Re: [Freesurfer] ROI analysis and whitening in fsfast - Percent activity change

[Clark Fisher]

Thanks - it turned out that the zero voxels I put in my fake ROI volumes were 
causing the cesvar voxels to be misaligned relative to the ces voxels.  All 
seems to be right for the moment.

-Clark


On Feb 14, 2013, at 12:47 PM, Douglas N Greve wrote:

> You can compute the t = ces/sqrt(cesvar) and from that (and the DOF) you can 
> compute the p to see if it is  consistent with pValue.
> doug
> ps. I don't know that your conf interval formula is correct. I don't have a 
> reason to think it is wrong, I just don't know, so you might want to double 
> check it
> 
> 
> On 02/14/2013 07:25 AM, Clark Fisher wrote:
>> Hi Doug and the list,
>> 
>> I think I still have a problem understanding what cesvar.nii contains.  As a 
>> sanity check, I tried to create 95% confidence intervals around my CES. I 
>> found that in some voxels (or ROIs in my case) that had a p-value of less 
>> than 0.05, my 95% confidence interval for my CES included zero.  Here's one 
>> example:
>> 
>> 
>> >> clear
>> >> cesNii = MRIread('ces.nii');
>> >> cesVol = cesNii.vol;
>> >> cesVarNii = MRIread('cesvar.nii');
>> >> cesVarVol = cesVarNii.vol;
>> >> sigNii = MRIread('sig.nii');
>> >> sigVol = sigNii.vol;
>> >> pValue = 10^-abs(sigVol(4,1,1))
>> 
>> pValue =
>> 
>>0.0199
>> 
>> >> ces = cesVol(4,1,1)
>> 
>> ces =
>> 
>>   -0.0028
>> 
>> >> cesVar = cesVarVol(4,1,1)
>> 
>> cesVar =
>> 
>>   6.4511e-06
>> 
>> >> ces95pctCI = ces + [ -1 +1 ] .* sqrt(cesVar) * 1.96
>> 
>> ces95pctCI =
>> 
>>   -0.00780.0022
>> 
>> 
>> Are the p-values calculated in a way that assumes non-Gaussian error of the 
>> ces, or am I otherwise doing something wrong?
>> 
>> Thanks,
>> Clark
>> 
>> 
>> 
>>> Douglas N Greve 
>>> 
>>>  Wed, 13 Feb 2013 15:11:27 -0800 
>>> 
>>> 
>>> 1). Yes
>>> 2) Right, pull the scale outside of the sqrt()
>>> 
>>> doug
>>> On 02/13/2013 03:36 PM, Clark Fisher wrote:
>>> > Hi Doug,
>>> >
>>> > Thanks for the help, that seemed to worked great.   I have a few
>>> > follow up questions about how to process the resulting statistics.
>>> >
>>> > I'm still using v4.5 (can't switch to v5 yet), as I mentioned, and
>>> > would like to get the % signal change for certain contrasts with error
>>> > bars.  Looking through the listserv, I see that the values in
>>> > cespct.nii require correction by a scale factor in this version of
>>> > fsfast.  The most recent conversation I could find on this comes from
>>> > 2010, when you told Thomas Janssens:
>>> >> Hi Thomas, you may have found a bug in my scale factor calculation. Can
>>> >> you compute the new scale factor as described below? BTW, these issues
>>> >> are fixed in version 5.
>>> >>
>>> >> cd bold/analysis
>>> >> x = load('X');
>>> >> tirf = x.flac0.ev(3).tirf;
>>> >> Xirf = x.flac0.ev(3).Xirf;
>>> >> scalefOld = sum(Xirf .* repmat(tirf,[1 size(Xirf,2)]));
>>> >> TR = x.flac0.TR;
>>> >> dt = tirf(2)-tirf(1);
>>> >> scalefNew = sum(Xirf)*TR/dt;
>>> > I can't find a follow up to this message. 2 questions.
>>> > 1) The results with scalefNew look reasonable to me; do you still think 
>>> > that
>>> > this is the proper way to adjust cespct.nii in v4.5?
>>> > 2) If I want to put error bars on my % signal change, how do I scale the
>>> > values in cesvarpct.nii?  I would guess that if I wanted to put a 95% CI 
>>> > on
>>> > my % signal change, it would be:
>>> >   (cespct * scalefNew) +/- ( sqrt(cesvarpct) * scalefNew * 1.96)  and 
>>> > NOT
>>> > (cespct * scalefNew) +/- ( sqrt(cesvarpct * scalefNew) * 1.96)
>>> > Does this sound right, or am I misinterpreting what cesvarpct.nii 
>>> > contains?
>>> > Thanks again,
>>> > Clark
>>> >
>>> >> Hi Clark,
>>> >>
>>> >> On 02/06/2013 05:55 PM, Clark Fisher wrote:
>>> >> > Hi everyone,
>>> >> >
>>> >> > In a previous discussion on this list
>>> >> > (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17681.html),
>>> >> > Pablo Polosecki was asking the best way to perform hypothesis testing
>>> >> > using functional data within an ROI.  The final opinion was that it
>>> >> > was best to average all of the time courses in the ROI, and re-run the
>>> >> > analysis from scratch, so that all of the appropriate whitening, etc.
>>> >> > occurred.
>>> >> >
>>> >> > I was considering doing this, creating a small volume (say, 10 voxels
>>> >> > total) that had each voxel holding the average time course from one of
>>> >> > 10 ROIs.  I would then set up and run a usual fsfast analysis using
>>> >> > these tiny volumes.  I am using freesurfer 4.5.  I have a few 
>>> >> > questions.
>>> >> >
>>> >> > 1) Is this reasonable?
>>> >> In general, it is reasonable. Though I'm curious what you are ultimately
>>> >> trying to do. Do you want p-values for each subject in each ROI? Or will
>>> >> you be combining the ROI beta values across subject in a group analysis?
>

