[Freesurfer] Segmentation of thalamic nuclei - FreeSurferColorLUT

2018-09-11 Thread stdp82 
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Hi list,
where can I find the list of regions that I obtain by trough the segmentation 
of thalamic nuclei? Are they in FreeSurferColorLUT? Which are the codes for 
right and left regions?
Thanks
Stefano___
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[Freesurfer] Amygdala subfields segmentation

2018-09-11 Thread Miguel Ángel Rivas Fernández 
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Hi Freesurfer developes,

I am trying to execute the hippocampal and amygdala segmentation command "
segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1
[SUBJECTS_DIR]" but freesurfer gave to me this error
*command not found. *


However, when I use the command that segment only the hippocampal subfields
(recon-all -s  -hippocampal-subfields-T2  ) I don´t have any problem.


What would be the reason?


Thanks in advance.


Best,

-- 
*Miguel Ángel Rivas Fernández*
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Re: [Freesurfer] Using the new Thalamus tool

2018-09-11 Thread Erik O'Hanlon 
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Thanks Eugenio,


I'll intall the latest dev version so. How long does it typically take to run a 
subject through the thalamus pipeline typically?


Thanks again for the prompt reply. Very much appreciated.


Cheers


Erik


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, 
Eugenio 
Sent: 10 September 2018 18:00:20
To: freesurfer@nmr.mgh.harvard.edu; Freesurfer support list
Subject: Re: [Freesurfer] Using the new Thalamus tool


External Email - Use Caution

Dear Erik,
Installing only the thalamic tool is technically possible but requires a level 
of hacking that i don't want to encourage or support ;-)
Please install the new dev on a separate directory, and make FREESURFER_HOME 
point to that the directory (and source freesurfer) to run the thalamic tool. 
No need to rerun recon-all on the subjects.
Cheers
Eugenio

Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Erik O'Hanlon 

Sent: Thursday, September 6, 2018 3:44:57 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Using the new Thalamus tool


External Email - Use Caution

Hi FS Experts


I've run my data through the brainstem, hippocampus and amygdala following the 
usual Recon_all and using the developmental version downloaded and stalled 
around Jan2018. I'd like to use the new thalamus tool and am wondering if I 
need to do a full install of the latest DEV version to do so. As I am still 
working on certain aspects of the analyses I've run so far, I don't want to 
overwrite my main FS installation mid analysis. Is it possible to download the 
toolbox and add it to my current dev version or is it best just to do another 
install with teh complete new Dev version?  Is it possible to run the Thalamus 
analysis as an addtional component without having to rerun the recon_all again?


Thanks and 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


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


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


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

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Re: [Freesurfer] Using the new Thalamus tool

2018-09-11 Thread Iglesias Gonzalez, Eugenio 
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10-15 mins or so

Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Erik O'Hanlon 

Sent: Tuesday, September 11, 2018 12:32:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Using the new Thalamus tool


External Email - Use Caution

Thanks Eugenio,


I'll intall the latest dev version so. How long does it typically take to run a 
subject through the thalamus pipeline typically?


Thanks again for the prompt reply. Very much appreciated.


Cheers


Erik


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, 
Eugenio 
Sent: 10 September 2018 18:00:20
To: freesurfer@nmr.mgh.harvard.edu; Freesurfer support list
Subject: Re: [Freesurfer] Using the new Thalamus tool


External Email - Use Caution

Dear Erik,
Installing only the thalamic tool is technically possible but requires a level 
of hacking that i don't want to encourage or support ;-)
Please install the new dev on a separate directory, and make FREESURFER_HOME 
point to that the directory (and source freesurfer) to run the thalamic tool. 
No need to rerun recon-all on the subjects.
Cheers
Eugenio

Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Erik O'Hanlon 

Sent: Thursday, September 6, 2018 3:44:57 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Using the new Thalamus tool


External Email - Use Caution

Hi FS Experts


I've run my data through the brainstem, hippocampus and amygdala following the 
usual Recon_all and using the developmental version downloaded and stalled 
around Jan2018. I'd like to use the new thalamus tool and am wondering if I 
need to do a full install of the latest DEV version to do so. As I am still 
working on certain aspects of the analyses I've run so far, I don't want to 
overwrite my main FS installation mid analysis. Is it possible to download the 
toolbox and add it to my current dev version or is it best just to do another 
install with teh complete new Dev version?  Is it possible to run the Thalamus 
analysis as an addtional component without having to rerun the recon_all again?


Thanks and 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


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


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


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

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Re: [Freesurfer] Amygdala subfields segmentation

2018-09-11 Thread Iglesias Gonzalez, Eugenio 
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Dear MA
Please download the latest dev version and the command will be there
Cheers
Eugenio

Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Miguel Ángel Rivas 
Fernández 
Sent: Tuesday, September 11, 2018 12:20:55 PM
To: Freesurfer support list
Subject: [Freesurfer] Amygdala subfields segmentation


External Email - Use Caution

Hi Freesurfer developes,

I am trying to execute the hippocampal and amygdala segmentation command " 
segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 [SUBJECTS_DIR]" 
but freesurfer gave to me this error command not found.


