Re: [Freesurfer] eccentricity and polar maps?

[Douglas N Greve]

Hi Dan, I just put rtview back on the server. You can also run 
tksurfer-sess as shown on the web page to view the angles (tksurfer-sess 
-a rtopy.self.?h -s sessid -map angle)
doug

On 08/03/2012 05:15 PM, dgw wrote:
> Hi,
>
> I am trying to process a small amount of retinotopy data. I have one run
> of positive polar stimuli with 64 second cycle and another of positive
> eccentricity data with a 64 second cycle (I realize that I could use
> better parameters). I have followed the tutorial on
>
> http://www.freesurfer.net/fswiki/FsFastIndividualRetinotopyAnalysis
>
> I was able to get through all of the steps on that page, but now I want to
> look at the polar and eccentricity maps. I couldn't find anything on the
> wiki about them. I did find this post on the list:
>
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-February/022464.html
>
> ; however, the rtview script is not located there on the ftp server (I
> assume it got deleted at some point). Can anyone point me to the next
> step(s)?
>
> Thanks,
> Dan
> ___
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>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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[Freesurfer] eccentricity and polar maps?

[dgw]

Hi,

I am trying to process a small amount of retinotopy data. I have one run
of positive polar stimuli with 64 second cycle and another of positive
eccentricity data with a 64 second cycle (I realize that I could use
better parameters). I have followed the tutorial on

http://www.freesurfer.net/fswiki/FsFastIndividualRetinotopyAnalysis

I was able to get through all of the steps on that page, but now I want to
look at the polar and eccentricity maps. I couldn't find anything on the
wiki about them. I did find this post on the list:

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-February/022464.html

; however, the rtview script is not located there on the ftp server (I
assume it got deleted at some point). Can anyone point me to the next
step(s)?

Thanks,
Dan
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Re: [Freesurfer] expert option error in recon-all

[Mehul Sampat]

Hi James,
I had the same issue. The following workaround was mentioned on the FS
mailing list:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20335.html
It works for me.
Mehul

On Fri, Aug 3, 2012 at 10:11 AM, Douglas N Greve
wrote:

> Delete that dir and run recon-all with -debug as the first option. Pipe
> the output to a file, eg,
> recon-all -debug ... |& tee recon-all.log
> And send me recon-all.log. Note it will likely be very big!
> doug
>
> On 08/03/2012 12:52 PM, james pardon wrote:
> > works fine. Even I can cp expert.opts to scripts folder on my own.
> > Sorry forgot to reply all at first
> >
> > On Fri, Aug 3, 2012 at 9:13 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > So /home/dir/subject/subname/scripts does not exist? If so that is
> > wrong. What happens if you
> > mkdir /home/dir/subject/subname/scripts
> > doug
> >
> >
> > On 08/03/2012 12:09 PM, james pardon wrote:
> >
> > Nick or Doug could you help us here?
> >
> > On Fri, Aug 3, 2012 at 8:05 PM, Bruce Fischl
> >  > 
> >  > >> wrote:
> >
> > Hi James
> > can you post to the list so others can answer? I'm not
> > sure what's
> > going on, but Nick or Doug might
> >
> >
> > Bruce
> >
> > On Fri, 3 Aug 2012, james pardon wrote:
> >
> > Hi Bruce,
> > subject's folder is empty,  there is no scripts folder,
> or
> > anything else.
> > Again if I omit -expert everything works fine.
> >
> > Thanks
> >
> > On Fri, Aug 3, 2012 at 7:29 PM, Bruce Fischl
> >  > 
> >  > >>
> >
> > wrote:
> >   Hi James
> >
> >   what happens if you run:
> >
> >   ls -l
> > /home/dir/subject/subname/scripts/expert-options
> >   touch
> > /home/dir/subject/subname/scripts/expert-options
> >
> >   Bruce
> >
> >   On Fri, 3 Aug 2012, james pardon wrote:
> >
> > Dear all,
> > I'm trying to pass the following flags for
> > mri_normalize through -expert
> > flag in recon-all, with a file, named
> > expert.opts
> > with the following single
> > line:
> > mri_normalize -b 20 -n 5
> >
> > my command line is:
> >
> > recon-all -i inputfile -subject subname
> > -all -expert
> > /expert.opts
> >
> > I receive the following error:
> >
> > cp: cannot create regular file:
> >
> > '/home/dir/subject/subname/scripts/expert-options'
> >
> > The directory of the subject has been
> > created, but
> > it is completely empty.
> > At first glance I thought it might be some
> > sort of
> > permission problems,
> > however I have rwx permission for all the
> > paths
> > (even running under the root
> > username the same error comes up). Secondly,
> I
> > checked my disk quota, it is
> > completely fine. Please note that, if I do
> > not pass
> > -expert flag recon-all
> > works completely fine.
> >
> > Any input is much appreciated.
> >
> > Regards,
> > James
> >
> >
> >
> >
> > 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.
> >
> >
> >
> >
> >
> > --
> > Douglas N. Greve, P

