Re: [Freesurfer] Hippo subfields long

[Iglesias Gonzalez, Juan E.]

External Email - Use Caution

Dear Andrei,
The script requires that you’ve run the main FreeSurfer longitudinal pipeline 
(see Longitudinal Processing in the wiki).
Don’t worry about the files, they have different names and can coexist without 
issues 
Cheers,
/E


--
Juan Eugenio Iglesias
http://secure-web.cisco.com/10fTQ42u4_V7tprrGhZtquem9C8ol86QGWI0WSKTeJmrMNbbbBfv6TXMg2qxFleC48s3zH-4u9m5nfjQS7_fKmUn6GkY2oZQkRwX92k2LGnbYgF_waVU7auGmc9AaJyX02KjoIWf9lngiEqNjnRAzHQVFVbuxXlEuDN515b1WjioA5LC96IYogsYAvNT7xnoMaT-_kJw0wnWXkvlLzMnewj7RVJWE0ZyKP6Te_bsblaEFj0_W9B0HtJv3BHbTIaEK09xDOxjj1HFdS6U6mLna4w/http%3A%2F%2Fwww.jeiglesias.com

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Andrei Bieger 

Date: Sunday, July 2, 2023 at 17:27
To: Freesurfer support list 
Subject: [Freesurfer] Hippo subfields long

External Email - Use Caution
Hello everyone,

Quick question.
After running the longitudinal recon-all pipeline, is it required to run all 
subjects/tps through the segmentHA before running the segmentHA_long?
If no, since I already ran the segment_HA in a few subjects, if I stop and 
start running the segmentHA_long, will I have any trouble in overlaying output 
files?

Thank you in advance!
Andrei
--
Andrei Bieger
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[Freesurfer] Hippo subfields long

[Andrei Bieger]

External Email - Use Caution

Hello everyone,

Quick question.
After running the longitudinal recon-all pipeline, is it required to run
all subjects/tps through the segmentHA before running the segmentHA_long?
If no, since I already ran the segment_HA in a few subjects, if I stop and
start running the segmentHA_long, will I have any trouble in overlaying
output files?

Thank you in advance!
Andrei
-- 
Andrei Bieger
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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 
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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] hippo subfields and amygdala

[Erik O'Hanlon]

External Email - Use Caution

Thanks a mill Eugenio,


Best regards


Erik


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, 
Eugenio 
Sent: 29 May 2018 13:02:07
To: Freesurfer support list
Subject: Re: [Freesurfer] hippo subfields and amygdala


External Email - Use Caution

Yes the LUT evolves but remains backwards compatible.

And yes, the command looks OK to me!

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 Erik O'Hanlon 


Erik O'Hanlon
Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

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


Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
2018-2022<http://www.rcsi.ie/strategy2018>


RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]


Reply-To: Freesurfer support list 
Date: Tuesday, 29 May 2018 at 13:00
To: Freesurfer support list 
Subject: Re: [Freesurfer] hippo subfields and amygdala



External Email - Use Caution

Hi Eugenio,



Thanks, I'll give that a try. Just a quick question, the correct ROI id's for 
each subfield are in the LUT ? Is there a different LUT in the DEV version for 
the hippo and Amy subdivisions individually and also the anterior /posterior 
divisions and are there different numbers for each hemisphere?   If I use the 
MRI_segment_Label can I make a mask for the whole structure volumes for the 
hippo and Amy just by listing all the ID's i.e.

mri_segment lh.hippoAmygLabels-T1.v2x.FSvoxelSpace.mgz 7001 7003  7005 7006 
7007 7008 7009 7010 7015 LeftAmygdala.nii



Thanks again Eugenio really appreciate the help



Cheers



Erik



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, 
Eugenio 
Sent: 29 May 2018 11:44:41
To: Freesurfer support list
Subject: Re: [Freesurfer] hippo subfields and amygdala



External Email - Use Caution

Hi Erik,

The subfield module gives you a segmentation in the same space as brain.mgz and 
the rest of volumes in the recon-all stream:

[lr]h.hippoAmygLabels-T1.v2x.FSvoxelSpace.mgz

You can use mri_extract_label to create binary masks.

Cheers,

/Eugenio



--

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/





From:  on behalf of Erik O'Hanlon 


Erik O'Hanlon
Postdoctoral researcher

[cid:image001.png@01D3F74D.423505F0]

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

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
2018-2022<http://www.rcsi.ie/strategy2018>

RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:image002.png@01D3F74D.423505F0]

Reply-To: Freesurfer support list 
Date: Tuesday, 29 May 2018 at 11:07
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippo subfields and amygdala



External Email - Use Caution

Hi FS experts,



I have run my analysis using the dev version and have all the necessary 
volume.txt files. As a secondary step, I want to use some of the subfields as 
seed volumes for tractography (using ExploreDTI). I have may diffusion data in 
the same space as the FS brain.mgz but am wondering how I should make the 
subfield masks so that they will be in the same coordinate space when exported 
as a nii file. If I use Freeview and load the brain.mgz and then the subfield 
volumes, is it simply a case of reducing the LUT to the specific subfield and 
then save that as a volume/mask ? Will that mask be in the same coordinate 
space and regsitered the brain.nii too.