Re: [Freesurfer] talairach transformation troubleshooting problem

[Rongxiang Tang]

Hi Bruce,

The aseg is also problematic for several slicesI uploaded the subject dir 
on theMatinos center file drop...since the file is too big, I separated into 
two parts.

Thanks,
Catherine




 From: Bruce Fischl 
To: Rongxiang Tang  
Cc: "freesurfer@nmr.mgh.harvard.edu"  
Sent: Thursday, February 14, 2013 2:42 PM
Subject: Re: [Freesurfer] talairach transformation troubleshooting problem
 
probably not, although it's hard to say. If you upload the whole subject dir 
I'll take a look. How does the aseg look?
On Thu, 14 Feb 2013, Rongxiang Tang wrote:

> Hi Bruce,
> 
> I checked the skullstrip stage using this command:
> 
> tkmedit subjectid brainmask.mgz -aux T1.mgz -surfs
> and both of the brainmask and T1 images look fine the wm.mgz is problema
> tic, with some area missing. I was wondering if I need to manually adding 
> control points to solve the pro
> blem.
> Thanks,
> Catherine
> 
> 
> From: Bruce Fischl 
> To: Rongxiang Tang 
> Sent: Thursday, February 14, 2013 2:03 PM
> Subject: Re: [Freesurfer] talairach transformation troubleshooting problem
> 
> Hi Catherine
> 
> that looks like something went wrong in the surface recon, not in the
> talairaching. Maybe a skullstrip problem? You need to investigate. Also,
> please cc the list so that others can answer!
> 
> thanks
> Bruce
> On Thu, 14 Feb 2013, Rongxiang Tang wrote:
> 
> > Hi Bruce,
> >
> > I attached two images...one is the target view and the other is the
> moveable
> > view.
> >
> > Thanks,
> > Catherine
> >
> >
> >___
> _
> > From: Bruce Fischl 
> > To: Rongxiang Tang 
> > Cc: "freesurfer@nmr.mgh.harvard.edu" 
> > Sent: Thursday, February 14, 2013 1:33 PM
> > Subject: Re: [Freesurfer] talairach transformation troubleshooting problem
> >
> > Hi Catherine
> >
> > can you send us an image of what you are looking at?
> >
> > thanks
> > Bruce
> > On Thu, 14 Feb 2013,
> > Rongxiang Tang wrote:
> >
> >
 > Dear All,
> > >
> > > When I was checking the talairach transformation output, I noticed that
> > some of the white matter was not included inside
> > > the green line. Instead of drawing the green line to include all of the
> > white matter of the whole brain, it somehow only
> > > includes the bottom half of the white matter of the brain.
> > >
> > > Is there a way to fix that? 
> > >
> > > Thanks,
> > > Catherine
> > >
> > >
> >
> >
> > 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] talairach transformation troubleshooting problem

[Douglas N Greve]

Hi Catherine, if the skull strip is ok, then it might be that there were 
some defects that messed things up. Try running defect-segto generate 
segmentations of the defects. Look in the help for how to view the 
segmentations.
doug


