eventqueue18UserEventQueueImpl5flushEv+1205

[ 24] 0x00010fa83a65 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwuix.dylib+00043621 
_Z25isHandleUserEventCallbackPFvPvE+0501

[ 25] 0x00010155da45 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01047109 
_Z21svWS_ProcessCallbacksv+00016693

[ 26] 0x000101559152 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01028434 
_Z25svWS_ProcessPendingEventsiib+0834

[ 27] 0x000101558e5e 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01027678 
_Z25svWS_ProcessPendingEventsiib+0078

[ 28] 0x00010ebfa18f 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00119183 
_ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+0095

[ 29] 0x00010ebfa49f 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00119967 
_ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+0335

[ 30] 0x00010ebe0d1b 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00015643 
_Z26run_init_and_handle_eventsPv+0059

[ 31] 0x7fff20454950
/usr/lib/system/libsystem_pthread.dylib+00026960 _pthread_start+0224

[ 32] 0x7fff2045047b
/usr/lib/system/libsystem_pthread.dylib+9339 thread_start+0015



If this problem is reproducible, please submit a Service Request via:

http://www.mathworks.com/support/contact_us/


A technical support engineer might contact you with further information.


Thank you for your help.** This crash report has been saved to disk as 
/Users/tilak/matlab_crash_dump.2179-1 **




MATLAB is exiting because of fatal error

/Applications/freesurfer/7.1.1/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
 line 33:  2179 Killed: 9   
/Applications/freesurfer/7.1.1/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
 Amy_Damboise /Users/tilak/Desktop/Work/CNS_cases/Hipps 
0. 
/Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasMesh.gz 
/Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasDump.mgz 
/Applications/freesurfer/7.1.1/average/HippoSF/atlas/compressionLookupTable.txt 
0.05 left L-BFGS v21 '/Applications/freesurfer/7.1.1/bin/fs_run_from_mcr 
/Applications/freesurfer/7.1.1/bin/' 0

Darwin tilak.lan 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 00:07:06 PST 
2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64


T1 hippocampal subfields exited with ERRORS at Wed Mar 24 00:59:59 EDT 2021


For more details, see the log file 
/Users/tilak/Desktop/Work/CNS_cases/Hipps/Amy_Damboise/scripts/hippocampal-subfields-T1.log


tilak@tilak Hipps %




From: fsbuild 
Sent: Tuesday, March 23, 2021 11:00 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Ramtilak Gattu 
Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

[EXTERNAL]
I”m wondering if this is an issue with the version of Java installed on the 
machine and Matlab.  I’ve seen the latest MCR Matlab installer try to make 
changes to java installed on a Mac.  So maybe updating or re-installing the 
Matlab software on your machine could force a java update.  You should be able 
to exit the installer before it makes any changes if you decide not to go thru 
with it.

- R.

On Mar 23, 2021, at 17:45, Ramtilak Gattu  wrote:

External Email - Use Caution
External Email - Use Caution
Hi,

I am also encountering the same issue as WON JONG CHWA on my macbo

Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

[fsbuild]

External Email - Use Caution

I”m wondering if this is an issue with the version of Java installed on the 
machine and Matlab. I’ve seen the latest MCR Matlab installer try to make 
changes to java installed on a Mac. So maybe updating or re-installing 
the Matlab software on your machine could force a java update. You should 
be able to exit the installer before it makes any changes if you decide not to 
go thru with it.
- R..

On Mar 23, 2021, at 17:45, Ramtilak Gattu rg...@med.wayne..edu 
wrote:External Email - Use 
CautionExternal
 Email - Use CautionHi,I am 
also encountering the same issue as WON JONG CHWA on my macbook pro (16gb ram) 
and I even tried the same on imac (8gb ram). I ran recon-all successfully on 
both systems. Here are my system detailsHardware Overview:Model 
Name:MacBook ProModel 
Identifier:MacBookPro16,1Processor Name:6-Core Intel 
Core i7Processor Speed:2.6 GHzNumber of 
Processors:1Total Number of Cores:6L2 Cache 
(per Core):256 KBL3 Cache:12 
MBHyper-Threading 
Technology:EnabledMemory:16 GBSystem 
Firmware Version:1554.80.3.0.0 (iBridge: 
18.16.14347.0.0,0)Serial Number 
(system):C02DPB3BMD6MHardware 
UUID:D313516B-A3B9-500F-9303-EB0F4D4946A4Provisioning 
UDID:D313516B-A3B9-500F-9303-EB0F4D4946A4Activation Lock 
Status:EnabledHere is the log for segmentation violation 
error***Fitting mesh to image 
data took 742.9022 secondsTransforming pointsTransforming pointsWrote image to 
file image.mgzConstructing image-to-world transform from header information 
(asmr1.mgz)Constructing image-to-world transform from header information 
(/Users/tilak/Desktop/Work/CNS_cases/Hipps/AD/tmp/hippoSF_T1_v21_left/imageDump.mgz)Wrote
 image to file asmr2.mgzThis file does not contain MRI parametersCaught 
unexpected exception of unknown 
type.
   Segmentation violation detected at Tue Mar 23 15:53:07 
2021Configuration:
 Crash Decoding   : Disabled Current Visual   : 
Quartz Default Encoding  : ISO-8859-1 MATLAB Architecture: 
maci64 MATLAB Root: 
/Applications/freesurfer/7.1.1/MCRv84 MATLAB Version   : 
8.4.0.150421 (R2014b) Operating System  : Darwin 20..3.0 Darwin 
Kernel Version 20.3.0: Thu Jan 21 00:07:06 PST 2021; 
root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64 Processor ID   
 : x86 Family 6 Model 158 Stepping 10, GenuineIntel Software OpenGL 
 : 0 Virtual Machine  : Java 1.7.0_55-b13 with 
Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode Window 
System   : QuartzFault Count: 1Abnormal 
termination:Segmentation violationRegister State (from fault): RAX = 
0003 RBX = 000102cde080 RCX = 7ff4ce00 
RDX = 7624c180 RSP = 7ff4ce00 RBP = 
7fff2041595e RSI = 7000 RDI = 
7fff204171f9 R8 = 660333a0  R9 = 
7624c180 R10 = 7fff20410002 R11 = 
7ff4ce05b4e0 R12 = 7624c498 R13 = 
 R14 = 00010e5fbd9b R15 = 
0060 RIP = 7624c498 RFL = 
7624c1e0 CS = 00010e49227b  FS = 7624c1c0 
 GS = 0001Stack Trace (from fault):[ 0] 
0x0001048a9e64 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+0052[ 
1] 0x0001048ada2a 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 
_ZN2fl4test17terminate_handledEv+0906[ 2] 0x0001048ad477 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 
_ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+0119[ 3] 
0x000107e39b7a 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 
_Z32mnRunPathDependentInitializationv+3146[ 4] 0x000107e39e58 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 
_Z32mnRunPathDependentInitializationv+3880[ 5] 0x000107e37733 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 
mnFatalSignalHandler+0275[ 6] 0x7fff20630d7d
  /usr/lib/system/libsystem_platform.dylib+00015741 
_sigtramp+0029[ 7] 0x 
   
  unknown-module+[ 8] 0x00010e49227b 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01782395
 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00010667[ 
9] 0x00010e3eba17 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01100311
 _Z15inRunFinalizers7opcodesPS_Pi+0119[ 10] 0x00010e49029d 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01774237
 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+2509[ 11] 
0x00010f0b9c55 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_dispatcher.dylib+00400469
 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+0645[ 12] 
0x00010e43348b 

[Freesurfer] Hippocampal Subfields Segmentation Violation-error

[Ramtilak Gattu]

External Email - Use Caution

Hi,

I am also encountering the same issue as WON JONG CHWA on my macbook pro (16gb 
ram) and I even tried the same on imac (8gb ram). I ran recon-all successfully 
on both systems. Here are my system details


Hardware Overview:


  Model Name: MacBook Pro

  Model Identifier: MacBookPro16,1

  Processor Name: 6-Core Intel Core i7

  Processor Speed: 2.6 GHz

  Number of Processors: 1

  Total Number of Cores: 6

  L2 Cache (per Core): 256 KB

  L3 Cache: 12 MB

  Hyper-Threading Technology: Enabled

  Memory: 16 GB

  System Firmware Version: 1554.80.3.0.0 (iBridge: 18.16.14347.0.0,0)

  Serial Number (system): C02DPB3BMD6M

  Hardware UUID: D313516B-A3B9-500F-9303-EB0F4D4946A4

  Provisioning UDID: D313516B-A3B9-500F-9303-EB0F4D4946A4

  Activation Lock Status: Enabled


Here is the log for segmentation violation error
***
Fitting mesh to image data took 742.9022 seconds
Transforming points
Transforming points
Wrote image to file image.mgz
Constructing image-to-world transform from header information (asmr1.mgz)
Constructing image-to-world transform from header information 
(/Users/tilak/Desktop/Work/CNS_cases/Hipps/AD/tmp/hippoSF_T1_v21_left/imageDump.mgz)
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
Caught unexpected exception of unknown type.


   Segmentation violation detected at Tue Mar 23 15:53:07 2021


Configuration:
  Crash Decoding : Disabled
  Current Visual : Quartz
  Default Encoding   : ISO-8859-1
  MATLAB Architecture: maci64
  MATLAB Root: /Applications/freesurfer/7.1.1/MCRv84
  MATLAB Version : 8.4.0.150421 (R2014b)
  Operating System   : Darwin 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 
00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64
  Processor ID   : x86 Family 6 Model 158 Stepping 10, GenuineIntel
  Software OpenGL: 0
  Virtual Machine: Java 1.7.0_55-b13 with Oracle Corporation Java 
HotSpot(TM) 64-Bit Server VM mixed mode
  Window System  : Quartz

Fault Count: 1


Abnormal termination:
Segmentation violation

Register State (from fault):
  RAX = 0003  RBX = 000102cde080
  RCX = 7ff4ce00  RDX = 7624c180
  RSP = 7ff4ce00  RBP = 7fff2041595e
  RSI = 7000  RDI = 7fff204171f9

   R8 = 660333a0   R9 = 7624c180
  R10 = 7fff20410002  R11 = 7ff4ce05b4e0
  R12 = 7624c498  R13 = 
  R14 = 00010e5fbd9b  R15 = 0060

  RIP = 7624c498  RFL = 7624c1e0

   CS = 00010e49227b   FS = 7624c1c0   GS = 0001

Stack Trace (from fault):
[  0] 0x0001048a9e64 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+0052
[  1] 0x0001048ada2a 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 
_ZN2fl4test17terminate_handledEv+0906
[  2] 0x0001048ad477 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 
_ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+0119
[  3] 0x000107e39b7a 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 
_Z32mnRunPathDependentInitializationv+3146
[  4] 0x000107e39e58 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 
_Z32mnRunPathDependentInitializationv+3880
[  5] 0x000107e37733 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 
mnFatalSignalHandler+0275
[  6] 0x7fff20630d7d   
/usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+0029
[  7] 0x   
+
[  8] 0x00010e49227b 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01782395
 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00010667
[  9] 0x00010e3eba17 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01100311
 _Z15inRunFinalizers7opcodesPS_Pi+0119
[ 10] 0x00010e49029d 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01774237
 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+2509
[ 11] 0x00010f0b9c55 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_dispatcher.dylib+00400469
 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+0645
[ 12] 0x00010e43348b 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01393803
 
_Z23inEvalPcodeHeaderToWordP15_memory_contextiPP11mxArray_tagP12_pcodeheaderP6Mfh_mpj+0219
[ 13] 0x00010e3e5f4b 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01077067
 

Re: [Freesurfer] Hippocampal subfields questions

[Iglesias Gonzalez, Juan E.]

Hi Steve,
Thank you very much for the interest in our tool!
Q1. Yes, mm^3.
Q2. I’ll defer to Doug Greve (CCed) 
Cheers,
/E

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From:  on behalf of Steve Petersen 

Reply-To: Freesurfer support list 
Date: Saturday, October 24, 2020 at 05:07
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfields questions


External Email - Use Caution
Dear Eugenio,

Just two simple questions about hippocampal subfields:

Q1. The volume of each hippocampal subfield is exported in mm3?

Q2. I would like to compare hippocampal subfields volume measures between three 
groups by including the eTIV as covariate. Can I perform this group analysis by 
using the command line (with mri_glmfit command as for the thickness for 
example)?. In that case should I include some specific argument to consider in 
the analysis the hippocampal subfield stats of each subject?.


Thank you in advance.


Best,

Steve
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[Freesurfer] Hippocampal subfields questions

[Steve Petersen]

External Email - Use Caution

Dear Eugenio,

Just two simple questions about hippocampal subfields:

Q1. The volume of each hippocampal subfield is exported in mm3?

Q2. I would like to compare hippocampal subfields volume measures between
three groups by including the eTIV as covariate. Can I perform this group
analysis by using the command line (with mri_glmfit command as for the
thickness for example)?. In that case should I include some specific
argument to consider in the analysis the hippocampal subfield stats of each
subject?.


Thank you in advance.


Best,

Steve
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Re: [Freesurfer] Hippocampal subfields error

[Emily K Clarke]

External Email - Use Caution

Hi Eugenio,

No, I don't think so - we're running recon-all and using the hippocampal 
pipeline from FS 6.0. I bug tested with the FS 6.0dev version and found that 
that hippocampal pipeline worked okay, but since we're combining data with an 
older dataset we need to be able to extract the older hippocampal subfields, 
starting with the recon-all hippocampal subfields processing.

Thanks,
Emily


Date: Wed, 9 Sep 2020 21:21:41 +
From: "Iglesias Gonzalez, Juan E." 
Subject: Re: [Freesurfer] Hippocampal subfields error
To: Freesurfer support list 
Message-ID: <25df95c0-873a-4906-9d51-a94cf0223...@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Emily.
Is it possibly that you may be mixing FS versions, by any chance?
Cheers,
/Eugenio


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)

https://urldefense.com/v3/__http://www.jeiglesias.com__;!!OToaGQ!54kYqoLJMazG-e4wE3yKpehQ-BMMjAGSsGWeQv_zzG6tzdVr_8s9dgvsAg3rWMo$
 



From:  on behalf of Emily K Clarke 

Reply-To: Freesurfer support list 
Date: Wednesday, September 9, 2020 at 15:53
To: "freesurfer@nmr.mgh.harvard.edu" 
    Subject: [Freesurfer] Hippocampal subfields error


External Email - Use Caution
Hi Eugenio,

We?re still running into the issue where running recon-all with the 
hippocampal subfields tag isn?t actually generating any of the hippocampal 
files. I?ve included our full recon-all log below. We already examined the 
scans, and they look perfectly normal ? do you know why this might be happening?

Thanks,
Emily Clarke-Rubright
Morey Neuroimaging Lab



The whole log message:

#

#@# Hippocampal Subfields processing (T1 only) left Mon Aug 10 18:54:21 EDT

2020

--

Setting up environment variables

---

LD_LIBRARY_PATH is


.:/usr/local/packages/freesurfer_v6.0.0/MCRv80/runtime/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/bin/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/os/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/usr/lib64/qt5/plugins/platforms:/usr/local/packages/ants-2.3.4/lib:/usr/lib64/openmpi/lib:

Warning: application is running on a locale different from the original

platform locale.