Is it just a matter of doing this process numerous times in Freeview and each 
time simply changing the LUT corresponding to the specific ROI needed to get 
the masks I want to use for each subject.



Thanks for any information you can offer



Best regards



Erik



Erik O'Hanlon
Postdoctoral researcher

[cid:image003.png@01D3F74D.423505F0]

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

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
2018-2022<http://www.rcsi.ie/strategy2018>

RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:image004.png@01D3F74D.423505F0]
___
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Re: [Freesurfer] hippo subfields and amygdala

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Yes the LUT evolves but remains backwards compatible.
And yes, the command looks OK to me!
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 Erik O'Hanlon 

Reply-To: Freesurfer support list 
Date: Tuesday, 29 May 2018 at 13:00
To: Freesurfer support list 
Subject: Re: [Freesurfer] hippo subfields and amygdala


External Email - Use Caution

Hi Eugenio,



Thanks, I'll give that a try. Just a quick question, the correct ROI id's for 
each subfield are in the LUT ? Is there a different LUT in the DEV version for 
the hippo and Amy subdivisions individually and also the anterior /posterior 
divisions and are there different numbers for each hemisphere?   If I use the 
MRI_segment_Label can I make a mask for the whole structure volumes for the 
hippo and Amy just by listing all the ID's i.e.

mri_segment lh.hippoAmygLabels-T1.v2x.FSvoxelSpace.mgz 7001 7003  7005 7006 
7007 7008 7009 7010 7015 LeftAmygdala.nii



Thanks again Eugenio really appreciate the help



Cheers



Erik


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, 
Eugenio 
Sent: 29 May 2018 11:44:41
To: Freesurfer support list
Subject: Re: [Freesurfer] hippo subfields and amygdala


External Email - Use Caution

Hi Erik,

The subfield module gives you a segmentation in the same space as brain.mgz and 
the rest of volumes in the recon-all stream:

[lr]h.hippoAmygLabels-T1.v2x.FSvoxelSpace.mgz

You can use mri_extract_label to create binary masks.

Cheers,

/Eugenio



--

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/





From:  on behalf of Erik O'Hanlon 


Erik O'Hanlon
Postdoctoral researcher

[cid:image001.png@01D3F74D.423505F0]

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

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
2018-2022<http://www.rcsi.ie/strategy2018>

RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:image002.png@01D3F74D.423505F0]
Reply-To: Freesurfer support list 
Date: Tuesday, 29 May 2018 at 11:07
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippo subfields and amygdala



External Email - Use Caution

Hi FS experts,



I have run my analysis using the dev version and have all the necessary 
volume.txt files. As a secondary step, I want to use some of the subfields as 
seed volumes for tractography (using ExploreDTI). I have may diffusion data in 
the same space as the FS brain.mgz but am wondering how I should make the 
subfield masks so that they will be in the same coordinate space when exported 
as a nii file. If I use Freeview and load the brain.mgz and then the subfield 
volumes, is it simply a case of reducing the LUT to the specific subfield and 
then save that as a volume/mask ? Will that mask be in the same coordinate 
space and regsitered the brain.nii too.

Is it just a matter of doing this process numerous times in Freeview and each 
time simply changing the LUT corresponding to the specific ROI needed to get 
the masks I want to use for each subject.



Thanks for any information you can offer



Best regards



Erik



Erik O'Hanlon
Postdoctoral researcher

[cid:image003.png@01D3F74D.423505F0]

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

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
2018-2022<http://www.rcsi.ie/strategy2018>

RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:image004.png@01D3F74D.423505F0]
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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] hippo subfields and amygdala

[Erik O'Hanlon]

External Email - Use Caution

Hi Eugenio,


Thanks, I'll give that a try. Just a quick question, the correct ROI id's for 
each subfield are in the LUT ? Is there a different LUT in the DEV version for 
the hippo and Amy subdivisions individually and also the anterior /posterior 
divisions and are there different numbers for each hemisphere?   If I use the 
MRI_segment_Label can I make a mask for the whole structure volumes for the 
hippo and Amy just by listing all the ID's i.e.

mri_segment lh.hippoAmygLabels-T1.v2x.FSvoxelSpace.mgz 7001 7003  7005 7006 
7007 7008 7009 7010 7015 LeftAmygdala.nii


Thanks again Eugenio really appreciate the help


Cheers


Erik


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, 
Eugenio 
Sent: 29 May 2018 11:44:41
To: Freesurfer support list
Subject: Re: [Freesurfer] hippo subfields and amygdala


External Email - Use Caution

Hi Erik,

The subfield module gives you a segmentation in the same space as brain.mgz and 
the rest of volumes in the recon-all stream:

[lr]h.hippoAmygLabels-T1.v2x.FSvoxelSpace.mgz

You can use mri_extract_label to create binary masks.