On 02/14/2013 03:36 PM, Rongxiang Tang wrote:
> Hi Bruce,
>
> I checked the skullstrip stage using this command:
> tkmedit subjectid brainmask.mgz -aux T1.mgz -surfs
>
> and both of the brainmask and T1 images look fine the wm.mgz is 
> problematic, with some area missing.
> I was wondering if I need to manually adding control points to solve the 
> problem.
>
> Thanks,
> Catherine
> 
> *From:* Bruce Fischl 
> *To:* Rongxiang Tang 
> *Sent:* Thursday, February 14, 2013 2:03 PM
> *Subject:* Re: [Freesurfer] talairach transformation troubleshooting 
> problem
>
> Hi Catherine
>
> that looks like something went wrong in the surface recon, not in the 
> talairaching. Maybe a skullstrip problem? You need to investigate. 
> Also, please cc the list so that others can answer!
>
> thanks
> Bruce
> On Thu, 14 Feb 2013, Rongxiang Tang wrote:
>
> > Hi Bruce,
> >
> > I attached two images...one is the target view and the other is the 
> moveable
> > view.
> >
> > Thanks,
> > Catherine
> >
> >
> > 
> 
> > From: Bruce Fischl  >
> > To: Rongxiang Tang  >
> > Cc: "freesurfer@nmr.mgh.harvard.edu 
> " 
> mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Sent: Thursday, February 14, 2013 1:33 PM
> > Subject: Re: [Freesurfer] talairach transformation troubleshooting 
> problem
> >
> > Hi Catherine
> >
> > can you send us an image of what you are looking at?
> >
> > thanks
> > Bruce
> > On Thu, 14 Feb 2013,
> > Rongxiang Tang wrote:
> >
> > > Dear All,
> > >
> > > When I was checking the talairach transformation output, I noticed 
> that
> > some of the white matter was not included inside
> > > the green line. Instead of drawing the green line to include all 
> of the
> > white matter of the whole brain, it somehow only
> > > includes the bottom half of the white matter of the brain.
> > >
> > > Is there a way to fix that?
> > >
> > > Thanks,
> > > Catherine
> > >
> > >
> >
> >
> > 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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-- 
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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
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Re: [Freesurfer] talairach transformation troubleshooting problem

[Bruce Fischl]

probably not, although it's hard to say. If you upload the whole subject 
dir I'll take a look. How does the aseg look?
On Thu, 14 Feb 2013, Rongxiang 
Tang wrote:



Hi Bruce,

I checked the skullstrip stage using this command:

tkmedit subjectid brainmask.mgz -aux T1.mgz -surfs
and both of the brainmask and T1 images look fine the wm.mgz is problema
tic, with some area missing. 
I was wondering if I need to manually adding control points to solve the pro

blem.
Thanks,
Catherine


From: Bruce Fischl 
To: Rongxiang Tang 
Sent: Thursday, February 14, 2013 2:03 PM
Subject: Re: [Freesurfer] talairach transformation troubleshooting problem

Hi Catherine

that looks like something went wrong in the surface recon, not in the
talairaching. Maybe a skullstrip problem? You need to investigate. Also,
please cc the list so that others can answer!

thanks
Bruce
On Thu, 14 Feb 2013, Rongxiang Tang wrote:

> Hi Bruce,
>
> I attached two images...one is the target view and the other is the
moveable
> view.
>
> Thanks,
> Catherine
>
>
>___
_
> From: Bruce Fischl 
> To: Rongxiang Tang 
> Cc: "freesurfer@nmr.mgh.harvard.edu" 
> Sent: Thursday, February 14, 2013 1:33 PM
> Subject: Re: [Freesurfer] talairach transformation troubleshooting problem
>
> Hi Catherine
>
> can you send us an image of what you are looking at?
>
> thanks
> Bruce
> On Thu, 14 Feb 2013,
> Rongxiang Tang wrote:
>
> > Dear All,
> >
> > When I was checking the talairach transformation output, I noticed that
> some of the white matter was not included inside
> > the green line. Instead of drawing the green line to include all of the
> white matter of the whole brain, it somehow only
> > includes the bottom half of the white matter of the brain.
> >
> > Is there a way to fix that? 
> >
> > Thanks,
> > Catherine
> >
> >
>
>
> 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] "nu_estimate_np_and_em" error during recon-all

[Nick Schmansky]

Tudor,

In the default installation, there should be 2GB of free space on the
default disk, so somehow it got filled.  Try deleting unnecessary stuff
(packages added during an upgrade I think mentioned doing, or subjects in
the freesurfer/subjects dir).  Freeing just a few tens of MB should be
enough to get things working again.

