Check the User contribution section of the FreeSurfer wiki. I've put there a small script to do this.
Sent from my Nokia phone @E71 -----Msg original----- De: Marina.Lopez@crccorp.es Enviada: 22/04/2009 05:43:39 Assunto: [Freesurfer] Individual thickness data extraction from plot
Hello all,
I have the following plot of thickness value in a specific vertex for all my subjects:
My single question is: how can I take the data list of y-values (vertex thickness for all subjects) in this plot in an automatic manner (and have them in a table)? I have to extract thickness values of a lot of vertices and a quick manner will help me a lot.
Thank you very much for your help,
marina
Av�s | Aquest correu i qualsevol fitxer adjunt existent, contenen informaci� confidencial que van dirigits �nica i exclusivament al seu destinatari. Queda totalment prohibit realitzar-ne c�pies, aix� com difondre el seu contingut a altres persones que no siguin les destin�taries.
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This message and any files attached are confidential. It is intended solely for the use of the addressee(s). If you are not the intended recipient of this e-mail, please note that any review, dissemination, disclosure, alteration, printing, copying or transmission of this e-mail and/or any file transmitted with it, is prohibited and may be unlawful.
2009/4/23 Marina.Lopez@crccorp.es
Hi Pedro Paulo,
I tried to use your script (qdec-coord) to extract individual thickness data from my plot in qdec, but I have a couple of questions:
- I found the output from the instruction in a file called* lh.l.asc *in my
working directory (.../qdec/FolderOfTheSpecificAnalysis).
This file contains 160000 rows approx and 5 columns. I suppose the first column is the vertex number, but I am not sure about which value is represented in each column. What are them, please?
It's VertexNum, X, Y, Z, val
Val depends on what you ran on QDEC. If you did a thickness experiment it's tickness.
- I have tried different numbers in *set numsubject *but I have always
recieved the same output. I need to have the thickness values in the plot (1 cortical thickness value for each of 50 subjects). I am sure I am missing something. Could you please help me?
What you mean by same output?
I think you should plot the "val" for the same X,Y,Z coords
Thanks a lot for that!! and sorry for my basic questions
Marina -----freesurfer-bounces@nmr.mgh.harvard.edu escribió: -----
Para: "Marina.Lopez@crccorp.es" Marina.Lopez@crccorp.es De: "Pedro Paulo de Magalhaes Oliveira Junior" ppj@netfilter.com.br Enviado por: freesurfer-bounces@nmr.mgh.harvard.edu Fecha: 22/04/2009 11:08 cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Asunto: RES: [Freesurfer] Individual thickness data extraction from plot
Check the User contribution section of the FreeSurfer wiki. I've put there a small script to do this.
Sent from my Nokia phone @E71 -----Msg original----- De: Marina.Lopez@crccorp.es Enviada: 22/04/2009 05:43:39 Assunto: [Freesurfer] Individual thickness data extraction from plot
Hello all,
I have the following plot of thickness value in a specific vertex for all my subjects:
My single question is: how can I take the data list of y-values (vertex thickness for all subjects) in this plot in an automatic manner (and have them in a table)? I have to extract thickness values of a lot of vertices and a quick manner will help me a lot.
Thank you very much for your help,
marina
Av�s | Aquest correu i qualsevol fitxer adjunt existent, contenen informaci� confidencial que van dirigits �nica i exclusivament al seu destinatari. Queda totalment prohibit realitzar-ne c�pies, aix� com difondre el seu contingut a altres persones que no siguin les destin�taries.
Aviso | Este correo y cualquier fichero adjunto existente, contienen informaci�n confidencial que va dirigida �nica y exclusivamente a su destinatario. Est� completamente prohibido hacer copias, as� como difundir su contenido a otras personas que no sean los destinatarios.
This message and any files attached are confidential. It is intended solely for the use of the addressee(s). If you are not the intended recipient of this e-mail, please note that any review, dissemination, disclosure, alteration, printing, copying or transmission of this e-mail and/or any file transmitted with it, is prohibited and may be unlawful.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Avís | Aquest correu i qualsevol fitxer adjunt existent, contenen informació confidencial que van dirigits única i exclusivament al seu destinatari. Queda totalment prohibit realitzar-ne còpies, així com difondre el seu contingut a altres persones que no siguin les destinàtaries.
