I've checked my table and included an empty line after the last subject. I made my table first in excell and I have also to include an empty space after it cell content. And it worked.
Thank you for your help,
Best regards, Carolina
Em 12/08/2011 12:58, freesurfer-requ...@nmr.mgh.harvard.edu escreveu:
To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
freesurfer-requ...@nmr.mgh.harvard.edu
You can reach the person managing the list at
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. QATools (Knut J Bjuland)
2. Error with mri_preproc (Antonella Kis)
3. Re: Fwd: qdec (Nick Schmansky)
4. Re: Tracula and number of fibres per voxel (J?rgen H?nggi)
----------------------------------------------------------------------
Message: 1
Date: Fri, 12 Aug 2011 17:13:35 +0200
From: Knut J Bjuland
Subject: [Freesurfer ] QATools
To: "freesurfer@nmr.mgh.harvard.edu >> Freesurfer Mailing List"
Message-ID: <4e45431f.6000...@hotmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi
I have looked at QAtools at
https://surfer.nmr.mgh.harvard.edu/fswiki/QATools.
But there seem to be some trouble. I have fixed up the wrong file issue
but there is problem with my files being in the wrong order. Should I
try to reorder the files to reflect the new situation or is there
something wrong with my processing of recon-all.
Knut J
mri/transforms/talairach.xfm mri/rawavg.mgz
mri/rawavg.mgz mri/orig.mgz
mri/orig.mgz mri/nu.mgz
mri/transforms/talairach.auto.xfm mri/transforms/talairach.auto.xfm
mri/nu.mgz mri/transforms/talairach.xfm
.......... .........
.......... .........
......... . .........
14 outputfiles_NOTOK
-------------- next part --------------
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------------------------------
Message: 2
Date: Fri, 12 Aug 2011 08:50:02 -0700 (PDT)
From: Antonella Kis
Subject: [Freesurfer] Error with mri_preproc
To: "fis...@nmr.mgh.harvard.edu"
Cc: "freesurfer@nmr.mgh.harvard.edu"
Message-ID:
<1313164202.99199.yahoomail...@web121718.mail.ne1.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear freesurfers,
I am trying to see what are the group differences in cortical thickness of patients with right and left FLE compared to controls using the GLM.
I created a txt file in gedit called my_age_fsgd.txt (please see the attachment) containing my subjects (patients and controls) and their age. I am not interested in doing a study versus gender just versus age.
Following the instructions from the tutorial I was running the mri_preproc:
mris_preproc --fsgd my_age_fsgd.txt \
? --target fsaverage \
? --hemi lh \?????????????????????? ?
? --meas thickness \
? --out lh.gender_age.thickness.mgh
?
but I got an error: ERROR: no subjects specified. Also, what should be my contrast vector if I am not interested in considering the gender. I found in one tutorial that I should create age.mat if it does not exist and it should contain this line:
????????????????????????????????????
0 0 1
Why this numbers?
Can anyone give a hint please in how to eliminate my error and how to create the contrast vector in order to take in consideration only my subject's age?
Many thanks,
Antonella
-------------- next p art --------------
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------------------------------
Message: 3
Date: Fri, 12 Aug 2011 11:51:11 -0400 (EDT)
From: "Nick Schmansky"
Subject: Re: [Freesurfer] Fwd: qdec
To: "carolina.mr"
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<50022.128.148.107.167.1313164271.squir...@mail.nmr.mgh.harvard.edu>
Content-Type: text/plain;charset=iso-8859-1
Carolina,
make sure the file has an empty line at the very end of the file. If that
still doesnt work, you can send me the file and i can have a look.
n.
>
>
> Mensagem original
De: carolina.mr
> < carolina...@uol.com.br >
Para:
> freesurfer-requ...@nmr.mgh.harvard.edu
Assunto:
> qdec
Enviada: 12/08/2011 00:43
>
>
>
>
>
>
Reading
> /Applications/freesurfer/tktools/tkUtils.tcl
>
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 4
Date: Fri, 12 Aug 2011 17:58:41 +0200
From: J?rgen H?nggi
Subject: Re: [Freesurfer] Tracula and number of fibres per voxel
To: Priti Srinivasan
Cc: Freesurfer Mailinglist
Message-ID:
Content-Type: text/plain; charset="ISO-8859-1"
Hi Priti
Thanks for the information. Is there any rule of thumb or recommendations
wrt to how many anisotropic compartments in a voxel in bedpostx should be
modeled?