Re: [Freesurfer] expert option error in recon-all

[Douglas N Greve]

Delete that dir and run recon-all with -debug as the first option. Pipe 
the output to a file, eg,
recon-all -debug ... |& tee recon-all.log
And send me recon-all.log. Note it will likely be very big!
doug

On 08/03/2012 12:52 PM, james pardon wrote:
> works fine. Even I can cp expert.opts to scripts folder on my own. 
> Sorry forgot to reply all at first
>
> On Fri, Aug 3, 2012 at 9:13 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> So /home/dir/subject/subname/scripts does not exist? If so that is
> wrong. What happens if you
> mkdir /home/dir/subject/subname/scripts
> doug
>
>
> On 08/03/2012 12:09 PM, james pardon wrote:
>
> Nick or Doug could you help us here?
>
> On Fri, Aug 3, 2012 at 8:05 PM, Bruce Fischl
>  
>  >> wrote:
>
> Hi James
> can you post to the list so others can answer? I'm not
> sure what's
> going on, but Nick or Doug might
>
>
> Bruce
>
> On Fri, 3 Aug 2012, james pardon wrote:
>
> Hi Bruce,
> subject's folder is empty,  there is no scripts folder, or
> anything else.
> Again if I omit -expert everything works fine.
>
> Thanks
>
> On Fri, Aug 3, 2012 at 7:29 PM, Bruce Fischl
>  
>  >>
>
> wrote:
>   Hi James
>
>   what happens if you run:
>
>   ls -l
> /home/dir/subject/subname/scripts/expert-options
>   touch
> /home/dir/subject/subname/scripts/expert-options
>
>   Bruce
>
>   On Fri, 3 Aug 2012, james pardon wrote:
>
> Dear all,
> I'm trying to pass the following flags for
> mri_normalize through -expert
> flag in recon-all, with a file, named
> expert.opts
> with the following single
> line:
> mri_normalize -b 20 -n 5
>
> my command line is:
>
> recon-all -i inputfile -subject subname
> -all -expert
> /expert.opts
>
> I receive the following error:
>
> cp: cannot create regular file:
>
> '/home/dir/subject/subname/scripts/expert-options'
>
> The directory of the subject has been
> created, but
> it is completely empty.
> At first glance I thought it might be some
> sort of
> permission problems,
> however I have rwx permission for all the
> paths
> (even running under the root
> username the same error comes up). Secondly, I
> checked my disk quota, it is
> completely fine. Please note that, if I do
> not pass
> -expert flag recon-all
> works completely fine.
>
> Any input is much appreciated.
>
> Regards,
> James
>
>
>
>
> 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.
>
>
>
>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Nu

Re: [Freesurfer] expert option error in recon-all

[james pardon]

works fine. Even I can cp expert.opts to scripts folder on my own. Sorry
forgot to reply all at first

On Fri, Aug 3, 2012 at 9:13 PM, Douglas N Greve
wrote:

> So /home/dir/subject/subname/**scripts does not exist? If so that is
> wrong. What happens if you
> mkdir /home/dir/subject/subname/**scripts
> doug
>
>
> On 08/03/2012 12:09 PM, james pardon wrote:
>
>> Nick or Doug could you help us here?
>>
>> On Fri, Aug 3, 2012 at 8:05 PM, Bruce Fischl 
>> > fis...@nmr.mgh.**harvard.edu >> wrote:
>>
>> Hi James
>> can you post to the list so others can answer? I'm not sure what's
>> going on, but Nick or Doug might
>>
>>
>> Bruce
>>
>> On Fri, 3 Aug 2012, james pardon wrote:
>>
>> Hi Bruce,
>> subject's folder is empty,  there is no scripts folder, or
>> anything else.
>> Again if I omit -expert everything works fine.
>>
>> Thanks
>>
>> On Fri, Aug 3, 2012 at 7:29 PM, Bruce Fischl
>> > > >>
>>
>> wrote:
>>   Hi James
>>
>>   what happens if you run:
>>
>>   ls -l /home/dir/subject/subname/**scripts/expert-options
>>   touch /home/dir/subject/subname/**scripts/expert-options
>>
>>   Bruce
>>
>>   On Fri, 3 Aug 2012, james pardon wrote:
>>
>> Dear all,
>> I'm trying to pass the following flags for
>> mri_normalize through -expert
>> flag in recon-all, with a file, named expert.opts
>> with the following single
>> line:
>> mri_normalize -b 20 -n 5
>>
>> my command line is:
>>
>> recon-all -i inputfile -subject subname -all -expert
>> /expert.opts
>>
>> I receive the following error:
>>
>> cp: cannot create regular file:
>> '/home/dir/subject/subname/**scripts/expert-options'
>>
>> The directory of the subject has been created, but
>> it is completely empty.
>> At first glance I thought it might be some sort of
>> permission problems,
>> however I have rwx permission for all the paths
>> (even running under the root
>> username the same error comes up). Secondly, I
>> checked my disk quota, it is
>> completely fine. Please note that, if I do not pass
>> -expert flag recon-all
>> works completely fine.
>>
>> Any input is much appreciated.
>>
>> Regards,
>> James
>>
>>
>>
>>
>> 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.
>>
>>
>>
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: 
> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
> FileDrop: 
> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
>
>
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Re: [Freesurfer] expert option error in recon-all

[Douglas N Greve]

So /home/dir/subject/subname/scripts does not exist? If so that is 
wrong. What happens if you
mkdir /home/dir/subject/subname/scripts
doug

On 08/03/2012 12:09 PM, james pardon wrote:
> Nick or Doug could you help us here?
>
> On Fri, Aug 3, 2012 at 8:05 PM, Bruce Fischl 
> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>
> Hi James
> can you post to the list so others can answer? I'm not sure what's
> going on, but Nick or Doug might
>
>
> Bruce
>
> On Fri, 3 Aug 2012, james pardon wrote:
>
> Hi Bruce,
> subject's folder is empty,  there is no scripts folder, or
> anything else.
> Again if I omit -expert everything works fine.
>
> Thanks
>
> On Fri, Aug 3, 2012 at 7:29 PM, Bruce Fischl
> mailto:fis...@nmr.mgh.harvard.edu>>
> wrote:
>   Hi James
>
>   what happens if you run:
>
>   ls -l /home/dir/subject/subname/scripts/expert-options
>   touch /home/dir/subject/subname/scripts/expert-options
>
>   Bruce
>
>   On Fri, 3 Aug 2012, james pardon wrote:
>
> Dear all,
> I'm trying to pass the following flags for
> mri_normalize through -expert
> flag in recon-all, with a file, named expert.opts
> with the following single
> line:
> mri_normalize -b 20 -n 5
>
> my command line is:
>
> recon-all -i inputfile -subject subname -all -expert
> /expert.opts
>
> I receive the following error:
>
> cp: cannot create regular file:
> '/home/dir/subject/subname/scripts/expert-options'
>
> The directory of the subject has been created, but
> it is completely empty.
> At first glance I thought it might be some sort of
> permission problems,
> however I have rwx permission for all the paths
> (even running under the root
> username the same error comes up). Secondly, I
> checked my disk quota, it is
> completely fine. Please note that, if I do not pass
> -expert flag recon-all
> works completely fine.
>
> Any input is much appreciated.
>
> Regards,
> James
>
>
>
>
> 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.
>
>
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Thresholding using FDR

[Douglas N Greve]

Yes, it will not continue to update. When nothing is significant, it 
always uses a threshold that is just over the maximally significant voxel.
doug