Aviso | Este correo y cualquier fichero adjunto existente, contienen información confidencial que va dirigida única y exclusivamente a su destinatario. Está completamente prohibido hacer copias, así como difundir su contenido a otras personas que no sean los destinatarios.
This message and any files attached are confidential. It is intended solely for the use of the addressee(s). If you are not the intended recipient of this e-mail, please note that any review, dissemination, disclosure, alteration, printing, copying or transmission of this e-mail and/or any file transmitted with it, is prohibited and may be unlawful.
#!/bin/bash
cd #your directory where qdec data are stored.
set numsubject = 17 #your value
for i in `seq 1 $numsubject` do mri_convert --frame $i y.mgh ../../fsaverage/surf/lh.$i.mgh mris_convert -c $i.mgh ../../fsaverage/surf/lh.inflated lh.$i.asc done
Did you use bash? It should create
lh.1.asc lh.2.asc lh.3.asc
and so on.
And then you run an equivalent script changing lh to rh
Hope it helps. ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.netfilter.com.br
2009/4/24 Marina.Lopez@crccorp.es
Thanks a lot! Then, the info that I see in the file lh.l.asc is VertexNum, X, Y, Z,(talairach?) val *for only one subject *corresponding to the number that I have put in *numsubject*, correct? ** In my case, I need to extract the precise values from the plot (cortical thickness) in a specific vertex but I have applied an *smoothing of 15mm*, and I would need those smoothed values for the specific vertex for each subject.
In my previous mail I commented that when I changed the numsubject number, and run again the script, the new file lh.l.asc contained exactly the same info than before (when I entered a different number in numsubject), so I am confused about how to prepare the script in order to recieve the info from my 53 subjects in the specific 15mm smoothed vertex.
Thanks again for everything,
Marina
**
2009/4/23 < Marina.Lopez@crccorp.es >
Hi Pedro Paulo,
I tried to use your script (qdec-coord) to extract individual thickness data from my plot in qdec, but I have a couple of questions:
- I found the output from the instruction in a file called *lh.l.asc *in my
working directory (.../qdec/FolderOfTheSpecificAnalysis).
This file contains 160000 rows approx and 5 columns. I suppose the first column is the vertex number, but I am not sure about which value is represented in each column. What are them, please?
It's VertexNum, X, Y, Z, val
Val depends on what you ran on QDEC. If you did a thickness experiment it's tickness.
- I have tried different numbers in *set numsubject *but I have always
recieved the same output. I need to have the thickness values in the plot (1 cortical thickness value for each of 50 subjects). I am sure I am missing something. Could you please help me?
What you mean by same output?
I think you should plot the "val" for the same X,Y,Z coords
Thanks a lot for that!! and sorry for my basic questions
Marina ----- freesurfer-bounces@nmr.mgh.harvard.edu escribió: -----
Para: " Marina.Lopez@crccorp.es " < Marina.Lopez@crccorp.es > De: "Pedro Paulo de Magalhaes Oliveira Junior" < ppj@netfilter.com.br > Enviado por: freesurfer-bounces@nmr.mgh.harvard.edu Fecha: 22/04/2009 11:08 cc: Freesurfer Mailing List < freesurfer@nmr.mgh.harvard.edu > Asunto: RES: [Freesurfer] Individual thickness data extraction from plot
Check the User contribution section of the FreeSurfer wiki. I've put there a small script to do this.
Sent from my Nokia phone @E71 -----Msg original----- De: Marina.Lopez@crccorp.es Enviada: 22/04/2009 05:43:39 Assunto: [Freesurfer] Individual thickness data extraction from plot
Hello all,
I have the following plot of thickness value in a specific vertex for all my subjects:
My single question is: how can I take the data list of y-values (vertex thickness for all subjects) in this plot in an automatic manner (and have them in a table)? I have to extract thickness values of a lot of vertices and a quick manner will help me a lot.
Thank you very much for your help,
marina
Av�s | Aquest correu i qualsevol fitxer adjunt existent, contenen informaci� confidencial que van dirigits �nica i exclusivament al seu destinatari. Queda totalment prohibit realitzar-ne c�pies, aix� com difondre el seu contingut a altres persones que no siguin les destin�taries.