Cheers,

/Eugenio



--

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/





From:  on behalf of Erik O'Hanlon 


Erik O'Hanlon
Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

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


Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
2018-2022<http://www.rcsi.ie/strategy2018>


RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]


Reply-To: Freesurfer support list 
Date: Tuesday, 29 May 2018 at 11:07
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippo subfields and amygdala



External Email - Use Caution

Hi FS experts,



I have run my analysis using the dev version and have all the necessary 
volume.txt files. As a secondary step, I want to use some of the subfields as 
seed volumes for tractography (using ExploreDTI). I have may diffusion data in 
the same space as the FS brain.mgz but am wondering how I should make the 
subfield masks so that they will be in the same coordinate space when exported 
as a nii file. If I use Freeview and load the brain.mgz and then the subfield 
volumes, is it simply a case of reducing the LUT to the specific subfield and 
then save that as a volume/mask ? Will that mask be in the same coordinate 
space and regsitered the brain.nii too.

Is it just a matter of doing this process numerous times in Freeview and each 
time simply changing the LUT corresponding to the specific ROI needed to get 
the masks I want to use for each subject.



Thanks for any information you can offer



Best regards



Erik



Erik O'Hanlon
Postdoctoral researcher

[cid:image001.png@01D3F742.70D780F0]

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

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
2018-2022<http://www.rcsi.ie/strategy2018>

RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:image002.png@01D3F742.70D780F0]
___
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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] hippo subfields and amygdala

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Erik,
The subfield module gives you a segmentation in the same space as brain.mgz and 
the rest of volumes in the recon-all stream:
[lr]h.hippoAmygLabels-T1.v2x.FSvoxelSpace.mgz
You can use mri_extract_label to create binary masks.
Cheers,
/Eugenio

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


From:  on behalf of Erik O'Hanlon 

Reply-To: Freesurfer support list 
Date: Tuesday, 29 May 2018 at 11:07
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippo subfields and amygdala


External Email - Use Caution

Hi FS experts,



I have run my analysis using the dev version and have all the necessary 
volume.txt files. As a secondary step, I want to use some of the subfields as 
seed volumes for tractography (using ExploreDTI). I have may diffusion data in 
the same space as the FS brain.mgz but am wondering how I should make the 
subfield masks so that they will be in the same coordinate space when exported 
as a nii file. If I use Freeview and load the brain.mgz and then the subfield 
volumes, is it simply a case of reducing the LUT to the specific subfield and 
then save that as a volume/mask ? Will that mask be in the same coordinate 
space and regsitered the brain.nii too.

Is it just a matter of doing this process numerous times in Freeview and each 
time simply changing the LUT corresponding to the specific ROI needed to get 
the masks I want to use for each subject.



Thanks for any information you can offer



Best regards



Erik



Erik O'Hanlon
Postdoctoral researcher

[cid:image001.png@01D3F742.70D780F0]

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

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
2018-2022<http://www.rcsi.ie/strategy2018>

RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:image002.png@01D3F742.70D780F0]
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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] hippo subfields and amygdala

[Erik O'Hanlon]

External Email - Use Caution

Hi FS experts,


I have run my analysis using the dev version and have all the necessary 
volume.txt files. As a secondary step, I want to use some of the subfields as 
seed volumes for tractography (using ExploreDTI). I have may diffusion data in 
the same space as the FS brain.mgz but am wondering how I should make the 
subfield masks so that they will be in the same coordinate space when exported 
as a nii file. If I use Freeview and load the brain.mgz and then the subfield 
volumes, is it simply a case of reducing the LUT to the specific subfield and 
then save that as a volume/mask ? Will that mask be in the same coordinate 
space and regsitered the brain.nii too.

Is it just a matter of doing this process numerous times in Freeview and each 
time simply changing the LUT corresponding to the specific ROI needed to get 
the masks I want to use for each subject.


Thanks for any information you can offer


Best regards


Erik


Erik O'Hanlon
Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

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


Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
2018-2022


RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

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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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dispose of the e-mail.

Re: [Freesurfer] hippo-subfields analysis 6.0v

[Iglesias Gonzalez, Eugenio]

Hi Stefano,

When segmenting 1 mm scans, the position of the internal boundaries between the 
hippocampal substructures largely relies on prior knowledge acquired from our 
ex vivo training data and summarized in our statistical atlas. For this reason, 
volumes of internal subfields (especially GC-DG, CA4 and molecular layer) must 
be interpreted with caution, and further validation with higher resolution data 
should ideally be carried out to confirm the results. On the other end of the 
spectrum, we have substructures such as the fimbria and tail, which are 
reliable at 1 mm.

Cheers,

/Eugenio


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


On 24 Jan 2017, at 21:35, std...@virgilio.it wrote:

Hi list,
I'm performing hippo-subfields analysis on T1 having the followed parameters:

data_type  INT32
dim1   170
dim2   256
dim3   256
dim4   1
datatype   8
pixdim11.25
pixdim21.00
pixdim31.00
pixdim41.00
cal_max0.
cal_min0.
file_type  NIFTI-1+

Does my result will be reliable also whether I avoid to add the T2 scan?