However, when I use the command that segment only the hippocampal subfields 
(recon-all -s  -hippocampal-subfields-T2  ) I don´t have any problem.


What would be the reason?


Thanks in advance.


Best,

--
Miguel Ángel Rivas Fernández
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Re: [Freesurfer] Using the new Thalamus tool

2018-09-11 Thread Erik O'Hanlon 
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That's super.


Thanks again Eugenio,


Best regards


Erik


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, 
Eugenio 
Sent: 11 September 2018 16:44:34
To: Freesurfer support list; Freesurfer support list
Subject: Re: [Freesurfer] Using the new Thalamus tool


External Email - Use Caution

10-15 mins or so

Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Erik O'Hanlon 

Sent: Tuesday, September 11, 2018 12:32:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Using the new Thalamus tool


External Email - Use Caution

Thanks Eugenio,


I'll intall the latest dev version so. How long does it typically take to run a 
subject through the thalamus pipeline typically?


Thanks again for the prompt reply. Very much appreciated.


Cheers


Erik


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, 
Eugenio 
Sent: 10 September 2018 18:00:20
To: freesurfer@nmr.mgh.harvard.edu; Freesurfer support list
Subject: Re: [Freesurfer] Using the new Thalamus tool


External Email - Use Caution

Dear Erik,
Installing only the thalamic tool is technically possible but requires a level 
of hacking that i don't want to encourage or support ;-)
Please install the new dev on a separate directory, and make FREESURFER_HOME 
point to that the directory (and source freesurfer) to run the thalamic tool. 
No need to rerun recon-all on the subjects.
Cheers
Eugenio

Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Erik O'Hanlon 

Sent: Thursday, September 6, 2018 3:44:57 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Using the new Thalamus tool


External Email - Use Caution

Hi FS Experts


I've run my data through the brainstem, hippocampus and amygdala following the 
usual Recon_all and using the developmental version downloaded and stalled 
around Jan2018. I'd like to use the new thalamus tool and am wondering if I 
need to do a full install of the latest DEV version to do so. As I am still 
working on certain aspects of the analyses I've run so far, I don't want to 
overwrite my main FS installation mid analysis. Is it possible to download the 
toolbox and add it to my current dev version or is it best just to do another 
install with teh complete new Dev version?  Is it possible to run the Thalamus 
analysis as an addtional component without having to rerun the recon_all again?


Thanks and 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


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


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


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


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


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

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Re: [Freesurfer] Amygdala subfields segmentation

2018-09-11 Thread Miguel Ángel Rivas Fernández 
External Email - Use Caution

Hi Eugenio,


Where can I find the link for download the latest dev version?


The latest version is this?:

*freesurfer-darwin-OSX-ElCapitan-dev.tar.gz*


Thanks in advance,


Best,


El mar., 11 sept. 2018 a las 17:47, Iglesias Gonzalez, Eugenio (<
e.igles...@ucl.ac.uk>) escribió:

> External Email - Use Caution
>
> Dear MA
> Please download the latest dev version and the command will be there
> Cheers
> Eugenio
>
> Sent from my phone, please excuse brevity and typos
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas
> Fernández 
> *Sent:* Tuesday, September 11, 2018 12:20:55 PM
> *To:* Freesurfer support list
> *Subject:* [Freesurfer] Amygdala subfields segmentation
>
>
> External Email - Use Caution
>
>
> Hi Freesurfer developes,
>
> I am trying to execute the hippocampal and amygdala segmentation command "
> segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1
> [SUBJECTS_DIR]" but freesurfer gave to me this error
> *command not found. *
>
>
> However, when I use the command that segment only the hippocampal
> subfields (recon-all -s  -hippocampal-subfields-T2  of additional scan> ) I don´t have any problem.
>
>
> What would be the reason?
>
>
> Thanks in advance.
>
>
> Best,
>
> --
> *Miguel Ángel Rivas Fernández*
> ___
> 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.
>


-- 
*Miguel Ángel Rivas Fernández*
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Re: [Freesurfer] Using the new Thalamus tool

2018-09-11 Thread Douglas N. Greve 
And just to be clear, you should  run only the thalamus,  hippo, amyg, 
brainstem segmentations in dev. Do not run recon-all using the dev version.