Warning: No display specified.  You will not be able to display graphics on

the screen.

Registering imageDump.mgz to hippocampal mask from ASEG

This file does not contain MRI parameters

$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $



--mov: Using imageDump.mgz as movable/source volume.

--dst: Using /mnt/BIAC/.users/ch186/


duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/addl/cch/12588326/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask_autoCropped.mgz

as target volume.

--lta: Output transform as trash.lta .

--mapmovhdr: Will save header adjusted movable as

imageDump_coregistered.mgz !

--sat: Using saturation 50 in M-estimator!



reading source 'imageDump.mgz'...

reading target '/mnt/BIAC/.users/ch186/


duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/addl/cch/12588326/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask_autoCropped.mgz'.

..



Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE )

   Type Source : 0  Type Target : 3  ensure both FLOAT (3)

   Reordering axes in mov to better fit dst... ( -1 3 -2 )

MRIreorder() ---

xdim=-1 ydim=3 zdim=-2

src 131 241 99, 0.25 0.25 0.25

dst 131 99 241, 0.25 0.25 0.25

 Determinant after swap : 0.015625

   Mov: (0.25, 0.25, 0.25)mm  and dim (131, 99, 241)

   Dst: (1, 1, 1)mm  and dim (38, 40, 59)

   Asserting both images: 1mm isotropic

- reslicing Mov ...

   -- changing data type from 0 to 3 (noscale = 0)...

   -- Original : (0.25, 0.25, 0.25)mm and (131, 99, 241) voxels.

   -- Resampled: (1, 1, 1)mm and (38, 40, 61) voxels.

   -- Reslicing using cubic bspline

MRItoBSpline degree 3

- reslicing Dst ...

   -- Original : (1, 1, 1)mm and (38, 40, 59) voxels.

   -- Resampled: (1, 1, 1)mm and (38, 40, 61) voxels.

   -- Reslicing using cubic bspline

MRItoBSpline degree 3





 Registration::computeMultiresRegistration

   - computing centroids

   - computing initial transform

 -- 

Re: [Freesurfer] hippocampal subfields error

[Courtney Haswell]

External Email - Use Caution

The whole log message:

#
#@# Hippocampal Subfields processing (T1 only) left Mon Aug 10 18:54:21 EDT
2020
--
Setting up environment variables
---
LD_LIBRARY_PATH is
.:/usr/local/packages/freesurfer_v6.0.0/MCRv80/runtime/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/bin/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/os/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/usr/lib64/qt5/plugins/platforms:/usr/local/packages/ants-2.3.4/lib:/usr/lib64/openmpi/lib:
Warning: application is running on a locale different from the original
platform locale.
Warning: No display specified.  You will not be able to display graphics on
the screen.
Registering imageDump.mgz to hippocampal mask from ASEG
This file does not contain MRI parameters
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $

--mov: Using imageDump.mgz as movable/source volume.
--dst: Using /mnt/BIAC/.users/ch186/
duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/addl/cch/12588326/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask_autoCropped.mgz
as target volume.
--lta: Output transform as trash.lta .
--mapmovhdr: Will save header adjusted movable as
imageDump_coregistered.mgz !
--sat: Using saturation 50 in M-estimator!

reading source 'imageDump.mgz'...
reading target '/mnt/BIAC/.users/ch186/
duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/addl/cch/12588326/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask_autoCropped.mgz'.
..

Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE )
   Type Source : 0  Type Target : 3  ensure both FLOAT (3)
   Reordering axes in mov to better fit dst... ( -1 3 -2 )
MRIreorder() ---
xdim=-1 ydim=3 zdim=-2
src 131 241 99, 0.25 0.25 0.25
dst 131 99 241, 0.25 0.25 0.25
 Determinant after swap : 0.015625
   Mov: (0.25, 0.25, 0.25)mm  and dim (131, 99, 241)
   Dst: (1, 1, 1)mm  and dim (38, 40, 59)
   Asserting both images: 1mm isotropic
- reslicing Mov ...
   -- changing data type from 0 to 3 (noscale = 0)...
   -- Original : (0.25, 0.25, 0.25)mm and (131, 99, 241) voxels.
   -- Resampled: (1, 1, 1)mm and (38, 40, 61) voxels.
   -- Reslicing using cubic bspline
MRItoBSpline degree 3
- reslicing Dst ...
   -- Original : (1, 1, 1)mm and (38, 40, 59) voxels.
   -- Resampled: (1, 1, 1)mm and (38, 40, 61) voxels.
   -- Reslicing using cubic bspline
MRItoBSpline degree 3


 Registration::computeMultiresRegistration
   - computing centroids
   - computing initial transform
 -- using translation info
   - Get Gaussian Pyramid Limits ( min size: 16 max size: -1 )
   - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 1 )
   - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 1 )
   - initial transform:
Ti = [ ...
 1.000  1.1459029727155
   0  1.00 -0.0876360601093
   00  1.0 -2.9034875996918
   000  1.0  ]

   - initial iscale:  Ii =1

Resolution: 1  S( 19 20 30 )  T( 19 20 30 )
 Iteration(f): 1
 -- diff. to prev. transform: 7.11234
 Iteration(f): 2
 -- diff. to prev. transform: 5.92976
 Iteration(f): 3
 -- diff. to prev. transform: 7.00993
 Iteration(f): 4
 -- diff. to prev. transform: 4.91305
 Iteration(f): 5
 -- diff. to prev. transform: 0.781018 max it: 5 reached!

Resolution: 0  S( 38 40 61 )  T( 38 40 61 )
 Iteration(f): 1
 -- diff. to prev. transform: 8.1296
 Iteration(f): 2
 -- diff. to prev. transform: 1.32542
 Iteration(f): 3
 -- diff. to prev. transform: 0.660013
 Iteration(f): 4
 -- diff. to prev. transform: 0.272219
 Iteration(f): 5
 -- diff. to prev. transform: 0.0943126 max it: 5 reached!

   - final transform:
Tf = [ ...
 0.9986737402682 -0.0371977207162  0.0355962086772  0.4749903609000
 0.0194355513105  0.9126027300469  0.4083852549446 -14.0571487737101
-0.0476761978762 -0.4071517980857  0.9121153400046  9.9144950322154
   000  1.0  ]

   - final iscale:  If = 1

**
*
* WARNING: Registration did not converge in 5 steps!
*  Problem might be ill posed.
*  Please inspect output manually!
*
**

Final Transform:
Adjusting final transform due to initial resampling (voxel or size changes)
...
M = [ ...
-0.2496684350671  

Re: [Freesurfer] hippocampal subfields error

[Iglesias Gonzalez, Juan E.]

Dear Courtney,
You can safely ignore “This file does not contain MRI parameters”. If the 
output files are not created, there must be another error further down. Could 
you please send us the whole output?
Cheers,
/Eugenio


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From:  on behalf of Courtney Haswell 

Reply-To: Freesurfer support list 
Date: Wednesday, August 12, 2020 at 09:34
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippocampal subfields error


External Email - Use Caution
We are getting an error after running the hippocampal subfields pipeline that 
we have never received before. It is happening for all subjects. We run 
recon-all and then the hippocampal pipeline and the output files are not being 
created. Below is the beginning of the log and it seems like the relevant part 
is "This file does not contain MRI parameters" when referring to the imageDump 
file. I was able to open that file and it seems ok. What could be the problem? 
Thank you!


#
#@# Hippocampal Subfields processing (T1 only) left Mon Aug 10 18:54:21 EDT 2020
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/packages/freesurfer_v6.0.0/MCRv80/runtime/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/bin/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/os/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/usr/lib64/qt5/plugins/platforms:/usr/local/packages/ants-2.3.4/lib:/usr/lib64/openmpi/lib:
Warning: application is running on a locale different from the original 
platform locale.
Warning: No display specified.  You will not be able to display graphics on the 
screen.
Registering imageDump.mgz to hippocampal mask from ASEG
This file does not contain MRI parameters
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $

--mov: Using imageDump.mgz as movable/source volume.
--dst: Using 
/mnt/BIAC/.users/ch186/duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/addl/cch/12588326/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask_autoCropped.mgz<http://duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/addl/cch/12588326/tmp/hippoSF_T1_v10_left/hippoAmygBinaryMask_autoCropped.mgz>
 as target volume.
--lta: Output transform as trash.lta .
--mapmovhdr: Will save header adjusted movable as imageDump_coregistered.mgz !
--sat: Using saturation 50 in M-estimator!

reading source 'imageDump.mgz'...
reading target 
'/mnt/BIAC/.users/ch186/duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/addl/cch/12588326/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask_autoCropped.mgz'.<http://duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/addl/cch/12588326/tmp/hippoSF_T1_v10_left/hippoAmygBinaryMask_autoCropped.mgz'.>..
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[Freesurfer] hippocampal subfields error

[Courtney Haswell]

External Email - Use Caution

We are getting an error after running the hippocampal subfields pipeline
that we have never received before. It is happening for all subjects. We
run recon-all and then the hippocampal pipeline and the output files are
not being created. Below is the beginning of the log and it seems like the
relevant part is "This file does not contain MRI parameters" when
referring to the imageDump file. I was able to open that file and it seems
ok. What could be the problem? Thank you!


#
#@# Hippocampal Subfields processing (T1 only) left Mon Aug 10 18:54:21 EDT
2020
--
Setting up environment variables
---
LD_LIBRARY_PATH is
.:/usr/local/packages/freesurfer_v6.0.0/MCRv80/runtime/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/bin/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/os/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/usr/lib64/qt5/plugins/platforms:/usr/local/packages/ants-2.3.4/lib:/usr/lib64/openmpi/lib:
Warning: application is running on a locale different from the original
platform locale.
Warning: No display specified.  You will not be able to display graphics on
the screen.
Registering imageDump.mgz to hippocampal mask from ASEG
This file does not contain MRI parameters
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $

--mov: Using imageDump.mgz as movable/source volume.
--dst: Using /mnt/BIAC/.users/ch186/
duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/addl/cch/12588326/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask_autoCropped.mgz
as target volume.
--lta: Output transform as trash.lta .
--mapmovhdr: Will save header adjusted movable as
imageDump_coregistered.mgz !
--sat: Using saturation 50 in M-estimator!

reading source 'imageDump.mgz'...
reading target '/mnt/BIAC/.users/ch186/
duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/addl/cch/12588326/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask_autoCropped.mgz'.
..
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Re: [Freesurfer] Hippocampal subfields --> normalization

[Iglesias Gonzalez, Juan E.]

Dear Hae Won,
Normalizing by ICV and whole hippocampal volume simply attempt to answer two 
different questions:
Is the volume of subfield X, accounting for head size, [insert analysis 
question here]?
Is the % of hippocampal volume covered by subfield X, [insert analysis question 
here]?
(where [analysis question] could be “smaller in Alzheimer’s than in controls”, 
or “related to age”)
Cheers,
/Eugenio


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From:  on behalf of Haewon Roh 

Reply-To: Freesurfer support list 
Date: Wednesday, August 12, 2020 at 06:50
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfields --> normalization


External Email - Use Caution

Hi. team!

Recently,  I submitted a paper dealing with volumes of hippocampus and its 
subfields in epilepsy patients who have significantly reduced  hippocampal 
volume (compared with normal controls) and, in that paper, I used the 
normalization method using ICV, which was suggested by Jack CR in 1989: 
normalized volume = volume (observed) – b (ICV – mean ICV), where b is the 
slope of regression for each ICV.

But, one of the reviewers pointed out that I should use the method based on 
each patient's hippocampus rather than total intracranial volume. Since I've 
seen that a lot of papers, which dealt about these kinds of issues about 
hippocampus and subfields, used the same method with me, I am really doubtful 
that it is more appropriate if I should use the method using individual volume 
of hippocampus (rather than ICV) in order to normalize its volumes of 
substructures in the comparison analysis with those of controls.

# And, whether this is true or not, could you please recommend to me several 
literatures that can show which method of normalizing volumes of the 
hippocampus and its subfields is more appropriate for this kind of issue?

# Really sorry for bothering you. Thank you always for your kind and delicate 
solutions ! : )

--
Hae Won ROH, M.D.

H.P: +82-10-4341-8142
E-mail: rofree...@gmail.com<mailto:rofree...@gmail.com>
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[Freesurfer] Hippocampal subfields --> normalization

[Haewon Roh]

External Email - Use Caution

Hi. team!

Recently,  I submitted a paper dealing with volumes of hippocampus and
its subfields in epilepsy patients who have significantly reduced
 hippocampal volume (compared with normal controls) and, in that paper, I
used the normalization method using ICV, which was suggested by Jack CR in
1989: normalized volume = volume (observed) – b (ICV – mean ICV), where b
is the slope of regression for each ICV.

But, one of the reviewers pointed out that I should use the method based on
each patient's hippocampus rather than total intracranial volume. Since
I've seen that a lot of papers, which dealt about these kinds of issues
about hippocampus and subfields, used the same method with me, I am really
doubtful that it is more appropriate if I should use the method using
individual volume of hippocampus (rather than ICV) in order to normalize
its volumes of substructures in the comparison analysis with those of
controls.

# And, whether this is true or not, could you please recommend to me
several literatures that can show which method of normalizing volumes of
the hippocampus and its subfields is more appropriate for this kind of
issue?

# Really sorry for bothering you. Thank you always for your kind and
delicate solutions ! : )

-- 
Hae Won ROH, M.D.

H.P: +82-10-4341-8142
E-mail: rofree...@gmail.com
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Re: [Freesurfer] Hippocampal subfields

[Iglesias Gonzalez, Juan E.]

Dear Ioana,
This is tricky because the volumes are computed from soft segmentations, which 
are not the ones you’re editing. In general, editing outputs is a bad idea; it 
may be better to simply discard the cases for which quality control fails.
Having said that: if you want to use corrected cases, you could compute volumes 
by simply summing the number of voxels with each label, and multiplying by the 
volume of a voxel (which is 1/27=0.03703703703 cubic mm). But if you do this, 
then you need to compute the volume this way for all cases, including the ones 
you didn’t edit (you don’t want to mix 2 ways of estimating volumes).
Cheers,
/Eugenio


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From:  on behalf of ioana cracana 

Reply-To: Freesurfer support list 
Date: Wednesday, April 8, 2020 at 04:59
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfields


External Email - Use Caution
Hello,
I'm doing a study about hippocampal atrophy and I'm using the Segmentation of 
Hippocampal subfields tool. There were some minor errors and I edited them 
using Freeview, voxel edit tool.  I would like to generate a new 
[lr]h.hippoSfVolumes-T1.v10.txt file using the edited 
[lr]h.hippoSfLabels-T1.v10.mgz in order to see the new results. What command do 
i have to use? Is there another way to edit the hippocampal subfields?And how 
do i see the results?
I'm using Freesurfer v6.0.0. on macOS Mojave.