Thanks


Stefano
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] hippo-subfields analysis 6.0v

[stdp82]

Hi list,I'm performing hippo-subfields analysis on T1 having the followed 
parameters:
data_type  INT32dim1   170dim2   256dim3   256dim4  
 1datatype   8pixdim11.25pixdim21.00pixdim3 
   1.00pixdim41.00cal_max0.cal_min
0.file_type  NIFTI-1+
Does my result will be reliable also whether I avoid to add the T2 scan?
Thanks

Stefano___
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[Freesurfer] Hippo-subfields visualization

[stdp82]

Hi list, 
I'm using version 5.3 and I have performed hippo-subfields analysis.
A- I'd like to visualize the mask of each subfield on the T1. 
In subid/mri, I run the command line above:
freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz 
-p-labels posterior_right_* posterior_Right-Hippocampus.mgz -p-prefix 
posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt
but I can not visualize the subfields ROI on the T1
B- How I can visualize the entorhinal, perirhinal and parahippocampal on T1 of 
a subjects?
C- I would like to have the ROI entorhinal, perirhinal and parahippocampal for 
each subject and use it as masks. How can I do?
Thanks,

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Re: [Freesurfer] -hippo-subfields

[Marcos Martins da Silva]

Hi, Greg
I use to process my subjects with:

recon-all -s subjid -all -hippo-subfields

The -all flag makes the program run all the 3 stages (autorecon1,
autorecon2 and autorecon3) in sequence. Only after this it starts the
hippo-subfields stage. If you do not have any special reason to run each
autorecon in a different line in your script I suggest you just use the
-all flag. But if you need to separate each stage you can use:

recon-all -s subjid -autorecon1
recon-all -s subjid -autorecon2
recon-all -s subjid -autorecon3 -hippo-subfields

No need to add the hippo-subfields flag for each stage: you would just
repeat the same process and waste time. Indeed, if you check
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation you 
will see that ...the program needs the FreeSurfer-generated files aseg.mgz, 
nu.mgz and talairach.xfm
At least, aseg.mgz will not be available before completing autorecon2.
So I guess if you add the hippo-subfields flag after autorecon1 stage it
will return an error.
 
Marcos
Em Qui, 2014-08-07 às 16:05 -0500, Gregory Kirk escreveu:

 
 we have freesurfer set up on our big condor cluster, i asked that the
 
 -hippo-subfields be added. they have it set up to run in 3 stages
 autorecon1 autorecon2 autorecon3 
 they added the flag to all 3, i think it would only be needed on autorecon3, 
 but don't think it would
 cause harm, just be ignored in the first 2 ?
 
 thanks
 
 greg
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 properly
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Re: [Freesurfer] -hippo-subfields

[Eugenio Iglesias]

Hi Greg,
I would suggest that you only do it with either autorecon2 or  autorecon3. With 
autorecon1, it will fail because it won't find aseg.mgz. You should still be 
able to run autorecon2 after this mistake, but I wouldn't do it (why let the 
software exit with an error without need?). If you do it both with both 
autorecon2 and autorecon3, I believe that the code will be run twice.
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: Gregory Kirk gk...@wisc.edu
To: free freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, August 7, 2014 5:05:27 PM
Subject: [Freesurfer] -hippo-subfields



we have freesurfer set up on our big condor cluster, i asked that the

-hippo-subfields be added. they have it set up to run in 3 stages
autorecon1 autorecon2 autorecon3 
they added the flag to all 3, i think it would only be needed on autorecon3, 
but don't think it would
cause harm, just be ignored in the first 2 ?

thanks

greg
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[Freesurfer] -hippo-subfields

[Gregory Kirk]

we have freesurfer set up on our big condor cluster, i asked that the

-hippo-subfields be added. they have it set up to run in 3 stages
autorecon1 autorecon2 autorecon3 
they added the flag to all 3, i think it would only be needed on autorecon3, 
but don't think it would
cause harm, just be ignored in the first 2 ?

thanks

greg
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[Freesurfer] -hippo-subfields error

[Garikoitz Lerma-Usabiaga]

Hi,
I had a subject already run through recon-all.
After making recon-all -s ID -hippo-subfields
or
recon-all -s ID -hippo-subfields -make all

it is failing.

It is the first subject ever failing with the hippo-subfields. The rest of
the subjects are ok. This subject is properly segmented (tkmedit ID
brainmask.mgz -surfs -aseg is ok).

Any recommendations on what to do next?


thanks!
Gari

PS1 please find attached the last recon-all invocation log.
PS2 I have the screen output as well, there was more detail in that, in
case it would help recognizing the problem.


recon-all.log.last
Description: Binary data
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Re: [Freesurfer] -hippo-subfields error

[Juan Eugenio Iglesias]

Gari, can you send us the log of the hippo subfield module (or the 
screen output; they should be the same)

Cheers,
/Eugenio

On 10/16/2013 10:22 AM, Garikoitz Lerma-Usabiaga wrote:

Hi,
I had a subject already run through recon-all.
After making recon-all -s ID -hippo-subfields
or
recon-all -s ID -hippo-subfields -make all

it is failing.

It is the first subject ever failing with the hippo-subfields. The 
rest of the subjects are ok. This subject is properly segmented 
(tkmedit ID brainmask.mgz -surfs -aseg is ok).


