[Freesurfer] Hippocampal subfields

[von Polier, Georg Ferdinand Anto]

Dear FreeSurfers,

I am just finishing a paper using output from Hippocampal subfields and 
recognized that the current version has been deprecated. I am interested in 
volumes of the whole hippocampus.
Are these volumes still valid and can you estimate when a new version will be 
available? Can you provide maybe a brief comment on the decision to deprecate 
the current version?
Best regards,
Georg

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[Freesurfer] hippocampal subfields

[Erik O'Hanlon]

Hi FS experts,


I completed an analysis including the hippocampal subfield options using 5.3.0. I understand that the subfield options was then removed and I noticed that the new rev of the subfield code will be ready for the v6 FS update. Can I use this code with my
 5.3.0 code and if so what files /dirs will I have to remove and how can I run or rerun it to get the new subfield measures if it's possible. I would really like to obtain the subfield measures and am not sure if I can use the existing measures based on the
 5.3.0 code. Any advice would be very much appreciated.


Kind regards  and thanks in advance


Erik


Erik O'Hanlon 

Postdoctoral researcher



RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740

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[Freesurfer] hippocampal subfields

[Gabor Perlaki]

Dear all,

1. Which is the suggested resolution for hippocampal subfields segmentation
with freesurfer? I've seen articles with 0.5*0.5*0.5mm^3 and with
1.0*1.0*1.0mm^3 as well. Does the hippocampal subfields segmentation really
work with 1.0*1.0*1.0 resolution?
2. The article "Automated Segmentation of Hippocampal Subfields from
Ultra-High Resolution In Vivo
MRI."
suggested on Freesurfer's page uses FOV=448. We are unable to set up the
matrix to achieve 0.38mm resolution using this FOV. Is there any other
suggested article to set up our measurements?

Thanks,

-- 
Gabor Perlaki
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[Freesurfer] hippocampal subfields

[Ferdi van de Kamp]

Hi all,

I'm trying to perform the longitudinal hippocampal subfields processing on
a cluster.

When I simply access a core on the cluster directly and use it to run the
hippocampal subfields it will run, but if I try to submit the process to
the cluster, it will either throw errors as I have pasted below or stop
after some registration steps.

The recon-all steps have run on the cluster (submitted) without problems.

Some notes:
As I'm testing things, the data is not in the original folder, so the path
names in recon-all log are not correct, but if that is the problem I'd
imagine it would be a problem for both submitting and direct processing.

Matlab runtime is installed, though in a separate folder, linking it in the
way described on the Freesurfer website.

The problem persists no matter how much memory I allocate to the process
(20GB RAM was the highest I tried).


Kind regards,

Ferdi van de Kamp



#
#@# Longitudinal Hippocampal Subfields processing (T1) left Wed Jan  4
03:06:40 CET 2017
--
Setting up environment variables
---
LD_LIBRARY_PATH is
.:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/runtime/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/bin/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/os/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/usr/local/OpenGridScheduler/gridengine/lib/linux-x64/:/usr/local/jemalloc/current/lib/:/usr/local/lib/:/usr/local/ScaLAPACK/scalapack-2.0.2/lib/
Warning: Unable to open display 'localhost:10.0'.  You will not be able to
display graphics on the screen.
Registering imageDump.mgz to hippocampal mask from ASEG of Base Point
/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin//kvlAutoCrop:
line 3: 65931 Segmentation fault  (core dumped) kvlAutoCrop.bin "$@"
/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin//kvlAutoCrop
/exports/fsw/MBos/DevTest/P0392Base/tmp/hippoSF_T1_long.v10_left//hippoAmygBinaryMask.mgz
6 >/dev/null: Segmentation fault
gzip:
/exports/fsw/MBos/DevTest/P0392Base/tmp/hippoSF_T1_long.v10_left//hippoAmygBinaryMask_autoCropped.mgz.gz:
No such file or directory
ERROR: problem reading fname
SWITCH expression must be a scalar or string constant.

Error in myMRIread>load_mgh (line 550)



Error in myMRIread>myMRIread_aux (line 92)



Error in myMRIread (line 63)



Error in SegmentSubfieldsT1Longitudinal (line 228)



MATLAB:badSwitchExpression
@#@FSTIME  2017:01:04:03:06:40
/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin/segmentSF_T1_long.sh
N 8 e 12.17 S 0.80 U 3.63 P 36% M 680932 F 530 R 118193 W 0 c 10055 w 5994
I 439360 O 194448 L 4.58 4.59 4.59
@#@FSLOADPOST 2017:01:04:03:06:52
/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin/segmentSF_T1_long.sh
N 8 4.72 4.62 4.60
#
#@# Longitudinal Hippocampal Subfields processing (T1) right Wed Jan  4
03:06:52 CET 2017
--
Setting up environment variables
---
LD_LIBRARY_PATH is
.:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/runtime/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/bin/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/os/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/usr/local/OpenGridScheduler/gridengine/lib/linux-x64/:/usr/local/jemalloc/current/lib/:/usr/local/lib/:/usr/local/ScaLAPACK/scalapack-2.0.2/lib/
Warning: Unable to open display 'localhost:10.0'.  You will not be able to
display graphics on the screen.
Registering imageDump.mgz to hippocampal mask from ASEG of Base Point
/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//b

[Freesurfer] Hippocampal subfields

[Alan Francis]

Hi Eugenio:

Hope all is well. I have a question. I have run the HSF algorithm on 32
brains and they ran smoothly without problems. I used only T1 scans. I did
not have T2s. Now to extract the data, do I need to run the following:

*.FSspace.mgz*: the additional scan, rigidly registered to the
T1 data.

*[lr]h.hippoSfLabels--.v10.mgz*: they store the discrete
segmentation volume at 0.333 mm resolution in the physical space of the
FreeSurfer  T1 data
(and therefore of the aligned scan *.FSspace.mgz* as well).

*[lr]h.hippoSfLabels--.v10.1mm.mgz*: they store the
discrete segmentation volume in the 1 mm FreeSurfer
 voxel space.
*[lr]h.hippoSfVolumes--.v10.txt*: these text files store
the estimated volumes of the subfields and of the whole hippocampi.

Or can I go directly to :

quantifyHippocampalSubfields.sh - 



Thanks so much,

best regards,

Alan



-- 
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*Alan N. Francis PhD*
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu 
afran...@mclean.harvard.edu


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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,
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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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[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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[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


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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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[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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[Freesurfer] hippocampal subfields

[Thomas Wolbers]

Hi there,

I was wondering whether there is any chance the automated segmentation 
of hippocampal subfields might be incorporated in the next Freesurfer 
update...

Cheers,
Thomas Wolbers

-- 
-
Dr. rer. nat. Thomas Wolbers
Senior Lecturer
Centre for Cognitive and Neural Systems&
Centre for Cognitive Ageing and Cognitive Epidemiology
The University of Edinburgh
1 George Square
Edinburgh EH8 9JZ
-
email: twolb...@ed.ac.uk
url: www.sal.mvm.ed.ac.uk
--


On 09/03/2011 13:58, Thomas Wolbers wrote:
> Dear Koen,
>
> I found your email from early 2009 regarding segmentation of 
> hippocampal subfields - may I ask whether there is any chance that 
> this feature will be implemented in Freesurfer any time soon?
>
> Best,
> Thomas Wolbers
>
> We have recently developed a method for automatically segmenting the
> hippocampal subfields from ultra-high resolution MRI data. The 
> software code
> is not yet in FreeSurfer, but will be in the future. It produces 
> volumetric
> segmentations, rather than surface representations, though.
>
> - Koen
>
>>
>>  Can freesurfer flatten (and only display) a (or several) segmented
>>  subcortical area(s), e.g. hippocampal region? If yes, can the fine
>>  structures in such a region (such as CA1,2,3, DG, etc.) be labeled?
>>
>>
>>
>>  Thanks,
>>
>>  Mingwu
>
>

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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[Freesurfer] hippocampal subfields

[Wayne Su]

One quick question: how to convert hippocampal subfields back to FS space?
Wayne
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[Freesurfer] hippocampal subfields

[Lugar, Heather]

If I were to run the hippocampal subfields command on data that had been 
previously processed using Freesurfer 5.0 (rather than 5.1), would the results 
be valid?

Thanks,
Heather
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Re: [Freesurfer] Hippocampal subfields

[Eugenio Iglesias]

Hi Georg,
we will be releasing with FreeSurfer 6 a new hippocampal subfield module based 
on a more accurate atlas built upon ex vivo MRI scans. However, if what you are 
interested in is the whole hippocampal volume, the results from the new module 
won't be too different.
Cheers,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


- Original Message -
From: "Georg Ferdinand Anto von Polier" 
To: "Freesurfer support list" 
Sent: Tuesday, December 2, 2014 2:46:40 PM
Subject: [Freesurfer] Hippocampal subfields





Dear FreeSurfers, 



I am just finishing a paper using output from Hippocampal subfields and 
recognized that the current version has been deprecated. I am interested in 
volumes of the whole hippocampus. 

Are these volumes still valid and can you estimate when a new version will be 
available? Can you provide maybe a brief comment on the decision to deprecate 
the current version? 

Best regards, 

Georg 


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Re: [Freesurfer] Hippocampal subfields

[angela . favaro]

Hi all, this is really a terrible news!
I am writing a paper using hippocampal subfields (ver 5.3). What is the
problem with segmentation using this tool? Is it reliable at least on some
of the subfield?
When will Freesurfer 6 be released?

Thank you

Angela


> Hi Georg,
> we will be releasing with FreeSurfer 6 a new hippocampal subfield module
> based on a more accurate atlas built upon ex vivo MRI scans. However, if
> what you are interested in is the whole hippocampal volume, the results
> from the new module won't be too different.
> Cheers,
> /Eugenio
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
>
> - Original Message -
> From: "Georg Ferdinand Anto von Polier" 
> To: "Freesurfer support list" 
> Sent: Tuesday, December 2, 2014 2:46:40 PM
> Subject: [Freesurfer] Hippocampal subfields
>
>
>
>
>
> Dear FreeSurfers,
>
>
>
> I am just finishing a paper using output from Hippocampal subfields and
> recognized that the current version has been deprecated. I am interested
> in volumes of the whole hippocampus.
>
> Are these volumes still valid and can you estimate when a new version will
> be available? Can you provide maybe a brief comment on the decision to
> deprecate the current version?
>
> Best regards,
>
> Georg
>
>
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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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>



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Re: [Freesurfer] Hippocampal subfields

[Erik O'Hanlon]

Hi FS experts,

Yes, I'm in the same position and have been trying to do it longitudinally. 
Does this mean that the outputs are completely unreliable and unstable? Should 
it be parked until the release of version 6?

Thanks

Erik

Erik O'Hanlon
Postdoctoral researcher


RCSI Psychiatry
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From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of angela.fav...@unipd.it 
[angela.fav...@unipd.it]
Sent: 02 December 2014 21:53
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields

Hi all, this is really a terrible news!
I am writing a paper using hippocampal subfields (ver 5.3). What is the
problem with segmentation using this tool? Is it reliable at least on some
of the subfield?
When will Freesurfer 6 be released?

Thank you

Angela


> Hi Georg,
> we will be releasing with FreeSurfer 6 a new hippocampal subfield module
> based on a more accurate atlas built upon ex vivo MRI scans. However, if
> what you are interested in is the whole hippocampal volume, the results
> from the new module won't be too different.
> Cheers,
> /Eugenio
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
>
> - Original Message -
> From: "Georg Ferdinand Anto von Polier" 
> To: "Freesurfer support list" 
> Sent: Tuesday, December 2, 2014 2:46:40 PM
> Subject: [Freesurfer] Hippocampal subfields
>
>
>
>
>
> Dear FreeSurfers,
>
>
>
> I am just finishing a paper using output from Hippocampal subfields and
> recognized that the current version has been deprecated. I am interested
> in volumes of the whole hippocampus.
>
> Are these volumes still valid and can you estimate when a new version will
> be available? Can you provide maybe a brief comment on the decision to
> deprecate the current version?
>
> Best regards,
>
> Georg
>
>
> ___
> Freesurfer mailing list
> 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 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
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>



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Re: [Freesurfer] Hippocampal subfields

[Eugenio Iglesias]

Dear Erik / Angela,
the atlas in 5.3 was derived from manual annotations on in vivo images that 
relied largely on geometric rules, and led to volume estimates that did not 
agree well with histology studies. The new atlas is based on ex vivo MRI and 
agrees better with histology. Moreover, it also has the option to input higher 
resolution images (in addition to the standard 1 mm T1), which yield a much 
better fit of the internal structure of the hippocampus.
That said, IMHO you can still publish papers with the old tool; you just need 
to be careful with the interpretation of the results, and discuss these issues 
in the submission. 
Kind regards,
/Eugenio


Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


- Original Message -
From: "Erik O'Hanlon" 
To: "Freesurfer support list" 
Sent: Tuesday, December 2, 2014 11:20:35 PM
Subject: Re: [Freesurfer] Hippocampal subfields

Hi FS experts,

Yes, I'm in the same position and have been trying to do it longitudinally. 
Does this mean that the outputs are completely unreliable and unstable? Should 
it be parked until the release of version 6?

Thanks

Erik

Erik O'Hanlon
Postdoctoral researcher


RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie  W: www.rcsi.ie

RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of angela.fav...@unipd.it 
[angela.fav...@unipd.it]
Sent: 02 December 2014 21:53
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields

Hi all, this is really a terrible news!
I am writing a paper using hippocampal subfields (ver 5.3). What is the
problem with segmentation using this tool? Is it reliable at least on some
of the subfield?
When will Freesurfer 6 be released?

Thank you

Angela


> Hi Georg,
> we will be releasing with FreeSurfer 6 a new hippocampal subfield module
> based on a more accurate atlas built upon ex vivo MRI scans. However, if
> what you are interested in is the whole hippocampal volume, the results
> from the new module won't be too different.
> Cheers,
> /Eugenio
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
>
> - Original Message -
> From: "Georg Ferdinand Anto von Polier" 
> To: "Freesurfer support list" 
> Sent: Tuesday, December 2, 2014 2:46:40 PM
> Subject: [Freesurfer] Hippocampal subfields
>
>
>
>
>
> Dear FreeSurfers,
>
>
>
> I am just finishing a paper using output from Hippocampal subfields and
> recognized that the current version has been deprecated. I am interested
> in volumes of the whole hippocampus.
>
> Are these volumes still valid and can you estimate when a new version will
> be available? Can you provide maybe a brief comment on the decision to
> deprecate the current version?
>
> Best regards,
>
> Georg
>
>
> ___
> Freesurfer mailing list
> 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 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.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>



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Re: [Freesurfer] Hippocampal subfields

[_andreia_]

Hi,

Will it be possible to incorporate the new hippo subfields atlas and stats
generation in the 5.3 recon-all without having to process everything from
scratch with 6.0?

Thank you,
Andreia

 Citando Eugenio Iglesias :


Dear Erik / Angela,
the atlas in 5.3 was derived from manual annotations on in vivo images
that relied largely on geometric rules, and led to volume estimates that
did not agree well with histology studies. The new atlas is based on ex
vivo MRI and agrees better with histology. Moreover, it also has the
option to input higher resolution images (in addition to the standard 1
mm T1), which yield a much better fit of the internal structure of the
hippocampus.
That said, IMHO you can still publish papers with the old tool; you just
need to be careful with the interpretation of the results, and discuss
these issues in the submission.
Kind regards,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com[1]
www.bcbl.eu[2]

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer[3]

- Original Message -
From: "Erik O'Hanlon" 
To: "Freesurfer support list" 
Sent: Tuesday, December 2, 2014 11:20:35 PM
Subject: Re: [Freesurfer] Hippocampal subfields

Hi FS experts,

Yes, I'm in the same position and have been trying to do it
longitudinally. Does this mean that the outputs are completely
unreliable and unstable? Should it be parked until the release of
version 6?

Thanks

Erik

Erik O'Hanlon
Postdoctoral researcher

RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie  W: www.rcsi.ie[4]

RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE

From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of
angela.fav...@unipd.it [angela.fav...@unipd.it]
Sent: 02 December 2014 21:53
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields

Hi all, this is really a terrible news!
I am writing a paper using hippocampal subfields (ver 5.3). What is the
problem with segmentation using this tool? Is it reliable at least on

some

of the subfield?
When will Freesurfer 6 be released?

Thank you

Angela


Hi Georg,
we will be releasing with FreeSurfer 6 a new hippocampal subfield module
based on a more accurate atlas built upon ex vivo MRI scans. However, if
what you are interested in is the whole hippocampal volume, the results
from the new module won't be too different.
Cheers,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com[1]
www.bcbl.eu[2]

Legal disclaimer/Aviso legal/Lege-oharra:

www.bcbl.eu/legal-disclaimer[3]


- Original Message -
From: "Georg Ferdinand Anto von Polier" 
To: "Freesurfer support list" 
Sent: Tuesday, December 2, 2014 2:46:40 PM
Subject: [Freesurfer] Hippocampal subfields

Dear FreeSurfers,

I am just finishing a paper using output from Hippocampal subfields and
recognized that the current version has been deprecated. I am interested
in volumes of the whole hippocampus.

Are these volumes still valid and can you estimate when a new version
will
be available? Can you provide maybe a brief comment on the decision to
deprecate the current version?

Best regards,

Georg

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it

is
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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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Ligações:
-
[1] http://www.jeiglesias.com
[2] http://www.bcbl.eu
[3] http://www.bcbl.eu/legal-disclaimer
[4] http://www.rcsi.ie
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Re: [Freesurfer] Hippocampal subfields

[Eugenio Iglesias]

Hi Andreia,
Nothing will prevent you from running FS6's hippocampal subfields on 
5.3-processed subjects, even though I'd recommend processing everything with 
the same version for the sake of reproducibility.
Cheers,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


- Original Message -
From: " andreia " <_andre...@sapo.pt>
To: "Freesurfer support list" , "Eugenio 
Iglesias" 
Sent: Wednesday, December 3, 2014 2:40:33 PM
Subject: Re: [Freesurfer] Hippocampal subfields



Hi, 

Will it be possible to incorporate the new hippo subfields atlas and stats 
generation in the 5.3 recon-all without having to process everything from 
scratch with 6.0? 

Thank you, 
Andreia 



Citando Eugenio Iglesias < e.igles...@bcbl.eu >: 



Dear Erik / Angela, 
the atlas in 5.3 was derived from manual annotations on in vivo images that 
relied largely on geometric rules, and led to volume estimates that did not 
agree well with histology studies. The new atlas is based on ex vivo MRI and 
agrees better with histology. Moreover, it also has the option to input higher 
resolution images (in addition to the standard 1 mm T1), which yield a much 
better fit of the internal structure of the hippocampus. 
That said, IMHO you can still publish papers with the old tool; you just need 
to be careful with the interpretation of the results, and discuss these issues 
in the submission. 
Kind regards, 
/Eugenio 


Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


- Original Message - 
From: "Erik O'Hanlon" < erikohan...@rcsi.ie > 
To: "Freesurfer support list" < freesurfer@nmr.mgh.harvard.edu > 
Sent: Tuesday, December 2, 2014 11:20:35 PM 
Subject: Re: [Freesurfer] Hippocampal subfields 

Hi FS experts, 

Yes, I'm in the same position and have been trying to do it longitudinally. 
Does this mean that the outputs are completely unreliable and unstable? Should 
it be parked until the release of version 6? 