We sampled 64 non-collinear diffusion directions and I ask me whether this
is enough for modeling 3 anisotropic compartments?
Thanks
Cheers
J?rgen
On [DATE], "Priti Srinivasan" <[ADDRESS]> wrote:
> Hi J?rgen,
>
> To chage the no. of anisotropic compartments in a voxel in bedpostx you
> might have to run bedpostx_seychelles outside of tracula (instead of
> running trac-all -bedp)
>
> bedpostx_seychelles -n 3
>
> You can try this out to see if it works for you.
>
> -Priti
>
>
>> Dear Tracula experts
>>
>> Is it possible to change the number of fibres per voxel in bedpostx (from
>> 2
>> to 3) within the trac-all command?
>>
>> I did not see any option for that.
>>
>> Thanks in advance
>> Cheers
>> J?rgen
>>
>> ----------------------------------------------------------------------------
>> J?rgen H?nggi, Ph.D.
>> Division Neuropsychology
>> Institute of Psychology
>> University of Zurich
>> Binzmuehlestrasse 14, PO Box 25
>> 8050 Zurich, Switzerland
>> 0041 44 635 73 97 (phone office)
>> 0041 76 445 86 84 (phone mobile)
>> 0041 44 635 74 09 (fax office)
>> BIN 4.D.04 (office room number)
>> j.haenggi[at]psychologie.uzh.ch (email)
>> http://www.psychologie.uzh.ch/neuropsy/ (website)
>> http://www.juergenhaenggi.ch (private website)
>>
>> This e-mail (and any attachment/s) contains confidential and/or privileged
>> information. If you are not the intended recipient (or have received this
>> e-mail in error) please notify the sender immediately and destroy this
>> e-mail. Any unauthorised copying, disclosure or distribution of the
>> material in this e-mail is strictly forbidden.
>> ------------------------------------------------------------ ----------------
>>
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain pat ient information, please contact the sender and
> properly
> dispose of the e-mail.
>
----------------------------------------------------------------------------
J?rgen H?nggi, Ph.D.
Division Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
j.haenggi[at]psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged
information. If you are not the intended recipient (or have received this
e-mail in error) please notify the sender immediately and destroy this
e-mail. Any unauthorised copying, disclosure or distributio n of the
material in this e-mail is strictly forbidden.
----------------------------------------------------------------------------
------------------------------
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
End of Freesurfer Digest, Vol 90, Issue 54
******************************************
Em 12/08/2011 12:58, freesurfer-requ...@nmr.mgh.harvard.edu escreveu:
To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
freesurfer-requ...@nmr.mgh.harvard.edu
You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. QATools (Knut J Bjuland)
2. Error with mri_preproc (Antonella Kis)
3. Re: Fwd: qdec (Nick Schmansky)
4. Re: Tracula and number of fibres per voxel (J?rgen H?nggi)
----------------------------------------------------------------------
Message: 1
Date: Fri, 12 Aug 2011 17:13:35 +0200
From: Knut J Bjuland
Subject: [Freesurfer ] QATools
To: "freesurfer@nmr.mgh.harvard.edu >> Freesurfer Mailing List"
Message-ID: <4e45431f.6000...@hotmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi
I have looked at QAtools at
https://surfer.nmr.mgh.harvard.edu/fswiki/QATools.
But there seem to be some trouble. I have fixed up the wrong file issue
but there is problem with my files being in the wrong order. Should I
try to reorder the files to reflect the new situation or is there
something wrong with my processing of recon-all.
Knut J
mri/transforms/talairach.xfm mri/rawavg.mgz
mri/rawavg.mgz mri/orig.mgz
mri/orig.mgz mri/nu.mgz
mri/transforms/talairach.auto.xfm mri/transforms/talairach.auto.xfm
mri/nu.mgz mri/transforms/talairach.xfm
.......... .........
.......... .........
......... . .........