On 09/11/2018 07:32 AM, Erik O'Hanlon wrote:
>
> External Email - Use Caution
>
> Thanks Eugenio,
>
>
> I'll intall the latest dev version so. How long does it typically take 
> to run a subject through the thalamus pipeline typically?
>
>
> Thanks again for the prompt reply. Very much appreciated.
>
>
> Cheers
>
>
> Erik
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Iglesias 
> Gonzalez, Eugenio 
> *Sent:* 10 September 2018 18:00:20
> *To:* freesurfer@nmr.mgh.harvard.edu; Freesurfer support list
> *Subject:* Re: [Freesurfer] Using the new Thalamus tool
>
> External Email - Use Caution
>
> Dear Erik,
> Installing only the thalamic tool is technically possible but requires 
> a level of hacking that i don't want to encourage or support ;-)
> Please install the new dev on a separate directory, and make 
> FREESURFER_HOME point to that the directory (and source freesurfer) to 
> run the thalamic tool. No need to rerun recon-all on the subjects.
> Cheers
> Eugenio
>
> Sent from my phone, please excuse brevity and typos
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Erik O'Hanlon 
> 
> *Sent:* Thursday, September 6, 2018 3:44:57 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] Using the new Thalamus tool
>
> External Email - Use Caution
>
> Hi FS Experts
>
>
> I've run my data through the brainstem, hippocampus and amygdala 
> following the usual Recon_all and using the developmental version 
> downloaded and stalled around Jan2018. I'd like to use the new 
> thalamus tool and am wondering if I need to do a full install of the 
> latest DEV version to do so. As I am still working on certain aspects 
> of the analyses I've run so far, I don't want to overwrite my main FS 
> installation mid analysis. Is it possible to download the toolbox and 
> add it to my current dev version or is it best just to do another 
> install with teh complete new Dev version?  Is it possible to run the 
> Thalamus analysis as an addtional component without having to rerun 
> the recon_all again?
>
>
> Thanks and regards
>
>
> 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.com 
>
> /Transforming Healthcare Education, Research and Service: RCSI 
> Strategic Plan 2018-2022 /
>
>
>
>
>
> *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.com 
>
> /Transforming Healthcare Education, Research and Service: RCSI 
> Strategic Plan 2018-2022 /
>
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Fwd: strange eTIV values

2018-09-11 Thread Miguel Ángel Rivas Fernández 
External Email - Use Caution

Hi Douglas,

Yes, I compared the eTIV values in the SPSS and in the individual
aseg.stats files and I noticed that Freesurfer export this kind of measures
with a precision of 6 decimals (eg. 1418761.222904)

The problem is that when I send these values from the txt (that contain all
the measures of the aseg.stats file) to SPSS.

I will try to send the data from the txt to the SPSS without any distortion
in the number of decimals.


Any help will be appreciated.


Best,

El jue., 6 sept. 2018 a las 20:16, Douglas N. Greve ()
escribió:

> Canyou give more info on how you arrived at those numbers? Eg, are those
> the numbers after you imported into SPSS? If you look in an individual's
> aseg.stats file, do you see the same value?
>
> On 09/06/2018 12:41 PM, Miguel Ángel Rivas Fernández wrote:
> >
> > External Email - Use Caution
> >
> > Hello Freesurfer developers,
> >
> >
> > Did hoy have chance to read this question?.
> >
> > Thank you very much for your help!
> >
> >
> > Best regards,
> >
> > -- Forwarded message -
> > From: *Miguel Ángel Rivas Fernández*  > >
> > Date: mar., 4 sept. 2018 20:37
> > Subject: strange eTIV values
> > To: Freesurfer support list  > >
> >
> >
> >
> > Hello Freesurfer experts,
> >
> >
> > When I exported the Destrieux and Desikian-Killiany volume values from
> > Freesurfer to SPSS I obtained "strange" eTIV values with 16 digits as
> > follows:
> >
> > 101,632,104,008.
> > 134,253,072,953.
> > 155,967,056,944.
> > 142,085,122,028.
> > 181,105,664,397.
> > 118,051,287,519.
> > 896,135,067,103.
> >
> > With how many decimals Freesurfer exports the eTIV values ?, that is,
> > what is the precision of this measure? I do not know how many decimals
> > this measure has.
> >
> > Another doubt, it is necessary to make some kind of numerical
> > transformation on the eTIV values before including it as a covariate
> > in the statistical analysis (for example, a logarithmic transformation).
> >
> >
> > Best,
> >
> > --
> > *Miguel Ángel Rivas Fernández*
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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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.
>


-- 
*Miguel Ángel Rivas Fernández*
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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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[Freesurfer] Download and Registration issue

2018-09-11 Thread Juliane Corlier 
External Email - Use Caution

Dear list, 

I have to issues:

1) I am trying to download a dmg installer file for Freesurfer from this 
website: 
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall 

I get an error that the page is not working/can’t be opened. 


2) I am trying to set up an account via the new registration link, but I get an 
error code saying “You are not allowed to do newaccount on this page. Login and 
try again.”

Please let me know if those are only temporary problems or how could I resolve 
them.


Thank you, 

Juliana
 




 

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[Freesurfer] questions about trac-all -stat

2018-09-11 Thread ?????? 
External Email - Use Caution

Dear experts,I have some questions about along-path analysis:
(1)how to determine the first position and last position of all subjects' 
pathway when converting all pathstats.byvoxel.txt files to a table for group 
analyses?


(2)how to complete correspondence of  points between subjects?


(3)what is values in table for group analyses,diffusion measure of center or 
something else?


Thanks!
Qianwen___
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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.