Thanks 

Erik 

Erik O'Hanlon 
Postdoctoral researcher 


RCSI Psychiatry 
Royal College of Surgeons in Ireland 
Beaumont Road, Beaumont, D9, Ireland 
T: 8093740 
E: erikohan...@rcsi.ie W: www.rcsi.ie 

RCSI DEVELOPING HEALTHCARE LEADERS 
WHO MAKE A DIFFERENCE WORLDWIDE 
 
From: freesurfer-boun...@nmr.mgh.harvard.edu [ 
freesurfer-boun...@nmr.mgh.harvard.edu ] on behalf of angela.fav...@unipd.it [ 
angela.fav...@unipd.it ] 
Sent: 02 December 2014 21:53 
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampal subfields 

Hi all, this is really a terrible news! 
I am writing a paper using hippocampal subfields (ver 5.3). What is the 
problem with segmentation using this tool? Is it reliable at least on some 
of the subfield? 
When will Freesurfer 6 be released? 

Thank you 

Angela 





Hi Georg, 
we will be releasing with FreeSurfer 6 a new hippocampal subfield module 
based on a more accurate atlas built upon ex vivo MRI scans. However, if 
what you are interested in is the whole hippocampal volume, the results 
from the new module won't be too different. 
Cheers, 
/Eugenio 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


- Original Message - 
From: "Georg Ferdinand Anto von Polier" < gvonpol...@ukaachen.de > 
To: "Freesurfer support list" < freesurfer@nmr.mgh.harvard.edu > 
Sent: Tuesday, December 2, 2014 2:46:40 PM 
Subject: [Freesurfer] Hippocampal subfields 





Dear FreeSurfers, 



I am just finishing a paper using output from Hippocampal subfields and 
recognized that the current version has been deprecated. I am interested 
in volumes of the whole hippocampus. 

Are these volumes still valid and can you estimate when a new version will 
be available? Can you provide maybe a brief comment on the decision to 
deprecate the current version? 

Best regards, 

Georg 


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The information in this e-mail is intended only for the person to whom it 
is 
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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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https://ma

Re: [Freesurfer] hippocampal subfields

[Eugenio Iglesias]

Hi Erik,
the 6.0 subfield code won't overwrite your 5.3 results, so if you run the 6.0 
module on data analyzed with 5.3, both results will co-exist in the MRI 
directory of each subject.
Kind regards,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


- Original Message -
From: "Erik O'Hanlon" 
To: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, May 8, 2015 2:07:18 PM
Subject: [Freesurfer] hippocampal subfields



Hi FS experts, 


I completed an analysis including the hippocampal subfield options using 5.3.0. 
I understand that the subfield options was then removed and I noticed that the 
new rev of the subfield code will be ready for the v6 FS update. Can I use this 
code with my 5.3.0 code and if so what files /dirs will I have to remove and 
how can I run or rerun it to get the new subfield measures if it's possible. I 
would really like to obtain the subfield measures and am not sure if I can use 
the existing measures based on the 5.3.0 code. Any advice would be very much 
appreciated. 


Kind regards and thanks in advance 


Erik 

Erik O'Hanlon 
Postdoctoral researcher 




RCSI Psychiatry 
Royal College of Surgeons in Ireland 
Beaumont Road, Beaumont, D9, Ireland 
T: 8093740 
E: erikohan...@rcsi.ie W: www.rcsi.ie 

RCSI DEVELOPING HEALTHCARE LEADERS 
WHO MAKE A DIFFERENCE WORLDWIDE 
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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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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] hippocampal subfields

[Erik O'Hanlon]

Hi Eugenio,

That's brilliant, thanks so much for the quick response. So I will download the v6 code and how do I call the command so that it runs the v6 subfield analysis from the recon_all command?

Thanks again for the guidance. Very much appreciated

Cheers

Erik

From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias [e.igles...@bcbl.eu]
Sent: 08 May 2015 13:16
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields

Hi Erik,
the 6.0 subfield code won't overwrite your 5.3 results, so if you run the 6.0 module on data analyzed with 5.3, both results will co-exist in the MRI directory of each subject.
Kind regards,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: 
www.bcbl.eu/legal-disclaimer


- Original Message -
From: "Erik O'Hanlon" 
To: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, May 8, 2015 2:07:18 PM
Subject: [Freesurfer] hippocampal subfields



Hi FS experts,


I completed an analysis including the hippocampal subfield options using 5.3.0. I understand that the subfield options was then removed and I noticed that the new rev of the subfield code will be ready for the v6 FS update. Can I use this code with my 5.3.0
 code and if so what files /dirs will I have to remove and how can I run or rerun it to get the new subfield measures if it's possible. I would really like to obtain the subfield measures and am not sure if I can use the existing measures based on the 5.3.0
 code. Any advice would be very much appreciated.


Kind regards and thanks in advance


Erik

Erik O'Hanlon
Postdoctoral researcher




RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.ie

RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE
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contains patient information, please contact the Partners Compliance HelpLine at
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dispose of the e-mail.




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dispose of the e-mail.

Re: [Freesurfer] hippocampal subfields

[Erik O'Hanlon]

Hi Eugenio,


Sorry, forgot to ask if I can run it with the longitudinal pipeline too?


Best regards


Erik


From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohan...@rcsi.ie]
Sent: 08 May 2015 14:36
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields




Hi Eugenio,

That's brilliant, thanks so much for the quick response. So I will download the v6 code and how do I call the command so that it runs the v6 subfield analysis from the recon_all command?

Thanks again for the guidance. Very much appreciated

Cheers

Erik

From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias [e.igles...@bcbl.eu]
Sent: 08 May 2015 13:16
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields

Hi Erik,
the 6.0 subfield code won't overwrite your 5.3 results, so if you run the 6.0 module on data analyzed with 5.3, both results will co-exist in the MRI directory of each subject.
Kind regards,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: 
www.bcbl.eu/legal-disclaimer


- Original Message -
From: "Erik O'Hanlon" 
To: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, May 8, 2015 2:07:18 PM
Subject: [Freesurfer] hippocampal subfields



Hi FS experts,


I completed an analysis including the hippocampal subfield options using 5.3.0. I understand that the subfield options was then removed and I noticed that the new rev of the subfield code will be ready for the v6 FS update. Can I use this code with my 5.3.0
 code and if so what files /dirs will I have to remove and how can I run or rerun it to get the new subfield measures if it's possible. I would really like to obtain the subfield measures and am not sure if I can use the existing measures based on the 5.3.0
 code. Any advice would be very much appreciated.


Kind regards and thanks in advance


Erik

Erik O'Hanlon
Postdoctoral researcher




RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.ie

RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE
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contains patient information, please contact the Partners Compliance HelpLine at
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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.

Re: [Freesurfer] hippocampal subfields

[Eugenio Iglesias]

Hi again,
FS6 is not out yet,  but hopefully soon.
The instructions for the new hippocampal subfield module are here: 
http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
Cheers,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


- Original Message -
From: "Erik O'Hanlon" 
To: "Freesurfer support list" 
Sent: Friday, May 8, 2015 3:36:21 PM
Subject: Re: [Freesurfer] hippocampal subfields



Hi Eugenio, 

That's brilliant, thanks so much for the quick response. So I will download the 
v6 code and how do I call the command so that it runs the v6 subfield analysis 
from the recon_all command? 

Thanks again for the guidance. Very much appreciated 

Cheers 

Erik 
 
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias 
[e.igles...@bcbl.eu] 
Sent: 08 May 2015 13:16 
To: Freesurfer support list 
Subject: Re: [Freesurfer] hippocampal subfields 

Hi Erik, 
the 6.0 subfield code won't overwrite your 5.3 results, so if you run the 6.0 
module on data analyzed with 5.3, both results will co-exist in the MRI 
directory of each subject. 
Kind regards, 
/Eugenio 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


- Original Message - 
From: "Erik O'Hanlon"  
To: freesurfer@nmr.mgh.harvard.edu 
Sent: Friday, May 8, 2015 2:07:18 PM 
Subject: [Freesurfer] hippocampal subfields 



Hi FS experts, 


I completed an analysis including the hippocampal subfield options using 5.3.0. 
I understand that the subfield options was then removed and I noticed that the 
new rev of the subfield code will be ready for the v6 FS update. Can I use this 
code with my 5.3.0 code and if so what files /dirs will I have to remove and 
how can I run or rerun it to get the new subfield measures if it's possible. I 
would really like to obtain the subfield measures and am not sure if I can use 
the existing measures based on the 5.3.0 code. Any advice would be very much 
appreciated. 


Kind regards and thanks in advance 


Erik 

Erik O'Hanlon 
Postdoctoral researcher 




RCSI Psychiatry 
Royal College of Surgeons in Ireland 
Beaumont Road, Beaumont, D9, Ireland 
T: 8093740 
E: erikohan...@rcsi.ie W: www.rcsi.ie 

RCSI DEVELOPING HEALTHCARE LEADERS 
WHO MAKE A DIFFERENCE WORLDWIDE 
___ 
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The information in this e-mail is intended only for the person to whom it is 
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at 
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The information in this e-mail is intended only for the person to whom it is
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The information in this e-mail is intended only for the person to whom it is
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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

[Eugenio Iglesias]

Hi once more,
there is no specific longitudinal subfield module, BUT you can run the subfield 
code on the longitudinally processed subjects (i.e., those with 
.long. added to their name). 
Cheers,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


- Original Message -
From: "Erik O'Hanlon" 
To: "Freesurfer support list" 
Sent: Friday, May 8, 2015 3:42:26 PM
Subject: Re: [Freesurfer] hippocampal subfields



Hi Eugenio, 


Sorry, forgot to ask if I can run it with the longitudinal pipeline too? 


Best regards 


Erik 



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon 
[erikohan...@rcsi.ie] 
Sent: 08 May 2015 14:36 
To: Freesurfer support list 
Subject: Re: [Freesurfer] hippocampal subfields 




Hi Eugenio, 

That's brilliant, thanks so much for the quick response. So I will download the 
v6 code and how do I call the command so that it runs the v6 subfield analysis 
from the recon_all command? 

Thanks again for the guidance. Very much appreciated 

Cheers 

Erik 
 
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias 
[e.igles...@bcbl.eu] 
Sent: 08 May 2015 13:16 
To: Freesurfer support list 
Subject: Re: [Freesurfer] hippocampal subfields 

Hi Erik, 
the 6.0 subfield code won't overwrite your 5.3 results, so if you run the 6.0 
module on data analyzed with 5.3, both results will co-exist in the MRI 
directory of each subject. 
Kind regards, 
/Eugenio 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


- Original Message - 
From: "Erik O'Hanlon"  
To: freesurfer@nmr.mgh.harvard.edu 
Sent: Friday, May 8, 2015 2:07:18 PM 
Subject: [Freesurfer] hippocampal subfields 



Hi FS experts, 


I completed an analysis including the hippocampal subfield options using 5.3.0. 
I understand that the subfield options was then removed and I noticed that the 
new rev of the subfield code will be ready for the v6 FS update. Can I use this 
code with my 5.3.0 code and if so what files /dirs will I have to remove and 
how can I run or rerun it to get the new subfield measures if it's possible. I 
would really like to obtain the subfield measures and am not sure if I can use 
the existing measures based on the 5.3.0 code. Any advice would be very much 
appreciated. 


Kind regards and thanks in advance 


Erik 

Erik O'Hanlon 
Postdoctoral researcher 




RCSI Psychiatry 
Royal College of Surgeons in Ireland 
Beaumont Road, Beaumont, D9, Ireland 
T: 8093740 
E: erikohan...@rcsi.ie W: www.rcsi.ie 

RCSI DEVELOPING HEALTHCARE LEADERS 
WHO MAKE A DIFFERENCE WORLDWIDE 
___ 
Freesurfer mailing list 
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 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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] hippocampal subfields

[Nick Schmansky, MGH]

Erik,

If you wanted to test a 'beta' of v6, which has the new hippocampal
stream, then our current internal 'dev' build, which is very close to
being the upcoming v6, can be downloaded from here:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/

This goes for anyone else on the list who would like to help us test v6
prior to release.

Nick


On Fri, 2015-05-08 at 13:36 +, Erik O'Hanlon wrote:
> Hi Eugenio,
> 
> That's brilliant, thanks so much for the quick response. So I will
> download the v6 code and how do I call the command so that it runs the
> v6 subfield analysis from the recon_all command?
> 
> Thanks again for the guidance. Very much appreciated
> 
> Cheers
> 
> Erik
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
> [e.igles...@bcbl.eu]
> Sent: 08 May 2015 13:16
> To: Freesurfer support list
> Subject: Re: [Freesurfer] hippocampal subfields
> 
> Hi Erik,
> the 6.0 subfield code won't overwrite your 5.3 results, so if you run
> the 6.0 module on data analyzed with 5.3, both results will co-exist
> in the MRI directory of each subject.
> Kind regards,
> /Eugenio
> 
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
> 
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
> 
> 
> ----- Original Message -----
> From: "Erik O'Hanlon" 
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Friday, May 8, 2015 2:07:18 PM
> Subject: [Freesurfer] hippocampal subfields
> 
> 
> 
> Hi FS experts,
> 
> 
> I completed an analysis including the hippocampal subfield options
> using 5.3.0. I understand that the subfield options was then removed
> and I noticed that the new rev of the subfield code will be ready for
> the v6 FS update. Can I use this code with my 5.3.0 code and if so
> what files /dirs will I have to remove and how can I run or rerun it
> to get the new subfield measures if it's possible. I would really like
> to obtain the subfield measures and am not sure if I can use the
> existing measures based on the 5.3.0 code. Any advice would be very
> much appreciated.
> 
> 
> Kind regards and thanks in advance
> 
> 
> Erik
> 
> Erik O'Hanlon
> Postdoctoral researcher
> 
> 
> 
> 
> RCSI Psychiatry
> Royal College of Surgeons in Ireland
> Beaumont Road, Beaumont, D9, Ireland
> T: 8093740
> E: erikohan...@rcsi.ie W: www.rcsi.ie
> 
> RCSI DEVELOPING HEALTHCARE LEADERS
> WHO MAKE A DIFFERENCE WORLDWIDE
> ___
> Freesurfer mailing list
> 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 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.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] hippocampal subfields

[Erik O'Hanlon]

That is super Nick,

I'll download it next week and try it out. Will I need to just run the subfield part based on the 5.3.0 analysis I have or do it from scratch with the beta v6?

Thanks again for all the help

Erik

Erik O'Hanlon 

Postdoctoral researcher



RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740

E: erikohan...@rcsi.ie W: www.rcsi.ie

RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE 


From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH [ni...@nmr.mgh.harvard.edu]
Sent: 08 May 2015 19:05
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields

Erik,

If you wanted to test a 'beta' of v6, which has the new hippocampal
stream, then our current internal 'dev' build, which is very close to
being the upcoming v6, can be downloaded from here:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/

This goes for anyone else on the list who would like to help us test v6
prior to release.

Nick


On Fri, 2015-05-08 at 13:36 +, Erik O'Hanlon wrote:
> Hi Eugenio,
>
> That's brilliant, thanks so much for the quick response. So I will
> download the v6 code and how do I call the command so that it runs the
> v6 subfield analysis from the recon_all command?
>
> Thanks again for the guidance. Very much appreciated
>
> Cheers
>
> Erik
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
> [e.igles...@bcbl.eu]
> Sent: 08 May 2015 13:16
> To: Freesurfer support list
> Subject: Re: [Freesurfer] hippocampal subfields
>
> Hi Erik,
> the 6.0 subfield code won't overwrite your 5.3 results, so if you run
> the 6.0 module on data analyzed with 5.3, both results will co-exist
> in the MRI directory of each subject.
> Kind regards,
> /Eugenio
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: 
www.bcbl.eu/legal-disclaimer
>
>
> ----- Original Message -----
> From: "Erik O'Hanlon" 
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Friday, May 8, 2015 2:07:18 PM
> Subject: [Freesurfer] hippocampal subfields
>
>
>
> Hi FS experts,
>
>
> I completed an analysis including the hippocampal subfield options
> using 5.3.0. I understand that the subfield options was then removed
> and I noticed that the new rev of the subfield code will be ready for
> the v6 FS update. Can I use this code with my 5.3.0 code and if so
> what files /dirs will I have to remove and how can I run or rerun it
> to get the new subfield measures if it's possible. I would really like
> to obtain the subfield measures and am not sure if I can use the
> existing measures based on the 5.3.0 code. Any advice would be very
> much appreciated.
>
>
> Kind regards and thanks in advance
>
>
> Erik
>
> Erik O'Hanlon
> Postdoctoral researcher
>
>
>
>
> RCSI Psychiatry
> Royal College of Surgeons in Ireland
> Beaumont Road, Beaumont, D9, Ireland
> T: 8093740
> E: erikohan...@rcsi.ie W: www.rcsi.ie
>
> RCSI DEVELOPING HEALTHCARE LEADERS
> WHO MAKE A DIFFERENCE WORLDWIDE
> ___
> Freesurfer mailing list
> 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 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.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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




___
Freesurfer mailing list
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 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.

Re: [Freesurfer] hippocampal subfields

[Nick Schmansky, MGH]

Erik,

I haven't tried, but I'm pretty certain that you can use v5.3 results.
I'm not aware of any dependency built-in to the v6 stream that the new
hippocampal-subfields stream uses.