Any recommendations on what to do next?


thanks!
Gari

PS1 please find attached the last recon-all invocation log.
PS2 I have the screen output as well, there was more detail in that, 
in case it would help recognizing the problem.



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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] Hippo-subfields

[Marcos Martins da Silva]

TYVM, Juan Eugenio and Bruce.
I am a neurologist and Professor in Federal University of Rio de
Janeiro. I am confortable with Linux and scripts but, as a physician,
eigenvectors  will be really hard. I will try to get some help inside
University. But if I correctly understood, it seems an elegant way to
make tool that will work with several hippocampi with greater
consistency than manual approach. Your step by step directions worked
great, Juan. But I had to make a Left and a Right file. When I tried to
concat right and left subfields in teh same file I got an error saying
that right and left Ca1 dimensions did not match. Thank you again. 
Em Qui, 2013-04-18 às 11:29 -0400, Juan Eugenio Iglesias escreveu:

 I agree with Bruce. You can use MRIread.m to read in the data.
 
 Regarding the other question: first you need to combine the posteriors
 of all the subfields into a single posterior for the whole hippocampus.
 You can do that like this:
 
 mri_concat posterior_fimbria.mgz posterior_CA1.mgz ... --sum --o
 posteriorWholeHippocampus.mgz
 
 Then you can threshold the posterior at probability 0.5 to obtain a
 binary hippocampal mask:
 
 mri_binarize --i posteriorWholeHippocampus.mgz --min 127 --o
 binaryHippocampalMask.mgz
 
 Finally, you can generate a surface by tesselating the mask:
 
 mri_tesselate binaryHippocampalMask.mgz 1 surfaceFile
 
 You can visualize the output with
 
 freeview -v posteriorWholeHippocampus.mgz -f surfaceFile
 
 Cheers,
 
 /Eugenio
 
 
 
 
 
 
 
 On Thu, 2013-04-18 at 11:22 -0400, Bruce Fischl wrote:
  Hi Marcos
  
  I would do it in matlab. Compute the spatial eigenvectors then divide the 
  hippocampus up along the primary eigenvector
  
  cheers
  Bruce
  On Thu, 18 Apr 2013, Marcos 
  Martins da Silva wrote:
  
   Thank you for your answer, Juan.
   
Yes, I want a surface of the whole hippocampus and I thought I had just 
   obtained that using
   freeview and adding all hippo-subfield files. That resulted in the 
   screenshot I previously
   attached. I just do not know how I can save the resultant surface.
   
   After I checked show as isosurface in 3D view the low and high 
   threshold controls appeared.
   The default threshold values on Freeview for low was 127.5 and high was 
   255. When I played
   with these controls, the size of the surfaces changed on 3D view. That is 
   why I made the
   second question. I was trying to select the correct values for low and 
   high threshoulds so I
   get an image consistent with the volume values we get after running
   kvlQuantifyPosteriorProbabilityImages. After setting the correct values I 
   would like to save
   the work as a surface so I could load the whole surface instead of 
   loading each individual
   subfield file. But I did not find a save as surface option. So I used 
   the screenshot tool to
   save the work. This way I could at least show you what I got but I 
   thought it was not the
   best way to do it.
   
   Relating to the last question about generating a new segmentation 
   (anterior, body and
   posterior), you said I could use simple geometric rules to get it. Could 
   you tell me where I
   can find instructions about how to do it?
   
   Sorry, I am afraid I am a novice here and my questions are the best proof 
   of this, so I would
   like to thank you for all your patience.
   
   Em Qua, 2013-04-17 às 21:19 -0400, Juan Eugenio Iglesias escreveu:
   Dear Marcos,
   
 1- How do I save the combined 3D view I got as a surface?
   
Do you want a surface of the whole hippocampus? In that case I would
suggest adding up the probability volumes from all the subfields and
thresholding the resulting volume.
   
   
 2-I know the hippo-subifields .mgz files are probability maps and if I
 guess right kvlQuantifyPosteriorProbabilityImages read these files to
 count how many voxels you have in each subfield. I also guess it count
 only the voxels with reasonable high probability to be part of each
 subfield. If so, what is the minimum value between 1 and 255 the
 program use to decide if a particular voxel is valid?
   
The estimates of the volumes are based on soft probabilities, so all
voxels with non-zero probability contribute towards the estimate. For
instance, a voxel with value 255 contributes to the volume 255 times as
much as a voxel with a value of 1.
   
   
 3- Is it possible to merge hippo-subfield .mgz files data and to
 generate a different segmentation like anterior (anterior quarter),
 body (the2 intermediate quarters) and posterior (posterior quarter).
   
There are currently no scripts in FreeSurfer to generate such a
partition. But you could always take a mask of the whole hippocampus
(either from aseg.mgz of from the combination of all the subfields, like
I mentioned in 1) and define some simple geometric rules to create it.
   