Thanks,
Ioana
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[Freesurfer] Hippocampal subfields

[ioana cracana]

External Email - Use Caution

Hello,
I'm doing a study about hippocampal atrophy and I'm using the Segmentation of 
Hippocampal subfields tool. There were some minor errors and I edited them 
using Freeview, voxel edit tool.  I would like to generate a new 
[lr]h.hippoSfVolumes-T1.v10.txt file using the edited 
[lr]h.hippoSfLabels-T1.v10.mgz in order to see the new results. What command do 
i have to use? Is there another way to edit the hippocampal subfields?And how 
do i see the results?
I'm using Freesurfer v6.0.0. on macOS Mojave.

Thanks,
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Re: [Freesurfer] hippocampal-subfields-T1 error

[Duvnjak, Aleksandar]

External Email - Use Caution

Dear Juan,

Thank you so much. This has sorted our issue. You're a lifesaver.

Kind regards,
Aleks Duvnjak

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, Juan 
E. 
Sent: 27 March 2020 19:07
To: Freesurfer support list 
Subject: Re: [Freesurfer] hippocampal-subfields-T1 error


This email from jiglesiasgonza...@mgh.harvard.edu originates from outside 
Imperial. Do not click on links and attachments unless you recognise the 
sender. If you trust the sender, add them to your safe senders 
list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping 
for this address.



Dear Aleks,

Please try:  chmod u+x /rds/general/project/amyloidpet/live/freesurfer/bin/*

Cheers,

/Eugenio





Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com







From:  on behalf of "Duvnjak, 
Aleksandar" 
Reply-To: Freesurfer support list 
Date: Friday, March 27, 2020 at 14:39
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippocampal-subfields-T1 error



External Email - Use Caution

Dear FreeSurfer Experts,



FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0

Platform: Secure Shell port of a high performance computer (HPC) accessed via 
Ubuntu 18.04 WSL



Having processed a cohort of 1mm^3 MRI images via the recon-all command, we 
have had issues processing the hippocampal subfield command as described: 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields



Although we eventually want to run the command in array, we are currently 
attempting it on individual subjects to ensure a good output. Upon running the 
command we receive a "permission denied" error. The HPC is a shared cluster, 
and the FreeSurfer 6.0.0 app is downloaded in a shared dir which we cannot 
edit, and thus couldn't download the Matlab runtime to.



We initially thought this may be the issue, and so tried multiple workarounds, 
including copying the entirety of the FreeSurfer installation package from the 
shared directory to our own directory, within which we have editing 
permissions. This didn't help, even when setting our personal directory as the 
FREESURFER_HOME. As you can see from the end of the recon-all.log file, we 
tried numerous attempts with various workarounds and all have the same outcome.



I appreciate this may still be more of an issue with running FreeSurfer via a 
secure shell port to a HPC cluster rather than an issue with FreeSurfer itself, 
but I'm sure you have many research labs asking questions regarding using HPC 
systems to run FreeSurfer, so any recommendations or thoughts would be welcome.



Kind Regards,
Aleks Duvnjak
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Re: [Freesurfer] hippocampal-subfields-T1 error

[Iglesias Gonzalez, Juan E.]

Dear Aleks,
Please try:  chmod u+x /rds/general/project/amyloidpet/live/freesurfer/bin/*
Cheers,
/Eugenio


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From:  on behalf of "Duvnjak, 
Aleksandar" 
Reply-To: Freesurfer support list 
Date: Friday, March 27, 2020 at 14:39
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippocampal-subfields-T1 error


External Email - Use Caution
Dear FreeSurfer Experts,

FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0
Platform: Secure Shell port of a high performance computer (HPC) accessed via 
Ubuntu 18.04 WSL

Having processed a cohort of 1mm^3 MRI images via the recon-all command, we 
have had issues processing the hippocampal subfield command as described: 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

Although we eventually want to run the command in array, we are currently 
attempting it on individual subjects to ensure a good output. Upon running the 
command we receive a "permission denied" error. The HPC is a shared cluster, 
and the FreeSurfer 6.0.0 app is downloaded in a shared dir which we cannot 
edit, and thus couldn't download the Matlab runtime to.

We initially thought this may be the issue, and so tried multiple workarounds, 
including copying the entirety of the FreeSurfer installation package from the 
shared directory to our own directory, within which we have editing 
permissions. This didn't help, even when setting our personal directory as the 
FREESURFER_HOME. As you can see from the end of the recon-all.log file, we 
tried numerous attempts with various workarounds and all have the same outcome.

I appreciate this may still be more of an issue with running FreeSurfer via a 
secure shell port to a HPC cluster rather than an issue with FreeSurfer itself, 
but I'm sure you have many research labs asking questions regarding using HPC 
systems to run FreeSurfer, so any recommendations or thoughts would be welcome.

Kind Regards,
Aleks Duvnjak
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Re: [Freesurfer] hippocampal-subfields-T1 error

[Duvnjak, Aleksandar]

External Email - Use Caution

To clarify, upon copying the entire FreeSurfer 6.0 package to our personal 
directory, we have then downloaded the matlab runtime MCRv80 folder to that 
directory and the issue does not appear to be the hippocampal-subfields-T1 
pipeline accessing that.

Regards,
Aleks Duvnjak

From: Duvnjak, Aleksandar
Sent: 27 March 2020 18:38
To: freesurfer@nmr.mgh.harvard.edu 
Subject: hippocampal-subfields-T1 error

Dear FreeSurfer Experts,

FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0
Platform: Secure Shell port of a high performance computer (HPC) accessed via 
Ubuntu 18.04 WSL

Having processed a cohort of 1mm^3 MRI images via the recon-all command, we 
have had issues processing the hippocampal subfield command as described: 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

Although we eventually want to run the command in array, we are currently 
attempting it on individual subjects to ensure a good output. Upon running the 
command we receive a "permission denied" error. The HPC is a shared cluster, 
and the FreeSurfer 6.0.0 app is downloaded in a shared dir which we cannot 
edit, and thus couldn't download the Matlab runtime to.

We initially thought this may be the issue, and so tried multiple workarounds, 
including copying the entirety of the FreeSurfer installation package from the 
shared directory to our own directory, within which we have editing 
permissions. This didn't help, even when setting our personal directory as the 
FREESURFER_HOME. As you can see from the end of the recon-all.log file, we 
tried numerous attempts with various workarounds and all have the same outcome.

I appreciate this may still be more of an issue with running FreeSurfer via a 
secure shell port to a HPC cluster rather than an issue with FreeSurfer itself, 
but I'm sure you have many research labs asking questions regarding using HPC 
systems to run FreeSurfer, so any recommendations or thoughts would be welcome.

Kind Regards,
Aleks Duvnjak
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Re: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl Amygdala) FreeSurfer_dev version

[Iglesias Gonzalez, Juan E.]

Good question! It’s ok if only the hippo is covered.
Cheers,
/E

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Rene Seiger 

Reply-To: Freesurfer support list 
Date: Friday, 24 January 2020 at 12:15
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool 
(incl Amygdala) FreeSurfer_dev version


External Email - Use Caution

Dear Juan,

Thank you very much for you answer! However, I ran into another issue using the 
new tool: It is stated:  'Using the additional scan in isolation is advised 
when it is of higher resolution than the T1 while covering the whole hippocampi 
and amygdalae'. Can I still use this processing mode, when my high-resolution 
scans only have the hippocampi covered, as I am not interested in the amygdala 
in the first place? Or is it mandatory to have both structures fully covered 
within the additional scan when I want to run it in isolation?
Thank you very much,
René



<http://www.meduniwien.ac.at/neuroimaging/>
<http://www.meduniwien.ac.at/neuroimaging/>
Am 23.01.2020 um 18:09 schrieb Iglesias Gonzalez, Juan E.:
Hi Rene,
The atlases are slightly different so the outputs will be a bit different. But 
the segmentations will indeed be comparable.
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Rene Seiger 
<mailto:rene.sei...@meduniwien.ac.at>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, 23 January 2020 at 07:48
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl 
Amygdala) FreeSurfer_dev version


External Email - Use Caution

Dear all,

I recently saw that the page of the hippocampal module for FS6 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) seems to be 
obsolete and it looks as if this module will be replaced by a newer version in 
the near future (now dev version, 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).

However, I am not entirely sure how those two modules differ in terms of 
hippocampal subfield segmentation, when the "FS60" parcellation scheme is used 
in the new module. It is stated that 'it mimics the FreeSurfer 6.0 hippocampal 
module', but is the output 1:1 comparable?
Thank you very much and kind regards,
René
--

Dr. René Seiger
Research Associate

Medical University of Vienna
Department of Psychiatry and Psychotherapy
Division of General Psychiatry
NEUROIMAGING LABS (NIL) - PET, MRI, EEG, TMS & Chemical Lab

Waehringer Guertel 18-20, A-1090 Vienna
Phone +43 (0) 1 40400-38250
rene.sei...@meduniwien.ac.at
<mailto:rene.sei...@meduniwien.ac.at>http://www.meduniwien.ac.at/neuroimaging/

<http://www.meduniwien.ac.at/neuroimaging/>



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Re: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl Amygdala) FreeSurfer_dev version

[Rene Seiger]

   External Email - Use Caution


Dear Juan,

Thank you very much for you answer! However, I ran into another issue 
using the new tool: It is stated:  'Using the additional scan in 
isolation is advised when it is of higher resolution than the T1 while 
covering the whole hippocampi and amygdalae'. Can I still use this 
processing mode, when my high-resolution scans only have the hippocampi 
covered, as I am not interested in the amygdala in the first place? Or 
is it mandatory to have both structures fully covered within the 
additional scan when I want to run it in isolation?


Thank you very much,
René



<http://www.meduniwien.ac.at/neuroimaging/>
<http://www.meduniwien.ac.at/neuroimaging/>
Am 23.01.2020 um 18:09 schrieb Iglesias Gonzalez, Juan E.:


Hi Rene,

The atlases are slightly different so the outputs will be a bit 
different. But the segmentations will indeed be comparable.


Cheers,

/Eugenio

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com

*From: * on behalf of Rene 
Seiger 

*Reply-To: *Freesurfer support list 
*Date: *Thursday, 23 January 2020 at 07:48
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *[Freesurfer] Hippocampal subfields FS6 vs. new hippocampus 
tool (incl Amygdala) FreeSurfer_dev version


*External Email - Use Caution *

Dear all,

I recently saw that the page of the hippocampal module for FS6 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) seems 
to be obsolete and it looks as if this module will be replaced by a 
newer version in the near future (now dev version, 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).


However, I am not entirely sure how those two modules differ in terms 
of hippocampal subfield segmentation, when the "FS60" parcellation 
scheme is used in the new module. It is stated that 'it mimics the 
FreeSurfer 6.0 hippocampal module', but is the output 1:1 comparable?


Thank you very much and kind regards,
René

--

*Dr. René Seiger*
Research Associate

*Medical University of Vienna*
Department of Psychiatry and Psychotherapy
Division of General Psychiatry
NEUROIMAGING LABS (NIL) - PET, MRI, EEG, TMS & Chemical Lab

Waehringer Guertel 18-20, A-1090 Vienna
Phone +43 (0) 1 40400-38250
rene.sei...@meduniwien.ac.at
<mailto:rene.sei...@meduniwien.ac.at>http://www.meduniwien.ac.at/neuroimaging/ 



<http://www.meduniwien.ac.at/neuroimaging/>


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Re: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl Amygdala) FreeSurfer_dev version

[Iglesias Gonzalez, Juan E.]

Hi Rene,
The atlases are slightly different so the outputs will be a bit different. But 
the segmentations will indeed be comparable.
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Rene Seiger 

Reply-To: Freesurfer support list 
Date: Thursday, 23 January 2020 at 07:48
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl 
Amygdala) FreeSurfer_dev version


External Email - Use Caution

Dear all,

I recently saw that the page of the hippocampal module for FS6 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) seems to be 
obsolete and it looks as if this module will be replaced by a newer version in 
the near future (now dev version, 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).

However, I am not entirely sure how those two modules differ in terms of 
hippocampal subfield segmentation, when the "FS60" parcellation scheme is used 
in the new module. It is stated that 'it mimics the FreeSurfer 6.0 hippocampal 
module', but is the output 1:1 comparable?
Thank you very much and kind regards,
René
--

Dr. René Seiger
Research Associate

Medical University of Vienna
Department of Psychiatry and Psychotherapy
Division of General Psychiatry
NEUROIMAGING LABS (NIL) - PET, MRI, EEG, TMS & Chemical Lab

Waehringer Guertel 18-20, A-1090 Vienna
Phone +43 (0) 1 40400-38250
rene.sei...@meduniwien.ac.at
<mailto:rene.sei...@meduniwien.ac.at>http://www.meduniwien.ac.at/neuroimaging/

<http://www.meduniwien.ac.at/neuroimaging/>
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[Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl Amygdala) FreeSurfer_dev version

[Rene Seiger]

   External Email - Use Caution


Dear all,

I recently saw that the page of the hippocampal module for FS6 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) seems 
to be obsolete and it looks as if this module will be replaced by a 
newer version in the near future (now dev version, 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).


However, I am not entirely sure how those two modules differ in terms of 
hippocampal subfield segmentation, when the "FS60" parcellation scheme 
is used in the new module. It is stated that 'it mimics the FreeSurfer 
6.0 hippocampal module', but is the output 1:1 comparable?


Thank you very much and kind regards,
René
--

*Dr. René Seiger*
Research Associate

*Medical University of Vienna*
Department of Psychiatry and Psychotherapy
Division of General Psychiatry
NEUROIMAGING LABS (NIL) - PET, MRI, EEG, TMS & Chemical Lab

Waehringer Guertel 18-20, A-1090 Vienna
Phone +43 (0) 1 40400-38250
rene.sei...@meduniwien.ac.at
http://www.meduniwien.ac.at/neuroimaging/ 




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Re: [Freesurfer] Hippocampal subfields: exporting results

[Iglesias Gonzalez, Juan E.]

Yes, you should be following the instructions here:
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
rather than the wiki page for 6.0 here:
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Steve Petersen 

Reply-To: Freesurfer support list 
Date: Wednesday, 11 December 2019 at 10:28
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Hippocampal subfields: exporting results


External Email - Use Caution
Dear Eugenio,

I noticed what was the problem. I used freesurfer dev version with the 
following command:

segmentHA_T2.sh

I tried to export the hippocampal and amygdala results of several subjects with 
these commands and now everything works fine.

quantifyHAsubregions.sh hippoSf HIPO-AMY hippocampal_results.txt

quantifyHAsubregions.sh amygNuc HIPO-AMY amygdala_results.txt



Is there some difference between the segmentHA_T2.sh  that I used and the 
command of the website? In that case I would like to use the most appropriated.



recon-all -s  -hippocampal-subfields-T2  

 Thanks in advance.


Best regards,



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Re: [Freesurfer] Hippocampal subfields: exporting results

[Steve Petersen]

External Email - Use Caution

Dear Eugenio,

I noticed what was the problem. I used freesurfer dev version with the
following command:

segmentHA_T2.sh

I tried to export the hippocampal and amygdala results of several subjects
with these commands and now everything works fine.

quantifyHAsubregions.sh hippoSf HIPO-AMY hippocampal_results.txt

quantifyHAsubregions.sh amygNuc HIPO-AMY amygdala_results.txt


Is there some difference between the *segmentHA_T2.sh*  that I used and the
command of the website? In that case I would like to use the most
appropriated.


recon-all -s  *-hippocampal-subfields-T2*  

 Thanks in advance.