14 outputfiles_NOTOK
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: recon_all_output_file_checker
Url: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20110812/04b85c15/attachment-0001.pl
------------------------------
Message: 2
Date: Fri, 12 Aug 2011 08:50:02 -0700 (PDT)
From: Antonella Kis
Subject: [Freesurfer] Error with mri_preproc
To: "fis...@nmr.mgh.harvard.edu"
Cc: "freesurfer@nmr.mgh.harvard.edu"
Message-ID:
<1313164202.99199.yahoomail...@web121718.mail.ne1.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear freesurfers,
I am trying to see what are the group differences in cortical thickness of patients with right and left FLE compared to controls using the GLM.
I created a txt file in gedit called my_age_fsgd.txt (please see the attachment) containing my subjects (patients and controls) and their age. I am not interested in doing a study versus gender just versus age.
Following the instructions from the tutorial I was running the mri_preproc:
mris_preproc --fsgd my_age_fsgd.txt \
? --target fsaverage \
? --hemi lh \?????????????????????? ?
? --meas thickness \
? --out lh.gender_age.thickness.mgh
?
but I got an error: ERROR: no subjects specified. Also, what should be my contrast vector if I am not interested in considering the gender. I found in one tutorial that I should create age.mat if it does not exist and it should contain this line:
????????????????????????????????????
0 0 1
Why this numbers?
Can anyone give a hint please in how to eliminate my error and how to create the contrast vector in order to take in consideration only my subject's age?
Many thanks,
Antonella
-------------- next p art --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20110812/8aca3ea3/attachment-0001.html
------------------------------
Message: 3
Date: Fri, 12 Aug 2011 11:51:11 -0400 (EDT)
From: "Nick Schmansky"
Subject: Re: [Freesurfer] Fwd: qdec
To: "carolina.mr"
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<50022.128.148.107.167.1313164271.squir...@mail.nmr.mgh.harvard.edu>
Content-Type: text/plain;charset=iso-8859-1
Carolina,
make sure the file has an empty line at the very end of the file. If that
still doesnt work, you can send me the file and i can have a look.
n.
>
>
> Mensagem original
De: carolina.mr
> < carolina...@uol.com.br >
Para:
> freesurfer-requ...@nmr.mgh.harvard.edu
Assunto:
> qdec
Enviada: 12/08/2011 00:43
>
Hello,
>
When I load my qdec table it apears an error that I don't know how to
> solve. It says that there is not a nemline after my last subject.
> solve. It says that there is not a nemline after my last subject.
>
Does anybody know how to solve it?
>
The text that appears in my terminal is pasted bellow.
>
Thank you, Carolina
>
Reading
> /Applications/freesurfer/tktools/tkUtils.tcl
>
Using /Applications/freesurfer//lib/tcl/fsgdfPlot.tcl
>
Loading data table /analise/qdec/MS1qdec.table.dat...
>
QdecDataTable::Load: will attempt to open as Mac text file...
>
Number of columns: ??148
>
fsid column: ?? ?? ?? ??1
>
Number of factors: ??147
>
Number of subjects: 59
>
ERROR: QdecDataTable::Load: problem parsing file
> /analise/qdec/MS1qdec.table.dat
> /analise/qdec/MS1qdec.table.dat
>
This line did not appear to end with a newline:
>
P29EX1 male> style="white-space: pre;"> 30.30
> MSRR 19.01> style="white-space: pre;"> 1.04
> 5690.0 814> style="white-space: pre;"> 456
> 525 318> style="white-space: pre;"> 419
> 2532 1.5607> style="white-space: pre;"> 0.543
> 0.5892 0.8853> style="white-space: pre;"> 0.6859
> 0.5815 0.4185> style="white-space: pre;"> 1.5971
> 0.6467 > >0.5325 0.9628> style="white-space: pre;"> 1.1932
> 0.6492 0.3508> style="white-space: pre;"> 1.4455
> 0.5872 0.5233> style="white-space: pre;"> 0.8733
> 0.7933 0.6767> style="white-space: pre;"> 0.3233
> 1.3922 0.6489> style="white-space: pre;"> 0.4694
> 0.8967 1.1003> style="white-space: pre;"> 0.7251
> 0.2749 1.8263> style="white-space: pre;"> ; 0.5703
> 0.639 0.989
> 1.1874 0.5183> style="white-space: pre;"> 0.4817