Kind regards,
   
Eugenio
   
   
   
   

 TY in 

Re: [Freesurfer] Hippo-subfields

[Juan Eugenio Iglesias]

Hi Marcos,
the subfields of the left and right hippocampi are defined on different
voxel spaces. If you want to combine them, you first need to reslice them
to a common voxel space (for instance using -rl in mri_convert)
Cheers,
/Eugenio


On Fri, April 19, 2013 9:57 pm, Marcos Martins da Silva wrote:
 TYVM, Juan Eugenio and Bruce.
 I am a neurologist and Professor in Federal University of Rio de
 Janeiro. I am confortable with Linux and scripts but, as a physician,
 eigenvectors  will be really hard. I will try to get some help inside
 University. But if I correctly understood, it seems an elegant way to
 make tool that will work with several hippocampi with greater
 consistency than manual approach. Your step by step directions worked
 great, Juan. But I had to make a Left and a Right file. When I tried to
 concat right and left subfields in teh same file I got an error saying
 that right and left Ca1 dimensions did not match. Thank you again.
 Em Qui, 2013-04-18 às 11:29 -0400, Juan Eugenio Iglesias escreveu:

 I agree with Bruce. You can use MRIread.m to read in the data.

 Regarding the other question: first you need to combine the posteriors
 of all the subfields into a single posterior for the whole hippocampus.
 You can do that like this:

 mri_concat posterior_fimbria.mgz posterior_CA1.mgz ... --sum --o
 posteriorWholeHippocampus.mgz

 Then you can threshold the posterior at probability 0.5 to obtain a
 binary hippocampal mask:

 mri_binarize --i posteriorWholeHippocampus.mgz --min 127 --o
 binaryHippocampalMask.mgz

 Finally, you can generate a surface by tesselating the mask:

 mri_tesselate binaryHippocampalMask.mgz 1 surfaceFile

 You can visualize the output with

 freeview -v posteriorWholeHippocampus.mgz -f surfaceFile

 Cheers,

 /Eugenio







 On Thu, 2013-04-18 at 11:22 -0400, Bruce Fischl wrote:
  Hi Marcos
 
  I would do it in matlab. Compute the spatial eigenvectors then divide
 the
  hippocampus up along the primary eigenvector
 
  cheers
  Bruce
  On Thu, 18 Apr 2013, Marcos
  Martins da Silva wrote:
 
   Thank you for your answer, Juan.
  
Yes, I want a surface of the whole hippocampus and I thought I had
 just obtained that using
   freeview and adding all hippo-subfield files. That resulted in the
 screenshot I previously
   attached. I just do not know how I can save the resultant surface.
  
   After I checked show as isosurface in 3D view the low and high
 threshold controls appeared.
   The default threshold values on Freeview for low was 127.5 and high
 was 255. When I played
   with these controls, the size of the surfaces changed on 3D view.
 That is why I made the
   second question. I was trying to select the correct values for low
 and high threshoulds so I
   get an image consistent with the volume values we get after running
   kvlQuantifyPosteriorProbabilityImages. After setting the correct
 values I would like to save
   the work as a surface so I could load the whole surface instead of
 loading each individual
   subfield file. But I did not find a save as surface option. So I
 used the screenshot tool to
   save the work. This way I could at least show you what I got but I
 thought it was not the
   best way to do it.
  
   Relating to the last question about generating a new segmentation
 (anterior, body and
   posterior), you said I could use simple geometric rules to get it.
 Could you tell me where I
   can find instructions about how to do it?
  
   Sorry, I am afraid I am a novice here and my questions are the best
 proof of this, so I would
   like to thank you for all your patience.
  
   Em Qua, 2013-04-17 às 21:19 -0400, Juan Eugenio Iglesias escreveu:
   Dear Marcos,
   
 1- How do I save the combined 3D view I got as a surface?
   
Do you want a surface of the whole hippocampus? In that case I
 would
suggest adding up the probability volumes from all the subfields
 and
thresholding the resulting volume.
   
   
 2-I know the hippo-subifields .mgz files are probability maps
 and if I
 guess right kvlQuantifyPosteriorProbabilityImages read these
 files to
 count how many voxels you have in each subfield. I also guess it
 count
 only the voxels with reasonable high probability to be part of
 each
 subfield. If so, what is the minimum value between 1 and 255 the
 program use to decide if a particular voxel is valid?
   
The estimates of the volumes are based on soft probabilities, so
 all
voxels with non-zero probability contribute towards the estimate.
 For
instance, a voxel with value 255 contributes to the volume 255
 times as
much as a voxel with a value of 1.
   
   
 3- Is it possible to merge hippo-subfield .mgz files data and to
 generate a different segmentation like anterior (anterior
 quarter),
 body (the2 intermediate quarters) and posterior (posterior
 quarter).
   
There are currently no scripts in FreeSurfer to generate such a
partition. But you could always 

Re: [Freesurfer] Hippo-subfields

[Marcos Martins da Silva]

Thank you for your answer, Juan.

 Yes, I want a surface of the whole hippocampus and I thought I had just
obtained that using freeview and adding all hippo-subfield files. That
resulted in the screenshot I previously attached. I just do not know how I
can save the resultant surface.