Best regards,
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Re: [Freesurfer] Hippocampal subfields: exporting results

[Iglesias Gonzalez, Juan E.]

Dear Steve,
Can you please send us:
- The segmentation command you used for a sample subject
- A list of the files under the mri directory for that subject.
Cheers,
/Eugenio


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Steve Petersen 

Reply-To: Freesurfer support list 
Date: Wednesday, 11 December 2019 at 03:54
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfields: exporting results


External Email - Use Caution
Dear Freesurfer experts,

I used the freesurfer dev version to estimate hippocampal subfields using mode 
B (additional scan).

All have worked fine although when I tried to export the results I can not find 
the txt file created

This is the output



rmnlab1:~ neucoga$ quantifyHippocampalSubfields.sh HIPOAMYG 
HipoAmyg_results.txt /Applications/freesurfer/subjects/4001T1

Gathering results from subjects in:

   /Applications/freesurfer/subjects/4001T1

Using the suffix name:

   HIPOAMYG

And writing them to:

   HipoAmyg_results.txt







Where is saved the HipoAmyg_results.txt file?? I have searched it and I can't 
find it...



Excuse me for this basic question.





Thanks in advance.





Best regards,
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[Freesurfer] Hippocampal subfields: exporting results

[Steve Petersen]

External Email - Use Caution

Dear Freesurfer experts,

I used the freesurfer dev version to estimate hippocampal subfields using
mode B (additional scan).

All have worked fine although when I tried to export the results I can not
find the txt file created

This is the output


rmnlab1:~ neucoga$ quantifyHippocampalSubfields.sh HIPOAMYG
HipoAmyg_results.txt /Applications/freesurfer/subjects/4001T1

Gathering results from subjects in:

   /Applications/freesurfer/subjects/4001T1

Using the suffix name:

   HIPOAMYG

And writing them to:

   HipoAmyg_results.txt




Where is saved the HipoAmyg_results.txt file?? I have searched it and I
can't find it...


Excuse me for this basic question.



Thanks in advance.



Best regards,
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Re: [Freesurfer] hippocampal subfields as masks for mri_segstats

[Greve, Douglas N.,Ph.D.]

Try using this instead
lh.hippoAmygLabels-T1.v21.FSvoxelSpace.mgz


On 12/4/19 5:09 PM, Marcel Heers wrote:
>
> External Email - Use Caution
>
> Dear all, (dear Eugenio),
>
> I would like to use hippocampal subfields as masks for mri_segstats to 
> retrieve intensity values. I am having problems loading the subfields 
> file although it works fine with aseg.mgz.
>
> Does  anyone know the cause?
>
> Thank you in advance!
>
> Best regards
> Marcel
>
> mri_segstats --seg $SUBJECTS_DIR/test/mri/aseg.mgz --ctab-default 
> --sum output.txt --in $SUBJECTS_DIR/test/mri/T1.mgz
>
> mri_segstats --seg 
> $SUBJECTS_DIR/test/mri/lh.hippoAymgLabels-T1.v21.HBT.mgz --sum 
> output.txt --in $SUBJECTS_DIR/test/mri/T1.mgz
>
> ERROR: loading $SUBJECTS_DIR/test/mri/lh.hippoAymgLabels-T1.v21.HBT.mgz
>
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Re: [Freesurfer] hippocampal subfields as masks for mri_segstats

[Iglesias Gonzalez, Juan E.]

I believe the problem is that they live in different voxel spaces (Doug, can 
you please clarify?)
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Marcel Heers 

Reply-To: Freesurfer support list 
Date: Wednesday, 4 December 2019 at 17:10
To: "Freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippocampal subfields as masks for mri_segstats


External Email - Use Caution
Dear all, (dear Eugenio),

I would like to use hippocampal subfields as masks for mri_segstats to retrieve 
intensity values. I am having problems loading the subfields file although it 
works fine with aseg.mgz.

Does  anyone know the cause?

Thank you in advance!

Best regards
Marcel

mri_segstats --seg $SUBJECTS_DIR/test/mri/aseg.mgz --ctab-default --sum 
output.txt --in $SUBJECTS_DIR/test/mri/T1.mgz

mri_segstats --seg $SUBJECTS_DIR/test/mri/lh.hippoAymgLabels-T1.v21.HBT.mgz 
--sum output.txt --in $SUBJECTS_DIR/test/mri/T1.mgz

ERROR: loading $SUBJECTS_DIR/test/mri/lh.hippoAymgLabels-T1.v21.HBT.mgz
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[Freesurfer] hippocampal subfields as masks for mri_segstats

[Marcel Heers]

External Email - Use Caution

Dear all, (dear Eugenio),

I would like to use hippocampal subfields as masks for mri_segstats to
retrieve intensity values. I am having problems loading the subfields file
although it works fine with aseg.mgz.

Does  anyone know the cause?

Thank you in advance!

Best regards
Marcel

mri_segstats --seg $SUBJECTS_DIR/test/mri/aseg.mgz --ctab-default --sum
output.txt --in $SUBJECTS_DIR/test/mri/T1.mgz

mri_segstats --seg $SUBJECTS_DIR/test/mri/lh.hippoAymgLabels-T1.v21.HBT.mgz
--sum output.txt --in $SUBJECTS_DIR/test/mri/T1.mgz

ERROR: loading $SUBJECTS_DIR/test/mri/lh.hippoAymgLabels-T1.v21.HBT.mgz
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[Freesurfer] ?????? Hippocampal Subfields Atlas

[ZZY]

External Email - Use Caution

Dear Doug??
I know the fsfast but have never used it 
before, and I just preprocessed my resting-state fMRI data by using SPM 
toolbox. Next, we want to analyze the functional connecitvity between
the hippocampal subregions.


Best,


Zhiyong


----
??:"Greve, Douglas N.,Ph.D."https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Hippocampal Subfields Atlas

[Greve, Douglas N.,Ph.D.]

Are you using fsfast?

On 9/25/19 7:00 AM, ZZY wrote:
>
> ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution
>
> Dear ?0?2Doug??
>
> ?0?2 ?0?2 ?0?2I have a group of multimode MRI data, including functional MRI, 
> T1WI and diffusion MRI. We want to analyze the functional and 
> structual connectivity between the hippocampal subregions.?0?2 Now, we 
> have obtained individual-level atlas of hippocampal subfields for each 
> subject by using FREESURFER 6.0 on the T1 image. What should we do 
> next step? How do get a group-level atlas of hippocampal subfields and 
> apply it to functuional and diffusion data?
>
> Best,
>
> Zhiyong
>
>
>
> ___
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[Freesurfer] Hippocampal Subfields Atlas

[ZZY]

External Email - Use Caution

Dear Doug??

  I have a group of multimode MRI data, including functional 
MRI, T1WI and diffusion MRI. We want to analyze the functional and structual 
connectivity between the hippocampal subregions. Now, we have obtained 
individual-level atlas of hippocampal subfields for each subject by using 
FREESURFER 6.0 on the T1 image. What should we do next step? How do get a 
group-level atlas of hippocampal subfields and apply it to functuional and 
diffusion data?







Best,


Zhiyong___
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[Freesurfer] Hippocampal Subfields Atlas

[ZZY]

External Email - Use Caution

Dear Freesurfer developer:
   I have a group of multimode 
MRI data, including functional MRI, T1WI and diffusion MRI. We want to analyze 
the functional and structual connectivity between the hippocampal subregions.
Now, we have obtained individual-level atlas of hippocampal subfields for each 
subject by using FREESURFER 6.0 on the T1 image. What should we do next step? 
How do get a group-level atlas of hippocampal subfields and apply it to 
functuional and diffusion data?


Best,
zhiyong___
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Re: [Freesurfer] Hippocampal-subfields-T1 interruption (Bruce Fischl)

[Bruce Fischl]

glad it worked out
Bruce
On Fri, 13 Sep 2019, 3 6 wrote:



External Email - Use Caution

Hi Bruce,
I checked the alias, I really aliased mv to “mv -i”, and it worked
automatically, after I unaliased.

Thanks for your help.

Best regards,
Guodong

  在
  2019年9月13日，上午12:00，freesurfer-requ...@nmr.mgh.harvard.edu
  写道：

Re: Hippocampal-subfields-T1 interruption (Bruce Fischl)



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Re: [Freesurfer] Hippocampal-subfields-T1 interruption (Bruce Fischl)

[3 6]

External Email - Use Caution

Hi Bruce,

I checked the alias, I really aliased mv to “mv -i”, and it worked 
automatically, after I unaliased.

Thanks for your help.

Best regards,
Guodong

> 在 2019年9月13日，上午12:00，freesurfer-requ...@nmr.mgh.harvard.edu 写道：
> 
> Re: Hippocampal-subfields-T1 interruption (Bruce Fischl)

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Re: [Freesurfer] Hippocampal-subfields-T1 interruption

[Bruce Fischl]

Hi Guodong

Hmmm, not sure what is doing that, but my guess is you have mv aliased. Can 
you type:


which mv

and see if you have it aliased to "mv -i" or some such?

cheers
Bruce


On Thu, 12 Sep 2019, 
3 6 wrote:


   External Email - Use Caution 


Hello FreeSurfer Developers,

I'm attempting to analyze hippocampal subfields for T1 scan, but when I run the command recon-all -s subjects -hippocampal-subfields-T1, I always get interrupted by the warning : 


mv: overwrite ‘imageDump.mgz’?

It keep running only when I type Y or N.

I've searched the list and no similar request have been submitted. Does anyone have any thoughts on how to make it automatically running? Also, I’ve attached the hippocampal-subfields-T1.log in case it's of any use. 


1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0
2) Platform: CentOS release 7 
3) recon-all.log: see attached


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[Freesurfer] hippocampal subfields {Disarmed}

[郑凤莲]

External Email - Use Caution

Dear experts,

I have segmented hippocampus into 13 subfields using FS6.0. Then, I want to 
study the function connectivity  between sibfields. How can I utilize this 
template to do this research? Is it possible? Thanks for your reply in advance.

Sincerely,
Zhemg


| |
郑凤莲
|
|
邮箱：zhengfenglian0...@163.com
|

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Re: [Freesurfer] Hippocampal subfields

[Iglesias Gonzalez, Juan E.]

Dear Zheng,
I believe you ran out of memory. How much RAM does your machine have? You need 
about 10GB to run this.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of 郑凤莲 

Reply-To: Freesurfer support list 
Date: Friday, 9 August 2019 at 01:19
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampal subfields


External Email - Use Caution
Dear /Eugenio,

Here is the log files and all results for one subject as the attachments. I 
have run a lots of subjects and all result directories didn't include 
l(r)h.hippoSfLabels-T1.v10.mgz file.

Sincerely,
Zheng



At 2019-08-08 09:49:30, "Iglesias Gonzalez, Juan E." 
 wrote:

Dear Zheng,
Can you please send us the log files?
Kind regards,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of 郑凤莲 

Reply-To: Freesurfer support list 
Date: Wednesday, 7 August 2019 at 21:19
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfields


External Email - Use Caution
Hi exports,

I am using FS6.0 to segment hippocampus. I run "recon-all -s bert 
-hippocampal-subfields-T1" and it said "recon all bert finished without error". 
However, in mri directory, there is no l(r)h.hippoSfLabels-T1.v10.mgz file. And 
in tmp directory, there are two directories, "hippoSF_T1_v10_left" and 
"hippoSF_T1_v10_right". But in these two directories, the 
l(r)h.hippoSfLabels-T1.v10.mgz file is still not exsit. What's the matter? I 
need your help. Thanks very muxh in advance.

Sincerely,
Zheng






从网易163邮箱发来的云附件
[Image removed by 
sender.]<http://fs.163.com/fs/display/?p=X-NETEASE-HUGE-ATTACHMENT=G-b3qYIpqPb3JDXJ0A047b7py5g69iVSmmIFcThcCOcB6oj2z_omEpB8wqbsFq50xOBA6-GnslKTWj_4hb3Fxw=Re%3ARe%3A%20%5BFreesurfer%5D%20Hippocampal%20subfields>
hippocampal-subfields-T1.log<http://fs.163.com/fs/display/?p=X-NETEASE-HUGE-ATTACHMENT=G-b3qYIpqPb3JDXJ0A047b7py5g69iVSmmIFcThcCOcB6oj2z_omEpB8wqbsFq50xOBA6-GnslKTWj_4hb3Fxw=Re%3ARe%3A%20%5BFreesurfer%5D%20Hippocampal%20subfields>
 (112.5K, 2019年8月24日 13:06 到期)
下载<http://fs.163.com/fs/display/?p=X-NETEASE-HUGE-ATTACHMENT=G-b3qYIpqPb3JDXJ0A047b7py5g69iVSmmIFcThcCOcB6oj2z_omEpB8wqbsFq50xOBA6-GnslKTWj_4hb3Fxw=Re%3ARe%3A%20%5BFreesurfer%5D%20Hippocampal%20subfields>
[Image removed by 
sender.]<http://fs.163.com/fs/display/?p=X-NETEASE-HUGE-ATTACHMENT=G-b3qYIpqPb3JDXJ0A047b7py5g69iVSmmIFcThcCOecwuYYtWpTYGGNnWS7Zp0VT-kslDawp64gaGy57xjFlw=Re%3ARe%3A%20%5BFreesurfer%5D%20Hippocampal%20subfields>
CQMS004.zip<http://fs.163.com/fs/display/?p=X-NETEASE-HUGE-ATTACHMENT=G-b3qYIpqPb3JDXJ0A047b7py5g69iVSmmIFcThcCOecwuYYtWpTYGGNnWS7Zp0VT-kslDawp64gaGy57xjFlw=Re%3ARe%3A%20%5BFreesurfer%5D%20Hippocampal%20subfields>
 (359.89M, 2019年8月24日 12:57 到期)
下载<http://fs.163.com/fs/display/?p=X-NETEASE-HUGE-ATTACHMENT=G-b3qYIpqPb3JDXJ0A047b7py5g69iVSmmIFcThcCOecwuYYtWpTYGGNnWS7Zp0VT-kslDawp64gaGy57xjFlw=Re%3ARe%3A%20%5BFreesurfer%5D%20Hippocampal%20subfields>





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Re: [Freesurfer] Hippocampal subfields

[郑凤莲]

External Email - Use Caution

Dear /Eugenio,


Here is the log files and all results for one subject as the attachments. I 
have run a lots of subjects and all result directories didn't include 
l(r)h.hippoSfLabels-T1.v10.mgz file.


Sincerely,
Zheng





At 2019-08-08 09:49:30, "Iglesias Gonzalez, Juan E." 
 wrote:


Dear Zheng,

Can you please send us the log files?