Nick

On Fri, 2015-05-08 at 18:10 +, Erik O'Hanlon wrote:
> That is super Nick,
> 
> I'll download it next week and try it out. Will I need to just run the
> subfield part based on the 5.3.0 analysis I have or do it from scratch
> with the beta v6?
> 
> Thanks again for all the help
> 
> Erik 
> 
> Erik O'Hanlon 
> Postdoctoral researcher
> 
> 
> 
> 
> RCSI Psychiatry
> Royal College of Surgeons in Ireland
> Beaumont Road, Beaumont, D9, Ireland
> T: 8093740 
> E: erikohan...@rcsi.ie W: www.rcsi.ie
> 
> RCSI DEVELOPING HEALTHCARE LEADERS
> WHO MAKE A DIFFERENCE WORLDWIDE 
> 
> 
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky,
> MGH [ni...@nmr.mgh.harvard.edu]
> Sent: 08 May 2015 19:05
> To: Freesurfer support list
> Subject: Re: [Freesurfer] hippocampal subfields
> 
> Erik,
> 
> If you wanted to test a 'beta' of v6, which has the new hippocampal
> stream, then our current internal 'dev' build, which is very close to
> being the upcoming v6, can be downloaded from here:
> 
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
> 
> This goes for anyone else on the list who would like to help us test
> v6
> prior to release.
> 
> Nick
> 
> 
> On Fri, 2015-05-08 at 13:36 +, Erik O'Hanlon wrote:
> > Hi Eugenio,
> >
> > That's brilliant, thanks so much for the quick response. So I will
> > download the v6 code and how do I call the command so that it runs
> the
> > v6 subfield analysis from the recon_all command?
> >
> > Thanks again for the guidance. Very much appreciated
> >
> > Cheers
> >
> > Erik
> > ____
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio
> Iglesias
> > [e.igles...@bcbl.eu]
> > Sent: 08 May 2015 13:16
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] hippocampal subfields
> >
> > Hi Erik,
> > the 6.0 subfield code won't overwrite your 5.3 results, so if you
> run
> > the 6.0 module on data analyzed with 5.3, both results will co-exist
> > in the MRI directory of each subject.
> > Kind regards,
> > /Eugenio
> >
> > Juan Eugenio Iglesias
> > Postdoctoral researcher BCBL
> > www.jeiglesias.com
> > www.bcbl.eu
> >
> > Legal disclaimer/Aviso legal/Lege-oharra:
> www.bcbl.eu/legal-disclaimer
> >
> >
> > - Original Message -
> > From: "Erik O'Hanlon" 
> > To: freesurfer@nmr.mgh.harvard.edu
> > Sent: Friday, May 8, 2015 2:07:18 PM
> > Subject: [Freesurfer] hippocampal subfields
> >
> >
> >
> > Hi FS experts,
> >
> >
> > I completed an analysis including the hippocampal subfield options
> > using 5.3.0. I understand that the subfield options was then removed
> > and I noticed that the new rev of the subfield code will be ready
> for
> > the v6 FS update. Can I use this code with my 5.3.0 code and if so
> > what files /dirs will I have to remove and how can I run or rerun it
> > to get the new subfield measures if it's possible. I would really
> like
> > to obtain the subfield measures and am not sure if I can use the
> > existing measures based on the 5.3.0 code. Any advice would be very
> > much appreciated.
> >
> >
> > Kind regards and thanks in advance
> >
> >
> > Erik
> >
> > Erik O'Hanlon
> > Postdoctoral researcher
> >
> >
> >
> >
> > RCSI Psychiatry
> > Royal College of Surgeons in Ireland
> > Beaumont Road, Beaumont, D9, Ireland
> > T: 8093740
> > E: erikohan...@rcsi.ie W: www.rcsi.ie
> >
> > RCSI DEVELOPING HEALTHCARE LEADERS
> > WHO MAKE A DIFFERENCE WORLDWIDE
> > ___
> > Freesurfer mailing list
> > 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 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 th

Re: [Freesurfer] hippocampal subfields

[Z K]

H. That's odd. Does the error appear if you source freesurfer and type 
"freeview" at the command line?

$> export FREESURFER_HOME=/Application/freesurfer
$> source $FREESURFER_HOME/SetUpFreeSurfer.sh
$> freeview

-Zeke


> On May 9, 2015, at 3:09 AM, Garikoitz Lerma-Usabiaga  
> wrote:
> 
> Hi Nick!
> just testing it in Yosemite and gives me this error, is there any dependency 
> I should consider?
> 
>  
> 
> 
>> On Fri, May 8, 2015 at 8:06 PM Nick Schmansky, MGH 
>>  wrote:
>> Erik,
>> 
>> If you wanted to test a 'beta' of v6, which has the new hippocampal
>> stream, then our current internal 'dev' build, which is very close to
>> being the upcoming v6, can be downloaded from here:
>> 
>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
>> 
>> This goes for anyone else on the list who would like to help us test v6
>> prior to release.
>> 
>> Nick
>> 
>> 
>> On Fri, 2015-05-08 at 13:36 +, Erik O'Hanlon wrote:
>> > Hi Eugenio,
>> >
>> > That's brilliant, thanks so much for the quick response. So I will
>> > download the v6 code and how do I call the command so that it runs the
>> > v6 subfield analysis from the recon_all command?
>> >
>> > Thanks again for the guidance. Very much appreciated
>> >
>> > Cheers
>> >
>> > Erik
>> > ________
>> > From: freesurfer-boun...@nmr.mgh.harvard.edu
>> > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
>> > [e.igles...@bcbl.eu]
>> > Sent: 08 May 2015 13:16
>> > To: Freesurfer support list
>> > Subject: Re: [Freesurfer] hippocampal subfields
>> >
>> > Hi Erik,
>> > the 6.0 subfield code won't overwrite your 5.3 results, so if you run
>> > the 6.0 module on data analyzed with 5.3, both results will co-exist
>> > in the MRI directory of each subject.
>> > Kind regards,
>> > /Eugenio
>> >
>> > Juan Eugenio Iglesias
>> > Postdoctoral researcher BCBL
>> > www.jeiglesias.com
>> > www.bcbl.eu
>> >
>> > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>> >
>> >
>> > - Original Message -
>> > From: "Erik O'Hanlon" 
>> > To: freesurfer@nmr.mgh.harvard.edu
>> > Sent: Friday, May 8, 2015 2:07:18 PM
>> > Subject: [Freesurfer] hippocampal subfields
>> >
>> >
>> >
>> > Hi FS experts,
>> >
>> >
>> > I completed an analysis including the hippocampal subfield options
>> > using 5.3.0. I understand that the subfield options was then removed
>> > and I noticed that the new rev of the subfield code will be ready for
>> > the v6 FS update. Can I use this code with my 5.3.0 code and if so
>> > what files /dirs will I have to remove and how can I run or rerun it
>> > to get the new subfield measures if it's possible. I would really like
>> > to obtain the subfield measures and am not sure if I can use the
>> > existing measures based on the 5.3.0 code. Any advice would be very
>> > much appreciated.
>> >
>> >
>> > Kind regards and thanks in advance
>> >
>> >
>> > Erik
>> >
>> > Erik O'Hanlon
>> > Postdoctoral researcher
>> >
>> >
>> >
>> >
>> > RCSI Psychiatry
>> > Royal College of Surgeons in Ireland
>> > Beaumont Road, Beaumont, D9, Ireland
>> > T: 8093740
>> > E: erikohan...@rcsi.ie W: www.rcsi.ie
>> >
>> > RCSI DEVELOPING HEALTHCARE LEADERS
>> > WHO MAKE A DIFFERENCE WORLDWIDE
>> > ___
>> > Freesurfer mailing list
>> > 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 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.
>> >
>> > ___

Re: [Freesurfer] hippocampal subfields

[Garikoitz Lerma-Usabiaga]

Thanks Zeke,
I did that and the terminal gave me an error saying that it couldn't find
libgomp.1.dylib,
so I did:
$> brew install gcc
and then added this to .bash_profile
export
DYLD_LIBRARY_PATH=/Applications/freesurfer/lib/gcc/lib:/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/
and now it is working :)
thanks!
Gari

On Sat, May 9, 2015 at 5:25 PM Z K  wrote:

>
> H. That's odd. Does the error appear if you source freesurfer and type
> "freeview" at the command line?
>
> $> export FREESURFER_HOME=/Application/freesurfer
> $> source $FREESURFER_HOME/SetUpFreeSurfer.sh
> $> freeview
>
> -Zeke
>
>
> On May 9, 2015, at 3:09 AM, Garikoitz Lerma-Usabiaga 
> wrote:
>
> Hi Nick!
> just testing it in Yosemite and gives me this error, is there any
> dependency I should consider?
>
>
>
> 
>
>
>
> On Fri, May 8, 2015 at 8:06 PM Nick Schmansky, MGH <
> ni...@nmr.mgh.harvard.edu> wrote:
>
>> Erik,
>>
>> If you wanted to test a 'beta' of v6, which has the new hippocampal
>> stream, then our current internal 'dev' build, which is very close to
>> being the upcoming v6, can be downloaded from here:
>>
>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
>>
>> This goes for anyone else on the list who would like to help us test v6
>> prior to release.
>>
>> Nick
>>
>>
>> On Fri, 2015-05-08 at 13:36 +, Erik O'Hanlon wrote:
>> > Hi Eugenio,
>> >
>> > That's brilliant, thanks so much for the quick response. So I will
>> > download the v6 code and how do I call the command so that it runs the
>> > v6 subfield analysis from the recon_all command?
>> >
>> > Thanks again for the guidance. Very much appreciated
>> >
>> > Cheers
>> >
>> > Erik
>> > 
>> > From: freesurfer-boun...@nmr.mgh.harvard.edu
>> > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
>> > [e.igles...@bcbl.eu]
>> > Sent: 08 May 2015 13:16
>> > To: Freesurfer support list
>> > Subject: Re: [Freesurfer] hippocampal subfields
>> >
>> > Hi Erik,
>> > the 6.0 subfield code won't overwrite your 5.3 results, so if you run
>> > the 6.0 module on data analyzed with 5.3, both results will co-exist
>> > in the MRI directory of each subject.
>> > Kind regards,
>> > /Eugenio
>> >
>> > Juan Eugenio Iglesias
>> > Postdoctoral researcher BCBL
>> > www.jeiglesias.com
>> > www.bcbl.eu
>> >
>> > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>> >
>> >
>> > - Original Message -
>> > From: "Erik O'Hanlon" 
>> > To: freesurfer@nmr.mgh.harvard.edu
>> > Sent: Friday, May 8, 2015 2:07:18 PM
>> > Subject: [Freesurfer] hippocampal subfields
>> >
>> >
>> >
>> > Hi FS experts,
>> >
>> >
>> > I completed an analysis including the hippocampal subfield options
>> > using 5.3.0. I understand that the subfield options was then removed
>> > and I noticed that the new rev of the subfield code will be ready for
>> > the v6 FS update. Can I use this code with my 5.3.0 code and if so
>> > what files /dirs will I have to remove and how can I run or rerun it
>> > to get the new subfield measures if it's possible. I would really like
>> > to obtain the subfield measures and am not sure if I can use the
>> > existing measures based on the 5.3.0 code. Any advice would be very
>> > much appreciated.
>> >
>> >
>> > Kind regards and thanks in advance
>> >
>> >
>> > Erik
>> >
>> > Erik O'Hanlon
>> > Postdoctoral researcher
>> >
>> >
>> >
>> >
>> > RCSI Psychiatry
>> > Royal College of Surgeons in Ireland
>> > Beaumont Road, Beaumont, D9, Ireland
>> > T: 8093740
>> > E: erikohan...@rcsi.ie W: www.rcsi.ie
>> >
>> > RCSI DEVELOPING HEALTHCARE LEADERS
>> > WHO MAKE A DIFFERENCE WORLDWIDE
>> > ___
>> > Freesurfer mailing list
>> > 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 person to whom
>> > it is
>> > addressed. If yo

Re: [Freesurfer] hippocampal subfields

[Erik O'Hanlon]

Hi FS Experts,

I'm trying the v6 hippocampal subfield code on a subject processed with 5.3.0 and I encountered the following error in the log file

Making Unknown map to reduced label 13
Computing hyperparameters for estimation of Gaussian parameters
Estimating typical intensities of  alveus
/home/support/tcin/apps/freesurfer/6-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 43:  2675 Killed  "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args
~

It appears that the process finished prematurely and didn't write out anything in the mri/ dir.

Any pointers how to resolve ? Any help greatly appreciated

Cheers

Erik

Erik O'Hanlon 

Postdoctoral researcher



RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740

E: erikohan...@rcsi.ie W: www.rcsi.ie

RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE 


From: Erik O'Hanlon
Sent: 08 May 2015 19:10
To: Freesurfer support list
Subject: RE: [Freesurfer] hippocampal subfields

That is super Nick,

I'll download it next week and try it out. Will I need to just run the subfield part based on the 5.3.0 analysis I have or do it from scratch with the beta v6?

Thanks again for all the help

Erik

From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH [ni...@nmr.mgh.harvard.edu]
Sent: 08 May 2015 19:05
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields

Erik,

If you wanted to test a 'beta' of v6, which has the new hippocampal
stream, then our current internal 'dev' build, which is very close to
being the upcoming v6, can be downloaded from here:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/

This goes for anyone else on the list who would like to help us test v6
prior to release.

Nick


On Fri, 2015-05-08 at 13:36 +, Erik O'Hanlon wrote:
> Hi Eugenio,
>
> That's brilliant, thanks so much for the quick response. So I will
> download the v6 code and how do I call the command so that it runs the
> v6 subfield analysis from the recon_all command?
>
> Thanks again for the guidance. Very much appreciated
>
> Cheers
>
> Erik
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
> [e.igles...@bcbl.eu]
> Sent: 08 May 2015 13:16
> To: Freesurfer support list
> Subject: Re: [Freesurfer] hippocampal subfields
>
> Hi Erik,
> the 6.0 subfield code won't overwrite your 5.3 results, so if you run
> the 6.0 module on data analyzed with 5.3, both results will co-exist
> in the MRI directory of each subject.
> Kind regards,
> /Eugenio
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: 
www.bcbl.eu/legal-disclaimer
>
>
> - Original Message -
> From: "Erik O'Hanlon" 
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Friday, May 8, 2015 2:07:18 PM
> Subject: [Freesurfer] hippocampal subfields
>
>
>
> Hi FS experts,
>
>
> I completed an analysis including the hippocampal subfield options
> using 5.3.0. I understand that the subfield options was then removed
> and I noticed that the new rev of the subfield code will be ready for
> the v6 FS update. Can I use this code with my 5.3.0 code and if so
> what files /dirs will I have to remove and how can I run or rerun it
> to get the new subfield measures if it's possible. I would really like
> to obtain the subfield measures and am not sure if I can use the
> existing measures based on the 5.3.0 code. Any advice would be very
> much appreciated.
>
>
> Kind regards and thanks in advance
>
>
> Erik
>
> Erik O'Hanlon
> Postdoctoral researcher
>
>
>
>
> RCSI Psychiatry
> Royal College of Surgeons in Ireland
> Beaumont Road, Beaumont, D9, Ireland
> T: 8093740
> E: erikohan...@rcsi.ie W: www.rcsi.ie
>
> RCSI DEVELOPING HEALTHCARE LEADERS
> WHO MAKE A DIFFERENCE WORLDWIDE
> ___
> Freesurfer mailing list
> 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 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 patien

Re: [Freesurfer] hippocampal subfields

[Eugenio Iglesias]

Hi Erik, 
I guess your process was killed by the kernel. Maybe you ran out of RAM memory? 
How much RAM do you have?
Cheers,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


- Original Message -
From: "Erik O'Hanlon" 
To: "Freesurfer support list" 
Sent: Monday, May 25, 2015 6:53:54 PM
Subject: Re: [Freesurfer] hippocampal subfields



Hi FS Experts, 

I'm trying the v6 hippocampal subfield code on a subject processed with 5.3.0 
and I encountered the following error in the log file 

Making Unknown map to reduced label 13 
Computing hyperparameters for estimation of Gaussian parameters 
Estimating typical intensities of alveus 
/home/support/tcin/apps/freesurfer/6-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
 line 43: 2675 Killed "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args 
~ 

It appears that the process finished prematurely and didn't write out anything 
in the mri/ dir. 

Any pointers how to resolve ? Any help greatly appreciated 

Cheers 

Erik 

Erik O'Hanlon 
Postdoctoral researcher 




RCSI Psychiatry 
Royal College of Surgeons in Ireland 
Beaumont Road, Beaumont, D9, Ireland 
T: 8093740 
E: erikohan...@rcsi.ie W: www.rcsi.ie 

RCSI DEVELOPING HEALTHCARE LEADERS 
WHO MAKE A DIFFERENCE WORLDWIDE 
 
From: Erik O'Hanlon 
Sent: 08 May 2015 19:10 
To: Freesurfer support list 
Subject: RE: [Freesurfer] hippocampal subfields 

That is super Nick, 

I'll download it next week and try it out. Will I need to just run the subfield 
part based on the 5.3.0 analysis I have or do it from scratch with the beta v6? 

Thanks again for all the help 

Erik 
 
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH 
[ni...@nmr.mgh.harvard.edu] 
Sent: 08 May 2015 19:05 
To: Freesurfer support list 
Subject: Re: [Freesurfer] hippocampal subfields 

Erik, 

If you wanted to test a 'beta' of v6, which has the new hippocampal 
stream, then our current internal 'dev' build, which is very close to 
being the upcoming v6, can be downloaded from here: 

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ 

This goes for anyone else on the list who would like to help us test v6 
prior to release. 

Nick 


On Fri, 2015-05-08 at 13:36 +, Erik O'Hanlon wrote: 
> Hi Eugenio, 
> 
> That's brilliant, thanks so much for the quick response. So I will 
> download the v6 code and how do I call the command so that it runs the 
> v6 subfield analysis from the recon_all command? 
> 
> Thanks again for the guidance. Very much appreciated 
> 
> Cheers 
> 
> Erik 
>  
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias 
> [e.igles...@bcbl.eu] 
> Sent: 08 May 2015 13:16 
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] hippocampal subfields 
> 
> Hi Erik, 
> the 6.0 subfield code won't overwrite your 5.3 results, so if you run 
> the 6.0 module on data analyzed with 5.3, both results will co-exist 
> in the MRI directory of each subject. 
> Kind regards, 
> /Eugenio 
> 
> Juan Eugenio Iglesias 
> Postdoctoral researcher BCBL 
> www.jeiglesias.com 
> www.bcbl.eu 
> 
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 
> 
> 
> - Original Message - 
> From: "Erik O'Hanlon"  
> To: freesurfer@nmr.mgh.harvard.edu 
> Sent: Friday, May 8, 2015 2:07:18 PM 
> Subject: [Freesurfer] hippocampal subfields 
> 
> 
> 
> Hi FS experts, 
> 
> 
> I completed an analysis including the hippocampal subfield options 
> using 5.3.0. I understand that the subfield options was then removed 
> and I noticed that the new rev of the subfield code will be ready for 
> the v6 FS update. Can I use this code with my 5.3.0 code and if so 
> what files /dirs will I have to remove and how can I run or rerun it 
> to get the new subfield measures if it's possible. I would really like 
> to obtain the subfield measures and am not sure if I can use the 
> existing measures based on the 5.3.0 code. Any advice would be very 
> much appreciated. 
> 
> 
> Kind regards and thanks in advance 
> 
> 
> Erik 
> 
> Erik O'Hanlon 
> Postdoctoral researcher 
> 
> 
> 
> 
> RCSI Psychiatry 
> Royal College of Surgeons in Ireland 
> Beaumont Road, Beaumont, D9, Ireland 
> T: 8093740 
> E: erikohan...@rcsi.ie W: www.rcsi.ie 
> 
> RCSI DEVELOPING HEALTHCARE LEADERS 
> WHO MAKE A DIFFERENCE WORLDWIDE 
> _

Re: [Freesurfer] hippocampal subfields

[Erik O'Hanlon]

Hi Eugenio,

I'm trying to run in on a cluster and I think I have eight cores assigned with 2GB per core. I'm not sure if the process is parallelised though so it could be the case that I have the job running on one of the possible core and only using 2GB of RAM. I can
 ask the cluster support team to check but is it possible to run the job across the 8 cores and thus grab the 16GB of RAM or will the code only use the one  core and I will have to get the RAM assigned to it to be increased.

Any guidance much appreciated and maybe if you could outline a typical system requirement/setup to run a job. I have 200 subjects so your advice would super.

