[Freesurfer] Parenchyma over CSF rartio

[Mahmoud]

Dear all,

I used the the 3 steps of longitudinal analysis explained in freesurfer
longitudinal tutorial and need to compute the ratio Parenchyma/CSF for each
of time points. Is this equivalent to compute the  (total gray matter
volume + total cortical matter volume)/CSF from aseg.stats file ?

Thank you,
Mahmoud
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Re: [Freesurfer] mri_glmfit-sim error

[Douglas Greve]

Can you run mri_glmfit-sim with --debug as the first option, then 
capture the output by putting "|& tee new.log" (no quotes) and post new.log

doug

On 10/24/14 9:33 PM, wrz891...@163.com wrote:
Thanks   a lot !  It just stopped woking  at the  last line and it 
didn't generate the  results ,so I didn't konw how to deal whit it .



wrz891...@163.com

*From:* Douglas N Greve 
*Date:* 2014-10-25 00:32
*To:* freesurfer 
*Subject:* Re: [Freesurfer] mri_glmfit-sim error
what is the error? I did not see anything in the log file.
On 10/24/2014 04:18 AM, wrz891...@163.com wrote:
>
> Dear Freesurfer Experts,
> I'm a new freesurfer, it comes some errors whendoing mri_glmfit-sim
> analysis. I don't konw what is wrong about it ,it just never
work when
> # doning at mri_glmfit-sim ,and my
> commandsas follwing.
>
>
> mris_preproc --fsgd advsnc.fsgd \
> --cache-in thickness.fwhm10.fsaverage \
> --target fsaverage --hemi lh \
> --out lh.advsnc.thickness.10.mgh
>
> mri_glmfit --y lh.advsnc.thickness.10.mgh --fsgd advsnc.fsgd --C
> AD-NC.interecpt.mtx --surf fsaverage lh --cortex --glmdir
> lh.advsnc.glmdir
>
> mri_glmfit-sim \
> --glmdir lh.advsnc.glmdir \
> --cache 4 neg\
> --cwp 0.05\
> --2spaces
>
> Many thanks!
>

> wrz891...@163.com 
>
>
>
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Re: [Freesurfer] permission denied

[Douglas Greve]

Try chmod -R a+X freesurfer/bin


On 10/26/14 1:57 PM, Ali Radaideh wrote:

Dear FreeSurfer users,

I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs 
has the latest version of freesurfer 5.3.0 while the others have the 
version 5.0.0. The PC that is installed with the latest version 
freesurfer 5.3.0 does not allow me to run any command and everytime I 
try a command such such as tkmedit i get the following error

/usr/local/freesurfer/bin/tkmedit: permission denied.

I have tried to change the permission settings
sudo chown -R imaging:imaging freesurfer

but did not work.

Any ideas why is this happening although I have done the same thing to 
other PCs and they are working fine.


Thanks in advance,
Ali

--
/Ali M. Al-Radaideh. PhD
Assistant Professor
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 390 ext.5422, 5355, 5364
Email: ali.radai...@hu.edu.jo 
/
/webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/



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Re: [Freesurfer] (no subject)

[Douglas Greve]

Sorry, nothing has been decided yet.
doug


On 10/26/14 4:00 AM, Nagy Szilvia wrote:


Dear Freesurfers,

I would interest about when will the freesurfer course takes place  in 
2015? I realy need this info due to a travel grant deadline.


Thanks,

Szilvia Nagy



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Re: [Freesurfer] Changing subject names after processing

[Janosch Linkersdörfer]

Great, I'll do that. Thank you very much!

Am 26.10.2014 um 17:12 schrieb Martin Reuter :

> One possible solution:
> Rename the time point in cross, in the base txt file (directly under the base 
> directory, something with tps in it), in the base/mri/transforms/* files and 
> in the long directory names and long/mri/transform files. I think these are 
> all the places where subject names are stored, but no guarantee.
> Best Martin
> 
> 
> Sent via my smartphone, please excuse brevity.
> 
>  Original message 
> From: Janosch Linkersdörfer
> Date:10/26/2014 6:05 PM (GMT-05:00)
> To: mreu...@nmr.mgh.harvard.edu
> Cc: Freesurfer support list
> Subject: Re: [Freesurfer] Changing subject names after processing
> 
> Hi Martin and Doug,
> 
> thanks for your answers!
> 
> >>> theoretically it would be sufficient 
> to rename the longitudinal directories accordingly as the base should 
> not change at all, only some of the filenames -- not tested!
> 
> Did I understand it correctly that if one has gone through the whole 
> longitudinal processing stream (including corrections etc.), could one not 
> remove the crosses and the base and just rename the longs to the new name as 
> any further processing/stats is carried out only with them?
> 
> Thanks,
> 
> Janosch
> 
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
> 


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Re: [Freesurfer] Changing subject names after processing

[Martin Reuter]

One possible solution:
Rename the time point in cross, in the base txt file (directly under the base 
directory, something with tps in it), in the base/mri/transforms/* files and in 
the long directory names and long/mri/transform files. I think these are all 
the places where subject names are stored, but no guarantee.
Best Martin


Sent via my smartphone, please excuse brevity.