Aviso | Este correo y cualquier fichero adjunto existente, contienen informaci�n confidencial que va dirigida �nica y exclusivamente a su destinatario. Est� completamente prohibido hacer copias, as� como difundir su contenido a otras personas que no sean los destinatarios.
This message and any files attached are confidential. It is intended solely for the use of the addressee(s). If you are not the intended recipient of this e-mail, please note that any review, dissemination, disclosure, alteration, printing, copying or transmission of this e-mail and/or any file transmitted with it, is prohibited and may be unlawful.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Avís | Aquest correu i qualsevol fitxer adjunt existent, contenen informació confidencial que van dirigits única i exclusivament al seu destinatari. Queda totalment prohibit realitzar-ne còpies, així com difondre el seu contingut a altres persones que no siguin les destinàtaries.
Aviso | Este correo y cualquier fichero adjunto existente, contienen información confidencial que va dirigida única y exclusivamente a su destinatario. Está completamente prohibido hacer copias, así como difundir su contenido a otras personas que no sean los destinatarios.
This message and any files attached are confidential. It is intended solely for the use of the addressee(s). If you are not the intended recipient of this e-mail, please note that any review, dissemination, disclosure, alteration, printing, copying or transmission of this e-mail and/or any file transmitted with it, is prohibited and may be unlawful.
Avís | Aquest correu i qualsevol fitxer adjunt existent, contenen informació confidencial que van dirigits única i exclusivament al seu destinatari. Queda totalment prohibit realitzar-ne còpies, així com difondre el seu contingut a altres persones que no siguin les destinàtaries.
Aviso | Este correo y cualquier fichero adjunto existente, contienen información confidencial que va dirigida única y exclusivamente a su destinatario. Está completamente prohibido hacer copias, así como difundir su contenido a otras personas que no sean los destinatarios.
This message and any files attached are confidential. It is intended solely for the use of the addressee(s). If you are not the intended recipient of this e-mail, please note that any review, dissemination, disclosure, alteration, printing, copying or transmission of this e-mail and/or any file transmitted with it, is prohibited and may be unlawful.
Marina,
In each subjects 'surf' directory, assuming you have run the -qcache option of recon-all (which presumably you have), there will be files named like:
lh.thickness.fwhm##.fsaverage.mgh
where ## is one of 0,5,10,15,20, and corresponds to the smoothing level. When qdec is run, and thickness and say 15mm smoothing and lh is selected, then this file is gathered from each subjects directory and concatenated into one file named y.mgh., referenced in Pedro Paulo's script.
So in Pedro Paulo's script, $numsubject corresponds to the number of subjects in your group, say, 53 subjects. the script should produce numsubjects number of .asc files, one for each subject. that is why lh.1.asc is always the same (it is the data for the first subject).
XYZ in the file are surface coordinates (not too valuable for you). the fifth column is thickness.
Nick
On Fri, 2009-04-24 at 09:02 +0200, Marina.Lopez@crccorp.es wrote:
Thanks a lot!
Then, the info that I see in the file lh.l.asc is VertexNum, X, Y, Z, (talairach?) val for only one subject corresponding to the number that I have put in numsubject, correct?
In my case, I need to extract the precise values from the plot (cortical thickness) in a specific vertex but I have applied an smoothing of 15mm, and I would need those smoothed values for the specific vertex for each subject.
In my previous mail I commented that when I changed the numsubject number, and run again the script, the new file lh.l.asc contained exactly the same info than before (when I entered a different number in numsubject), so I am confused about how to prepare the script in order to recieve the info from my 53 subjects in the specific 15mm smoothed vertex.