Thanks again

Cheers

Erik

From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias [e.igles...@bcbl.eu]
Sent: 26 May 2015 10:33
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields

Hi Erik,
I guess your process was killed by the kernel. Maybe you ran out of RAM memory? How much RAM do you have?
Cheers,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: 
www.bcbl.eu/legal-disclaimer


- Original Message -
From: "Erik O'Hanlon" 
To: "Freesurfer support list" 
Sent: Monday, May 25, 2015 6:53:54 PM
Subject: Re: [Freesurfer] hippocampal subfields



Hi FS Experts,

I'm trying the v6 hippocampal subfield code on a subject processed with 5.3.0 and I encountered the following error in the log file

Making Unknown map to reduced label 13
Computing hyperparameters for estimation of Gaussian parameters
Estimating typical intensities of alveus
/home/support/tcin/apps/freesurfer/6-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 43: 2675 Killed "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args
~

It appears that the process finished prematurely and didn't write out anything in the mri/ dir.

Any pointers how to resolve ? Any help greatly appreciated

Cheers

Erik

Erik O'Hanlon
Postdoctoral researcher




RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.ie

RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE

From: Erik O'Hanlon
Sent: 08 May 2015 19:10
To: Freesurfer support list
Subject: RE: [Freesurfer] hippocampal subfields

That is super Nick,

I'll download it next week and try it out. Will I need to just run the subfield part based on the 5.3.0 analysis I have or do it from scratch with the beta v6?

Thanks again for all the help

Erik

From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH [ni...@nmr.mgh.harvard.edu]
Sent: 08 May 2015 19:05
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields

Erik,

If you wanted to test a 'beta' of v6, which has the new hippocampal
stream, then our current internal 'dev' build, which is very close to
being the upcoming v6, can be downloaded from here:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/

This goes for anyone else on the list who would like to help us test v6
prior to release.

Nick


On Fri, 2015-05-08 at 13:36 +, Erik O'Hanlon wrote:
> Hi Eugenio,
>
> That's brilliant, thanks so much for the quick response. So I will
> download the v6 code and how do I call the command so that it runs the
> v6 subfield analysis from the recon_all command?
>
> Thanks again for the guidance. Very much appreciated
>
> Cheers
>
> Erik
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
> [e.igles...@bcbl.eu]
> Sent: 08 May 2015 13:16
> To: Freesurfer support list
> Subject: Re: [Freesurfer] hippocampal subfields
>
> Hi Erik,
> the 6.0 subfield code won't overwrite your 5.3 results, so if you run
> the 6.0 module on data analyzed with 5.3, both results will co-exist
> in the MRI directory of each subject.
> Kind regards,
> /Eugenio
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: 
www.bcbl.eu/legal-disclaimer
>
>
> - Original Message -
> From: "Erik O'Hanlon" 
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Friday, May 8, 2015 2:07:18 PM
> Subject: [Freesurfer] hippocampal subfields
>
>
>
> Hi FS experts,
>
>
> I completed an analysis including the hippocampal subfield options
> using 5.3.0. I understand that the subfield options was then removed
> and I noticed that

Re: [Freesurfer] hippocampal subfields

[Eugenio Iglesias]

Hi again,
The software requires approximately 10GB of RAM
Cheers
Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


- Original Message -
From: Erik O'Hanlon 
To: Freesurfer support list 
Sent: Tue, 26 May 2015 12:16:00 +0200 (CEST)
Subject: Re: [Freesurfer] hippocampal subfields





<!-- .EmailQuote { margin-left: 1pt; padding-left: 4pt; border-left: 
#80 2px solid; } -->



Hi Eugenio,

I'm trying to run in on a cluster and I think I have eight cores assigned 
with 2GB per core. I'm not sure if the process is parallelised though so it 
could be the case that I have the job running on one of the possible core and 
only using 2GB of RAM. I can
 ask the cluster support team to check but is it possible to run the job across 
the 8 cores and thus grab the 16GB of RAM or will the code only use the 
one  core and I will have to get the RAM assigned to it to be 
increased.

Any guidance much appreciated and maybe if you could outline a typical system 
requirement/setup to run a job. I have 200 subjects so your advice would 
super.

Thanks again

Cheers

Erik

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias 
[e.igles...@bcbl.eu]
Sent: 26 May 2015 10:33
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields

Hi Erik,
I guess your process was killed by the kernel. Maybe you ran out of RAM memory? 
How much RAM do you have?
Cheers,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
http://www.jeiglesias.com"; target="_blank">www.jeiglesias.com
http://www.bcbl.eu"; target="_blank">www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: http://www.bcbl.eu/legal-disclaimer"; target="_blank">
www.bcbl.eu/legal-disclaimer


- Original Message -
From: "Erik O'Hanlon" <erikohan...@rcsi.ie>
To: "Freesurfer support list" 
<freesurfer@nmr.mgh.harvard.edu>
Sent: Monday, May 25, 2015 6:53:54 PM
Subject: Re: [Freesurfer] hippocampal subfields



Hi FS Experts,

I'm trying the v6 hippocampal subfield code on a subject processed with 
5.3.0 and I encountered the following error in the log file

Making Unknown map to reduced label 13
Computing hyperparameters for estimation of Gaussian parameters
Estimating typical intensities of alveus
/home/support/tcin/apps/freesurfer/6-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
 line 43: 2675 Killed 
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args
~

It appears that the process finished prematurely and didn't write out 
anything in the mri/ dir.

Any pointers how to resolve ? Any help greatly appreciated

Cheers

Erik

Erik O'Hanlon
Postdoctoral researcher




RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie W: http://www.rcsi.ie"; 
target="_blank">www.rcsi.ie

RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE
____
From: Erik O'Hanlon
Sent: 08 May 2015 19:10
To: Freesurfer support list
Subject: RE: [Freesurfer] hippocampal subfields

That is super Nick,

I'll download it next week and try it out. Will I need to just run the 
subfield part based on the 5.3.0 analysis I have or do it from scratch with the 
beta v6?

Thanks again for all the help

Erik

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH 
[ni...@nmr.mgh.harvard.edu]
Sent: 08 May 2015 19:05
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields

Erik,

If you wanted to test a 'beta' of v6, which has the new hippocampal
stream, then our current internal 'dev' build, which is very close 
to
being the upcoming v6, can be downloaded from here:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/"; 
target="_blank">ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/

This goes for anyone else on the list who would like to help us test v6
prior to release.

Nick


On Fri, 2015-05-08 at 13:36 +, Erik O'Hanlon wrote:
> Hi Eugenio,
>
> That's brilliant, thanks so much for the quick response. So I will
> download the v6 code and how do I call the command so that it runs the
> v6 subfield analysis from the recon_all command?
>
> Thanks again for the guidance. Very much appreciated
>
> Cheers
>
> Erik
> ____________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
> [e.igles...@bcbl.eu]
> Sent: 08 May 2015 13:16
> To: Freesurfer su

Re: [Freesurfer] hippocampal subfields

[Erik O'Hanlon]

Hi Eugenio,

I managed to get the subfield code process to run, my cluster wasn't using all the allotted RAM for the job, thank you for all the input. Can I ask how long it typically takes as it appears to have completed in about 30mins and gave me the left and right dirs
 with the volume txts etc. Just wanted to be sure before I kick it off on the complete data set.

Thanks again for all the help.

Cheers

Ertik

Erik O'Hanlon 

Postdoctoral researcher



RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740

E: erikohan...@rcsi.ie W: www.rcsi.ie

RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE 


From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias [e.igles...@bcbl.eu]
Sent: 26 May 2015 11:25
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields

Hi again,
The software requires approximately 10GB of RAM
Cheers
Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: 
www.bcbl.eu/legal-disclaimer


- Original Message -
From: Erik O'Hanlon 
To: Freesurfer support list 
Sent: Tue, 26 May 2015 12:16:00 +0200 (CEST)
Subject: Re: [Freesurfer] hippocampal subfields





<!-- .EmailQuote { margin-left: 1pt; padding-left: 4pt; border-left: #80 2px solid; } -->



Hi Eugenio,

I'm trying to run in on a cluster and I think I have eight cores assigned with 2GB per core. I'm not sure if the process is parallelised though so it could be the case that I have the job running on one of the possible core and only using 2GB of RAM.
 I can
 ask the cluster support team to check but is it possible to run the job across the 8 cores and thus grab the 16GB of RAM or will the code only use the one  core and I will have to get the RAM assigned to it to be increased.

Any guidance much appreciated and maybe if you could outline a typical system requirement/setup to run a job. I have 200 subjects so your advice would super.

Thanks again

Cheers

Erik

From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias [e.igles...@bcbl.eu]
Sent: 26 May 2015 10:33
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields

Hi Erik,
I guess your process was killed by the kernel. Maybe you ran out of RAM memory? How much RAM do you have?
Cheers,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
http://www.jeiglesias.com" target="_blank">www.jeiglesias.com
http://www.bcbl.eu" target="_blank">www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: http://www.bcbl.eu/legal-disclaimer" target="_blank">
www.bcbl.eu/legal-disclaimer>


- Original Message -
From: "Erik O'Hanlon" <erikohan...@rcsi.ie>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Monday, May 25, 2015 6:53:54 PM
Subject: Re: [Freesurfer] hippocampal subfields



Hi FS Experts,

I'm trying the v6 hippocampal subfield code on a subject processed with 5.3.0 and I encountered the following error in the log file

Making Unknown map to reduced label 13
Computing hyperparameters for estimation of Gaussian parameters
Estimating typical intensities of alveus
/home/support/tcin/apps/freesurfer/6-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 43: 2675 Killed "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args
~

It appears that the process finished prematurely and didn't write out anything in the mri/ dir.

Any pointers how to resolve ? Any help greatly appreciated

Cheers

Erik

Erik O'Hanlon
Postdoctoral researcher




RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie W: http://www.rcsi.ie" target="_blank">www.rcsi.ie

RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE

From: Erik O'Hanlon
Sent: 08 May 2015 19:10
To: Freesurfer support list
Subject: RE: [Freesurfer] hippocampal subfields

That is super Nick,

I'll download it next week and try it out. Will I need to just run the subfield part based on the 5.3.0 analysis I have or do it from scratch with the beta v6?

Thanks again for all the help

Erik

From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH [ni...@nmr.mgh.harvard.edu]
Sent: 08 May 2015 19:05
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields

Erik,

If you wanted to test a 'beta' of v6, which has the new hippocampal
stream, then our current internal 'dev' build, which is very cl

Re: [Freesurfer] hippocampal subfields

[Eugenio Iglesias]

Hi Erik,
30 mins for a subject sounds correct. If the text files with the volumes are 
there, and the segmentations look plausible, then everything should be fine.
One more thing: it the outputs are in specific directories, please note that we 
changed the naming convention and structure  of  the output last week - sorry 
about that! We believe that the changes made the module easier to use. Please 
see the updated instructions here:
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
Cheers,
/Eugenio


Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


- Original Message -
From: "Erik O'Hanlon" 
To: "Freesurfer support list" 
Sent: Wednesday, May 27, 2015 10:17:51 AM
Subject: Re: [Freesurfer] hippocampal subfields



Hi Eugenio, 

I managed to get the subfield code process to run, my cluster wasn't using all 
the allotted RAM for the job, thank you for all the input. Can I ask how long 
it typically takes as it appears to have completed in about 30mins and gave me 
the left and right dirs with the volume txts etc. Just wanted to be sure before 
I kick it off on the complete data set. 

Thanks again for all the help. 

Cheers 

Ertik 

Erik O'Hanlon 
Postdoctoral researcher 




RCSI Psychiatry 
Royal College of Surgeons in Ireland 
Beaumont Road, Beaumont, D9, Ireland 
T: 8093740 
E: erikohan...@rcsi.ie W: www.rcsi.ie 

RCSI DEVELOPING HEALTHCARE LEADERS 
WHO MAKE A DIFFERENCE WORLDWIDE 
 
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias 
[e.igles...@bcbl.eu] 
Sent: 26 May 2015 11:25 
To: Freesurfer support list 
Subject: Re: [Freesurfer] hippocampal subfields 

Hi again, 
The software requires approximately 10GB of RAM 
Cheers 
Eugenio 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


- Original Message - 
From: Erik O'Hanlon  
To: Freesurfer support list  
Sent: Tue, 26 May 2015 12:16:00 +0200 (CEST) 
Subject: Re: [Freesurfer] hippocampal subfields 

 
 


<!-- .EmailQuote { margin-left: 1pt; padding-left: 4pt; border-left: 
#80 2px solid; } --> 
 
 
 
Hi Eugenio, 
 
I'm trying to run in on a cluster and I think I have eight cores assigned 
with 2GB per core. I'm not sure if the process is parallelised though so it 
could be the case that I have the job running on one of the possible core and 
only using 2GB of RAM. I can 
ask the cluster support team to check but is it possible to run the job across 
the 8 cores and thus grab the 16GB of RAM or will the code only use the 
one  core and I will have to get the RAM assigned to it to be 
increased. 
 
Any guidance much appreciated and maybe if you could outline a typical system 
requirement/setup to run a job. I have 200 subjects so your advice would 
super. 
 
Thanks again 
 
Cheers 
 
Erik 
 
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias 
[e.igles...@bcbl.eu] 
Sent: 26 May 2015 10:33 
To: Freesurfer support list 
Subject: Re: [Freesurfer] hippocampal subfields 
 
Hi Erik, 
I guess your process was killed by the kernel. Maybe you ran out of RAM memory? 
How much RAM do you have? 
Cheers, 
/Eugenio 
 
Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
http://www.jeiglesias.com " 
target="_blank">www.jeiglesias.com 
http://www.bcbl.eu " target="_blank">www.bcbl.eu 
 
Legal disclaimer/Aviso legal/Lege-oharra: http://www.bcbl.eu/legal-disclaimer " target="_blank"> 
www.bcbl.eu/legal-disclaimer 
 
 
- Original Message - 
From: "Erik O'Hanlon" <erikohan...@rcsi.ie> 
To: "Freesurfer support list" 
<freesurfer@nmr.mgh.harvard.edu> 
Sent: Monday, May 25, 2015 6:53:54 PM 
Subject: Re: [Freesurfer] hippocampal subfields 
 
 
 
Hi FS Experts, 
 
I'm trying the v6 hippocampal subfield code on a subject processed with 
5.3.0 and I encountered the following error in the log file 
 
Making Unknown map to reduced label 13 
Computing hyperparameters for estimation of Gaussian parameters 
Estimating typical intensities of alveus 
/home/support/tcin/apps/freesurfer/6-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
 line 43: 2675 Killed 
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args 
~ 
 
It appears that the process finished prematurely and didn't write out 
anything in the mri/ dir. 
 
Any pointers how to resolve ? Any help greatly appreciated 
 
Cheers 
 
Erik 
 
Erik O'Hanlon 
Postdoctoral researcher 
 
 
 
 
RCSI Psychiatry 
Royal College of Surgeons in Ireland 
Beaumont Road, Beaumont,

[Freesurfer] Hippocampal subfields intensity

[Marcos Martins da Silva]

Hi, Freesurfer Experts

After usual processing with recon-all -all we get the aseg.stats file
with several data including intensity values like:
normMean normStdDev
normMin normMax normRange
Left-Hippocampus  77.8939 7.574846.
105.59.

How could I get similar results for each hippocampal subfield, assuming
I also generated all posterior*.mgz files corresponding to each
subfield?
I guess I should first binarize each of the subfields file with a
threshold=127 to map all the pertinent voxels, and then use these files
as masks over nu.mgz and calculate the intensities values. But I do not
know the best way to accomplish this after the binarize step.

Thank you in advance for any help.

Marcos
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[Freesurfer] hippocampal subfields question

[Salil Soman]

Hi,

I just wanted to confirm that label "hippocampus" in the hippocampal
subfields segmentation is simply parts of the hippocampus that do not fall
into one of the other major categories? Also, where can I find the units
for the hippocampal subfields? I am seeing some discrepancy between the
left and right hippocampal volumes generated by freesurfer and the summed
areas generated by the hippocampal subfield analysis.

Thank you,

-Sal
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[Freesurfer] Hippocampal subfields script.

[Alan Francis]

Hi Eugenio:

I have HSF data on 60 Asperger brains. Is there a script that will allow me
to extract the volumes into a single location?

thanks so much,

Alan Francis
Martinos Center
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Re: [Freesurfer] hippocampal subfields

[Juan Eugenio Iglesias]

Dear Gabor,
the segmentation benefits to some extent from higher resolution data,
but produces decent estimates of the subfields at 1x1x1. We are working
on a new atlas that will incorporate much more detail, and will more
effectively take advantage of high-resolution images. 
Kind regards,
Juan Eugenio Iglesias

On Mon, 2014-03-03 at 13:49 +0100, Gabor Perlaki wrote:
> Dear all,
> 
> 
> 1. Which is the suggested resolution for hippocampal subfields
> segmentation with freesurfer? I've seen articles with 0.5*0.5*0.5mm^3
> and with 1.0*1.0*1.0mm^3 as well. Does the hippocampal subfields
> segmentation really work with 1.0*1.0*1.0 resolution? 
> 2. The article "Automated Segmentation of Hippocampal Subfields from
> Ultra-High Resolution In Vivo MRI." suggested on Freesurfer's page
> uses FOV=448. We are unable to set up the matrix to achieve 0.38mm
> resolution using this FOV. Is there any other suggested article to set
> up our measurements?
> 
> Thanks,  
> 
> -- 
> Gabor Perlaki
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] hippocampal subfields

[Gregory Kirk]

Hi, just wondering if you have a guesstimate on the ETA of the new atlas ?

thanks



On 03/03/14, Juan Eugenio Iglesias  wrote:
> Dear Gabor,
> the segmentation benefits to some extent from higher resolution data,
> but produces decent estimates of the subfields at 1x1x1. We are working
> on a new atlas that will incorporate much more detail, and will more
> effectively take advantage of high-resolution images. 
> Kind regards,
> Juan Eugenio Iglesias
> 
> On Mon, 2014-03-03 at 13:49 +0100, Gabor Perlaki wrote:
> > Dear all,
> > 
> > 
> > 1. Which is the suggested resolution for hippocampal subfields
> > segmentation with freesurfer? I've seen articles with 0.5*0.5*0.5mm^3
> > and with 1.0*1.0*1.0mm^3 as well. Does the hippocampal subfields
> > segmentation really work with 1.0*1.0*1.0 resolution? 
> > 2. The article "Automated Segmentation of Hippocampal Subfields from
> > Ultra-High Resolution In Vivo MRI." suggested on Freesurfer's page
> > uses FOV=448. We are unable to set up the matrix to achieve 0.38mm
> > resolution using this FOV. Is there any other suggested article to set
> > up our measurements?
> > 
> > Thanks, 
> > 
> > -- 
> > Gabor Perlaki
> > 
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
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> 
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> 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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[Freesurfer] Hippocampal subfields error

[Greenberg, Jonathan]

Hi all
I ran recon-all on data from about 60 participants pre and post an 
intervention, with the hippocampal subfields flag
(e.g. "recon-all -all -subjid SPS01-1910_pre_lazar -hippocampal-subfields-T1"). 
The recon-all.log file states that the process finished without errors. 
However, the hippocampal-subfieldsT1.log indicated the following:
"Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
 (see below for the full content of hippocampal-subfieldsT1.log).
I tried to run only the hippocampal subfield recon-all again (e.g. "recon-all 
-s recon-all -all -subjid SPS01-1910_pre_lazar hippocampal-subfields-T1") and 
received the same error message. 
I tried to look in the indicated folder 
("/autofs/cluster/freesurfer/centos6_x86_64/dev/bin") and found a file named 
segmentSubjectT1_autoEstimateAlveusML (without the ctf extension). I do not 
know if this is the source of the problem. 