Kind regards,

/Eugenio

 

-- 

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com 

 

 

From:  on behalf of 郑凤莲 

Reply-To: Freesurfer support list 
Date: Wednesday, 7 August 2019 at 21:19
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfields

 

External Email - Use Caution

Hi exports,

 

I am using FS6.0 to segment hippocampus. I run "recon-all -s bert 
-hippocampal-subfields-T1" and it said "recon all bert finished without error". 
However, in mri directory, there is no l(r)h.hippoSfLabels-T1.v10.mgz file. And 
in tmp directory, there are two directories, "hippoSF_T1_v10_left" and 
"hippoSF_T1_v10_right". But in these two directories, the 
l(r)h.hippoSfLabels-T1.v10.mgz file is still not exsit. What's the matter? I 
need your help. Thanks very muxh in advance.

 

Sincerely,

Zheng






 

从网易163邮箱发来的云附件
hippocampal-subfields-T1.log (112.5K, 2019年8月24日 13:06 到期)
下载
CQMS004.zip (359.89M, 2019年8月24日 12:57 到期)
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Re: [Freesurfer] Hippocampal subfields

[Iglesias Gonzalez, Juan E.]

Dear Zheng,
Can you please send us the log files?
Kind regards,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of 郑凤莲 

Reply-To: Freesurfer support list 
Date: Wednesday, 7 August 2019 at 21:19
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfields


External Email - Use Caution
Hi exports,

I am using FS6.0 to segment hippocampus. I run "recon-all -s bert 
-hippocampal-subfields-T1" and it said "recon all bert finished without error". 
However, in mri directory, there is no l(r)h.hippoSfLabels-T1.v10.mgz file. And 
in tmp directory, there are two directories, "hippoSF_T1_v10_left" and 
"hippoSF_T1_v10_right". But in these two directories, the 
l(r)h.hippoSfLabels-T1.v10.mgz file is still not exsit. What's the matter? I 
need your help. Thanks very muxh in advance.

Sincerely,
Zheng





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[Freesurfer] Hippocampal subfields

[郑凤莲]

External Email - Use Caution

Hi exports,


I am using FS6.0 to segment hippocampus. I run "recon-all -s bert 
-hippocampal-subfields-T1" and it said "recon all bert finished without error". 
However, in mri directory, there is no l(r)h.hippoSfLabels-T1.v10.mgz file. And 
in tmp directory, there are two directories, "hippoSF_T1_v10_left" and 
"hippoSF_T1_v10_right". But in these two directories, the 
l(r)h.hippoSfLabels-T1.v10.mgz file is still not exsit. What's the matter? I 
need your help. Thanks very muxh in advance.


Sincerely,
Zheng___
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Re: [Freesurfer] hippocampal subfields error

[Bruce Fischl]

hmmm, that is strange. Can you tar and gzip the entire subject dir then 
upload it to our ftp site?


On Mon, 17 Jun 2019, Iglesias Gonzalez, Eugenio 
wrote:




External Email - Use Caution

OK yes this is a problem with the main recon-all stream. It’d have been a 
miracle for the subfield
module to recover from that…

At this point, I’ll defer to Doug / Bruce.

Cheers,

/E

-- 

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com 

 

 

From:  on behalf of "Mennecke, Angelika"

Reply-To: Freesurfer support list 
Date: Monday, 17 June 2019 at 10:11
To: Freesurfer support list 
Subject: Re: [Freesurfer] hippocampal subfields error

 

External Email - Use Caution

Dear Eugenio,

 

attached you’ll find the picture. Looks as though the left hippocampus has 
erroneously been
attributed to gray matter.

 

Cheers, Angelika

 

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im
Auftrag von Iglesias Gonzalez, Eugenio
Gesendet: Montag, 17. Juni 2019 15:49
An: Freesurfer support list
Betreff: Re: [Freesurfer] hippocampal subfields error

 

External Email - Use Caution

Dear Angelika,

Can you please send us a screenshot of the inaccurate T1 segmentation?

Cheers,

/Eugenio

 

-- 

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com 

 

 

From:  on behalf of "Mennecke, Angelika"

Reply-To: Freesurfer support list 
Date: Monday, 17 June 2019 at 06:36
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippocampal subfields error

 

External Email - Use Caution

Hi all,

 

I’m doing hippocampal subfields analysis with freesurfer 6.0 with T1 and high 
resolution T2 data
from a 7T MRT. With at least one of my datasets Matlab throws an error during 
the
hippocampal-subfields-T2 –pipeline:

 

Making Unknown map to reduced label 14

Computing hyperparameters for estimation of Gaussians of T2 data

Error using |

Inputs must have the same size.

 

Error in segmentSubjectT2_autoEstimateAlveusML (line 1064)

 

With other patients, the pipeline on the T2 images is correctly working without 
errors. I’m
wondering what is causing this error and whether there is something I can do to 
avoid it?

 

As far as I can see, the only difference between the “error” dataset and the 
others is that
hippocampal subfields-T1 is also not calculated correctly. It finishes without 
errors, but the final
result does not cover the hippocampus correctly (probably due to a 
T1-hypointense cyst in the
hippocampus of that patient).

 

Best regards,

 

Angelika


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Re: [Freesurfer] hippocampal subfields error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

OK yes this is a problem with the main recon-all stream. It’d have been a 
miracle for the subfield module to recover from that…
At this point, I’ll defer to Doug / Bruce.
Cheers,
/E
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of "Mennecke, 
Angelika" 
Reply-To: Freesurfer support list 
Date: Monday, 17 June 2019 at 10:11
To: Freesurfer support list 
Subject: Re: [Freesurfer] hippocampal subfields error


External Email - Use Caution
Dear Eugenio,

attached you’ll find the picture. Looks as though the left hippocampus has 
erroneously been attributed to gray matter.

Cheers, Angelika

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Iglesias 
Gonzalez, Eugenio
Gesendet: Montag, 17. Juni 2019 15:49
An: Freesurfer support list
Betreff: Re: [Freesurfer] hippocampal subfields error


External Email - Use Caution
Dear Angelika,
Can you please send us a screenshot of the inaccurate T1 segmentation?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of "Mennecke, 
Angelika" 
Reply-To: Freesurfer support list 
Date: Monday, 17 June 2019 at 06:36
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippocampal subfields error


External Email - Use Caution
Hi all,

I’m doing hippocampal subfields analysis with freesurfer 6.0 with T1 and high 
resolution T2 data from a 7T MRT. With at least one of my datasets Matlab 
throws an error during the hippocampal-subfields-T2 –pipeline:

Making Unknown map to reduced label 14
Computing hyperparameters for estimation of Gaussians of T2 data
Error using |
Inputs must have the same size.

Error in segmentSubjectT2_autoEstimateAlveusML (line 1064)

With other patients, the pipeline on the T2 images is correctly working without 
errors. I’m wondering what is causing this error and whether there is something 
I can do to avoid it?

As far as I can see, the only difference between the “error” dataset and the 
others is that hippocampal subfields-T1 is also not calculated correctly. It 
finishes without errors, but the final result does not cover the hippocampus 
correctly (probably due to a T1-hypointense cyst in the hippocampus of that 
patient).

Best regards,

Angelika
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Re: [Freesurfer] hippocampal subfields error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Angelika,
Can you please send us a screenshot of the inaccurate T1 segmentation?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of "Mennecke, 
Angelika" 
Reply-To: Freesurfer support list 
Date: Monday, 17 June 2019 at 06:36
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippocampal subfields error


External Email - Use Caution
Hi all,

I’m doing hippocampal subfields analysis with freesurfer 6.0 with T1 and high 
resolution T2 data from a 7T MRT. With at least one of my datasets Matlab 
throws an error during the hippocampal-subfields-T2 –pipeline:

Making Unknown map to reduced label 14
Computing hyperparameters for estimation of Gaussians of T2 data
Error using |
Inputs must have the same size.

Error in segmentSubjectT2_autoEstimateAlveusML (line 1064)

With other patients, the pipeline on the T2 images is correctly working without 
errors. I’m wondering what is causing this error and whether there is something 
I can do to avoid it?

As far as I can see, the only difference between the “error” dataset and the 
others is that hippocampal subfields-T1 is also not calculated correctly. It 
finishes without errors, but the final result does not cover the hippocampus 
correctly (probably due to a T1-hypointense cyst in the hippocampus of that 
patient).

Best regards,

Angelika
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[Freesurfer] hippocampal subfields error

[Mennecke, Angelika]

External Email - Use Caution

Hi all,

I'm doing hippocampal subfields analysis with freesurfer 6.0 with T1 and high 
resolution T2 data from a 7T MRT. With at least one of my datasets Matlab 
throws an error during the hippocampal-subfields-T2 -pipeline:

Making Unknown map to reduced label 14
Computing hyperparameters for estimation of Gaussians of T2 data
Error using |
Inputs must have the same size.

Error in segmentSubjectT2_autoEstimateAlveusML (line 1064)

With other patients, the pipeline on the T2 images is correctly working without 
errors. I'm wondering what is causing this error and whether there is something 
I can do to avoid it?

As far as I can see, the only difference between the "error" dataset and the 
others is that hippocampal subfields-T1 is also not calculated correctly. It 
finishes without errors, but the final result does not cover the hippocampus 
correctly (probably due to a T1-hypointense cyst in the hippocampus of that 
patient).

Best regards,

Angelika
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Re: [Freesurfer] Hippocampal subfields segmentation template

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Wu,
The “templates” are probabilistic atlases with no image intensities. All you 
can look at is images like the ones in the top panel of Figure 5 in the paper.
If you want to generate these, let me know and I’ll show you instructions (it’s 
a bit tricky, because it requires  combining different versions of FreeSurfer….)
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Dongsheng Wu 

Reply-To: Freesurfer support list 
Date: Tuesday, 30 April 2019 at 04:38
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfields segmentation template


External Email - Use Caution
Dear FS developers,

I uesd the ''recon-all command'' to get the volumes of the hippocampal 
subfields, and we would like to perform further analysis with  these subfields 
in MNI. Could you show us the templates which are used to perform hippocampal 
segmentation (CA1, CA3, HATA, etc.)?


Best wishes,
Wu





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[Freesurfer] Hippocampal subfields segmentation template

[Dongsheng Wu]

External Email - Use Caution

Dear FS developers,


I uesd the ''recon-all command'' to get the volumes of the hippocampal 
subfields, and we would like to perform further analysis with  these subfields 
in MNI. Could you show us the templates which are used to perform hippocampal 
segmentation (CA1, CA3, HATA, etc.)? 




Best wishes,
Wu___
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[Freesurfer] hippocampal-subfields segmentation failure

[Xiaofu]

External Email - Use Caution

Hello,

   I am running segmentation of hippocampal subfields in FreeSurfer 6.0 but
one subject failed running the segmentation with the following error
message.

Wrote image to file asmr2.mgz

This file does not contain MRI parameters

This file does not contain MRI parameters

In an assignment  A(:) = B, the number of elements in A and B must be the
same.

Error in segmentSubjectT1_autoEstimateAlveusML (line 1848)



Any suggestions on this?  Thank you very much!


Best,

Xiaofu
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Re: [Freesurfer] hippocampal subfields

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Thanks, Marcel. Can you please send us the whole output (can be found in the 
log file)
Cheers,
/E

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Marcel Heers 

Reply-To: Freesurfer support list 
Date: Monday, 8 October 2018 at 20:45
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippocampal subfields


External Email - Use Caution
Dear Eugenio,

there is one error in the error.log: 'Could not set locale'.

Best regards

Marcel
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[Freesurfer] hippocampal subfields

[Marcel Heers]

External Email - Use Caution

Dear Eugenio,

there is one error in the error.log: 'Could not set locale'.

Best regards

Marcel
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Re: [Freesurfer] hippocampal subfields error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

That sounds pretty weird… Did you get any error messages on the Linux server?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Marcel Heers 

Reply-To: Freesurfer support list 
Date: Wednesday, 3 October 2018 at 20:11
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippocampal subfields error


External Email - Use Caution
Dear Eugenio,

I am currently testing the newest version of your hippocampal subfield analysis 
script. If I process the data on my macbook the files 
hipposubfields.lh.T2.v21.file_ID contain the volumes of the different nuclei, 
but on the linux server these files remain empty. On the server I installed 
freesurfer as local user. Do you have any suggestions how to check what might 
go wrong?

Thanks for your help!

Marcel
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[Freesurfer] hippocampal subfields error

[Marcel Heers]

External Email - Use Caution

Dear Eugenio,

I am currently testing the newest version of your hippocampal subfield
analysis script. If I process the data on my macbook the files
hipposubfields.lh.T2.v21.file_ID contain the volumes of the different
nuclei, but on the linux server these files remain empty. On the server I
installed freesurfer as local user. Do you have any suggestions how to
check what might go wrong?

Thanks for your help!

Marcel
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Re: [Freesurfer] hippocampal subfields segmentation error

[오진영]

External Email - Use Caution

Dear Eugenio

Thank you for your help.
As I need to segment the nuclei of amygdala, I'll try to download the
development version.

Thanks!!