On 08/03/2012 12:31 PM, Ian Carroll wrote:
> Hello,
>
> When thresholding significance using FDR for one of my overlays, I
> noticed that a rate of .1 and .05 give me the same minimum and maximum
> threshold values. At both levels, there were no voxels of
> significance. Does this mean that freesurfer will not continue to
> update max and min values when nothing is significant?
>
> Thanks,
> Ian
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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[Freesurfer] Thresholding using FDR

[Ian Carroll]

Hello,

When thresholding significance using FDR for one of my overlays, I  
noticed that a rate of .1 and .05 give me the same minimum and maximum  
threshold values. At both levels, there were no voxels of  
significance. Does this mean that freesurfer will not continue to  
update max and min values when nothing is significant?

Thanks,
Ian 
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Re: [Freesurfer] expert option error in recon-all

[james pardon]

Nick or Doug could you help us here?

On Fri, Aug 3, 2012 at 8:05 PM, Bruce Fischl wrote:

> Hi James
> can you post to the list so others can answer? I'm not sure what's going
> on, but Nick or Doug might
>
>
> Bruce
>
> On Fri, 3 Aug 2012, james pardon wrote:
>
>  Hi Bruce,
>> subject's folder is empty,  there is no scripts folder, or anything else.
>> Again if I omit -expert everything works fine.
>>
>> Thanks
>>
>> On Fri, Aug 3, 2012 at 7:29 PM, Bruce Fischl 
>> wrote:
>>   Hi James
>>
>>   what happens if you run:
>>
>>   ls -l /home/dir/subject/subname/**scripts/expert-options
>>   touch /home/dir/subject/subname/**scripts/expert-options
>>
>>   Bruce
>>
>>   On Fri, 3 Aug 2012, james pardon wrote:
>>
>> Dear all,
>> I'm trying to pass the following flags for
>> mri_normalize through -expert
>> flag in recon-all, with a file, named expert.opts
>> with the following single
>> line:
>> mri_normalize -b 20 -n 5
>>
>> my command line is:
>>
>> recon-all -i inputfile -subject subname -all -expert
>> /expert.opts
>>
>> I receive the following error:
>>
>> cp: cannot create regular file:
>> '/home/dir/subject/subname/**scripts/expert-options'
>>
>> The directory of the subject has been created, but
>> it is completely empty.
>> At first glance I thought it might be some sort of
>> permission problems,
>> however I have rwx permission for all the paths
>> (even running under the root
>> username the same error comes up). Secondly, I
>> checked my disk quota, it is
>> completely fine. Please note that, if I do not pass
>> -expert flag recon-all
>> works completely fine.
>>
>> Any input is much appreciated.
>>
>> Regards,
>> James
>>
>>
>>
>>
>> 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] Longitudinal cortical thickness analysis

[Martin Reuter]

Hi Venkat,


in 5.0 images are not aligned as longitudinal runs are done in their
native (cross sectional spaces). since 5.1 we map everything to the base
in the initial conform reslicing step to make visualization and
debugging easier. this further decreases variability. Although 5.0 does
not align the images it should still work. So maybe you have no problem
at all.

If you rerun, make sure you re-run the base and the longitudinal
directories from scratch, not on top of the old ones.

About processing stats files, there are several options:
1. grab the measures from the stats files yourself and input them into
any statistic package you desire. For this asegstats2table may be
helpful (also aparcstats2table). This is recommended as it is most
flexible, e.g. you can run linear mixed models, which is better than
looking simply at slopes. In your case (only 2 time points) it may not
matter much, but linear mixed models can deal with missing data (e.g. if
you have subjects with a single time point only). 
2. (some quick stuff I implemented for simple analysis, similar to
long_mris_slopes)
get long_stats_slopes (and all the other files there) from:
http://martinos.org/~mreuter/long/
backup yours and replace with these.
long_stats_slopes works the same way as long_mris_slopes.
You can run the output (e.g. rate/year or percent change) through
glm_fit for your group analysis (there is a tutorial about glm_fit).


We are working on making available more powerful statistical tools for
longitudinal analyses in the future. Then we will also create a better
tutorial for it. 