My FREESURFER_HOME directory is 
/autofs/cluster/freesurfer/centos6_x86_64/stable6/. My SUBJECTS_DIR is 
/autofs/cluster/lazar/Projects/jonathan-miracle/unpacking-dicoms/SUBJECTS_DIR/.

Any suggestions? (full hippocampal-subfieldsT1.log below)
Thank you!
Jonathan

hippocampal-subfieldsT1.log content:

#
#@# Hippocampal Subfields processing (T1 only) left Thu Jun 16 09:58:23 EDT 2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
#
#@# Hippocampal Subfields processing (T1 only) right Thu Jun 16 09:58:26 EDT 
2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf


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[Freesurfer] Hippocampal Subfields Segmentation

[Permesh Dhillon]

Hello FreeSurfer Developers,

I’m having issues with the hippocampal subfields segmentation using OS X 
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer  Subject Stamp: 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0   Current Stamp: 
freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.

I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep getting 
an error message : Error:CTF file 
'/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' 
failed to open for 'Read' access. Error message: 'Open a zip file for 
read/modify failed.’

The segmented hippocampal files as described on free surfer wiki cannot be 
found under the subject ‘mri’ folder.
I understand other users have complained of a similar issue within the last 
week.

I’d ve grateful if you could assist me with the issue above.

Many thanks
Permesh




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[Freesurfer] Hippocampal Subfields Segmentation

[Permesh Dhillon]

Hello FreeSurfer Experts,

I’m having issues with the hippocampal subfields segmentation using OS X 
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer  Subject Stamp: 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0   Current Stamp: 
freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.

I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep getting 
an error message : Error:CTF file 
'/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' 
failed to open for 'Read' access. Error message: 'Open a zip file for 
read/modify failed.’

The segmented hippocampal files as described on free surfer wiki cannot be 
found under the subject ‘mri’ folder.
I understand other users have complained of a similar issue within the last 
week.

I’d ve grateful if you could assist me with the issue above.

Many thanks
Permesh




This message and any attachment are intended solely for the addressee
and may contain confidential information. If you have received this
message in error, please send it back to me, and immediately delete it. 

Please do not use, copy or disclose the information contained in this
message or in any attachment.  Any views or opinions expressed by the
author of this email do not necessarily reflect the views of the
University of Nottingham.

This message has been checked for viruses but the contents of an
attachment may still contain software viruses which could damage your
computer system, you are advised to perform your own checks. Email
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[Freesurfer] hippocampal subfields command

[Alexopoulos, Dimitrios]

A quick question re: hippocampal segmentation.

I have processed 1mm isotropic T1 data with 5.3 using the following command:
recon-all  -qcache -all  -hippo-subfields

How is this this different than using the following command I have found here: 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
-hippocampal-subfields-T1


Thanks.
Jim


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Re: [Freesurfer] hippocampal subfields

[Iglesias Gonzalez, Eugenio]

Dear Ferdi,
It is really hard for us to know why you‘re getting such a weird error 
(segfault of kvlAutoCrop) in a submitted job when you don’t get it in an 
interactive session … You will have to look into the peculiarities of the 
submission system to see what is changing from one setting to the other (maybe 
some permissions?).
What version of FreeSurfer are you exactly using?
Kind regards,
/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 Jan 2017, at 07:49, Ferdi van de Kamp 
mailto:ferdivdk...@gmail.com>> wrote:

Hi all,

I'm trying to perform the longitudinal hippocampal subfields processing on a 
cluster.

When I simply access a core on the cluster directly and use it to run the 
hippocampal subfields it will run, but if I try to submit the process to the 
cluster, it will either throw errors as I have pasted below or stop after some 
registration steps.

The recon-all steps have run on the cluster (submitted) without problems.

Some notes:
As I'm testing things, the data is not in the original folder, so the path 
names in recon-all log are not correct, but if that is the problem I'd imagine 
it would be a problem for both submitting and direct processing.

Matlab runtime is installed, though in a separate folder, linking it in the way 
described on the Freesurfer website.

The problem persists no matter how much memory I allocate to the process (20GB 
RAM was the highest I tried).


Kind regards,

Ferdi van de Kamp



#
#@# Longitudinal Hippocampal Subfields processing (T1) left Wed Jan  4 03:06:40 
CET 2017
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/runtime/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/bin/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/os/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/usr/local/OpenGridScheduler/gridengine/lib/linux-x64/:/usr/local/jemalloc/current/lib/:/usr/local/lib/:/usr/local/ScaLAPACK/scalapack-2.0.2/lib/
Warning: Unable to open display 'localhost:10.0'.  You will not be able to 
display graphics on the screen.
Registering imageDump.mgz to hippocampal mask from ASEG of Base Point
/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin//kvlAutoCrop:
 line 3: 65931 Segmentation fault  (core dumped) kvlAutoCrop.bin "$@"
/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin//kvlAutoCrop
 
/exports/fsw/MBos/DevTest/P0392Base/tmp/hippoSF_T1_long.v10_left//hippoAmygBinaryMask.mgz
 6 >/dev/null: Segmentation fault
gzip: 
/exports/fsw/MBos/DevTest/P0392Base/tmp/hippoSF_T1_long.v10_left//hippoAmygBinaryMask_autoCropped.mgz.gz:
 No such file or directory
ERROR: problem reading fname
SWITCH expression must be a scalar or string constant.

Error in myMRIread>load_mgh (line 550)



Error in myMRIread>myMRIread_aux (line 92)



Error in myMRIread (line 63)



Error in SegmentSubfieldsT1Longitudinal (line 228)



MATLAB:badSwitchExpression
@#@FSTIME  2017:01:04:03:06:40 
/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin/segmentSF_T1_long.sh
 N 8 e 12.17 S 0.80 U 3.63 P 36% M 680932 F 530 R 118193 W 0 c 10055 w 5994 I 
439360 O 194448 L 4.58 4.59 4.59
@#@FSLOADPOST 2017:01:04:03:06:52 
/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin/segmentSF_T1_long.sh
 N 8 4.72 4.62 4.60
#
#@# Longitudinal Hippocampal Subfields processing (T1) right Wed Jan  4 
03:06:52 CET 2017
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/runtime/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/bin/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/os/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/

[Freesurfer] -hippocampal-subfields-T1T2

[Daniele Orlandi]

Dear All,
I'm trying to run the flag  -hippocampal-subfields-T1T2 with the new FS
v6.0 but I get the following error:

>Fitting mesh to synthetic image from ASEG took 217.8633 seconds
>Transforming points
>Transforming points
>ltaReadFile(/media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta):
can't open file
>No such file or directory
>ERROR: Reading transform from file
/media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta

Do you have any suggestion?
thank you all for your collaboration
Daniele

___
 Daniele Orlandi, PsyD, Research Assistant
 Laboratory of Epidemiology, Neuroimaging Alzheimer
 IRCCS Centro San Giovanni di Dio, Fatebenefratelli
 Via Pilastroni 4
 25125 Brescia - Italy
 tel:+39 030/3501563
 cell: +39 3495119685
<%2B39%20030%2F3501563>
 email: dorla...@fatebenefratelli.it; daniele.orlandi@gmail.com
 (http://www.centroalzheimer.org/sito/chi_staff_e.php)
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[Freesurfer] -hippocampal-subfields-T1

[Daniele Orlandi]

dear all,
I'm running analysis with the new FS-v6.0 using the flag
-hippocampal-subfields-T1 and  I get the following error:

none
  Matrix:
-3.3 0 0
0 0 -3.3
0 3.3 0
  Offset: [-34.0783, 128.423, -71.9905]
  Center: [0, 0, 0]
  Translation: [-34.0783, 128.423, -71.9905]
  Inverse:
-0.3 0 0
0 0 0.3
0 -0.3 0
  Singular: 0
I am WriteImage and I'm running!
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
Error using zeros
NaN and Inf not allowed.

Error in segmentSubjectT1_autoEstimateAlveusML (line 1396)

MATLAB:nonaninf


How I can solve it?

Best,
Daniele
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Re: [Freesurfer] Hippocampal subfields

[Eugenio Iglesias]

Hi Alan,
If you only want volumes, you can use quantifyHippocampalSubfields.sh. If you 
want to use the segmentations for something else (eg building ROIs for 
functional or diffusion), then you need to look into the mgz segmentation files.
Cheers
Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


- Original Message -
From: Alan Francis 
To: Juan Eugenio Iglesias , Freesurfer 

Sent: Tue, 19 Jan 2016 20:26:13 +0100 (CET)
Subject: Hippocampal subfields

Hi Eugenio:

Hope all is well. I have a question. I have run the HSF algorithm on 32
brains and they ran smoothly without problems. I used only T1 scans. I did
not have T2s. Now to extract the data, do I need to run the following:

*.FSspace.mgz*: the additional scan, rigidly registered to the
T1 data.

*[lr]h.hippoSfLabels--.v10.mgz*: they store the discrete
segmentation volume at 0.333 mm resolution in the physical space of the
FreeSurfer  T1 data
(and therefore of the aligned scan *.FSspace.mgz* as well).

*[lr]h.hippoSfLabels--.v10.1mm.mgz*: they store the
discrete segmentation volume in the 1 mm FreeSurfer
 voxel space.
*[lr]h.hippoSfVolumes--.v10.txt*: these text files store
the estimated volumes of the subfields and of the whole hippocampi.

Or can I go directly to :

quantifyHippocampalSubfields.sh - 



Thanks so much,

best regards,

Alan



-- 
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

*Alan N. Francis PhD*
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu 
afran...@mclean.harvard.edu


|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

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Re: [Freesurfer] Hippocampal subfields

[Alan Francis]

Thanks Eugenio.

On Thu, Jan 21, 2016 at 5:56 AM, Eugenio Iglesias 
wrote:

> Hi Alan,
> If you only want volumes, you can use quantifyHippocampalSubfields.sh. If
> you want to use the segmentations for something else (eg building ROIs for
> functional or diffusion), then you need to look into the mgz segmentation
> files.
> Cheers
> Eugenio
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
>
> - Original Message -
> From: Alan Francis 
> To: Juan Eugenio Iglesias , Freesurfer <
> freesurfer@nmr.mgh.harvard.edu>
> Sent: Tue, 19 Jan 2016 20:26:13 +0100 (CET)
> Subject: Hippocampal subfields
>
> Hi Eugenio:
>
> Hope all is well. I have a question. I have run the HSF algorithm on 32
> brains and they ran smoothly without problems. I used only T1 scans. I did
> not have T2s. Now to extract the data, do I need to run the following:
>
> *.FSspace.mgz*: the additional scan, rigidly registered to the
> T1 data.
>
> *[lr]h.hippoSfLabels--.v10.mgz*: they store the discrete
> segmentation volume at 0.333 mm resolution in the physical space of the
> FreeSurfer  T1 data
> (and therefore of the aligned scan *.FSspace.mgz* as well).
>
> *[lr]h.hippoSfLabels--.v10.1mm.mgz*: they store the
> discrete segmentation volume in the 1 mm FreeSurfer
>  voxel space.
> *[lr]h.hippoSfVolumes--.v10.txt*: these text files store
> the estimated volumes of the subfields and of the whole hippocampi.
>
> Or can I go directly to :
>
> quantifyHippocampalSubfields.sh - 
> 
>
>
> Thanks so much,
>
> best regards,
>
> Alan
>
>
>
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[Freesurfer] Hippocampal subfields, stuck?

[BAUTISTA-PERPINYA Maximilià]

Dear all experts,

I am running FS 6dev version. This is my recon-all comand: "recon-all 
-nuintensitycor-3T -i [directory] -s [subjectname] -all 
-hippocampal-subfields-T1".

Everything goes fine until the ''Hippocampal Subfields processing (T1 only)''. 
At some point it says '"mv: overwrite `imageDump.mgz'?". It doesn't matter 
whether I say y or n; it seems it gets stuck and doesn't progress at all. There 
is no cpu usage. Any recommendations? I have attached the hippocampal subfields 
log.

More info:
-

FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Linux-centos6_x86_64-dev-20160202

RedHat release: CentOS release 6.7 (Final)

Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64

-


--
Maximilià Bautista-Perpinyà, BSc
Master student at Joint Master in Neuroscience (JMN)
Université de Strasbourg (in partnership with Universität Freiburg and 
Universität Basel)
&
Master Intern at Biological and Personality Psychology Laboratory
Department of Psychology, Universität Freiburg

(+49) 015759302368
maximila.bautista-perpi...@etu.unistra.fr
maxbau...@gmail.com
#
#@# Hippocampal Subfields processing (T1 only) left Mon Apr 18 10:49:08 CEST 2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
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
fixedImageFileName: imageDump.mgz
movingImageFileName: /usr/local/freesurfer/subjects/B_HA_30_MRI_E_T0/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask_autoCropped.mgz
degreesOfFreedom: 3
numberOfBins: 20
useDefaultSchedule: 1
initialTranslationMode: 2
extraInputImageFileNames: 
Initializing the parameters as follows: [0, -0, 0, -54.104, -70.9115, -45.3863, 1, 1, 1, 0, 0, 0]
Using fixedShrinkFactors: [4, 4, 4]
Shrinking fixed image: 
  0%
  0.999885%
  1.99977%
  2.99965%
  3.99954%
  4.99942%
  5.99931%
  6.99919%
  7.99908%
  8.99896%
  9.99885%
  10.9987%
  11.9986%
  12.9985%
  13.9984%
  14.9983%
  15.9982%
  16.998%
  17.9979%
  18.9978%
  19.9977%
  20.9976%
  21.9975%
  22.9973%
  23.9972%
  24.9971%
  25.997%
  26.9969%
  27.9968%
  28.9967%
  29.9965%
  30.9964%
  31.9963%
  32.9962%
  33.9961%
  34.996%
  35.9959%
  36.9957%
  37.9956%
  38.9955%
  39.9954%
  40.9953%
  41.9952%
  42.995%
  43.9949%
  44.9948%
  45.9947%
  46.9946%
  47.9945%
  48.9944%
  49.9942%
  50.9941%
  51.994%
  52.9939%
  53.9938%
  54.9937%
  55.9935%
  56.9934%
  57.9933%
  58.9932%
  59.9931%
  60.993%
  61.9929%
  62.9927%
  63.9926%
  64.9925%
  65.9924%
  66.9923%
  67.9922%
  68.9921%
  69.9919%
  70.9918%
  71.9917%
  72.9916%
  73.9915%
  74.9914%
  75.9912%
  76.9911%
  77.991%
  78.9909%
  79.9908%
  80.9907%
  81.9906%
  82.9904%
  83.9903%
  84.9902%
  85.9901%
  86.99%
  87.9899%
  88.9897%
  89.9896%
  90.9895%
  91.9894%
  92.9893%
  93.9892%
  94.9891%
  95.9889%
  96.9888%
  97.9887%
  98.9886%
  99.9885%
  100%
  100%
Using movingShrinkFactors: [1, 1, 1]
Shrinking moving image: 
  0%
  1%
  2%
  3%
  4%
  5%
  6%
  7%
  8%
  9%
  10%
  11%
  12%
  13%
  14%
  15%
  16%
  17%
  18%
  19%
  20%
  21%
  22%
  23%
  24%
  25%
  26%
  27%
  28%
  29%
  30%
  31%
  32%
  33%
  34%
  35%
  36%
  37%
  38%
  39%
  40%
  41%
  42%
  43%
  44%
  45%
  46%
  47%
  48%
  49%
  50%
  51%
  52%
  53%
  54%
  55%
  56%
  57%
  58%
  59%
  60%
  61%
  62%
  63%
  64%
  65%
  66%
  67%
  68%
  69%
  70%
  71%
  72%
  73%
  74%
  75%
  76%
  77%
  78%
  79%
  80%
  81%
  82%
  83%
  84%
  85%
  86%
  87%
  88%
  89%
  90%
  91%
  92%
  93%
  94%
  95%
  96%
  97%
  98%
  99%
  100%
  100%
  100%
Using fixedSchedule: [4, 4, 4]
[1, 1, 1]

Using movingSchedule: [4, 4, 4]
[1, 1, 1]

Using scales: [57.1429, 57.1429, 57.1429, 1, 1, 1, 100, 100, 100, 100, 100, 100]
Using parameterOrder: [0, 0, 0, 1, 2, 3, 0, 0, 0, 0, 0, 0]
Calculating fixed image pyramid: 
  0%
  50%
  100%
Calculating moving image pyramid: 
  0%
  50%
  100%
Doing registration at level 0 of 2
   Iteration 0: value = -0.172259
Current position: 
Rotation: 0  -0  0  
 Translation: -52.4992  -74.7962  -46.0813  
 Scaling: 1  1  1  
 Skewing: 0  0  0  
   Iteration 1

[Freesurfer] hippocampal subfields segmentation

[JOANA BRAGA PEREIRA]

Dear Koen & Freesurfers,

I've been working with the GEMS tool for hippocampal subfields  
segmentation and have a question I would like to ask you all.

I've noticed that the CA1 sector appears to be quite small compared to  
other subfields (CA2-3 seems to be the largest), while previous  
studies suggest that it should be the largest subfield of the  
hippocampus. Why?

On the other hand, I have read the paper by Van Leemput et al. [2009]  
and how the subfields were initially delineated and was wondering what  
atlas was the manual tracing based on?

Many thanks!

joana


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[Freesurfer] hippocampal subfields - T1

[Rizvi, Batool]

Hi,
I was wondering if the hippocampal subfields analysis can still run on a lower 
resolution T1 scan than 1mm? One of our datasets has T1 scans with these 
dimensions: .93 x .93 x 1.3 .

Would it still run on this dataset, if it's not the standard 1mm to begin with?