Jinyoung

2018-07-30 17:39 GMT+09:00 Iglesias Gonzalez, Eugenio 
:

> External Email - Use Caution
>
> Dear Jin,
>
> 6.0 does not segment the nuclei of the amygdala; you can ignore that line,
> assuming the code runs to completion (I am assuming it does?)
>
> If you want to segment the nuclei of the amygdala, you’ll have to download
> the development version:
>
> http://freesurfer.net/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of 오진영 <
> jinyoung.oh...@gmail.com>
> *Reply-To: *Freesurfer support list 
> *Date: *Monday, 30 July 2018 at 09:29
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] hippocampal subfields segmentation error
>
>
>
> *External Email - Use Caution*
>
> Dear Eugenio,
>
>
>
> Thanks for your reply.
>
> I am running version "freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" of
> freesurfer.
>
> As the log is so long, I attached whole log as a text file and I just
> copied few lines before the error below:
>
>
>
> WorldToImageTransform after cropping:
>
> AffineTransform (0x128c17790)
>
>   RTTI typeinfo:   itk::AffineTransform
>
>   Reference Count: 1
>
>   Modified Time: 377450804
>
>   Debug: Off
>
>   Object Name:
>
>   Observers:
>
> none
>
>   Matrix:
>
> -3.3 8.73125e-11 2.22045e-16
>
> -8.4821e-14 -2.67186e-12 -3.3
>
> 5.55112e-16 3.3 1.97674e-10
>
>   Offset: [15.4608, 101.71, 117.525]
>
>   Center: [0, 0, 0]
>
>   Translation: [15.4608, 101.71, 117.525]
>
>   Inverse:
>
> -0.3 4.85723e-17 9.7012e-12
>
> 8.32667e-17 2.19633e-11 0.3
>
> 9.42996e-15 -0.3 -2.96735e-13
>
>   Singular: 0
>
> I am WriteImage and I'm running!
>
> Wrote image to file asmr2.mgz
>
> This file does not contain MRI parameters
>
> This file does not contain MRI parameters
>
> numberOfLabels: 25
>
> Rasterizing mesh...here: 25
>
> here2: 25
>
> done
>
> mri_convert.bin discreteLabels.mgz discreteLabelsResampledT1.mgz -rt
> nearest -odt float -rl /Users/mnd_mac/Desktop/JY_
> surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/norm.mgz
>
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
>
> reading from discreteLabels.mgz...
>
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>
> i_ras = (-1, 0, 2.84217e-14)
>
> j_ras = (0, 6.58905e-11, -1)
>
> k_ras = (2.91038e-11, 1, -8.90815e-13)
>
> reading template info from volume /Users/mnd_mac/Desktop/JY_
> surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/norm.mgz...
>
> Reslicing using nearest
>
> writing to discreteLabelsResampledT1.mgz...
>
> mv: rename volumesAmygdala.txt to /Users/mnd_mac/Desktop/JY_
> surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/lh.
> hippoSfVolumes-T1.amygdala.v10.txt: No such file or directory
>
>
>
> Thank you so much.
>
> Hope to hear you soon!
>
>
>
> Jin Young
>
>
>
> 2018-07-30 17:01 GMT+09:00 Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk>:
>
> *External Email - Use Caution*
>
> Dear Jinyoung,
>
> Can you please send us the log, or at least the last few lines before the
> error?
>
> Also, which exact version are you using? 6.0 or dev?
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of 오진영 <
> jinyoung.oh...@gmail.com>
> *Reply-To: *Freesurfer support list 
> *Date: *Monday, 30 July 2018 at 06:41
> *To: *"freesurfer@nmr.mgh.harvard.edu" 
> *Cc: *JongHyun Lee 
> *Subject: *[Freesurfer] hippocampal subfields segmentation error
>
>
>
> *External Email - Use Caution*
>
> Hello, freesurfer experts
>
>
>
> I'm trying to run segmentation of hippocampal subfields and nuclei of
> amygdala by using "segmentSF_T1.sh" command.
>
> I have downloaded the newest development version(freesurfer v.6.0

Re: [Freesurfer] hippocampal subfields segmentation error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Jin,
6.0 does not segment the nuclei of the amygdala; you can ignore that line, 
assuming the code runs to completion (I am assuming it does?)
If you want to segment the nuclei of the amygdala, you’ll have to download the 
development version:
http://freesurfer.net/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of 오진영 

Reply-To: Freesurfer support list 
Date: Monday, 30 July 2018 at 09:29
To: Freesurfer support list 
Subject: Re: [Freesurfer] hippocampal subfields segmentation error


External Email - Use Caution
Dear Eugenio,

Thanks for your reply.
I am running version "freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" of 
freesurfer.
As the log is so long, I attached whole log as a text file and I just copied 
few lines before the error below:


WorldToImageTransform after cropping:

AffineTransform (0x128c17790)

  RTTI typeinfo:   itk::AffineTransform

  Reference Count: 1

  Modified Time: 377450804

  Debug: Off

  Object Name:

  Observers:

none

  Matrix:

-3.3 8.73125e-11 2.22045e-16

-8.4821e-14 -2.67186e-12 -3.3

5.55112e-16 3.3 1.97674e-10

  Offset: [15.4608, 101.71, 117.525]

  Center: [0, 0, 0]

  Translation: [15.4608, 101.71, 117.525]

  Inverse:

-0.3 4.85723e-17 9.7012e-12

8.32667e-17 2.19633e-11 0.3

9.42996e-15 -0.3 -2.96735e-13

  Singular: 0

I am WriteImage and I'm running!

Wrote image to file asmr2.mgz

This file does not contain MRI parameters

This file does not contain MRI parameters

numberOfLabels: 25

Rasterizing mesh...here: 25

here2: 25

done

mri_convert.bin discreteLabels.mgz discreteLabelsResampledT1.mgz -rt nearest 
-odt float -rl 
/Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/norm.mgz

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $

reading from discreteLabels.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 2.84217e-14)

j_ras = (0, 6.58905e-11, -1)

k_ras = (2.91038e-11, 1, -8.90815e-13)

reading template info from volume 
/Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/norm.mgz...

Reslicing using nearest

writing to discreteLabelsResampledT1.mgz...

mv: rename volumesAmygdala.txt to 
/Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/lh.hippoSfVolumes-T1.amygdala.v10.txt:
 No such file or directory

Thank you so much.
Hope to hear you soon!

Jin Young

2018-07-30 17:01 GMT+09:00 Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>>:

External Email - Use Caution
Dear Jinyoung,
Can you please send us the log, or at least the last few lines before the error?
Also, which exact version are you using? 6.0 or dev?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 오진영 mailto:jinyoung.oh...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, 30 July 2018 at 06:41
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: JongHyun Lee mailto:jonghyunlee1...@gmail.com>>
Subject: [Freesurfer] hippocampal subfields segmentation error


External Email - Use Caution
Hello, freesurfer experts

I'm trying to run segmentation of hippocampal subfields and nuclei of amygdala 
by using "segmentSF_T1.sh" command.
I have downloaded the newest development version(freesurfer v.6.0) and license, 
as well as the required matlab runtime.

However, I am getting the following error:
mv: rename volumesAmygdala.txt to 
/Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/lh.hippoSfVolumes-T1.amygdala.v10.txt:
 No such file or directory

and I have no idea how to find the text file and solve this problem out.
If you have any idea or recommends, please send me the e-mail back.

Thanks!

Jinyoung


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dispose of the e-mail.

__

Re: [Freesurfer] hippocampal subfields segmentation error

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Jinyoung,
Can you please send us the log, or at least the last few lines before the error?
Also, which exact version are you using? 6.0 or dev?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of 오진영 

Reply-To: Freesurfer support list 
Date: Monday, 30 July 2018 at 06:41
To: "freesurfer@nmr.mgh.harvard.edu" 
Cc: JongHyun Lee 
Subject: [Freesurfer] hippocampal subfields segmentation error


External Email - Use Caution
Hello, freesurfer experts

I'm trying to run segmentation of hippocampal subfields and nuclei of amygdala 
by using "segmentSF_T1.sh" command.
I have downloaded the newest development version(freesurfer v.6.0) and license, 
as well as the required matlab runtime.

However, I am getting the following error:
mv: rename volumesAmygdala.txt to 
/Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/lh.hippoSfVolumes-T1.amygdala.v10.txt:
 No such file or directory

and I have no idea how to find the text file and solve this problem out.
If you have any idea or recommends, please send me the e-mail back.

Thanks!

Jinyoung

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[Freesurfer] hippocampal subfields segmentation error

[오진영]

External Email - Use Caution

Hello, freesurfer experts

I'm trying to run segmentation of hippocampal subfields and nuclei of
amygdala by using "segmentSF_T1.sh" command.
I have downloaded the newest development version(freesurfer v.6.0) and
license, as well as the required matlab runtime.

However, I am getting the following error:
mv: rename volumesAmygdala.txt to /Users/mnd_mac/Desktop/JY_surf
er/T1_data/Jinyoung_T1/Jinyoung_test/mri/lh.hippoSfVolumes-T1.amygdala.v10.txt:
No such file or directory

and I have no idea how to find the text file and solve this problem out.
If you have any idea or recommends, please send me the e-mail back.

Thanks!

Jinyoung
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[Freesurfer] Hippocampal Subfields Logitudinal Processing Error

[Maksimovskiy, Arkadiy]

Dear Experts,

I am attempting to initiate a longitudinal portion of the hippocampal subfield 
module and am getting an error. I was wondering if someone might have a 
suggestion for troubleshooting.

I am using the following version of freesurfer: 
freesurfer-Darwin-OSX-ElCapitan-dev-20180124-2459312abf
I have the Matlab runtime installed using the following command:
curl 
"https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile=get=runtime2014bMAC.tar.gz;
 -o "runtime.tar.gz"
Here is the command I use to initiate the stream:
segmentHA_T1_long.sh SILVA008_Template
Here is the error message:
[arkadiysnewimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits]
 arkadiy% segmentHA_T1_long.sh SILVA008_Template
#
#@# Longitudinal Hippocampal Subfields processing (T1) left Fri Jul  6 12:43:59 
EDT 2018
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is 
.:/Applications/freesurfer_Dev_El_Capitan//MCRv84//runtime/maci64:/Applications/freesurfer_Dev_El_Capitan//MCRv84//bin/maci64:/Applications/freesurfer_Dev_El_Capitan//MCRv84//sys/os/maci64:/Applications/freesurfer_Dev_El_Capitan/lib/gcc/lib:/Applications/freesurfer_6.0/lib/gcc/lib:/opt/X11/lib/flat_namespace
dyld: Library not loaded: @loader_path/libmwmclmcrrt.8.0.dylib
  Referenced from: 
/Applications/freesurfer_Dev_El_Capitan/bin/SegmentSubfieldsT1Longitudinal.app/Contents/MacOS/SegmentSubfieldsT1Longitudinal
  Reason: image not found
/Applications/freesurfer_Dev_El_Capitan/bin/run_SegmentSubfieldsT1Longitudinal.sh:
 line 37: 58577 Abort trap: 6   
"${exe_dir}"/SegmentSubfieldsT1Longitudinal.app/Contents/MacOS/SegmentSubfieldsT1Longitudinal
 $args
Darwin arkadiysnewimac.mclean.harvard.edu 17.6.0 Darwin Kernel Version 17.6.0: 
Tue May  8 15:22:16 PDT 2018; root:xnu-4570.61.1~1/RELEASE_X86_64 x86_64

longitudinal subfields exited with ERRORS at Fri Jul  6 12:43:59 EDT 2018

For more details, see the log file 
/Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits/SILVA008_Template/scripts/long-hippocampal-subfields-T1.log


I would love to hear if anyone has suggestions for fixing this.
Thanks,
arkadiy

--
Arkadiy L. Maksimovskiy, Ph.D.
Postdoctoral Research Fellow
McLean Imaging Center, McLean Hospital
Department of Psychiatry, Harvard Medical School
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Re: [Freesurfer] Hippocampal Subfields Module, output error

[Hurtado, Aura Maria]

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.igles...@ucl.ac.uk<mailto:e.igles...@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.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


From: 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Hurtado, Aura Maria" 
<ahurt...@mgh.harvard.edu<mailto:ahurt...@mgh.harvard.edu>>
Reply-To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, 23 March 2018 at 05:28
To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto: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.igles...@ucl.ac.uk<mailto:e.igles...@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.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


From: 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Hurtado, Aura Maria" 
<ahurt...@mgh.harvard.edu<mailto:ahurt...@mgh.harvard.edu>>
Reply-To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, 21 March 2018 at 22:24
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
<freesurfer@nmr.mgh.harvard.edu<mailto: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(0x7fd7

Re: [Freesurfer] Hippocampal Subfields Module, output error

[Iglesias Gonzalez, Eugenio]

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-boun...@nmr.mgh.harvard.edu> on behalf of "Hurtado, Aura 
Maria" <ahurt...@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:
___
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Re: [Freesurfer] Hippocampal subfields

[Iglesias Gonzalez, Eugenio]

Dear Arsenije
The atlas is encoded in a tetrahedral mesh, so there is no nifti file for it.
Having said that, it is possible to rasterize the atlas at a target resolution.
The command is the following:

kvlRasterizeAtlasMesh $FREESURFER_HOME/average/HippoSF/atlas/AtlasMesh.gz  
$FREESURFER_HOME/average/HippoSF/atlas/AtlasDump.mgz X  -1

where X is the label number (see 
$FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt for a 
listing; 0 is cortex, 1 is cerebral white matter, etc). -1 indicates the 
reference position of the atlas, so do not modify that.

This command will create a file called rasterized.mgz. You can convert it to 
nifty with mri_convert, eg.
mri_convert rasterized.mgz probability_label_X.nii.gz

You can do this with all the different hippocampal labels. And if you want a 
probability for the whole hippocampus, which is probably what you need for the 
registration with your manual mask, you can sum the probabilities of the 
different subfields into a single volume (e.g., with fslmaths)

I hope this helps,

/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-boun...@nmr.mgh.harvard.edu> on behalf of Arsenije Subotic 
<arsenije.subot...@ucalgary.ca>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, 22 March 2018 at 15:15
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampal subfields

Hi all

I would like to use subfield specific hippocampus maps that were produced Dr 
Iglesias's Lab: https://sites.google.com/site/jeiglesias/hippocampal-subfields

These maps are available via FreeSurfer, however our lab is trying to segment 
hippocampus subregions from already manually extracted hippocampuses. In other 
words, we have manually traced hippocampus masks in a NIFTI format that we 
would like to co-register with these maps.

How can I directly download subfield specific hippocampal atlases in a NIFTI 
format so that we can use non linear co registration after?

Thank you very much.

Look forward hearing from you,

Arsenije
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[Freesurfer] Hippocampal subfields

[Arsenije Subotic]

Hi all

I would like to use subfield specific hippocampus maps that were produced Dr 
Iglesias's Lab: https://sites.google.com/site/jeiglesias/hippocampal-subfields

These maps are available via FreeSurfer, however our lab is trying to segment 
hippocampus subregions from already manually extracted hippocampuses. In other 
words, we have manually traced hippocampus masks in a NIFTI format that we 
would like to co-register with these maps.

How can I directly download subfield specific hippocampal atlases in a NIFTI 
format so that we can use non linear co registration after?

Thank you very much.

Look forward hearing from you,

Arsenije
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Hippocampal Subfields Module, output error

[Iglesias Gonzalez, Eugenio]

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-boun...@nmr.mgh.harvard.edu> on behalf of "Hurtado, Aura 
Maria" <ahurt...@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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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Hippocampal Subfields Module, output error

[Hurtado, Aura Maria]

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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but does not contain patient information, please contact the sender and properly
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[Freesurfer] Hippocampal subfields {Disarmed}

[郑凤莲]

Hi professors,

I ran the segmentation of hippocampus in Freesurfer dev version. The left or 
right whole volume isn't equal to the sum of 12 subfields. But it is equal to 
the sum of the volume of tail, whole head and body. Why?
 I am looking forward to your reply. Thank you very much.

Sincerely,
Zheng



| |
13181786167
邮箱：13181786...@163.com
|

签名由 网易邮箱大师 定制___
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Hippocampal subfields segmentation

[Iglesias Gonzalez, Eugenio]

Hi Alexis,
Yes please send me the images!
Cheers,
/E

--
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-boun...@nmr.mgh.harvard.edu> on behalf of Alexis Guyot 
<alexis.guyot@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, 22 January 2018 at 17:49
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampal subfields segmentation

Dear Freesurfer developers,

I have been trying to segment (with Freesurfer v6.0.0, on Ubuntu 14.04) the 
hippocampal subfields of two 7T MR images in NIFTI format: an isotropic 
(0.8*0.8*0.8 mm3) whole-brain T1-weighted source volume with an anisotropic 
(0.3*1.2*0.3 mm3) T2-weighted volume covering the brain partially and centred 
on a region comprising both hippocampi.