Best, Martin

On Fri, 2012-08-03 at 10:31 -0400, Rajagopalan, Venkateswaran wrote:
> Hi Martin,
>  
> Thanks for your immediate response. 
>  
> are you using version 5.1 ?
> No version 5.0 I am undating it.
> After the upgarde I will run the program again and see whether the
> same problem persists.
>  
> The most common
> reason is that skull strip fails in the cross sectional runs. Large
> chunks of skull can throw off the registration in the base.
> 
> I verified my skull strip (I always do) and it is fine in this case.
> In your case, you have only 2 time points and an error in the
> registration would immediately result in a messed up norm.mgz image in
> the base:nonhyper_24_templ/mri/norm.mgz would be very blurry or show
> two ghost
> images.
> 
> I didn't see base image being messed up in my case though. 
> 
> Also I am interested in seeing whether is there any reduction in
> cortical thickness between the two time points. In that case how to do
> stats. I am unable to find guidelines to do stats after the
> longitudinal processing (processing steps for longitudinal is very
> good but unfortunately I am unable to find one for stats part).
> 
> Thanks
> 
> Venkat
> 
>  
> 
> 
> 
> __
> From: Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu]
> Sent: Thu 8/2/2012 3:37 PM
> To: Rajagopalan, Venkateswaran
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Longitudinal cortical thickness analysis
> 
> 
> Hi Venkat,
> 
> are you using version 5.1 ? In earlier versions, time points were not
> aligned to the base, so they don't align. Since 5.1 they should
> perfectly align. If not it can have several reasons. The most common
> reason is that skull strip fails in the cross sectional runs. Large
> chunks of skull can throw off the registration in the base.
> 
> In your case, you have only 2 time points and an error in the
> registration would immediately result in a messed up norm.mgz image in
> the base:
> 
> nonhyper_24_templ/mri/norm.mgz would be very blurry or show two ghost
> images.
> 
> So take a look at that and also the skull strip in
> nonhyper_24_06/mri/brainmask.mgz
> nonhyper_24_07/mri/brainmask.mgz
> 
> and fix them if it they are bad.
> 
> Best, Martin
> 
> On Thu, 2012-08-02 at 13:48 -0400, Rajagopalan, Venkateswaran wrote:
> >
> > Dear All,
> >
> > I ran the following steps in a patient of mine at two time points
> > nonhyper_24_06 and nonhyper_24_07
> >
> > recon-all -autorecon1 -subjid nonhyper_24_06
> > recon-all -autorecon1 -subjid nonhyper_24_07
> > recon-all -autorecon2 -subjid nonhyper_24_06
> > recon-all -autorecon3 -subjid nonhyper_24_06
> > recon-all -autorecon2 -subjid nonhyper_24_07
> > recon-all -autorecon3 -subjid nonhyper_24_07
> >
> > # template creation
> >
> > recon-all -base nonhyper_24_templ -tp nonhyper_24_06 -tp
> > nonhyper_24_07 -all
> >
> > recon-all -long nonhyper_24_06 nonhyper_24_templ -all
> > recon-all -long nonhyper_24_07 nonhyper_24_templ -all
> >
> > When I tried to inspect my longitudinal result using
> > freeview -v nonhyper_24_06.long.nonhyper_24_templ/mri/norm.mgz \
> > nonhyper_24_07.long.nonhyper_24_templ/mri/norm.mgz \
> >  -f
> > nonhyper_24_06.long.nonhyper_24_templ/surf/lh.pial:edgecolor=red \
> >
> > nonhyper_24_06.long.nonhyper_24_templ/surf/lh.white:edgecolor=blue \
> >
> >
> nonhyper_2

Re: [Freesurfer] expert option error in recon-all

[james pardon]

Hi Bruce,

subject's folder is empty,  there is no scripts folder, or anything else.
Again if I omit -expert everything works fine.