Thanks!
Batool
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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

[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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Re: [Freesurfer] Hippocampal subfields

[郑凤莲]

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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






 

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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,
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&file=G-b3qYIpqPb3JDXJ0A047b7py5g69iVSmmIFcThcCOcB6oj2z_omEpB8wqbsFq50xOBA6-GnslKTWj_4hb3Fxw&title=Re%3ARe%3A%20%5BFreesurfer%5D%20Hippocampal%20subfields>
hippocampal-subfields-T1.log<http://fs.163.com/fs/display/?p=X-NETEASE-HUGE-ATTACHMENT&file=G-b3qYIpqPb3JDXJ0A047b7py5g69iVSmmIFcThcCOcB6oj2z_omEpB8wqbsFq50xOBA6-GnslKTWj_4hb3Fxw&title=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&file=G-b3qYIpqPb3JDXJ0A047b7py5g69iVSmmIFcThcCOcB6oj2z_omEpB8wqbsFq50xOBA6-GnslKTWj_4hb3Fxw&title=Re%3ARe%3A%20%5BFreesurfer%5D%20Hippocampal%20subfields>
[Image removed by 
sender.]<http://fs.163.com/fs/display/?p=X-NETEASE-HUGE-ATTACHMENT&file=G-b3qYIpqPb3JDXJ0A047b7py5g69iVSmmIFcThcCOecwuYYtWpTYGGNnWS7Zp0VT-kslDawp64gaGy57xjFlw&title=Re%3ARe%3A%20%5BFreesurfer%5D%20Hippocampal%20subfields>
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 (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&file=G-b3qYIpqPb3JDXJ0A047b7py5g69iVSmmIFcThcCOecwuYYtWpTYGGNnWS7Zp0VT-kslDawp64gaGy57xjFlw&title=Re%3ARe%3A%20%5BFreesurfer%5D%20Hippocampal%20subfields>





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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


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[Freesurfer] Hippocampal Subfields Atlas

[ZZY]

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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,
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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,


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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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[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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[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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[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



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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:  on behalf of Arsenije Subotic 

Reply-To: Freesurfer support list 
Date: Thursday, 22 March 2018 at 15:15
To: "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 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

[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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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


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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 *

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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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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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Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
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Re: [Freesurfer] Hippocampal Subfields

[Jindal, Saurabh]

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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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[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

[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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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.]

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:


External Email - Use Caution


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<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:

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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Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] Hippocampal subfields

[Erik O'Hanlon]

External Email - Use Caution

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:


External Email - Use Caution


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<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:

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 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 --> 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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[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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[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

[Thomas Wolbers]

Sorry to repost this question, but it would be great to know if there is 
a chance the automated segmentation of hippocampal subfields might be 
incorporated in Freesurfer any time soon.

Cheers,
Thomas

-- 
-
Dr. rer. nat. Thomas Wolbers
Senior Lecturer
Centre for Cognitive and Neural Systems&
Centre for Cognitive Ageing and Cognitive Epidemiology
The University of Edinburgh
1 George Square
Edinburgh EH8 9JZ
-
email: twolb...@ed.ac.uk
url: www.sal.mvm.ed.ac.uk
--


On 12/03/2011 22:41, Thomas Wolbers wrote:
> Hi there,
>
> I was wondering whether there is any chance the automated segmentation 
> of hippocampal subfields might be incorporated in the next Freesurfer 
> update...
>
> Cheers,
> Thomas Wolbers
>

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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[Freesurfer] Hippocampal subfields segmentation

[yunus soleymani]

External Email - Use Caution

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 intensity

[Juan Eugenio Iglesias]

Hi Marcos,
the right way of doing this is using the soft posteriors to compute the
mean and variance, rather than thresholding at p=0.5. For instance, if
you wanted to compute the mean and variance of the intensitites of the
subiculum, you would do something like this:
mean=sum(Ps.*NU)/sum(Ps);
variance=sum(Ps.*(NU-mean).^2)/sum(Ps);
(where Ps is the posterior of the subiculum)
Cheers,
/Eugenio



On Mon, 2013-06-10 at 15:12 -0300, Marcos Martins da Silva wrote:
> Hi, Freesurfer Experts
> 
> After usual processing with recon-all -all we get the aseg.stats file
> with several data including intensity values like:
> normMean normStdDev
> normMin normMax normRange
> Left-Hippocampus  77.8939 7.574846.
> 105.59.
> 
> How could I get similar results for each hippocampal subfield,
> assuming I also generated all posterior*.mgz files corresponding to
> each subfield?
> I guess I should first binarize each of the subfields file with a
> threshold=127 to map all the pertinent voxels, and then use these
> files as masks over nu.mgz and calculate the intensities values. But I
> do not know the best way to accomplish this after the binarize step.
> 
> Thank you in advance for any help.
> 
> Marcos 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.



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Re: [Freesurfer] Hippocampal subfields intensity

[Juan Eugenio Iglesias]

Hi Marcos,
1. your fix of MRIread.m is great. I forgot of this bug; we should
totally take care of it.
2. a problem is that nu.mgz (or norm.mgz) and the posteriors are in
difference voxel space. So, you need to resample norm.mgz to the space
of the subfields. To do so, you can use mri_convert with the option -rl
("reslice like"):
mri_convert norm.mgz norm_resampled.mgz -rl posterior_subiculum.mgz 
3. Now you can do:
A=MRIread('norm.mgz');
data=A.vol(:);
B=MRIread('posterior_subiculum.mgz');
post=double(B.vol(:));
mean=sum(data.*post)/sum(post);
variance=sum((data-mean).^2.*post)/sum(post);
Cheers,
/Eugenio

On Mon, 2013-06-10 at 17:17 -0300, Marcos Martins da Silva wrote:
> Hi, Eugenio
> TY for your fast help. I understood you were suggesting to compute
> that on MatLab and I tried this:
> 
> NU=MRIread('nu.mgz')### that runs ok
> Ps=MRIread('posterior_left_subiculum.mgz')  ### it fails with the
> following message 
> WARNING: error reading MR params
> Attempted to access mr_parms(1); index out of bounds because
> numel(mr_parms)=0.
> 
> Error in MRIread (line 100)
>   tr = mr_parms(1);
> 
> I solved creating a little customized nMRIread.m with the following
> changes:
> 
> if numel(mr_parms) > 0
> tr = mr_parms(1);
> flip_angle = mr_parms(2);
> te = mr_parms(3);
> ti = mr_parms(4);
>   else
> mr_parms(1) = 0;
> mr_parms(2) = 0;
> mr_parms(3) = 0;
> mr_parms(4) = 0;
> tr = mr_parms(1);
> flip_angle = mr_parms(2);
> te = mr_parms(3);
> ti = mr_parms(4);
>   end
>   
> With those changes I assigned 0 to mr-parms elements so it runs
> without errors
> But whe I tried the following line I copy and pasted from your
> message:
>mean=sum(Ps.*NU)/sum(Ps);  ### I got the following error
> Undefined function 'times' for input arguments of type 'struct'.
> 
> Any help?
> Cheers, Marcos
> 
> PS: I promised I will post the final solution to list. But I guess it
> is more didactic if these little problems are solved before.
> TY, again.
> Em Seg, 2013-06-10 às 14:19 -0400, Juan Eugenio Iglesias escreveu: 
> > Hi Marcos,
> > the right way of doing this is using the soft posteriors to compute the
> > mean and variance, rather than thresholding at p=0.5. For instance, if
> > you wanted to compute the mean and variance of the intensitites of the
> > subiculum, you would do something like this:
> > mean=sum(Ps.*NU)/sum(Ps);
> > variance=sum(Ps.*(NU-mean).^2)/sum(Ps);
> > (where Ps is the posterior of the subiculum)
> > Cheers,
> > /Eugenio
> > 
> > 
> > 
> > On Mon, 2013-06-10 at 15:12 -0300, Marcos Martins da Silva wrote:
> > > Hi, Freesurfer Experts
> > > 
> > > After usual processing with recon-all -all we get the aseg.stats file
> > > with several data including intensity values like:
> > > normMean normStdDev
> > > normMin normMax normRange
> > > Left-Hippocampus  77.8939 7.574846.
> > > 105.59.
> > > 
> > > How could I get similar results for each hippocampal subfield,
> > > assuming I also generated all posterior*.mgz files corresponding to
> > > each subfield?
> > > I guess I should first binarize each of the subfields file with a
> > > threshold=127 to map all the pertinent voxels, and then use these
> > > files as masks over nu.mgz and calculate the intensities values. But I
> > > do not know the best way to accomplish this after the binarize step.
> > > 
> > > Thank you in advance for any help.
> > > 
> > > Marcos 
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> 

-- 
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.



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Re: [Freesurfer] Hippocampal subfields intensity

[Marcos Martins da Silva]

Hi, Eugenio,
TY again for your help. I did the computing without errors after your
suggestions. I also computed the intensities based on nu.mgz, norm.mgz
and T1.mgz. I would like to know the best  measure I should consider,
including because I intend to compare these values with intensity data
from basal ganglia and cortical areas as I can find in aseg.stats. It
follows my results:
norm.mgz based
meannorm= 78.725
variancenorm =  20.258(stdev = 4.50001)

nu.mgz based
meannu =  87.362
variancenu =  26.343  (stdev =5.132543229)

T1.mgz based
meant1 =  84.023
variancet1 =  23.277  (stdev =4.824624338)


It follows the MatLab/Octave code I used
Norm=MRIread('norm_postres.mgz');
datanorm=Norm.vol(:);
Ps=nMRIread('posterior_right_subiculum.mgz');
postsub=double(Ps.vol(:));
meannorm=sum(datanorm.*postsub)/sum(postsub);
variancenorm=sum((datanorm-meannorm).^2.*postsub)/sum(postsub);
Nu=MRIread('nu_postres.mgz');
datanu=Nu.vol(:);
meannu=sum(datanu.*postsub)/sum(postsub);
variancenu=sum((datanu-meannu).^2.*postsub)/sum(postsub);
T1=MRIread('T1_postres.mgz');
datat1=T1.vol(:);
meant1=sum(datat1.*postsub)/sum(postsub);
variancet1=sum((datat1-meant1).^2.*postsub)/sum(postsub);

The *postres.mgz files are nu, norm and T1 resampled as you suggested.
And nMRIread is the workarounded version of MRIread I said in previous
message.
Cheers,
Marcos
Em Seg, 2013-06-10 às 16:58 -0400, Juan Eugenio Iglesias escreveu:

> Hi Marcos,
> 1. your fix of MRIread.m is great. I forgot of this bug; we should
> totally take care of it.
> 2. a problem is that nu.mgz (or norm.mgz) and the posteriors are in
> difference voxel space. So, you need to resample norm.mgz to the space
> of the subfields. To do so, you can use mri_convert with the option -rl
> ("reslice like"):
> mri_convert norm.mgz norm_resampled.mgz -rl posterior_subiculum.mgz 
> 3. Now you can do:
> A=MRIread('norm.mgz');
> data=A.vol(:);
> B=MRIread('posterior_subiculum.mgz');
> post=double(B.vol(:));
> mean=sum(data.*post)/sum(post);
> variance=sum((data-mean).^2.*post)/sum(post);
> Cheers,
> /Eugenio
> 
> On Mon, 2013-06-10 at 17:17 -0300, Marcos Martins da Silva wrote:
> > Hi, Eugenio
> > TY for your fast help. I understood you were suggesting to compute
> > that on MatLab and I tried this:
> > 
> > NU=MRIread('nu.mgz')### that runs ok
> > Ps=MRIread('posterior_left_subiculum.mgz')  ### it fails with the
> > following message 
> > WARNING: error reading MR params
> > Attempted to access mr_parms(1); index out of bounds because
> > numel(mr_parms)=0.
> > 
> > Error in MRIread (line 100)
> >   tr = mr_parms(1);
> > 
> > I solved creating a little customized nMRIread.m with the following
> > changes:
> > 
> > if numel(mr_parms) > 0
> > tr = mr_parms(1);
> > flip_angle = mr_parms(2);
> > te = mr_parms(3);
> > ti = mr_parms(4);
> >   else
> > mr_parms(1) = 0;
> > mr_parms(2) = 0;
> > mr_parms(3) = 0;
> > mr_parms(4) = 0;
> > tr = mr_parms(1);
> > flip_angle = mr_parms(2);
> > te = mr_parms(3);
> > ti = mr_parms(4);
> >   end
> >   
> > With those changes I assigned 0 to mr-parms elements so it runs
> > without errors
> > But whe I tried the following line I copy and pasted from your
> > message:
> >mean=sum(Ps.*NU)/sum(Ps);  ### I got the following error
> > Undefined function 'times' for input arguments of type 'struct'.
> > 
> > Any help?
> > Cheers, Marcos
> > 
> > PS: I promised I will post the final solution to list. But I guess it
> > is more didactic if these little problems are solved before.
> > TY, again.
> > Em Seg, 2013-06-10 às 14:19 -0400, Juan Eugenio Iglesias escreveu: 
> > > Hi Marcos,
> > > the right way of doing this is using the soft posteriors to compute the
> > > mean and variance, rather than thresholding at p=0.5. For instance, if
> > > you wanted to compute the mean and variance of the intensitites of the
> > > subiculum, you would do something like this:
> > > mean=sum(Ps.*NU)/sum(Ps);
> > > variance=sum(Ps.*(NU-mean).^2)/sum(Ps);
> > > (where Ps is the posterior of the subiculum)
> > > Cheers,
> > > /Eugenio
> > > 
> > > 
> > > 
> > > On Mon, 2013-06-10 at 15:12 -0300, Marcos Martins da Silva wrote:
> > > > Hi, Freesurfer Experts
> > > > 
> > > > After usual processing with recon-all -all we get the aseg.stats file
> > > > with several data including intensity values like:
> > > > normMean normStdDev
> > > > normMin normMax normRange
> > > > Left-Hippocampus  77.8939 7.574846.
> > > > 105.59.
> > > > 
> > > > How could I get similar results for each hippocampal subfield,
> > > > assuming I also generated all posterior*.mgz files corresponding to
> > > > each subfield?
> > > > I guess I should first binarize each of the subfields file with a
> > > > threshold=127 to map all the pertinent voxels, and then use these
> > > > files as masks over nu.mgz and calculate the intensities values. But I
> 

Re: [Freesurfer] Hippocampal subfields intensity

[Juan Eugenio Iglesias]

Dear Marcos,
these are just mean and standard deviations of intensities of the images
at different levels of processing. What the best measure is depends on
what you want to do with them.
Cheers,
/Eugenio

On Tue, 2013-06-11 at 11:46 -0300, Marcos Martins da Silva wrote:
> Hi, Eugenio,
> TY again for your help. I did the computing without errors after your
> suggestions. I also computed the intensities based on nu.mgz, norm.mgz
> and T1.mgz. I would like to know the best  measure I should consider,
> including because I intend to compare these values with intensity data
> from basal ganglia and cortical areas as I can find in aseg.stats. It
> follows my results:
> norm.mgz based
> meannorm= 78.725
> variancenorm =  20.258(stdev = 4.50001)
> 
> nu.mgz based
> meannu =  87.362
> variancenu =  26.343  (stdev =5.132543229)
> 
> T1.mgz based
> meant1 =  84.023
> variancet1 =  23.277  (stdev =4.824624338)
> 
> 
> It follows the MatLab/Octave code I used
> Norm=MRIread('norm_postres.mgz');
> datanorm=Norm.vol(:);
> Ps=nMRIread('posterior_right_subiculum.mgz');
> postsub=double(Ps.vol(:));
> meannorm=sum(datanorm.*postsub)/sum(postsub);
> variancenorm=sum((datanorm-meannorm).^2.*postsub)/sum(postsub);
> Nu=MRIread('nu_postres.mgz');
> datanu=Nu.vol(:);
> meannu=sum(datanu.*postsub)/sum(postsub);
> variancenu=sum((datanu-meannu).^2.*postsub)/sum(postsub);
> T1=MRIread('T1_postres.mgz');
> datat1=T1.vol(:);
> meant1=sum(datat1.*postsub)/sum(postsub);
> variancet1=sum((datat1-meant1).^2.*postsub)/sum(postsub);
> 
> The *postres.mgz files are nu, norm and T1 resampled as you suggested.
> And nMRIread is the workarounded version of MRIread I said in previous
> message.
> Cheers,
> Marcos
> Em Seg, 2013-06-10 às 16:58 -0400, Juan Eugenio Iglesias escreveu: 
> > Hi Marcos,
> > 1. your fix of MRIread.m is great. I forgot of this bug; we should
> > totally take care of it.
> > 2. a problem is that nu.mgz (or norm.mgz) and the posteriors are in
> > difference voxel space. So, you need to resample norm.mgz to the space
> > of the subfields. To do so, you can use mri_convert with the option -rl
> > ("reslice like"):
> > mri_convert norm.mgz norm_resampled.mgz -rl posterior_subiculum.mgz 
> > 3. Now you can do:
> > A=MRIread('norm.mgz');
> > data=A.vol(:);
> > B=MRIread('posterior_subiculum.mgz');
> > post=double(B.vol(:));
> > mean=sum(data.*post)/sum(post);
> > variance=sum((data-mean).^2.*post)/sum(post);
> > Cheers,
> > /Eugenio
> > 
> > On Mon, 2013-06-10 at 17:17 -0300, Marcos Martins da Silva wrote:
> > > Hi, Eugenio
> > > TY for your fast help. I understood you were suggesting to compute
> > > that on MatLab and I tried this:
> > > 
> > > NU=MRIread('nu.mgz')### that runs ok
> > > Ps=MRIread('posterior_left_subiculum.mgz')  ### it fails with the
> > > following message 
> > > WARNING: error reading MR params
> > > Attempted to access mr_parms(1); index out of bounds because
> > > numel(mr_parms)=0.
> > > 
> > > Error in MRIread (line 100)
> > >   tr = mr_parms(1);
> > > 
> > > I solved creating a little customized nMRIread.m with the following
> > > changes:
> > > 
> > > if numel(mr_parms) > 0
> > > tr = mr_parms(1);
> > > flip_angle = mr_parms(2);
> > > te = mr_parms(3);
> > > ti = mr_parms(4);
> > >   else
> > > mr_parms(1) = 0;
> > > mr_parms(2) = 0;
> > > mr_parms(3) = 0;
> > > mr_parms(4) = 0;
> > > tr = mr_parms(1);
> > > flip_angle = mr_parms(2);
> > > te = mr_parms(3);
> > > ti = mr_parms(4);
> > >   end
> > >   
> > > With those changes I assigned 0 to mr-parms elements so it runs
> > > without errors
> > > But whe I tried the following line I copy and pasted from your
> > > message:
> > >mean=sum(Ps.*NU)/sum(Ps);  ### I got the following error
> > > Undefined function 'times' for input arguments of type 'struct'.
> > > 
> > > Any help?
> > > Cheers, Marcos
> > > 
> > > PS: I promised I will post the final solution to list. But I guess it
> > > is more didactic if these little problems are solved before.
> > > TY, again.
> > > Em Seg, 2013-06-10 às 14:19 -0400, Juan Eugenio Iglesias escreveu: 
> > > > Hi Marcos,
> > > > the right way of doing this is using the soft posteriors to compute the
> > > > mean and variance, rather than thresholding at p=0.5. For instance, if
> > > > you wanted to compute the mean and variance of the intensitites of the
> > > > subiculum, you would do something like this:
> > > > mean=sum(Ps.*NU)/sum(Ps);
> > > > variance=sum(Ps.*(NU-mean).^2)/sum(Ps);
> > > > (where Ps is the posterior of the subiculum)
> > > > Cheers,
> > > > /Eugenio
> > > > 
> > > > 
> > > > 
> > > > On Mon, 2013-06-10 at 15:12 -0300, Marcos Martins da Silva wrote:
> > > > > Hi, Freesurfer Experts
> > > > > 
> > > > > After usual processing with recon-all -all we get the aseg.stats file
> > > > > with several data including intensity values like:
> > > > > normMean normStdDev
> > > > > normMi

