Re: [Freesurfer] Longitudinal hippocampal subfields analysis problem

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

It depends heavily on the number of time points… I’d say ~20 mins per time 
point and side.

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


From: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu>
Date: Tuesday, 8 May 2018 at 16:27
To: "Iglesias Gonzalez, Eugenio" <e.igles...@ucl.ac.uk>, Freesurfer support 
list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Longitudinal hippocampal subfields analysis problem

I’m not sure. How long do these runs usually take Eugenio? I’m noticing that 
the process only used 9% of the cpu, which is odd since it ran for 10+ hours
Andrew


From: "Iglesias Gonzalez, Eugenio" <e.igles...@ucl.ac.uk>
Date: Tuesday, May 8, 2018 at 4:18 AM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Cc: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Longitudinal hippocampal subfields analysis problem


External Email - Use Caution
Is it possible that it ran out of memory? Andrew, what do you think?

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


From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Tamir Eisenstein 
<tami...@mail.tau.ac.il>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Sunday, 6 May 2018 at 08:22
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Longitudinal hippocampal subfields analysis problem


External Email - Use Caution
Hi FreeSurfer experts,

I've tried running the longHippoSubfieldsT1.sh command on a subject with 2 time 
points on FS 6.0, and it seemed working well while running.
However, after about 10 hours of processing it "ended" with the following 
message, and no files have been created in any of the subject's /mri folders:




Applying LTAtransformInterp (resample_type 0)
writing to discreteLabelsResampledT1_tp_1.mgz...
numberOfLabels: 25
Rasterizing mesh...here: 25
/usr/local/freesurfer/bin/run_SegmentSubfieldsT1Longitudinal.sh: line 45: 
103248 Killed  "${exe_dir}"/SegmentSubfieldsT1Longitudinal $args
@#@FSTIME  2018:05:05:21:24:27 /usr/local/freesurfer/bin/segmentSF_T1_long.sh N 
7 e 36809.26 S 113.13 U 3327.28 P 9% M 1402760 F 150217 R 19897260 W 0 c 213280 
w 30 I 48432510 O 1579840 L 5.28 3.10 2.20
@#@FSLOADPOST 2018:05:06:07:37:57 
/usr/local/freesurfer/bin/segmentSF_T1_long.sh N 7 6.10 6.21 4.49


With appreciation for your help,
Best,
Tamir

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Re: [Freesurfer] Longitudinal hippocampal subfields analysis problem

[Hoopes, Andrew]

I’m not sure. How long do these runs usually take Eugenio? I’m noticing that 
the process only used 9% of the cpu, which is odd since it ran for 10+ hours
Andrew


From: "Iglesias Gonzalez, Eugenio" <e.igles...@ucl.ac.uk>
Date: Tuesday, May 8, 2018 at 4:18 AM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Cc: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Longitudinal hippocampal subfields analysis problem


External Email - Use Caution
Is it possible that it ran out of memory? Andrew, what do you think?

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


From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Tamir Eisenstein 
<tami...@mail.tau.ac.il>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Sunday, 6 May 2018 at 08:22
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Longitudinal hippocampal subfields analysis problem


External Email - Use Caution
Hi FreeSurfer experts,

I've tried running the longHippoSubfieldsT1.sh command on a subject with 2 time 
points on FS 6.0, and it seemed working well while running.
However, after about 10 hours of processing it "ended" with the following 
message, and no files have been created in any of the subject's /mri folders:



Applying LTAtransformInterp (resample_type 0)
writing to discreteLabelsResampledT1_tp_1.mgz...
numberOfLabels: 25
Rasterizing mesh...here: 25
/usr/local/freesurfer/bin/run_SegmentSubfieldsT1Longitudinal.sh: line 45: 
103248 Killed  "${exe_dir}"/SegmentSubfieldsT1Longitudinal $args
@#@FSTIME  2018:05:05:21:24:27 /usr/local/freesurfer/bin/segmentSF_T1_long.sh N 
7 e 36809.26 S 113.13 U 3327.28 P 9% M 1402760 F 150217 R 19897260 W 0 c 213280 
w 30 I 48432510 O 1579840 L 5.28 3.10 2.20
@#@FSLOADPOST 2018:05:06:07:37:57 
/usr/local/freesurfer/bin/segmentSF_T1_long.sh N 7 6.10 6.21 4.49


With appreciation for your help,
Best,
Tamir
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Re: [Freesurfer] Longitudinal hippocampal subfields analysis problem

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Is it possible that it ran out of memory? Andrew, what do you think?