Thanks again for everything,
Marina
2009/4/23 < Marina.Lopez@crccorp.es > Hi Pedro Paulo, I tried to use your script (qdec-coord) to extract individual thickness data from my plot in qdec, but I have a couple of questions: - I found the output from the instruction in a file called lh.l.asc in my working directory (.../qdec/FolderOfTheSpecificAnalysis). This file contains 160000 rows approx and 5 columns. I suppose the first column is the vertex number, but I am not sure about which value is represented in each column. What are them, please? It's VertexNum, X, Y, Z, val Val depends on what you ran on QDEC. If you did a thickness experiment it's tickness. - I have tried different numbers in set numsubject but I have always recieved the same output. I need to have the thickness values in the plot (1 cortical thickness value for each of 50 subjects). I am sure I am missing something. Could you please help me? What you mean by same output? I think you should plot the "val" for the same X,Y,Z coords Thanks a lot for that!! and sorry for my basic questions Marina ----- freesurfer-bounces@nmr.mgh.harvard.edu escribió: ----- Para: " Marina.Lopez@crccorp.es " < Marina.Lopez@crccorp.es > De: "Pedro Paulo de Magalhaes Oliveira Junior" < ppj@netfilter.com.br > Enviado por: freesurfer- bounces@nmr.mgh.harvard.edu Fecha: 22/04/2009 11:08 cc: Freesurfer Mailing List < freesurfer@nmr.mgh.harvard.edu > Asunto: RES: [Freesurfer] Individual thickness data extraction from plot Check the User contribution section of the FreeSurfer wiki. I've put there a small script to do this. Sent from my Nokia phone @E71 -----Msg original----- De: Marina.Lopez@crccorp.es Enviada: 22/04/2009 05:43:39 Assunto: [Freesurfer] Individual thickness data extraction from plot Hello all, I have the following plot of thickness value in a specific vertex for all my subjects: My single question is: how can I take the data list of y-values (vertex thickness for all subjects) in this plot in an automatic manner (and have them in a table)? I have to extract thickness values of a lot of vertices and a quick manner will help me a lot. Thank you very much for your help, marina Av�s | Aquest correu i qualsevol fitxer adjunt existent, contenen informaci� confidencial que van dirigits �nica i exclusivament al seu destinatari. Queda totalment prohibit realitzar-ne c�pies, aix� com difondre el seu contingut a altres persones que no siguin les destin�taries. Aviso | Este correo y cualquier fichero adjunto existente, contienen informaci�n confidencial que va dirigida �nica y exclusivamente a su destinatario. Est� completamente prohibido hacer copias, as� como difundir su contenido a otras personas que no sean los destinatarios. This message and any files attached are confidential. It is intended solely for the use of the addressee(s). If you are not the intended recipient of this e-mail, please note that any review, dissemination, disclosure, alteration, printing, copying or transmission of this e-mail and/or any file transmitted with it, is prohibited and may be unlawful. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Avís | Aquest correu i qualsevol fitxer adjunt existent, contenen informació confidencial que van dirigits única i exclusivament al seu destinatari. Queda totalment prohibit realitzar-ne còpies, així com difondre el seu contingut a altres persones que no siguin les destinàtaries. Aviso | Este correo y cualquier fichero adjunto existente, contienen información confidencial que va dirigida única y exclusivamente a su destinatario. Está completamente prohibido hacer copias, así como difundir su contenido a otras personas que no sean los destinatarios. This message and any files attached are confidential. It is intended solely for the use of the addressee(s). If you are not the intended recipient of this e-mail, please note that any review, dissemination, disclosure, alteration, printing, copying or transmission of this e-mail and/or any file transmitted with it, is prohibited and may be unlawful.Avís | Aquest correu i qualsevol fitxer adjunt existent, contenen informació confidencial que van dirigits única i exclusivament al seu destinatari. Queda totalment prohibit realitzar-ne còpies, així com difondre el seu contingut a altres persones que no siguin les destinàtaries.
Aviso | Este correo y cualquier fichero adjunto existente, contienen información confidencial que va dirigida única y exclusivamente a su destinatario. Está completamente prohibido hacer copias, así como difundir su contenido a otras personas que no sean los destinatarios.
This message and any files attached are confidential. It is intended solely for the use of the addressee(s). If you are not the intended recipient of this e-mail, please note that any review, dissemination, disclosure, alteration, printing, copying or transmission of this e- mail and/or any file transmitted with it, is prohibited and may be unlawful.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Marina.Lopez＠crccorp.es -
Nick Schmansky -
Pedro Paulo de Magalhaes Oliveira Junior -
Pedro Paulo de Magalhães Oliveira Junior