 Original message From: Janosch Linkersdörfer 
 Date:10/26/2014  6:05 PM  (GMT-05:00) 
To: mreu...@nmr.mgh.harvard.edu Cc: Freesurfer support 
list  Subject: Re: [Freesurfer] 
Changing subject names after processing 
Hi Martin and Doug,

thanks for your answers!

>>> theoretically it would be sufficient 
to rename the longitudinal directories accordingly as the base should 
not change at all, only some of the filenames -- not tested!

Did I understand it correctly that if one has gone through the whole 
longitudinal processing stream (including corrections etc.), could one not 
remove the crosses and the base and just rename the longs to the new name as 
any further processing/stats is carried out only with them?

Thanks,

Janosch


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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Changing subject names after processing

[Martin Reuter]

Hi Janosch,

You could do that, but no further processing will be possible. The long runs 
take the asegs from the cross sectional runs and many other results from the 
base. Without base and long they can probably be used for statistical analysis 
(the roi stuff should work ,  for surfaces the base may be necessary). So in 
short it will create a mess. Some things may still work others not.
Martin


Sent via my smartphone, please excuse brevity.

 Original message From: Janosch Linkersdörfer 
 Date:10/26/2014  6:05 PM  (GMT-05:00) 
To: mreu...@nmr.mgh.harvard.edu Cc: Freesurfer support 
list  Subject: Re: [Freesurfer] 
Changing subject names after processing 
Hi Martin and Doug,

thanks for your answers!

>>> theoretically it would be sufficient 
to rename the longitudinal directories accordingly as the base should 
not change at all, only some of the filenames -- not tested!

Did I understand it correctly that if one has gone through the whole 
longitudinal processing stream (including corrections etc.), could one not 
remove the crosses and the base and just rename the longs to the new name as 
any further processing/stats is carried out only with them?

Thanks,

Janosch


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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Changing subject names after processing

[Janosch Linkersdörfer]

Hi Martin and Doug,

thanks for your answers!

>>> theoretically it would be sufficient 
to rename the longitudinal directories accordingly as the base should 
not change at all, only some of the filenames -- not tested!

Did I understand it correctly that if one has gone through the whole 
longitudinal processing stream (including corrections etc.), could one not 
remove the crosses and the base and just rename the longs to the new name as 
any further processing/stats is carried out only with them?

Thanks,

Janosch
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Re: [Freesurfer] Freesurfer course 2015 Brazil

[andrhorvath]

Thank you very much for your reply!

Cheers,
   Andrea





From: Pedro Paulo de Magalhães Oliveira Junior
Sent: ‎Sunday‎, ‎October‎ ‎26‎, ‎2014 ‎7‎:‎19‎ ‎PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Andrea Horváth





We don't have a date yet. An estimate would be March/April



-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441




On Fri, Oct 24, 2014 at 3:00 PM, Andrea Horváth  wrote:


Dear Freesurfers,

Does anyone know the exact date of the upcoming Freesurfer course in Sao Paolo, 
Brazil? I know that it is too early, but we need the date for a travel grant 
application. Thank you for your help in advance!
Cheers,
   Andrea





-- 


Andrea Horvath M.D.
PhD Fellow
Diagnostic Centre of Pécs


horvath.andr...@pte.hu


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Re: [Freesurfer] Freesurfer course 2015 Brazil

[Pedro Paulo de Magalhães Oliveira Junior]

We don't have a date yet. An estimate would be March/April

-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441


On Fri, Oct 24, 2014 at 3:00 PM, Andrea Horváth 
wrote:

> Dear Freesurfers,
>
> Does anyone know the exact date of the upcoming Freesurfer course in Sao
> Paolo, Brazil? I know that it is too early, but we need the date for a
> travel grant application. Thank you for your help in advance!
> Cheers,
>Andrea
>
>
>
> --
> *Andrea Horvath M.D.*
> PhD Fellow
> Diagnostic Centre of Pécs
> horvath.andr...@pte.hu
>
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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.
>
>
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[Freesurfer] permission denied

[Ali Radaideh]

Dear FreeSurfer users,

I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs has
the latest version of freesurfer 5.3.0 while the others have the version
5.0.0. The PC that is installed with the latest version freesurfer 5.3.0
does not allow me to run any command and everytime I try a command such
such as tkmedit i get the following error
/usr/local/freesurfer/bin/tkmedit: permission denied.

I have tried to change the permission settings
sudo chown -R imaging:imaging freesurfer

but did not work.

Any ideas why is this happening although I have done the same thing to
other PCs and they are working fine.

​Thanks in advance,
Ali​

-- 








*Ali M. Al-Radaideh. PhDAssistant ProfessorHead of Department of Medical
ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite
University, Zarqa, JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo *
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
*
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[Freesurfer] (no subject)

[Nagy Szilvia]

Dear Freesurfers,

I would interest about when will the freesurfer course takes place  in
2015? I realy need this info due to a travel grant deadline.

Thanks,

Szilvia Nagy
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