> 1.5847 0.5872> style="white-space: pre;"> 0.5642
> 0.9197 0.949> style="white-space: pre;"> 0.6148
> 0.3852
> MSRR 19.01> style="white-space: pre;"> 1.04
> 5690.0 814> style="white-space: pre;"> 456
> 525 318> style="white-space: pre;"> 419
> 2532 1.5607> style="white-space: pre;"> 0.543
> 0.5892 0.8853> style="white-space: pre;"> 0.6859
> 0.5815 0.4185> style="white-space: pre;"> 1.5971
> 0.6467
> 0.6492 0.3508> style="white-space: pre;"> 1.4455
> 0.5872 0.5233> style="white-space: pre;"> 0.8733
> 0.7933 0.6767> style="white-space: pre;"> 0.3233
> 1.3922 0.6489> style="white-space: pre;"> 0.4694
> 0.8967 1.1003> style="white-space: pre;"> 0.7251
> 0.2749 1.8263> style="white-space: pre;"> ; 0.5703
> 0.639 0.989
> 1.1874 0.5183> style="white-space: pre;"> 0.4817
> 1.5847 0.5872> style="white-space: pre;"> 0.5642
> 0.9197 0.949> style="white-space: pre;"> 0.6148
> 0.3852
>
Error loading the data table.
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 4
Date: Fri, 12 Aug 2011 17:58:41 +0200
From: J?rgen H?nggi
Subject: Re: [Freesurfer] Tracula and number of fibres per voxel
To: Priti Srinivasan
Cc: Freesurfer Mailinglist
Message-ID:
Content-Type: text/plain; charset="ISO-8859-1"
Hi Priti
Thanks for the information. Is there any rule of thumb or recommendations
wrt to how many anisotropic compartments in a voxel in bedpostx should be
modeled?
We sampled 64 non-collinear diffusion directions and I ask me whether this
is enough for modeling 3 anisotropic compartments?
Thanks
Cheers
J?rgen
On [DATE], "Priti Srinivasan" <[ADDRESS]> wrote:
> Hi J?rgen,
>
> To chage the no. of anisotropic compartments in a voxel in bedpostx you
> might have to run bedpostx_seychelles outside of tracula (instead of
> running trac-all -bedp)
>
> bedpostx_seychelles -n 3
>
> You can try this out to see if it works for you.
>
> -Priti
>
>
>> Dear Tracula experts
>>
>> Is it possible to change the number of fibres per voxel in bedpostx (from
>> 2
>> to 3) within the trac-all command?
>>
>> I did not see any option for that.
>>
>> Thanks in advance
>> Cheers
>> J?rgen
>>
>> ----------------------------------------------------------------------------
>> J?rgen H?nggi, Ph.D.
>> Division Neuropsychology
>> Institute of Psychology
>> University of Zurich
>> Binzmuehlestrasse 14, PO Box 25
>> 8050 Zurich, Switzerland
>> 0041 44 635 73 97 (phone office)
>> 0041 76 445 86 84 (phone mobile)
>> 0041 44 635 74 09 (fax office)
>> BIN 4.D.04 (office room number)
>> j.haenggi[at]psychologie.uzh.ch (email)
>> http://www.psychologie.uzh.ch/neuropsy/ (website)
>> http://www.juergenhaenggi.ch (private website)
>>
>> This e-mail (and any attachment/s) contains confidential and/or privileged
>> information. If you are not the intended recipient (or have received this
>> e-mail in error) please notify the sender immediately and destroy this
>> e-mail. Any unauthorised copying, disclosure or distribution of the
>> material in this e-mail is strictly forbidden.
>> ------------------------------------------------------------ ----------------
>>
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain pat ient information, please contact the sender and
> properly
> dispose of the e-mail.
>
----------------------------------------------------------------------------
J?rgen H?nggi, Ph.D.
Division Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
j.haenggi[at]psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged
information. If you are not the intended recipient (or have received this
e-mail in error) please notify the sender immediately and destroy this
e-mail. Any unauthorised copying, disclosure or distributio n of the
material in this e-mail is strictly forbidden.
----------------------------------------------------------------------------
------------------------------
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
End of Freesurfer Digest, Vol 90, Issue 54
******************************************
_______________________________________________ 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.