Thanks

On Fri, Aug 3, 2012 at 7:36 PM, james pardon wrote:

> Hi Bruce,
>
> subject's folder is empty,  there is no scripts folder, or anything else.
> Again if I omit -expert everything works fine.
>
> Thanks
>
>
> On Fri, Aug 3, 2012 at 7:29 PM, Bruce Fischl 
> wrote:
>
>> Hi James
>>
>> what happens if you run:
>>
>> ls -l /home/dir/subject/subname/**scripts/expert-options
>> touch /home/dir/subject/subname/**scripts/expert-options
>>
>> Bruce
>>
>>
>> On Fri, 3 Aug 2012, james pardon wrote:
>>
>>  Dear all,
>>> I'm trying to pass the following flags for mri_normalize through -expert
>>> flag in recon-all, with a file, named expert.opts with the following
>>> single
>>> line:
>>> mri_normalize -b 20 -n 5
>>>
>>> my command line is:
>>>
>>> recon-all -i inputfile -subject subname -all -expert
>>> /expert.opts
>>>
>>> I receive the following error:
>>>
>>> cp: cannot create regular file:
>>> '/home/dir/subject/subname/**scripts/expert-options'
>>>
>>> The directory of the subject has been created, but it is completely
>>> empty.
>>> At first glance I thought it might be some sort of permission problems,
>>> however I have rwx permission for all the paths (even running under the
>>> root
>>> username the same error comes up). Secondly, I checked my disk quota, it
>>> is
>>> completely fine. Please note that, if I do not pass -expert flag
>>> recon-all
>>> works completely fine.
>>>
>>> Any input is much appreciated.
>>>
>>> Regards,
>>> James
>>>
>>>
>>>
>>
>> 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] expert option error in recon-all

[Bruce Fischl]

Hi James

what happens if you run:

ls -l /home/dir/subject/subname/scripts/expert-options
touch /home/dir/subject/subname/scripts/expert-options

Bruce

On Fri, 3 Aug 2012, 
james pardon wrote:



Dear all,
I'm trying to pass the following flags for mri_normalize through -expert
flag in recon-all, with a file, named expert.opts with the following single
line:
mri_normalize -b 20 -n 5

my command line is:

recon-all -i inputfile -subject subname -all -expert /expert.opts

I receive the following error:

cp: cannot create regular file:
'/home/dir/subject/subname/scripts/expert-options'

The directory of the subject has been created, but it is completely empty.
At first glance I thought it might be some sort of permission problems,
however I have rwx permission for all the paths (even running under the root
username the same error comes up). Secondly, I checked my disk quota, it is
completely fine. Please note that, if I do not pass -expert flag recon-all
works completely fine. 

Any input is much appreciated. 

Regards,
James

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[Freesurfer] expert option error in recon-all

[james pardon]

Dear all,

I'm trying to pass the following flags for mri_normalize through -expert
flag in recon-all, with a file, named expert.opts with the following single
line:
mri_normalize -b 20 -n 5

my command line is:

recon-all -i inputfile -subject subname -all -expert /expert.opts

I receive the following error:

cp: cannot create regular file:
'/home/dir/subject/subname/scripts/expert-options'

The directory of the subject has been created, but it is completely empty.
At first glance I thought it might be some sort of permission problems,
however I have rwx permission for all the paths (even running under the
root username the same error comes up). Secondly, I checked my disk quota,
it is completely fine. Please note that, if I do not pass -expert flag
recon-all works completely fine.

Any input is much appreciated.

Regards,
James
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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] Lesion segmentation

[Bruce Fischl]

Hi Alexander

we do segment damaged white matter, although it's more accurate if you have 
a T2 or FLAIR. Check the aseg labels if you have run recon-all

Bruce


On Fri, 3 Aug 2012, Hunold, Alexander 
wrote:

> Dear Experts,
>
>> From my understanding, the segmentation of lesions within the brain tissue 
>> is none of your main interests. However earlier threads indicated that there 
>> are some tools related to FreeSurfer which could help with such a task.
>
> Precisely, I am looking for a way to segment the surface of a lesion in a T1 
> dataset. I am not afraid of doing the segmentation manually (only 2 
> participants), but I would prefer receiving an output in FreeSurfer surface 
> format which is coregistered with the regular output, e.g. lh.white, rh.pial, 
> etc. Can you point me to a procedure within FreeSurfer or to a tool 
> associated to FreeSurfer, to fulfill this task?
>
> Any hint is appreciated very much. Thanks a lot in advance.
>
> Best regards,
> Alexander Hunold
>
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>
>
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