I have followed the instructions in 
https://surfer.nmr.mgh.harvard.edu/fswiki/HighFieldRecon to correct the bias in 
the two 7T volumes ('T1_biasCorrected.png', 'T2_biasCorrected.png'). I have run 
'recon-all -hires [...] -expert expert.txt' ('expert.txt') on my bias-corrected 
T1 volume, which produced an accurate segmentation ('aseg.png', 
'recon-all.log'). Following this, I have run 'recon-all 
-hippocampal-subfields-T2' on the bias-corrected T2 volume 
('hippocampal-subfields-T2.log').
Looking at the resulting segmentation, I am unsure the molecular layer has been 
properly delineated in the body of the hippocampus 
('right_hippocampus_body.png', 'right_hippocampus_body_seg.png'). In addition, 
it appears the convolutions in the hippocampal head have not been correctly 
segmented ('right_hippocampus_head.png', 'right_hippocampus_head_seg.png').

I am not certain this is the expected behaviour when running the hippocampal 
subfields module on high-res data. Is it possible the recon-all output is not 
accurate enough (should I adjust the mres_inflate value prior to segmenting the 
brain)? Could the high anisotropy of the T2 volume hinder the segmentation 
process?
Any thoughts on this? Screenshots/attachments are available on request, as my 
previous message was rejected for being too big.

Thanks for your help,
Alexis
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Hippocampal subfields segmentation

[Alexis Guyot]

Dear Freesurfer developers,

I have been trying to segment (with Freesurfer v6.0.0, on Ubuntu 14.04) the
hippocampal subfields of two 7T MR images in NIFTI format: an isotropic
(0.8*0.8*0.8 mm3) whole-brain T1-weighted source volume with an anisotropic
(0.3*1.2*0.3 mm3) T2-weighted volume covering the brain partially and
centred on a region comprising both hippocampi.

I have followed the instructions in https://surfer.nmr.mgh.
harvard.edu/fswiki/HighFieldRecon to correct the bias in the two 7T volumes
('T1_biasCorrected.png', 'T2_biasCorrected.png'). I have run 'recon-all
-hires [...] -expert expert.txt' ('expert.txt') on my bias-corrected T1
volume, which produced an accurate segmentation ('aseg.png',
'recon-all.log'). Following this, I have run 'recon-all
-hippocampal-subfields-T2' on the bias-corrected T2 volume
('hippocampal-subfields-T2.log').
Looking at the resulting segmentation, I am unsure the molecular layer has
been properly delineated in the body of the hippocampus
('right_hippocampus_body.png', 'right_hippocampus_body_seg.png'). In
addition, it appears the convolutions in the hippocampal head have not been
correctly segmented ('right_hippocampus_head.png',
'right_hippocampus_head_seg.png').

I am not certain this is the expected behaviour when running the
hippocampal subfields module on high-res data. Is it possible the recon-all
output is not accurate enough (should I adjust the mres_inflate value prior
to segmenting the brain)? Could the high anisotropy of the T2 volume hinder
the segmentation process?
Any thoughts on this? Screenshots/attachments are available on request, as
my previous message was rejected for being too big.

Thanks for your help,
Alexis
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] hippocampal subfields in younger populations

[Iglesias Gonzalez, Eugenio]

Dear Christian,

They atlas is built using subfield segmentations on scans of older adult 
brains, but:
1. it’s also built with whole hippocampus segmentations of scans of subjects of 
a wider age range.
2. the deformation model should be able to account for large parts of the 
anatomical differences between subjects of different ages.

> I would think this would be an issue for young kids that have markedly 
> different brain volumes, but not for older kids and young adults that differ 
> less dramatically from older adults.

I agree with this statement.

I hope this helps!

/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-boun...@nmr.mgh.harvard.edu> on behalf of Christian Krog 
Tamnes <c.k.tam...@psykologi.uio.no>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, 10 January 2018 at 11:33
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] hippocampal subfields in younger populations


Dear FreeSurfer and hippocampal subfield segmentation developers,



I have noted that the FS6.0 hippocampal subfield segmentation procedure was 
developed using scans of older adult brains. Has the application of this method 
to kids, adolescents and/or young adults in any way been validated? Or do you 
have any thoughts regarding such use of the method?



I would think this would be an issue for young kids that have markedly 
different brain volumes, but not for older kids and young adults that differ 
less dramatically from older adults. But I would greatly appreciate any input 
regarding this.



Best regards,

Christian
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[Freesurfer] hippocampal subfields in younger populations

[Christian Krog Tamnes]

Dear FreeSurfer and hippocampal subfield segmentation developers,



I have noted that the FS6.0 hippocampal subfield segmentation procedure was 
developed using scans of older adult brains. Has the application of this method 
to kids, adolescents and/or young adults in any way been validated? Or do you 
have any thoughts regarding such use of the method?



I would think this would be an issue for young kids that have markedly 
different brain volumes, but not for older kids and young adults that differ 
less dramatically from older adults. But I would greatly appreciate any input 
regarding this.



Best regards,

Christian
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Re: [Freesurfer] hippocampal subfields stats

[Iglesias Gonzalez, Eugenio]

Dear Donatas,
I believe that mri_segstats is just counting voxels using the hard 
segmentation, whereas the volume in lh.hippoSfVolumes-T1.long.v20.txt is 
obtained using a soft segmentation. If you’re interested in this, look up the 
WRITE_POSTERIORS option in the wiki.
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/
 

On 21/11/2017, 18:00, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Donatas Sederevicius"  wrote:

Dear Freesurfer Developers,

I’ve run the new longitudinal hippocampal subfields segmentation using 
Freesurfer’s developer version. Then I decided to extract stats for each 
hierarchy: HBT, FS60 and CA. I used the following command, for example: 

mri_segstats —seg lh.hippoAmygLabels-T1.long.v20.CA.mgz —ctab-default —sum 
output.txt

I got what I wanted but decided to compare the results of one subject for 
Hippocampal_tail for each hierarchy and with the text file 
lh.hippoSfVolumes-T1.long.v20.txt. I got the following volume values:


lh.hippoSfVolumes-T1.long.v20.txt: 583.65
HBT: 593.4
FS60: 593.4
CA: 598.3

I wonder how do you actually extract stats that are present in 
lh.hippoSfVolumes-T1.long.v20.txt file? What is the reason for different 
values? I’m very curious since I cannot get the exact same stats as in the 
lh.hippoSfVolumes-T1.long.v20.txt file.

Thanks a lot!
Donatas




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[Freesurfer] hippocampal subfields stats

[Donatas Sederevicius]

Dear Freesurfer Developers,

I’ve run the new longitudinal hippocampal subfields segmentation using 
Freesurfer’s developer version. Then I decided to extract stats for each 
hierarchy: HBT, FS60 and CA. I used the following command, for example: 

mri_segstats —seg lh.hippoAmygLabels-T1.long.v20.CA.mgz —ctab-default —sum 
output.txt

I got what I wanted but decided to compare the results of one subject for 
Hippocampal_tail for each hierarchy and with the text file 
lh.hippoSfVolumes-T1.long.v20.txt. I got the following volume values:


lh.hippoSfVolumes-T1.long.v20.txt: 583.65
HBT: 593.4
FS60: 593.4
CA: 598.3

I wonder how do you actually extract stats that are present in 
lh.hippoSfVolumes-T1.long.v20.txt file? What is the reason for different 
values? I’m very curious since I cannot get the exact same stats as in the 
lh.hippoSfVolumes-T1.long.v20.txt file.

Thanks a lot!
Donatas




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Re: [Freesurfer] hippocampal subfields downsampling question

[Joost Janssen]

Great question!

El 26/10/2017 17:09, "NIELS JANSSEN ."  escribió:

> In the mri output folder, I noticed that both the 0.33 mm and 1 mm
> (voxelspace) maps have subfields that do not overlap in space, meaning that
> each subfield occupies a unique location in space that does not overlap
> with other subfields (i.e., 12 subfields and 12 unique voxel intensities).
> I am wondering how this is achieved for both resolutions simultaneously. Do
> you 'fit' the subfields first to the 0.33 mm data and then transform the
> data to the 1mm space, or do you fit to both spaces separately? I would
> like to transform the subfields to 1.5 mm data and are able to do so
> accurately, but I run into problems with subfield overlap because of the
> down sampling. I am wondering how to best deal with this issue, and from
> seeing non-overlapping subfields at both 0.33 and 1 mm I am thinking there
> must be someway to deal with this issue.
>
>
> --
> Niels Janssen
> Brain Imaging Laboratory
> Institute of Biomedical Technologies
> Center for Biomedical Research of the Canary Islands
> University of La Laguna
> Tenerife, Spain
> https://sites.google.com/view/nielsjanssen/
>
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>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] hippocampal subfields downsampling question

[Iglesias Gonzalez, Eugenio]

Hi Niels,

The code works at .33 mm and ends up with a soft segmentation for each voxel, 
i.e., each voxel has a vector of probabilities corresponding to the different 
structures. So, they DO overlap. However, we don’t write those probabilities by 
default. Instead, we take the most likely label at each location (the one with 
the maximal probability), to create the discrete segmentation you’ve seen. 
Then, I do a simple nearest neighbor resampling to 1mm space, which I admit is 
a bit ugly (but fast).

My recommendation would be the following:

1. For each label of the discrete segmentation, including the background (treat 
is as any other subfield):
   1a. First extract it from the segmentation, to create a binary mask (e.g., 
CA1 vs everything else).
   1b. Resample this mask to your new space with linear interpolation. This 
will create a deformed mask that is not binary anymore, but will have values 
between 0 and 1 (or 0 and 255, depending on how you binarize in step 1a).

2. Go over all voxels in the target space. For each voxel, look at the values 
of the deformed masks. Assign the label of the mask with the highest value.

This procedure will create a smooth segmentation.

If you’re feeling really inspired, you’ve got another (prettier) option. Run 
the code with WRITE_POSTERIORS (see the wiki). Then, you can do the same thing, 
but skipping step 1a, and using the posteriors in step 1b directly instead. 
Note that the code does not write the posterior for the background, but you can 
easily calculate this as one minus the sum of all other posteriors (at each 
voxel).

I hope this helps!

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-boun...@nmr.mgh.harvard.edu> on behalf of "NIELS JANSSEN ." 
<njans...@ull.edu.es>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, 26 October 2017 at 16:08
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] hippocampal subfields downsampling question

In the mri output folder, I noticed that both the 0.33 mm and 1 mm (voxelspace) 
maps have subfields that do not overlap in space, meaning that each subfield 
occupies a unique location in space that does not overlap with other subfields 
(i.e., 12 subfields and 12 unique voxel intensities). I am wondering how this 
is achieved for both resolutions simultaneously. Do you 'fit' the subfields 
first to the 0.33 mm data and then transform the data to the 1mm space, or do 
you fit to both spaces separately? I would like to transform the subfields to 
1.5 mm data and are able to do so accurately, but I run into problems with 
subfield overlap because of the down sampling. I am wondering how to best deal 
with this issue, and from seeing non-overlapping subfields at both 0.33 and 1 
mm I am thinking there must be someway to deal with this issue.


--
Niels Janssen
Brain Imaging Laboratory
Institute of Biomedical Technologies
Center for Biomedical Research of the Canary Islands
University of La Laguna
Tenerife, Spain
https://sites.google.com/view/nielsjanssen/
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[Freesurfer] hippocampal subfields downsampling question

[NIELS JANSSEN .]

In the mri output folder, I noticed that both the 0.33 mm and 1 mm
(voxelspace) maps have subfields that do not overlap in space, meaning that
each subfield occupies a unique location in space that does not overlap
with other subfields (i.e., 12 subfields and 12 unique voxel intensities).
I am wondering how this is achieved for both resolutions simultaneously. Do
you 'fit' the subfields first to the 0.33 mm data and then transform the
data to the 1mm space, or do you fit to both spaces separately? I would
like to transform the subfields to 1.5 mm data and are able to do so
accurately, but I run into problems with subfield overlap because of the
down sampling. I am wondering how to best deal with this issue, and from
seeing non-overlapping subfields at both 0.33 and 1 mm I am thinking there
must be someway to deal with this issue.


-- 
Niels Janssen
Brain Imaging Laboratory
Institute of Biomedical Technologies
Center for Biomedical Research of the Canary Islands
University of La Laguna
Tenerife, Spain
https://sites.google.com/view/nielsjanssen/
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[Freesurfer] Hippocampal subfields - molecular layer labelling Freesurfer 6.0

[Roddy Darren William]

Hi,
I know this has been addressed a bit before, but I remain confused! Apologies.

1….
The dentate anatomically has 3 layers [molecular layer/granular 
layer/polymorphic layer]. What layers exactly do Freesurfer output “GC_ML_DG” 
or “CG_ML" correspond to?

Granular layer only?
Or
Granular layer with polymorphic layer?
Or
Granular layer, polymorphic layer and molecular layer?

It’s mentioned in the Eugenio Iglesias’ article that the molecular layer of the 
dentate is included in the CA4 region. Is this where is it, or is it in the 
GC_ML_DG?

2….
By “molecular_layer_HP” does Freesurfer mean the ‘molecular layer’ i.e. 
‘outermost’ band of

Subiculum, CA1, CA2/3?
Or
Subiculum, CA1, CA2/3 and molecular layer of dentate?

I would appreciate some clarification..
Wonderful application by the way. A great step forward for hippocampal research

Many thanks..



Dr Darren Roddy

Trinity College Institute of Neuroscience

Room 3.36, The Lloyd Institute

Trinity College Dublin

Dublin 2

+353 86 6087927
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Re: [Freesurfer] hippocampal subfields: which are previous step result (files) needed for the process?

[Iglesias Gonzalez, Eugenio]

Hi Guido,
I think you should wait until recon-all is done. Running 2 recon-all commands 
on the same subject simultaneously: a) would need hacking recon-all; b) it’s a 
bad idea. Moreover, the subfields make use of wmparc.mgz, which is produced 
towards the very end of recon-all -all anyway.
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/


On 11 May 2017, at 15:10, Guido Pascariello 
> wrote:

Hi Experts,

I am running Freesurfer v6.0 on a Cluster. I've traied this command:

recon-all -i $IMAGEN -s $SUJETO -all -hippocampal-subfields-T1 
-brainstem-structures

Although all step in recon-all works fine, hippocampal-subfields process 
allocate much more RAM than previous step (10 GB of RAM more or less, and take 
about 30 mins to be completed, according to other post in the forum).

I am thinking in run these one after another, in order to not need to reserve a 
lot of memory for a long period of time (just for optimization)

I want to know which are the files (from recon-all process) that 
hippocampal-subfields process needs? Just to be sure that these will be 
transferred to the node before the process starts.

If you please help me

Cheers

--
Bioing. Guido Pascariello
Becario Doctoral CIFASIS - CONICET
Grupo de Procesamiento de Señales Multimediales
http://www.cifasis-conicet.gov.ar/
Tel/Fax: 54 341 482 6300/ 1771/ 72 Int. 386
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[Freesurfer] hippocampal subfields: which are previous step result (files) needed for the process?

[Guido Pascariello]

Hi Experts,

I am running Freesurfer v6.0 on a Cluster. I've traied this command:

*recon-all -i $IMAGEN -s $SUJETO -all -hippocampal-subfields-T1
-brainstem-structures*

Although all step in recon-all works fine, hippocampal-subfields process
allocate much more RAM than previous step (10 GB of RAM more or less, and
take about 30 mins to be completed, according to other post in the forum).