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


From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Tamir Eisenstein 
<tami...@mail.tau.ac.il>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Sunday, 6 May 2018 at 08:22
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Longitudinal hippocampal subfields analysis problem


External Email - Use Caution
Hi FreeSurfer experts,

I've tried running the longHippoSubfieldsT1.sh command on a subject with 2 time 
points on FS 6.0, and it seemed working well while running.
However, after about 10 hours of processing it "ended" with the following 
message, and no files have been created in any of the subject's /mri folders:


Applying LTAtransformInterp (resample_type 0)
writing to discreteLabelsResampledT1_tp_1.mgz...
numberOfLabels: 25
Rasterizing mesh...here: 25
/usr/local/freesurfer/bin/run_SegmentSubfieldsT1Longitudinal.sh: line 45: 
103248 Killed  "${exe_dir}"/SegmentSubfieldsT1Longitudinal $args
@#@FSTIME  2018:05:05:21:24:27 /usr/local/freesurfer/bin/segmentSF_T1_long.sh N 
7 e 36809.26 S 113.13 U 3327.28 P 9% M 1402760 F 150217 R 19897260 W 0 c 213280 
w 30 I 48432510 O 1579840 L 5.28 3.10 2.20
@#@FSLOADPOST 2018:05:06:07:37:57 
/usr/local/freesurfer/bin/segmentSF_T1_long.sh N 7 6.10 6.21 4.49


With appreciation for your help,
Best,
Tamir
___
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Longitudinal hippocampal subfields analysis problem

[Tamir Eisenstein]

External Email - Use Caution

Hi FreeSurfer experts,

I've tried running the longHippoSubfieldsT1.sh command on a subject with 2
time points on FS 6.0, and it seemed working well while running.
However, after about 10 hours of processing it "ended" with the following
message, and no files have been created in any of the subject's /mri
folders:

Applying LTAtransformInterp (resample_type 0)
writing to discreteLabelsResampledT1_tp_1.mgz...
numberOfLabels: 25
Rasterizing mesh...here: 25
/usr/local/freesurfer/bin/run_SegmentSubfieldsT1Longitudinal.sh: line 45:
103248 Killed  "${exe_dir}"/SegmentSubfieldsT1Longitudinal
$args
@#@FSTIME  2018:05:05:21:24:27
/usr/local/freesurfer/bin/segmentSF_T1_long.sh N 7 e 36809.26 S 113.13 U
3327.28 P 9% M 1402760 F 150217 R 19897260 W 0 c 213280 w 30 I 48432510
O 1579840 L 5.28 3.10 2.20
@#@FSLOADPOST 2018:05:06:07:37:57
/usr/local/freesurfer/bin/segmentSF_T1_long.sh N 7 6.10 6.21 4.49


With appreciation for your help,
Best,
Tamir
___
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addressed. If you believe this e-mail was sent to you in error and the e-mail
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Longitudinal hippocampal subfields analysis

[Martin Reuter]

Hi Manuel, 

smoothing is usually only necessary for surface data. 

You should have crated the subfields on top of the longitudinal directories, so:
> recon-all -long   -hippocampal-subfields-T1
> 

Else they will only be available in the cross dirs. The longs will have better 
reliability. 

Best, Martin


> On 12 May 2017, at 10:30, Manuel Delgado  wrote:
> 
> Dear all,
> 
> I set out to perform a longitudinal analysis of hippocampal subfields. I have 
> already edited the cross and/or the bases when necessary and obtained the 
> longs.
> 
> Then I have obtained the hippocampal subfields by the automated pipeline: 
> recon-all -s  -hippocampal-subfields-T1.
> 
> Now I am going to create the qdec table to proceed with the analysis, but I 
> don't know whether I have to smooth the data by recon-all -long  
>  -qcahe before the analysis, or given that hippocampal subregions 
> have been extracted by using its own pipeline it is not necessary to do any 
> smoothing.
> 
> Thanks
> 
> -- 
> Manuel Delgado Alvarado, MD
> Neurology Department
> Neuroimaging Unit
> Valdecilla Biomedical Research Institute, IDIVAL
> Santander, SPAIN
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] Longitudinal hippocampal subfields analysis

[Manuel Delgado]

Dear all,

I set out to perform a longitudinal analysis of hippocampal subfields. I
have already edited the cross and/or the bases when necessary and obtained
the longs.

Then I have obtained the hippocampal subfields by the automated pipeline:
recon-all -s  -hippocampal-subfields-T1.

Now I am going to create the qdec table to proceed with the analysis, but I
don't know whether I have to smooth the data by recon-all -long 
 -qcahe before the analysis, or given that hippocampal subregions
have been extracted by using its own pipeline it is not necessary to do any
smoothing.

Thanks
-- 
*Manuel Delgado Alvarado, MD*
Neurology Department
Neuroimaging Unit
Valdecilla Biomedical Research Institute, IDIVAL
Santander, SPAIN
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Re: [Freesurfer] longitudinal hippocampal subfields analysis

[Salil Soman]

Thank you Martin.

I will try this approach.  I was able to temporarily move the longitudinal
subject data to its own folder to run aparc2table and aseg2table. Hopefully
this will also work for the hippocampal subfield script.

Best wishes,

Sal

Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
On Jan 7, 2014 8:07 AM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote:

  Hi Salil,

 just run the hippo-subfields on the longitudinal results like this:

 recon-all -long tpNi templateid -hippo-subfields

 to generate the subfield data. I am not familiar with the kvlQuantify...
 script and think it works on all subjects in the Subjects dir. Not sure
 what the best way is to solve this as your subject dir contains also the
 cross and base results. Probably you can run the script and it will simply
 skip the cross and base directories (as no -hippo-subfields was run on
 them).