After I checked show as isosurface in 3D view the low and high threshold
controls appeared. The default threshold values on Freeview for low was
127.5 and high was 255. When I played with these controls, the size of the
surfaces changed on 3D view. That is why I made the second question. I was
trying to select the correct values for low and high threshoulds so I get
an image consistent with the volume values we get after running
kvlQuantifyPosteriorProbabilityImages. After setting the correct values I
would like to save the work as a surface so I could load the whole surface
instead of loading each individual subfield file. But I did not find a
save as surface option. So I used the screenshot tool to save the work.
This way I could at least show you what I got but I thought it was not the
best way to do it.

Relating to the last question about generating a new segmentation
(anterior, body and posterior), you said I could use simple geometric rules
to get it. Could you tell me where I can find instructions about how to do
it?

Sorry, I am afraid I am a novice here and my questions are the best proof
of this, so I would like to thank you for all your patience.

Em Qua, 2013-04-17 às 21:19 -0400, Juan Eugenio Iglesias escreveu:
Dear Marcos,

  1- How do I save the combined 3D view I got as a surface?

 Do you want a surface of the whole hippocampus? In that case I would
 suggest adding up the probability volumes from all the subfields and
 thresholding the resulting volume.


  2-I know the hippo-subifields .mgz files are probability maps and if I
  guess right kvlQuantifyPosteriorProbabilityImages read these files to
  count how many voxels you have in each subfield. I also guess it count
  only the voxels with reasonable high probability to be part of each
  subfield. If so, what is the minimum value between 1 and 255 the
  program use to decide if a particular voxel is valid?

 The estimates of the volumes are based on soft probabilities, so all
 voxels with non-zero probability contribute towards the estimate. For
 instance, a voxel with value 255 contributes to the volume 255 times as
 much as a voxel with a value of 1.


  3- Is it possible to merge hippo-subfield .mgz files data and to
  generate a different segmentation like anterior (anterior quarter),
  body (the2 intermediate quarters) and posterior (posterior quarter).

 There are currently no scripts in FreeSurfer to generate such a
 partition. But you could always take a mask of the whole hippocampus
 (either from aseg.mgz of from the combination of all the subfields, like
 I mentioned in 1) and define some simple geometric rules to create it.

 Kind regards,

 Eugenio




 
  TY in advance
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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.

Re: [Freesurfer] Hippo-subfields

[Juan Eugenio Iglesias]

I agree with Bruce. You can use MRIread.m to read in the data.

Regarding the other question: first you need to combine the posteriors
of all the subfields into a single posterior for the whole hippocampus.
You can do that like this:

mri_concat posterior_fimbria.mgz posterior_CA1.mgz ... --sum --o
posteriorWholeHippocampus.mgz

Then you can threshold the posterior at probability 0.5 to obtain a
binary hippocampal mask:

mri_binarize --i posteriorWholeHippocampus.mgz --min 127 --o
binaryHippocampalMask.mgz

Finally, you can generate a surface by tesselating the mask:

mri_tesselate binaryHippocampalMask.mgz 1 surfaceFile

You can visualize the output with

freeview -v posteriorWholeHippocampus.mgz -f surfaceFile

Cheers,

/Eugenio







On Thu, 2013-04-18 at 11:22 -0400, Bruce Fischl wrote:
 Hi Marcos
 
 I would do it in matlab. Compute the spatial eigenvectors then divide the 
 hippocampus up along the primary eigenvector
 
 cheers
 Bruce
 On Thu, 18 Apr 2013, Marcos 
 Martins da Silva wrote:
 
  Thank you for your answer, Juan.
  
   Yes, I want a surface of the whole hippocampus and I thought I had just 
  obtained that using
  freeview and adding all hippo-subfield files. That resulted in the 
  screenshot I previously
  attached. I just do not know how I can save the resultant surface.
  
  After I checked show as isosurface in 3D view the low and high threshold 
  controls appeared.
  The default threshold values on Freeview for low was 127.5 and high was 
  255. When I played
  with these controls, the size of the surfaces changed on 3D view. That is 
  why I made the
  second question. I was trying to select the correct values for low and high 
  threshoulds so I
  get an image consistent with the volume values we get after running
  kvlQuantifyPosteriorProbabilityImages. After setting the correct values I 
  would like to save
  the work as a surface so I could load the whole surface instead of loading 
  each individual
  subfield file. But I did not find a save as surface option. So I used the 
  screenshot tool to
  save the work. This way I could at least show you what I got but I 
  thought it was not the
  best way to do it.
  
  Relating to the last question about generating a new segmentation 
  (anterior, body and
  posterior), you said I could use simple geometric rules to get it. Could 
  you tell me where I
  can find instructions about how to do it?
  
  Sorry, I am afraid I am a novice here and my questions are the best proof 
  of this, so I would
  like to thank you for all your patience.
  
  Em Qua, 2013-04-17 às 21:19 -0400, Juan Eugenio Iglesias escreveu:
  Dear Marcos,
  
1- How do I save the combined 3D view I got as a surface?
  
   Do you want a surface of the whole hippocampus? In that case I would
   suggest adding up the probability volumes from all the subfields and
   thresholding the resulting volume.
  