I am thinking in run these one after another, in order to not need to
reserve a lot of memory for a long period of time (just for optimization)

*I want to know which are the files (from recon-all process) that
hippocampal-subfields process needs?* Just to be sure that these will be
transferred to the node before the process starts.

If you please help me

Cheers

-- 
*Bioing. Guido Pascariello*
Becario Doctoral CIFASIS - CONICET
Grupo de Procesamiento de Señales Multimediales
http://www.cifasis-conicet.gov.ar/
Tel/Fax: 54 341 482 6300/ 1771/ 72 Int. 386
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Re: [Freesurfer] Hippocampal Subfields Posterior Probability

[Bharadwaj, Pradyumna - (prad)]

Great! Thank you for taking that time to clarify that.


-Prad


From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, 
Eugenio <e.igles...@ucl.ac.uk>
Sent: Wednesday, March 22, 2017 11:34 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal Subfields Posterior Probability

Hi again, Prad,
In that case, you don’t need the discrete segmentations. Just look at the 
posteriors directly.
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/


On 22 Mar 2017, at 18:26, Bharadwaj, Pradyumna - (prad) 
<p...@email.arizona.edu<mailto:p...@email.arizona.edu>> wrote:

Sorry about that. I should have stated what I was trying to do. I'm trying to 
see if the posterior probability changes when using a certain combination of 
the different T1 and T2 weighted scans that we have in our lab. I thought using 
the binary masks to extract the probabilities as they were the final volumes of 
the subfields would be a better way.


As an example,
when I extract some basic stats on the left CA1 posteriors for one subject, 
these are the values I get,
range: 0.15 to 1, with a mean (sd) of 0.245258 (0.335046);

and , when I use the binary mask of the CA1 from lh.hippoSfLabels-T1.v10.mgz 
and then extract the same basic stats, I get,

range: 0.247501 to 1, with a mean (sd) of 0.770796 (0.175752)

Is my approach incorrect ?

Thanks!,
-Prad



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Iglesias Gonzalez, Eugenio 
<e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>>
Sent: Wednesday, March 22, 2017 11:06 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal Subfields Posterior Probability

Hi Prad,
The final probabilities are in the posterior files. There’s no need to binarize 
?h.hippoSfLabels if what you’re interested in is the soft segmentations.
Or maybe I’m missing something? What are you exactly trying to do?
Cheers,
/E

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


On 22 Mar 2017, at 18:02, Bharadwaj, Pradyumna - (prad) 
<p...@email.arizona.edu<mailto:p...@email.arizona.edu>> wrote:

Hi Dr. Iglesias,

Thank you for the overview of the labeling rules. I have also tried setting 
WRITE_POSTERIORS to 1 to write out the posteriors.

I had a follow up question about obtaining the probabilities for the final 
subfield labels as available in the ?h.hippoSfLabels-T1.v10.mgz

I use mri_binarize on ?h.hippoSfLabels-T1.v10.mgz to obtain binary masks for 
each subfield, and then used these masks with their respective posteriors to 
obtain the distributions.

Is this procedure correct or is there a better way ?

Thanks,
-Prad

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Iglesias Gonzalez, Eugenio 
<e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>>
Sent: Tuesday, March 21, 2017 2:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal Subfields Posterior Probability

Dear Prad,
There is a “secret” way of getting the posteriors. You need to set the 
environment variable WRITE_POSTERIORS to 1 before you call recon-all.
In (t)csh:
setenv WRITE_POSTERIORS 1
In bash:
export WRITE_POSTERIORS=1
And then call recon-all -hippocampal-subfields-T1(T2) as usual.

The discrete segmentation picks, for each voxel, the most likely label. The 
posterior of this label might or might not be above 0.5. For instance, if a 
voxel has p=0.4 of being CA1, p=0.3 of being background, and p=0.3 of being 
fimbria, it will be labeled as CA1 (even though p<0.5 for such subfield). Some 
people seem to prefer a 2-stage approach, in which a hippocampal mask is first 
created by selecting the voxels for which p(background)<0.5, and then each 
voxel within that mask is colored with the most likely subfield at that 
location.

I hope this helps!

Cheers,

/Eugenio



Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


On 21 Mar 2017, at 20:09, Bharadwaj, Pradyumna - (prad) 
<p...@email.arizona.edu<mailto:p...@email.arizona.edu>> wrote:

Hello Dr. Iglesias,

I'm currently examining the distributions of the posterior probabilities of the 
different

Re: [Freesurfer] Hippocampal Subfields Posterior Probability

[Iglesias Gonzalez, Eugenio]

Hi again, Prad,
In that case, you don’t need the discrete segmentations. Just look at the 
posteriors directly.
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/


On 22 Mar 2017, at 18:26, Bharadwaj, Pradyumna - (prad) 
<p...@email.arizona.edu<mailto:p...@email.arizona.edu>> wrote:

Sorry about that. I should have stated what I was trying to do. I'm trying to 
see if the posterior probability changes when using a certain combination of 
the different T1 and T2 weighted scans that we have in our lab. I thought using 
the binary masks to extract the probabilities as they were the final volumes of 
the subfields would be a better way.


As an example,
when I extract some basic stats on the left CA1 posteriors for one subject, 
these are the values I get,
range: 0.15 to 1, with a mean (sd) of 0.245258 (0.335046);

and , when I use the binary mask of the CA1 from lh.hippoSfLabels-T1.v10.mgz 
and then extract the same basic stats, I get,

range: 0.247501 to 1, with a mean (sd) of 0.770796 (0.175752)

Is my approach incorrect ?

Thanks!,
-Prad



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Iglesias Gonzalez, Eugenio 
<e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>>
Sent: Wednesday, March 22, 2017 11:06 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal Subfields Posterior Probability

Hi Prad,
The final probabilities are in the posterior files. There’s no need to binarize 
?h.hippoSfLabels if what you’re interested in is the soft segmentations.
Or maybe I’m missing something? What are you exactly trying to do?
Cheers,
/E

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


On 22 Mar 2017, at 18:02, Bharadwaj, Pradyumna - (prad) 
<p...@email.arizona.edu<mailto:p...@email.arizona.edu>> wrote:

Hi Dr. Iglesias,

Thank you for the overview of the labeling rules. I have also tried setting 
WRITE_POSTERIORS to 1 to write out the posteriors.

I had a follow up question about obtaining the probabilities for the final 
subfield labels as available in the ?h.hippoSfLabels-T1.v10.mgz

I use mri_binarize on ?h.hippoSfLabels-T1.v10.mgz to obtain binary masks for 
each subfield, and then used these masks with their respective posteriors to 
obtain the distributions.

Is this procedure correct or is there a better way ?

Thanks,
-Prad

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Iglesias Gonzalez, Eugenio 
<e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>>
Sent: Tuesday, March 21, 2017 2:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal Subfields Posterior Probability

Dear Prad,
There is a “secret” way of getting the posteriors. You need to set the 
environment variable WRITE_POSTERIORS to 1 before you call recon-all.
In (t)csh:
setenv WRITE_POSTERIORS 1
In bash:
export WRITE_POSTERIORS=1
And then call recon-all -hippocampal-subfields-T1(T2) as usual.

The discrete segmentation picks, for each voxel, the most likely label. The 
posterior of this label might or might not be above 0.5. For instance, if a 
voxel has p=0.4 of being CA1, p=0.3 of being background, and p=0.3 of being 
fimbria, it will be labeled as CA1 (even though p<0.5 for such subfield). Some 
people seem to prefer a 2-stage approach, in which a hippocampal mask is first 
created by selecting the voxels for which p(background)<0.5, and then each 
voxel within that mask is colored with the most likely subfield at that 
location.

I hope this helps!

Cheers,

/Eugenio



Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


On 21 Mar 2017, at 20:09, Bharadwaj, Pradyumna - (prad) 
<p...@email.arizona.edu<mailto:p...@email.arizona.edu>> wrote:

Hello Dr. Iglesias,

I'm currently examining the distributions of the posterior probabilities of the 
different hippocampal subfields, and I'm interested in obtaining the 
probability distribution images for the subfields that correspond to the 
volumes output in the subjects text file.

While I can use mri_binarize on ?h.hippoSfLabels-T1.v10.mgz to obtain the 
subfield masks and use them to obtain the posterior probabilities distribution 
after soft segmentation,
is there some other straighforward way to obtain 

Re: [Freesurfer] Hippocampal Subfields Posterior Probability

[Bharadwaj, Pradyumna - (prad)]

Sorry about that. I should have stated what I was trying to do. I'm trying to 
see if the posterior probability changes when using a certain combination of 
the different T1 and T2 weighted scans that we have in our lab. I thought using 
the binary masks to extract the probabilities as they were the final volumes of 
the subfields would be a better way.


As an example,
when I extract some basic stats on the left CA1 posteriors for one subject, 
these are the values I get,
range: 0.15 to 1, with a mean (sd) of 0.245258 (0.335046);

and , when I use the binary mask of the CA1 from lh.hippoSfLabels-T1.v10.mgz 
and then extract the same basic stats, I get,

range: 0.247501 to 1, with a mean (sd) of 0.770796 (0.175752)

Is my approach incorrect ?

Thanks!,
-Prad



From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, 
Eugenio <e.igles...@ucl.ac.uk>
Sent: Wednesday, March 22, 2017 11:06 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal Subfields Posterior Probability

Hi Prad,
The final probabilities are in the posterior files. There’s no need to binarize 
?h.hippoSfLabels if what you’re interested in is the soft segmentations.
Or maybe I’m missing something? What are you exactly trying to do?
Cheers,
/E

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 22 Mar 2017, at 18:02, Bharadwaj, Pradyumna - (prad) 
<p...@email.arizona.edu<mailto:p...@email.arizona.edu>> wrote:

Hi Dr. Iglesias,

Thank you for the overview of the labeling rules. I have also tried setting 
WRITE_POSTERIORS to 1 to write out the posteriors.

I had a follow up question about obtaining the probabilities for the final 
subfield labels as available in the ?h.hippoSfLabels-T1.v10.mgz

I use mri_binarize on ?h.hippoSfLabels-T1.v10.mgz to obtain binary masks for 
each subfield, and then used these masks with their respective posteriors to 
obtain the distributions.

Is this procedure correct or is there a better way ?

Thanks,
-Prad

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Iglesias Gonzalez, Eugenio 
<e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>>
Sent: Tuesday, March 21, 2017 2:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal Subfields Posterior Probability

Dear Prad,
There is a “secret” way of getting the posteriors. You need to set the 
environment variable WRITE_POSTERIORS to 1 before you call recon-all.
In (t)csh:
setenv WRITE_POSTERIORS 1
In bash:
export WRITE_POSTERIORS=1
And then call recon-all -hippocampal-subfields-T1(T2) as usual.

The discrete segmentation picks, for each voxel, the most likely label. The 
posterior of this label might or might not be above 0.5. For instance, if a 
voxel has p=0.4 of being CA1, p=0.3 of being background, and p=0.3 of being 
fimbria, it will be labeled as CA1 (even though p<0.5 for such subfield). Some 
people seem to prefer a 2-stage approach, in which a hippocampal mask is first 
created by selecting the voxels for which p(background)<0.5, and then each 
voxel within that mask is colored with the most likely subfield at that 
location.

I hope this helps!

Cheers,

/Eugenio



Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


On 21 Mar 2017, at 20:09, Bharadwaj, Pradyumna - (prad) 
<p...@email.arizona.edu<mailto:p...@email.arizona.edu>> wrote:

Hello Dr. Iglesias,

I'm currently examining the distributions of the posterior probabilities of the 
different hippocampal subfields, and I'm interested in obtaining the 
probability distribution images for the subfields that correspond to the 
volumes output in the subjects text file.

While I can use mri_binarize on ?h.hippoSfLabels-T1.v10.mgz to obtain the 
subfield masks and use them to obtain the posterior probabilities distribution 
after soft segmentation,
is there some other straighforward way to obtain these posterior probabilities 
for the volumes stated in the output text file ?

A follow up question - It appears that the soft segmentation approach 
approximates thresholding the posteriors by a value around 0.5 ? In your 
opinion, is this value acceptable and have you found similar values in your 
testing ?

Thanks!
-Prad


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the

Re: [Freesurfer] Hippocampal Subfields Posterior Probability

[Iglesias Gonzalez, Eugenio]

Hi Prad,
The final probabilities are in the posterior files. There’s no need to binarize 
?h.hippoSfLabels if what you’re interested in is the soft segmentations.
Or maybe I’m missing something? What are you exactly trying to do?
Cheers,
/E

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 22 Mar 2017, at 18:02, Bharadwaj, Pradyumna - (prad) 
<p...@email.arizona.edu<mailto:p...@email.arizona.edu>> wrote:

Hi Dr. Iglesias,

Thank you for the overview of the labeling rules. I have also tried setting 
WRITE_POSTERIORS to 1 to write out the posteriors.

I had a follow up question about obtaining the probabilities for the final 
subfield labels as available in the ?h.hippoSfLabels-T1.v10.mgz

I use mri_binarize on ?h.hippoSfLabels-T1.v10.mgz to obtain binary masks for 
each subfield, and then used these masks with their respective posteriors to 
obtain the distributions.

Is this procedure correct or is there a better way ?

Thanks,
-Prad

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Iglesias Gonzalez, Eugenio 
<e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>>
Sent: Tuesday, March 21, 2017 2:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal Subfields Posterior Probability

Dear Prad,
There is a “secret” way of getting the posteriors. You need to set the 
environment variable WRITE_POSTERIORS to 1 before you call recon-all.
In (t)csh:
setenv WRITE_POSTERIORS 1
In bash:
export WRITE_POSTERIORS=1
And then call recon-all -hippocampal-subfields-T1(T2) as usual.

The discrete segmentation picks, for each voxel, the most likely label. The 
posterior of this label might or might not be above 0.5. For instance, if a 
voxel has p=0.4 of being CA1, p=0.3 of being background, and p=0.3 of being 
fimbria, it will be labeled as CA1 (even though p<0.5 for such subfield). Some 
people seem to prefer a 2-stage approach, in which a hippocampal mask is first 
created by selecting the voxels for which p(background)<0.5, and then each 
voxel within that mask is colored with the most likely subfield at that 
location.

I hope this helps!

Cheers,

/Eugenio



Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


On 21 Mar 2017, at 20:09, Bharadwaj, Pradyumna - (prad) 
<p...@email.arizona.edu<mailto:p...@email.arizona.edu>> wrote:

Hello Dr. Iglesias,

I'm currently examining the distributions of the posterior probabilities of the 
different hippocampal subfields, and I'm interested in obtaining the 
probability distribution images for the subfields that correspond to the 
volumes output in the subjects text file.

While I can use mri_binarize on ?h.hippoSfLabels-T1.v10.mgz to obtain the 
subfield masks and use them to obtain the posterior probabilities distribution 
after soft segmentation,
is there some other straighforward way to obtain these posterior probabilities 
for the volumes stated in the output text file ?

A follow up question - It appears that the soft segmentation approach 
approximates thresholding the posteriors by a value around 0.5 ? In your 
opinion, is this value acceptable and have you found similar values in your 
testing ?

Thanks!
-Prad


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nm