Re: [Freesurfer] Hippocampal subfields intensity

[Marcos Martins da Silva]

Hi, Eugenio
Hmmm, I guessed the values I got were different because they represented
different stages of the processing. And you just confirmed that. Thank
you. I would like to compare these intensities with the intensities  I
can read in aseg.stats.  And I guess the comparison would be more
interesting if I use the same source.
Cheers,
Marcos
Em Ter, 2013-06-11 às 17:13 -0400, Juan Eugenio Iglesias escreveu:

> Dear Marcos,
> these are just mean and standard deviations of intensities of the images
> at different levels of processing. What the best measure is depends on
> what you want to do with them.
> Cheers,
> /Eugenio
> 
> On Tue, 2013-06-11 at 11:46 -0300, Marcos Martins da Silva wrote:
> > Hi, Eugenio,
> > TY again for your help. I did the computing without errors after your
> > suggestions. I also computed the intensities based on nu.mgz, norm.mgz
> > and T1.mgz. I would like to know the best  measure I should consider,
> > including because I intend to compare these values with intensity data
> > from basal ganglia and cortical areas as I can find in aseg.stats. It
> > follows my results:
> > norm.mgz based
> > meannorm= 78.725
> > variancenorm =  20.258(stdev = 4.50001)
> > 
> > nu.mgz based
> > meannu =  87.362
> > variancenu =  26.343  (stdev =5.132543229)
> > 
> > T1.mgz based
> > meant1 =  84.023
> > variancet1 =  23.277  (stdev =4.824624338)
> > 
> > 
> > It follows the MatLab/Octave code I used
> > Norm=MRIread('norm_postres.mgz');
> > datanorm=Norm.vol(:);
> > Ps=nMRIread('posterior_right_subiculum.mgz');
> > postsub=double(Ps.vol(:));
> > meannorm=sum(datanorm.*postsub)/sum(postsub);
> > variancenorm=sum((datanorm-meannorm).^2.*postsub)/sum(postsub);
> > Nu=MRIread('nu_postres.mgz');
> > datanu=Nu.vol(:);
> > meannu=sum(datanu.*postsub)/sum(postsub);
> > variancenu=sum((datanu-meannu).^2.*postsub)/sum(postsub);
> > T1=MRIread('T1_postres.mgz');
> > datat1=T1.vol(:);
> > meant1=sum(datat1.*postsub)/sum(postsub);
> > variancet1=sum((datat1-meant1).^2.*postsub)/sum(postsub);
> > 
> > The *postres.mgz files are nu, norm and T1 resampled as you suggested.
> > And nMRIread is the workarounded version of MRIread I said in previous
> > message.
> > Cheers,
> > Marcos
> > Em Seg, 2013-06-10 às 16:58 -0400, Juan Eugenio Iglesias escreveu: 
> > > Hi Marcos,
> > > 1. your fix of MRIread.m is great. I forgot of this bug; we should
> > > totally take care of it.
> > > 2. a problem is that nu.mgz (or norm.mgz) and the posteriors are in
> > > difference voxel space. So, you need to resample norm.mgz to the space
> > > of the subfields. To do so, you can use mri_convert with the option -rl
> > > ("reslice like"):
> > > mri_convert norm.mgz norm_resampled.mgz -rl posterior_subiculum.mgz 
> > > 3. Now you can do:
> > > A=MRIread('norm.mgz');
> > > data=A.vol(:);
> > > B=MRIread('posterior_subiculum.mgz');
> > > post=double(B.vol(:));
> > > mean=sum(data.*post)/sum(post);
> > > variance=sum((data-mean).^2.*post)/sum(post);
> > > Cheers,
> > > /Eugenio
> > > 
> > > On Mon, 2013-06-10 at 17:17 -0300, Marcos Martins da Silva wrote:
> > > > Hi, Eugenio
> > > > TY for your fast help. I understood you were suggesting to compute
> > > > that on MatLab and I tried this:
> > > > 
> > > > NU=MRIread('nu.mgz')### that runs ok
> > > > Ps=MRIread('posterior_left_subiculum.mgz')  ### it fails with the
> > > > following message 
> > > > WARNING: error reading MR params
> > > > Attempted to access mr_parms(1); index out of bounds because
> > > > numel(mr_parms)=0.
> > > > 
> > > > Error in MRIread (line 100)
> > > >   tr = mr_parms(1);
> > > > 
> > > > I solved creating a little customized nMRIread.m with the following
> > > > changes:
> > > > 
> > > > if numel(mr_parms) > 0
> > > > tr = mr_parms(1);
> > > > flip_angle = mr_parms(2);
> > > > te = mr_parms(3);
> > > > ti = mr_parms(4);
> > > >   else
> > > > mr_parms(1) = 0;
> > > > mr_parms(2) = 0;
> > > > mr_parms(3) = 0;
> > > > mr_parms(4) = 0;
> > > > tr = mr_parms(1);
> > > > flip_angle = mr_parms(2);
> > > > te = mr_parms(3);
> > > > ti = mr_parms(4);
> > > >   end
> > > >   
> > > > With those changes I assigned 0 to mr-parms elements so it runs
> > > > without errors
> > > > But whe I tried the following line I copy and pasted from your
> > > > message:
> > > >mean=sum(Ps.*NU)/sum(Ps);  ### I got the following error
> > > > Undefined function 'times' for input arguments of type 'struct'.
> > > > 
> > > > Any help?
> > > > Cheers, Marcos
> > > > 
> > > > PS: I promised I will post the final solution to list. But I guess it
> > > > is more didactic if these little problems are solved before.
> > > > TY, again.
> > > > Em Seg, 2013-06-10 às 14:19 -0400, Juan Eugenio Iglesias escreveu: 
> > > > > Hi Marcos,
> > > > > the right way of doing this is using the soft posteriors to compute 
> > > > > the
> > > > > mean and variance, rather than thresholding at p=0.5. For instance, if
> > > > > you wan

Re: [Freesurfer] Hippocampal subfields intensity

[Marcos Martins da Silva]

Hi, Eugenio
Just noticed the first lines of aseg.stats. From the command line
recon-all pipeline uses to make the original aseg.stats file it uses
norm.mgz so I think it is the best file to use for intensity comparisons
like I proposed.
Thank you.
Marcos 
Em Qua, 2013-06-12 às 13:33 -0300, Marcos Martins da Silva escreveu:

> Hi, Eugenio
> Hmmm, I guessed the values I got were different because they
> represented different stages of the processing. And you just confirmed
> that. Thank you. I would like to compare these intensities with the
> intensities  I can read in aseg.stats.  And I guess the comparison
> would be more interesting if I use the same source.
> Cheers,
> Marcos
> Em Ter, 2013-06-11 às 17:13 -0400, Juan Eugenio Iglesias escreveu: 
> 
> > Dear Marcos,
> > these are just mean and standard deviations of intensities of the images
> > at different levels of processing. What the best measure is depends on
> > what you want to do with them.
> > Cheers,
> > /Eugenio
> > 
> > On Tue, 2013-06-11 at 11:46 -0300, Marcos Martins da Silva wrote:
> > > Hi, Eugenio,
> > > TY again for your help. I did the computing without errors after your
> > > suggestions. I also computed the intensities based on nu.mgz, norm.mgz
> > > and T1.mgz. I would like to know the best  measure I should consider,
> > > including because I intend to compare these values with intensity data
> > > from basal ganglia and cortical areas as I can find in aseg.stats. It
> > > follows my results:
> > > norm.mgz based
> > > meannorm= 78.725
> > > variancenorm =  20.258(stdev = 4.50001)
> > > 
> > > nu.mgz based
> > > meannu =  87.362
> > > variancenu =  26.343  (stdev =5.132543229)
> > > 
> > > T1.mgz based
> > > meant1 =  84.023
> > > variancet1 =  23.277  (stdev =4.824624338)
> > > 
> > > 
> > > It follows the MatLab/Octave code I used
> > > Norm=MRIread('norm_postres.mgz');
> > > datanorm=Norm.vol(:);
> > > Ps=nMRIread('posterior_right_subiculum.mgz');
> > > postsub=double(Ps.vol(:));
> > > meannorm=sum(datanorm.*postsub)/sum(postsub);
> > > variancenorm=sum((datanorm-meannorm).^2.*postsub)/sum(postsub);
> > > Nu=MRIread('nu_postres.mgz');
> > > datanu=Nu.vol(:);
> > > meannu=sum(datanu.*postsub)/sum(postsub);
> > > variancenu=sum((datanu-meannu).^2.*postsub)/sum(postsub);
> > > T1=MRIread('T1_postres.mgz');
> > > datat1=T1.vol(:);
> > > meant1=sum(datat1.*postsub)/sum(postsub);
> > > variancet1=sum((datat1-meant1).^2.*postsub)/sum(postsub);
> > > 
> > > The *postres.mgz files are nu, norm and T1 resampled as you suggested.
> > > And nMRIread is the workarounded version of MRIread I said in previous
> > > message.
> > > Cheers,
> > > Marcos
> > > Em Seg, 2013-06-10 às 16:58 -0400, Juan Eugenio Iglesias escreveu: 
> > > > Hi Marcos,
> > > > 1. your fix of MRIread.m is great. I forgot of this bug; we should
> > > > totally take care of it.
> > > > 2. a problem is that nu.mgz (or norm.mgz) and the posteriors are in
> > > > difference voxel space. So, you need to resample norm.mgz to the space
> > > > of the subfields. To do so, you can use mri_convert with the option -rl
> > > > ("reslice like"):
> > > > mri_convert norm.mgz norm_resampled.mgz -rl posterior_subiculum.mgz 
> > > > 3. Now you can do:
> > > > A=MRIread('norm.mgz');
> > > > data=A.vol(:);
> > > > B=MRIread('posterior_subiculum.mgz');
> > > > post=double(B.vol(:));
> > > > mean=sum(data.*post)/sum(post);
> > > > variance=sum((data-mean).^2.*post)/sum(post);
> > > > Cheers,
> > > > /Eugenio
> > > > 
> > > > On Mon, 2013-06-10 at 17:17 -0300, Marcos Martins da Silva wrote:
> > > > > Hi, Eugenio
> > > > > TY for your fast help. I understood you were suggesting to compute
> > > > > that on MatLab and I tried this:
> > > > > 
> > > > > NU=MRIread('nu.mgz')### that runs ok
> > > > > Ps=MRIread('posterior_left_subiculum.mgz')  ### it fails with the
> > > > > following message 
> > > > > WARNING: error reading MR params
> > > > > Attempted to access mr_parms(1); index out of bounds because
> > > > > numel(mr_parms)=0.
> > > > > 
> > > > > Error in MRIread (line 100)
> > > > >   tr = mr_parms(1);
> > > > > 
> > > > > I solved creating a little customized nMRIread.m with the following
> > > > > changes:
> > > > > 
> > > > > if numel(mr_parms) > 0
> > > > > tr = mr_parms(1);
> > > > > flip_angle = mr_parms(2);
> > > > > te = mr_parms(3);
> > > > > ti = mr_parms(4);
> > > > >   else
> > > > > mr_parms(1) = 0;
> > > > > mr_parms(2) = 0;
> > > > > mr_parms(3) = 0;
> > > > > mr_parms(4) = 0;
> > > > > tr = mr_parms(1);
> > > > > flip_angle = mr_parms(2);
> > > > > te = mr_parms(3);
> > > > > ti = mr_parms(4);
> > > > >   end
> > > > >   
> > > > > With those changes I assigned 0 to mr-parms elements so it runs
> > > > > without errors
> > > > > But whe I tried the following line I copy and pasted from your
> > > > > message:
> > > > >mean=sum(Ps.*NU)/sum(Ps);  ### I got the following error
> > > > > Undefined function 

Re: [Freesurfer] hippocampal subfields question

[Juan Eugenio Iglesias]

Hi Sal,
yes, the label hippocampus corresponds to the tail.
The units for the segmentation are voxels of the subfield segmentation. 
Since these voxels are cubes with a .5mm side, you need to divide the 
volumes by 8 to convert to cubic mm.

Cheers,
/Eugenio

On 08/12/2013 09:13 PM, Salil Soman wrote:

Hi,

I just wanted to confirm that label "hippocampus" in the hippocampal 
subfields segmentation is simply parts of the hippocampus that do not 
fall into one of the other major categories? Also, where can I find 
the units for the hippocampal subfields? I am seeing some discrepancy 
between the left and right hippocampal volumes generated by freesurfer 
and the summed areas generated by the hippocampal subfield analysis.


Thank you,

-Sal


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--
-
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.

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Re: [Freesurfer] Hippocampal subfields script.

[Alan Francis]

Thanks Eugenio.


On Mon, Feb 3, 2014 at 2:57 PM, Juan Eugenio Iglesias <
igles...@nmr.mgh.harvard.edu> wrote:

> Hi Alan,
> there's indeed such a script:
> kvlQuantifyHippocampalSubfieldSegmentations.sh
> Check out the documentation at:
> http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation
> Cheers,
> /E
>
> On Mon, 2014-02-03 at 14:52 -0500, Alan Francis wrote:
> > Hi Eugenio:
> >
> >
> > I have HSF data on 60 Asperger brains. Is there a script that will
> > allow me to extract the volumes into a single location?
> >
> >
> > thanks so much,
> >
> >
> > Alan Francis
> > Martinos Center
>
>
>
>
> 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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Re: [Freesurfer] -hippocampal-subfields-T1T2

[Kanel, Prabesh]

Hi All,


Was this issue solved?? I am getting the similar error but couldn't find a 
solution on the mailing list.


Fitting mesh to synthetic image from ASEG took 362.0884 seconds
Transforming points
Transforming points
set final LTA type to 1
ltaReadFile(subject/mri/transforms/T1_to_T2.v10.lta): can't open file
No such file or directory
Segmentation fault (core dumped)
freesurfer/bin//mri_concatenate_lta -out_type   1 
subject/mri/transforms/T1_to_T2.v10.lta identity.nofile T1toT2.lta >/dev/null: 
Segmentation fault
Error using fgets
Invalid file identifier.  Use fopen to generate a valid file identifier.



Regards,


Prabesh


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Eugenio Iglesias 

Sent: Monday, October 19, 2015 8:59:59 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] -hippocampal-subfields-T1T2

Hi Daniel,
sorry for the late reply; I was on vacation.
It seems that the T1-T2 registration failed. Can you please send me the .log 
files for the hippocampal subfields? They should be in the following directory:
media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/scripts/
Cheers,
Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


From: "Daniele Orlandi" 
To: "Freesurfer support list" 
Sent: Monday, October 12, 2015 6:58:34 PM
Subject: [Freesurfer] -hippocampal-subfields-T1T2

Dear All,
I'm trying to run the flag  -hippocampal-subfields-T1T2 with the new FS v6.0 
but I get the following error:

>Fitting mesh to synthetic image from ASEG took 217.8633 seconds
>Transforming points
>Transforming points
>ltaReadFile(/media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta):
> can't open file
>No such file or directory
>ERROR: Reading transform from file 
>/media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta

Do you have any suggestion?
thank you all for your collaboration
Daniele

___
 Daniele Orlandi, PsyD, Research Assistant
 Laboratory of Epidemiology, Neuroimaging Alzheimer
 IRCCS Centro San Giovanni di Dio, Fatebenefratelli
 Via Pilastroni 4
 25125 Brescia - Italy
 tel:+39 030/3501563
 cell: +39 3495119685

 email: dorla...@fatebenefratelli.it<mailto:dorla...@fatebenefratelli.it>; 
daniele.orlandi@gmail.com<mailto:daniele.orlandi@gmail.com>
 (http://www.centroalzheimer.org/sito/chi_staff_e.php)



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Re: [Freesurfer] Hippocampal subfields error

[Hibert, Matthew Louis]

I've also gotten this error recently, with T1, T2, and combined T1+T2 
hippocampal segmentations.  It looks like the  files exist at 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
 exist, they just don't have the ".ctf" file extension.

Matt

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greenberg, Jonathan 
[jgreenbe...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 10:29 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Hippocampal subfields error

Hi all
I ran recon-all on data from about 60 participants pre and post an 
intervention, with the hippocampal subfields flag
(e.g. "recon-all -all -subjid SPS01-1910_pre_lazar -hippocampal-subfields-T1"). 
The recon-all.log file states that the process finished without errors. 
However, the hippocampal-subfieldsT1.log indicated the following:
"Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
 (see below for the full content of hippocampal-subfieldsT1.log).
I tried to run only the hippocampal subfield recon-all again (e.g. "recon-all 
-s recon-all -all -subjid SPS01-1910_pre_lazar hippocampal-subfields-T1") and 
received the same error message.
I tried to look in the indicated folder 
("/autofs/cluster/freesurfer/centos6_x86_64/dev/bin") and found a file named 
segmentSubjectT1_autoEstimateAlveusML (without the ctf extension). I do not 
know if this is the source of the problem.

My FREESURFER_HOME directory is 
/autofs/cluster/freesurfer/centos6_x86_64/stable6/. My SUBJECTS_DIR is 
/autofs/cluster/lazar/Projects/jonathan-miracle/unpacking-dicoms/SUBJECTS_DIR/.

Any suggestions? (full hippocampal-subfieldsT1.log below)
Thank you!
Jonathan

hippocampal-subfieldsT1.log content:

#
#@# Hippocampal Subfields processing (T1 only) left Thu Jun 16 09:58:23 EDT 2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
#
#@# Hippocampal Subfields processing (T1 only) right Thu Jun 16 09:58:26 EDT 
2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf


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Re: [Freesurfer] Hippocampal subfields error

[Greenberg, Jonathan]

Thanks Matt. Did you somehow get it to work or recognize the file without the 
ctf extension? 
Thanks
Jonathan

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis 
[mhib...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 11:10 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields error

I've also gotten this error recently, with T1, T2, and combined T1+T2 
hippocampal segmentations.  It looks like the  files exist at 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
 exist, they just don't have the ".ctf" file extension.

Matt

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greenberg, Jonathan 
[jgreenbe...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 10:29 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Hippocampal subfields error

Hi all
I ran recon-all on data from about 60 participants pre and post an 
intervention, with the hippocampal subfields flag
(e.g. "recon-all -all -subjid SPS01-1910_pre_lazar -hippocampal-subfields-T1"). 
The recon-all.log file states that the process finished without errors. 
However, the hippocampal-subfieldsT1.log indicated the following:
"Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
 (see below for the full content of hippocampal-subfieldsT1.log).
I tried to run only the hippocampal subfield recon-all again (e.g. "recon-all 
-s recon-all -all -subjid SPS01-1910_pre_lazar hippocampal-subfields-T1") and 
received the same error message.
I tried to look in the indicated folder 
("/autofs/cluster/freesurfer/centos6_x86_64/dev/bin") and found a file named 
segmentSubjectT1_autoEstimateAlveusML (without the ctf extension). I do not 
know if this is the source of the problem.

My FREESURFER_HOME directory is 
/autofs/cluster/freesurfer/centos6_x86_64/stable6/. My SUBJECTS_DIR is 
/autofs/cluster/lazar/Projects/jonathan-miracle/unpacking-dicoms/SUBJECTS_DIR/.