 Best, Martin


 On 01/05/2014 01:40 AM, Salil Soman wrote:

 Hi,

  I have been able to do the longitudinal processing steps for a number of
 subjects with 3 time points each, and then extract the generated statistics
 using aparcstats2table and asegstats2table. Is it possible to perform
 longitudinal analysis of the hippocampal subfields? If so, could someone
 point me to how to perform this analysis,
 as kvlQuantifyHippocampalSubfieldSegmentations.sh does not work on the
 output files I've generated.

  Thank you.

  Salil Soman, MD, MS


 ___
 Freesurfer mailing 
 listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 --
 Martin Reuter, Ph.D.
 Assistant in Neuroscience - Massachusetts General Hospital
 Instructor in Neurology   - Harvard Medical School
 MGH / HMS / MIT

 A.A.Martinos Center for Biomedical Imaging
 149 Thirteenth Street, Suite 2301
 Charlestown, MA 02129

 Phone: +1-617-724-5652
 Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
 Web  : http://reuter.mit.edu

  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] longitudinal hippocampal subfields analysis

[Martin Reuter]

Hi Sal,

asegstats2table (and aparc..) will take the longitudinal qdec file and 
then automatically select the *.long.* directories to create the table. 
So there is no need to move them to a separate folder.


The longitudinal qdec file is simply a table with at least 2 columns 
(for stacking results, 2 is enough):

fsid fsid-base

where fsid is the id of the time point and fsid-base is the name of the 
base :


fsid fsid-base
me1 me
me2 me
you1 you
you2 you
you3 you

etc.. It will then take the data from me1.long.me ...
You can have other columns, e.g. time_from_baseline, age, gender, 
disease_group, drug_status, ...


Best, Martin

On 01/08/2014 01:27 PM, Salil Soman wrote:


Thank you Martin.

I will try this approach.  I was able to temporarily move the 
longitudinal subject data to its own folder to run aparc2table and 
aseg2table. Hopefully this will also work for the hippocampal subfield 
script.


Best wishes,

Sal

Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care 
System


On Jan 7, 2014 8:07 AM, Martin Reuter mreu...@nmr.mgh.harvard.edu 
mailto:mreu...@nmr.mgh.harvard.edu wrote:


Hi Salil,

just run the hippo-subfields on the longitudinal results like this:

recon-all -long tpNi templateid -hippo-subfields

to generate the subfield data. I am not familiar with the
kvlQuantify... script and think it works on all subjects in the
Subjects dir. Not sure what the best way is to solve this as your
subject dir contains also the cross and base results. Probably you
can run the script and it will simply skip the cross and base
directories (as no -hippo-subfields was run on them).


Best, Martin


On 01/05/2014 01:40 AM, Salil Soman wrote:

Hi,

I have been able to do the longitudinal processing steps for a
number of subjects with 3 time points each, and then extract the
generated statistics using aparcstats2table and asegstats2table.
Is it possible to perform longitudinal analysis of the
hippocampal subfields? If so, could someone point me to how to
perform this analysis,
as kvlQuantifyHippocampalSubfieldSegmentations.sh does not work
on the output files I've generated.

Thank you.

Salil Soman, MD, MS


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-- 
Martin Reuter, Ph.D.

Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone:+1-617-724-5652  tel:%2B1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu  mailto:mreu...@nmr.mgh.harvard.edu
reu...@mit.edu  mailto:reu...@mit.edu
Web  :http://reuter.mit.edu  


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.



--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu

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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] longitudinal hippocampal subfields analysis

[Martin Reuter]

Hi Salil,

just run the hippo-subfields on the longitudinal results like this:

recon-all -long tpNi templateid -hippo-subfields

to generate the subfield data. I am not familiar with the kvlQuantify... 
script and think it works on all subjects in the Subjects dir. Not sure 
what the best way is to solve this as your subject dir contains also the 
cross and base results. Probably you can run the script and it will 
simply skip the cross and base directories (as no -hippo-subfields was 
run on them).



Best, Martin


On 01/05/2014 01:40 AM, Salil Soman wrote:

Hi,

I have been able to do the longitudinal processing steps for a number 
of subjects with 3 time points each, and then extract the generated 
statistics using aparcstats2table and asegstats2table. Is it possible 
to perform longitudinal analysis of the hippocampal subfields? If so, 
could someone point me to how to perform this analysis, 
as kvlQuantifyHippocampalSubfieldSegmentations.sh does not work on the 
output files I've generated.


Thank you.

Salil Soman, MD, MS


___
Freesurfer mailing list
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--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu

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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] longitudinal hippocampal subfields analysis

[Salil Soman]

Hi,

I have been able to do the longitudinal processing steps for a number of
subjects with 3 time points each, and then extract the generated statistics
using aparcstats2table and asegstats2table. Is it possible to perform
longitudinal analysis of the hippocampal subfields? If so, could someone
point me to how to perform this analysis,
as kvlQuantifyHippocampalSubfieldSegmentations.sh does not work on the
output files I've generated.

Thank you.

Salil Soman, MD, MS
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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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