  
2-I know the hippo-subifields .mgz files are probability maps and if I
guess right kvlQuantifyPosteriorProbabilityImages read these files to
count how many voxels you have in each subfield. I also guess it count
only the voxels with reasonable high probability to be part of each
subfield. If so, what is the minimum value between 1 and 255 the
program use to decide if a particular voxel is valid?
  
   The estimates of the volumes are based on soft probabilities, so all
   voxels with non-zero probability contribute towards the estimate. For
   instance, a voxel with value 255 contributes to the volume 255 times as
   much as a voxel with a value of 1.
  
  
3- Is it possible to merge hippo-subfield .mgz files data and to
generate a different segmentation like anterior (anterior quarter),
body (the2 intermediate quarters) and posterior (posterior quarter).
  
   There are currently no scripts in FreeSurfer to generate such a
   partition. But you could always take a mask of the whole hippocampus
   (either from aseg.mgz of from the combination of all the subfields, like
   I mentioned in 1) and define some simple geometric rules to create it.
  
   Kind regards,
  
   Eugenio
  
  
  
  
   
TY in advance
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http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
Department of Radiology, MGH, Harvard Medical School
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.


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Re: [Freesurfer] Hippo-subfields

[Juan Eugenio Iglesias]

Dear Marcos,

 1- How do I save the combined 3D view I got as a surface?

Do you want a surface of the whole hippocampus? In that case I would
suggest adding up the probability volumes from all the subfields and
thresholding the resulting volume.


 2-I know the hippo-subifields .mgz files are probability maps and if I
 guess right kvlQuantifyPosteriorProbabilityImages read these files to
 count how many voxels you have in each subfield. I also guess it count
 only the voxels with reasonable high probability to be part of each
 subfield. If so, what is the minimum value between 1 and 255 the
 program use to decide if a particular voxel is valid?

The estimates of the volumes are based on soft probabilities, so all
voxels with non-zero probability contribute towards the estimate. For
instance, a voxel with value 255 contributes to the volume 255 times as
much as a voxel with a value of 1. 


 3- Is it possible to merge hippo-subfield .mgz files data and to
 generate a different segmentation like anterior (anterior quarter),
 body (the2 intermediate quarters) and posterior (posterior quarter).

There are currently no scripts in FreeSurfer to generate such a
partition. But you could always take a mask of the whole hippocampus
(either from aseg.mgz of from the combination of all the subfields, like
I mentioned in 1) and define some simple geometric rules to create it.

Kind regards,

Eugenio




 
 TY in advance 
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Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
Department of Radiology, MGH, Harvard Medical School
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.


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[Freesurfer] hippo-subfields not creating some files

[Inge Knudson]

Hi Bruce et al.,

I have a problem with the -hippo-subfields segmentation not creating some files 
for the left side when I run it on our Linux box located at the Martinos 
Center, with Freesurfer sourced to /usr/local/freesurfer/nmr-stable51-env.  
Specifically, it runs to apparent completion and exits without error, but it 
does not create these three .mgz files:
posterior_Left-Cerebral-Cortex.mgz
posterior_Left-Cerebral-White-Matter.mgz
posterior_Left-Hippocampus.mgz

All the other posterior_*.mgz  files are created, however.  It is only these 
same 3 that are missing every time.   The hippo-subfields.log file also does 
not get created.  
This happens whether I run -hippo-subfields as part of the recon-all -all 
process, or as a stand-alone:
recon-all -s mysubject -hippo-subfields

The Freesurfer build stamp is 
freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110514

If I copy the subject's directory over to my iMac (OS 10.6.8) which has its own 
standalone copy of Freesurfer 5.1 installed, and run the same command line 
there, it runs fine.  All the files are created, including the 
hippo-subfields.log.  The build stamp on the iMac is 
freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0

Thank you,
Inge
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Re: [Freesurfer] hippo-subfields not creating some files

[Bruce Fischl]

Hi Inge

I think this is a question for Koen (ccd)

cheers
Bruce

On Fri, 14 Oct 2011, Inge Knudson wrote:

 Hi Bruce et al.,

 I have a problem with the -hippo-subfields segmentation not creating some 
 files for the left side when I run it on our Linux box located at the 
 Martinos Center, with Freesurfer sourced to 
 /usr/local/freesurfer/nmr-stable51-env.  Specifically, it runs to apparent 
 completion and exits without error, but it does not create these three .mgz 
 files:
 posterior_Left-Cerebral-Cortex.mgz
 posterior_Left-Cerebral-White-Matter.mgz
 posterior_Left-Hippocampus.mgz

 All the other posterior_*.mgz  files are created, however.  It is only these 
 same 3 that are missing every time.   The hippo-subfields.log file also does 
 not get created.
 This happens whether I run -hippo-subfields as part of the recon-all -all 
 process, or as a stand-alone:
 recon-all -s mysubject -hippo-subfields

 The Freesurfer build stamp is 
 freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110514

 If I copy the subject's directory over to my iMac (OS 10.6.8) which has its 
 own standalone copy of Freesurfer 5.1 installed, and run the same command 
 line there, it runs fine.  All the files are created, including the 
 hippo-subfields.log.  The build stamp on the iMac is 
 freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0

 Thank you,
 Inge
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