Any suggestions? (full hippocampal-subfieldsT1.log below)
Thank you!
Jonathan

hippocampal-subfieldsT1.log content:

#
#@# Hippocampal Subfields processing (T1 only) left Thu Jun 16 09:58:23 EDT 2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
#
#@# Hippocampal Subfields processing (T1 only) right Thu Jun 16 09:58:26 EDT 
2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf


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Re: [Freesurfer] Hippocampal subfields error

[Hibert, Matthew Louis]

No, I just wanted to mention that in case it helps with troubleshooting what 
went wrong with the new dev version build.

Matt

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greenberg, Jonathan 
[jgreenbe...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 11:24 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields error

Thanks Matt. Did you somehow get it to work or recognize the file without the 
ctf extension?
Thanks
Jonathan

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis 
[mhib...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 11:10 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields error

I've also gotten this error recently, with T1, T2, and combined T1+T2 
hippocampal segmentations.  It looks like the  files exist at 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
 exist, they just don't have the ".ctf" file extension.

Matt

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greenberg, Jonathan 
[jgreenbe...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 10:29 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Hippocampal subfields error

Hi all
I ran recon-all on data from about 60 participants pre and post an 
intervention, with the hippocampal subfields flag
(e.g. "recon-all -all -subjid SPS01-1910_pre_lazar -hippocampal-subfields-T1"). 
The recon-all.log file states that the process finished without errors. 
However, the hippocampal-subfieldsT1.log indicated the following:
"Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
 (see below for the full content of hippocampal-subfieldsT1.log).
I tried to run only the hippocampal subfield recon-all again (e.g. "recon-all 
-s recon-all -all -subjid SPS01-1910_pre_lazar hippocampal-subfields-T1") and 
received the same error message.
I tried to look in the indicated folder 
("/autofs/cluster/freesurfer/centos6_x86_64/dev/bin") and found a file named 
segmentSubjectT1_autoEstimateAlveusML (without the ctf extension). I do not 
know if this is the source of the problem.

My FREESURFER_HOME directory is 
/autofs/cluster/freesurfer/centos6_x86_64/stable6/. My SUBJECTS_DIR is 
/autofs/cluster/lazar/Projects/jonathan-miracle/unpacking-dicoms/SUBJECTS_DIR/.

Any suggestions? (full hippocampal-subfieldsT1.log below)
Thank you!
Jonathan

hippocampal-subfieldsT1.log content:

#
#@# Hippocampal Subfields processing (T1 only) left Thu Jun 16 09:58:23 EDT 2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
#
#@# Hippocampal Subfields processing (T1 only) right Thu Jun 16 09:58:26 EDT 
2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf


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Re: [Freesurfer] Hippocampal subfields error

[Greenberg, Jonathan]

Thanks.
Has anyone else encountered this error message or knows how it can be solved?
Thank you
Jonathan

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis 
[mhib...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 12:44 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields error

No, I just wanted to mention that in case it helps with troubleshooting what 
went wrong with the new dev version build.

Matt

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greenberg, Jonathan 
[jgreenbe...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 11:24 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields error

Thanks Matt. Did you somehow get it to work or recognize the file without the 
ctf extension?
Thanks
Jonathan

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis 
[mhib...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 11:10 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields error

I've also gotten this error recently, with T1, T2, and combined T1+T2 
hippocampal segmentations.  It looks like the  files exist at 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
 exist, they just don't have the ".ctf" file extension.

Matt

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greenberg, Jonathan 
[jgreenbe...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 10:29 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Hippocampal subfields error

Hi all
I ran recon-all on data from about 60 participants pre and post an 
intervention, with the hippocampal subfields flag
(e.g. "recon-all -all -subjid SPS01-1910_pre_lazar -hippocampal-subfields-T1"). 
The recon-all.log file states that the process finished without errors. 
However, the hippocampal-subfieldsT1.log indicated the following:
"Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
 (see below for the full content of hippocampal-subfieldsT1.log).
I tried to run only the hippocampal subfield recon-all again (e.g. "recon-all 
-s recon-all -all -subjid SPS01-1910_pre_lazar hippocampal-subfields-T1") and 
received the same error message.
I tried to look in the indicated folder 
("/autofs/cluster/freesurfer/centos6_x86_64/dev/bin") and found a file named 
segmentSubjectT1_autoEstimateAlveusML (without the ctf extension). I do not 
know if this is the source of the problem.

My FREESURFER_HOME directory is 
/autofs/cluster/freesurfer/centos6_x86_64/stable6/. My SUBJECTS_DIR is 
/autofs/cluster/lazar/Projects/jonathan-miracle/unpacking-dicoms/SUBJECTS_DIR/.

Any suggestions? (full hippocampal-subfieldsT1.log below)
Thank you!
Jonathan

hippocampal-subfieldsT1.log content:

#
#@# Hippocampal Subfields processing (T1 only) left Thu Jun 16 09:58:23 EDT 2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
#
#@# Hippocampal Subfields processing (T1 only) right Thu Jun 16 09:58:26 EDT 
2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf


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Re: [Freesurfer] Hippocampal subfields error

[June Kang]

I am also experiencing same problem.

I tried to change ct., but when I change the extension to ctf,It also give 
errors as below.
Error:CTF file 
'/usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' failed to 
open for 'Read' access. Error message: 'Open a zip file for read/modify failed.'
Ubuntu 14.04, nightly dev. version of freesurfer.I also use several mac on 
10.9~10.10.5, but they all works well with new hippocampal subfields 
segmentation function in latest dev. version.
June.


On Jun 17, 2016, at 2:01 AM, Greenberg, Jonathan  
wrote:Thanks.
Has anyone else encountered this error message or knows how it can be solved?
Thank you
Jonathan

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis 
[mhib...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 12:44 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields error

No, I just wanted to mention that in case it helps with troubleshooting what 
went wrong with the new dev version build.

Matt

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greenberg, Jonathan 
[jgreenbe...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 11:24 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields error

Thanks Matt. Did you somehow get it to work or recognize the file without the 
ctf extension?
Thanks
Jonathan

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis 
[mhib...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 11:10 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields error

I've also gotten this error recently, with T1, T2, and combined T1+T2 
hippocampal segmentations.  It looks like the  files exist at 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
 exist, they just don't have the ".ctf" file extension.

Matt

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greenberg, Jonathan 
[jgreenbe...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 10:29 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Hippocampal subfields error

Hi all
I ran recon-all on data from about 60 participants pre and post an 
intervention, with the hippocampal subfields flag
(e.g. "recon-all -all -subjid SPS01-1910_pre_lazar -hippocampal-subfields-T1"). 
The recon-all.log file states that the process finished without errors. 
However, the hippocampal-subfieldsT1.log indicated the following:
"Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
 (see below for the full content of hippocampal-subfieldsT1.log).
I tried to run only the hippocampal subfield recon-all again (e.g. "recon-all 
-s recon-all -all -subjid SPS01-1910_pre_lazar hippocampal-subfields-T1") and 
received the same error message.
I tried to look in the indicated folder 
("/autofs/cluster/freesurfer/centos6_x86_64/dev/bin") and found a file named 
segmentSubjectT1_autoEstimateAlveusML (without the ctf extension). I do not 
know if this is the source of the problem.

My FREESURFER_HOME directory is 
/autofs/cluster/freesurfer/centos6_x86_64/stable6/. My SUBJECTS_DIR is 
/autofs/cluster/lazar/Projects/jonathan-miracle/unpacking-dicoms/SUBJECTS_DIR/.

Any suggestions? (full hippocampal-subfieldsT1.log below)
Thank you!
Jonathan

hippocampal-subfieldsT1.log content:

#
#@# Hippocampal Subfields processing (T1 only) left Thu Jun 16 09:58:23 EDT 2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
#
#@# Hippocampal Subfields processing (T1 only) right Thu Jun 16 09:58:26 EDT 
2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stabl

Re: [Freesurfer] Hippocampal Subfields Segmentation

[pierre deman]

Hello,

I have similar problem. "
"Error:Cannot find CTF archive
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
the file is here but when I try to execute it, it's always missing some
library (libmwi18n.so for example, it was missing others before that I
added on my computer, but it never ends)
I am on ubuntu 14.04.
I thought that the problem is linked to the matlab runtime. I installed the
2012b. I tried newer version. installed again the 2012b.

Regards,
Pierre


On Mon, Jun 27, 2016 at 4:05 PM, Permesh Dhillon <
permesh.dhil...@nottingham.ac.uk> wrote:

> Hello FreeSurfer Developers,
>
> I’m having issues with the hippocampal subfields segmentation using OS X
> Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer  Subject Stamp:
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0   Current Stamp:
> freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.
>
> I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep
> getting an error message : Error:CTF file
> '/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf'
> failed to open for 'Read' access. Error message: 'Open a zip file for
> read/modify failed.’
>
> The segmented hippocampal files as described on free surfer wiki cannot
> be found under the subject ‘mri’ folder.
> I understand other users have complained of a similar issue within the
> last week.
>
> I’d ve grateful if you could assist me with the issue above.
>
> Many thanks
> Permesh
>
>
>
> This message and any attachment are intended solely for the addressee
> and may contain confidential information. If you have received this
> message in error, please send it back to me, and immediately delete it.
>
> Please do not use, copy or disclose the information contained in this
> message or in any attachment.  Any views or opinions expressed by the
> author of this email do not necessarily reflect the views of the
> University of Nottingham.
>
> This message has been checked for viruses but the contents of an
> attachment may still contain software viruses which could damage your
> computer system, you are advised to perform your own checks. Email
> communications with the University of Nottingham may be monitored as
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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
> 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.
>
>


-- 
DEMAN Pierre
Mobile : +33 7 82 57 80 94
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The information in this e-mail is intended only for the person to whom it is
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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.

Re: [Freesurfer] Hippocampal Subfields Segmentation

[Iglesias, Eugenio]

Hi everyone,
you need to install the Matlab 2012b runtime as explained in the wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
Cheers,
Eugenio



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


On 27 Jun 2016, at 15:16, pierre deman 
mailto:deman.pie...@gmail.com>> wrote:

Hello,

I have similar problem. "
"Error:Cannot find CTF archive
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
the file is here but when I try to execute it, it's always missing some library 
(libmwi18n.so for example, it was missing others before that I added on my 
computer, but it never ends)
I am on ubuntu 14.04.
I thought that the problem is linked to the matlab runtime. I installed the 
2012b. I tried newer version. installed again the 2012b.

Regards,
Pierre


On Mon, Jun 27, 2016 at 4:05 PM, Permesh Dhillon 
mailto:permesh.dhil...@nottingham.ac.uk>> 
wrote:
Hello FreeSurfer Developers,

I’m having issues with the hippocampal subfields segmentation using OS X 
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer  Subject Stamp: 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0   Current Stamp: 
freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.

I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep getting 
an error message : Error:CTF file 
'/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' 
failed to open for 'Read' access. Error message: 'Open a zip file for 
read/modify failed.’

The segmented hippocampal files as described on free surfer wiki cannot be 
found under the subject ‘mri’ folder.
I understand other users have complained of a similar issue within the last 
week.

I’d ve grateful if you could assist me with the issue above.

Many thanks
Permesh


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Re: [Freesurfer] Hippocampal Subfields Segmentation

[pierre deman]

I tried that. but didn't work.

Cheers,
Pierre

On Mon, Jun 27, 2016 at 4:32 PM, Iglesias, Eugenio 
wrote:

> Hi everyone,
> you need to install the Matlab 2012b runtime as explained in the wiki:
> https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
> Cheers,
> Eugenio
>
>
>
> Juan Eugenio Iglesias
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 27 Jun 2016, at 15:16, pierre deman  wrote:
>
> Hello,
>
> I have similar problem. "
> "Error:Cannot find CTF archive
>
> /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
> the file is here but when I try to execute it, it's always missing some
> library (libmwi18n.so for example, it was missing others before that I
> added on my computer, but it never ends)
> I am on ubuntu 14.04.
> I thought that the problem is linked to the matlab runtime. I installed
> the 2012b. I tried newer version. installed again the 2012b.
>
> Regards,
> Pierre
>
>
> On Mon, Jun 27, 2016 at 4:05 PM, Permesh Dhillon <
> permesh.dhil...@nottingham.ac.uk> wrote:
>
>> Hello FreeSurfer Developers,
>>
>> I’m having issues with the hippocampal subfields segmentation using OS X
>> Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer  Subject
>> Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0   Current
>> Stamp: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.
>>
>> I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep
>> getting an error message : Error:CTF file
>> '/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf'
>> failed to open for 'Read' access. Error message: 'Open a zip file for
>> read/modify failed.’
>>
>> The segmented hippocampal files as described on free surfer wiki cannot
>> be found under the subject ‘mri’ folder.
>> I understand other users have complained of a similar issue within the
>> last week.
>>
>> I’d ve grateful if you could assist me with the issue above.
>>
>> Many thanks
>> Permesh
>>
>> This message and any attachment are intended solely for the addressee
>> and may contain confidential information. If you have received this
>> message in error, please send it back to me, and immediately delete it.
>>
>> Please do not use, copy or disclose the information contained in this
>> message or in any attachment.  Any views or opinions expressed by the
>> author of this email do not necessarily reflect the views of the
>> University of Nottingham.
>>
>> This message has been checked for viruses but the contents of an
>> attachment may still contain software viruses which could damage your
>> computer system, you are advised to perform your own checks. Email
>> communications with the University of Nottingham may be monitored as
>> permitted by UK legislation.
>>
>>
>> ___
>> Freesurfer mailing list
>> 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 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.
>>
>>
>
>
> --
> DEMAN Pierre
> Mobile : +33 7 82 57 80 94
> ___
> Freesurfer mailing list
> 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 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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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
>


-- 
DEMAN Pierre
Mobile : +33 7 82 57 80 94
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The informati

Re: [Freesurfer] Hippocampal Subfields Segmentation

[Iglesias, Eugenio]

Hi Pierre,
Due to some technical problems, it might take me a couple of days to figure out 
what’s going on.  But it definitely sounds funny that it is asking for the CTF, 
since this is supposed to be embedded in the executable… I’ll get back to you 
as soon as possible.
Cheers,
Eugenio

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


On 27 Jun 2016, at 15:32, pierre deman 
mailto:deman.pie...@gmail.com>> wrote:

I tried that. but didn't work.

Cheers,
Pierre

On Mon, Jun 27, 2016 at 4:32 PM, Iglesias, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:
Hi everyone,
you need to install the Matlab 2012b runtime as explained in the wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
Cheers,
Eugenio



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


On 27 Jun 2016, at 15:16, pierre deman 
mailto:deman.pie...@gmail.com>> wrote:

Hello,

I have similar problem. "
"Error:Cannot find CTF archive
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
the file is here but when I try to execute it, it's always missing some library 
(libmwi18n.so for example, it was missing others before that I added on my 
computer, but it never ends)
I am on ubuntu 14.04.
I thought that the problem is linked to the matlab runtime. I installed the 
2012b. I tried newer version. installed again the 2012b.

Regards,
Pierre


On Mon, Jun 27, 2016 at 4:05 PM, Permesh Dhillon 
mailto:permesh.dhil...@nottingham.ac.uk>> 
wrote:
Hello FreeSurfer Developers,

I’m having issues with the hippocampal subfields segmentation using OS X 
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer  Subject Stamp: 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0   Current Stamp: 
freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.

I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep getting 
an error message : Error:CTF file 
'/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' 
failed to open for 'Read' access. Error message: 'Open a zip file for 
read/modify failed.’

The segmented hippocampal files as described on free surfer wiki cannot be 
found under the subject ‘mri’ folder.
I understand other users have complained of a similar issue within the last 
week.

I’d ve grateful if you could assist me with the issue above.

Many thanks
Permesh

This message and any attachment are intended solely for the addressee
and may contain confidential information. If you have received this
message in error, please send it back to me, and immediately delete it.

Please do not use, copy or disclose the information contained in this
message or in any attachment.  Any views or opinions expressed by the
author of this email do not necessarily reflect the views of the
University of Nottingham.

This message has been checked for viruses but the contents of an
attachment may still contain software viruses which could damage your
computer system, you are advised to perform your own checks. Email
communications with the University of Nottingham may be monitored as
permitted by UK legislation.


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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.




--
DEMAN Pierre
Mobile : +33 7 82 57 80 94
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Re: [Freesurfer] Hippocampal Subfields Segmentation

[Iglesias, Eugenio]

I could finally look into this. It is indeed weird. The CTF is indeed embedded 
in the executable…
Zeke/Nick, can you shed some light on this?
Cheers,
Eugenio

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


On 27 Jun 2016, at 15:43, Iglesias, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

Hi Pierre,
Due to some technical problems, it might take me a couple of days to figure out 
what’s going on.  But it definitely sounds funny that it is asking for the CTF, 
since this is supposed to be embedded in the executable… I’ll get back to you 
as soon as possible.
Cheers,
Eugenio

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


On 27 Jun 2016, at 15:32, pierre deman 
mailto:deman.pie...@gmail.com>> wrote:

I tried that. but didn't work.

Cheers,
Pierre

On Mon, Jun 27, 2016 at 4:32 PM, Iglesias, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:
Hi everyone,
you need to install the Matlab 2012b runtime as explained in the wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
Cheers,
Eugenio



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


On 27 Jun 2016, at 15:16, pierre deman 
mailto:deman.pie...@gmail.com>> wrote:

Hello,

I have similar problem. "
"Error:Cannot find CTF archive
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
the file is here but when I try to execute it, it's always missing some library 
(libmwi18n.so for example, it was missing others before that I added on my 
computer, but it never ends)
I am on ubuntu 14.04.
I thought that the problem is linked to the matlab runtime. I installed the 
2012b. I tried newer version. installed again the 2012b.

Regards,
Pierre


On Mon, Jun 27, 2016 at 4:05 PM, Permesh Dhillon 
mailto:permesh.dhil...@nottingham.ac.uk>> 
wrote:
Hello FreeSurfer Developers,

I’m having issues with the hippocampal subfields segmentation using OS X 
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer  Subject Stamp: 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0   Current Stamp: 
freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.

I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep getting 
an error message : Error:CTF file 
'/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' 
failed to open for 'Read' access. Error message: 'Open a zip file for 
read/modify failed.’

The segmented hippocampal files as described on free surfer wiki cannot be 
found under the subject ‘mri’ folder.
I understand other users have complained of a similar issue within the last 
week.

I’d ve grateful if you could assist me with the issue above.

Many thanks
Permesh

This message and any attachment are intended solely for the addressee
and may contain confidential information. If you have received this
message in error, please send it back to me, and immediately delete it.

Please do not use, copy or disclose the information contained in this
message or in any attachment.  Any views or opinions expressed by the
author of this email do not necessarily reflect the views of the
University of Nottingham.

This message has been checked for viruses but the contents of an
attachment may still contain software viruses which could damage your
computer system, you are advised to perform your own checks. Email
communications with the University of Nottingham may be monitored as
permitted by UK legislation.


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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.




--
DEMAN Pierre
Mobile : +33 7 82 57 80 94
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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.


_