Nick

> Hi Nick,
>
> I don't think there *is* any free space on the virtualbox ubuntu disk -
> that disk would presumably correspond to the first row in the "df -h"
> output, which shows as 0 free space. So even for recon-alls ran on data
> located on external HDDs, I would expect the nu_correct error to come up
> on
> all FS/VirtualBox installations, assuming that tmp space is a requirement
> (which makes sense).
>
> However, you mentioned at some point that bert runs to completion in the
> fsv5.1 WindowsVM for other users, which is intriguing...
>
> Tudor
>
>
>
> On 14 February 2013 15:29, Nick Schmansky 
> wrote:
>
>> Tudor,
>>
>> Now that there is free space on the virtualbox ubuntu disk, are you able
>> to complete recon-all's on data that is located on your external disk?
>> I
>> ask because although i'm not certain, i think nu_correct uses tmp space
>> on
>> the ubuntu local drive, which if it was full would cause recon failure
>> on
>> external data.  Thats my theory anyway.  We no longer have our local
>> VirtualBox expert that created this to support this issue, so this might
>> take some struggle.
>>
>> Nick
>>
>>
>> > Thanks Nick, it seems disk space is the issue after all, as /dev/sda1
>> has
>> > 0KB available space, due to the way the FS/Virtualbox drive was
>> created
>> > (i.e. size-tailored to the FS installation). My files were in the
>> folder
>> > that I shared through Virtualbox though (/media/Dell), which has
>> plenty
>> of
>> > space available, and that's where I ran recon-all from! Shouldn't I
>> have
>> >>2GB of space in *that* folder? If not, then the issue of making space
>> > available in the home drive (or whatver it's called), i.e. in
>> /dev/sda1,
>> > is, as it seems, a very non-trivial issue, which I have unsuccessfully
>> > tried to seek help with on the Virtualbox forum.
>> >
>> > Output of df -h below.
>> >
>> > *FreeSurfer:~> df -h
>> > FilesystemSize  Used Avail Use% Mounted on
>> > /dev/sda1  11G  9.8G 0 100% /
>> > tmpfs 755M 0  755M   0% /lib/init/rw
>> > varrun755M  104K  754M   1% /var/run
>> > varlock   755M 0  755M   0% /var/lock
>> > udev  755M  152K  754M   1% /dev
>> > tmpfs 755M 0  755M   0% /dev/shm
>> > lrm   755M  2.4M  752M   1%
>> > /lib/modules/2.6.28-11-generic/volatile
>> > overflow  1.0M   12K 1012K   2% /tmp
>> > Dell  173G  106G   68G  62% /media/Dell*
>> >
>> > On 13 February 2013 20:47, Nick Schmansky 
>> > wrote:
>> >
>> >> Tudor,
>> >>
>> >> I dont have any other suggestions, other than to make sure, as i
>> >> mentioned before, then you have free space on the disk that appears
>> >> within Xubuntu.  That is, from a terminal, when you type:
>> >>
>> >> df -h
>> >>
>> >> you should see that /dev/sda1 has about 2GB of space. the nu_correct
>> >> tools will fail if there is not enough disk space.
>> >>
>> >> Nick
>> >>
>> >>
>> >> On Wed, 2013-02-13 at 18:32 +, Tudor Popescu wrote:
>> >> > Hi Nick,
>> >> >
>> >> > I was wondering if there might be any other solutions left for me
>> to
>> >> > try, as I am currently stuck in the first (recon-all) stage of my
>> >> > cortical thickness analysis, not even being able to get the
>> baseline
>> >> > (bert) command past that nu_correct error.
>> >> >
>> >> > In the meantime I installed FreeSurfer on a different computer,
>> >> > running WinXP 64-bit, and tried the command there, only to obtain
>> the
>> >> > exact same error, even though the total amount of memory there was
>> >> > over 3GB, and disk space was plenty. I tried downloading FSL's
>> VMWare
>> >> > to use on the 64-bit OS, as you suggested, however their website is
>> >> > down at the moment.
>> >> >
>> >> > Many thanks for your help.
>> >> >
>> >> > Tudor
>> >> >
>> >> >
>> >> > On 6 February 2013 16:12, Tudor Popescu  wrote:
>> >> > Hi Nick,
>> >> > Unfortunately I don't think I can run that version, as my
>> OS
>> >> > (Win XP) is 32 bit. Is there nothing else I can try?
>> Searching
>> >> > the list for error messages related to those nu_
>> components,
>> >> > it seems that many people have had this problem before.
>> Were
>> >> > most of these cases related to N3/MNI? In my case, this
>> >> > doesn't seem to be the cause of the error.
>> >> > Tudor
>> >> >
>> >> >
>> >> > On 6 February 2013 16:06, Nick Schmansky
>> >> >  wrote:
>> >> > Tudor,
>> >> >
>> >> > Sorry to hear its not working.  There is a plan B:
>> >> > scra

Re: [Freesurfer] talairach transformation troubleshooting problem

[Bruce Fischl]

Hi Catherine

can you send us an image of what you are looking at?

thanks
Bruce
On Thu, 14 Feb 2013, 
Rongxiang Tang wrote:



Dear All,

When I was checking the talairach transformation output, I noticed that some of 
the white matter was not included inside
the green line. Instead of drawing the green line to include all of the white 
matter of the whole brain, it somehow only
includes the bottom half of the white matter of the brain.

Is there a way to fix that? 

Thanks,
Catherine

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Re: [Freesurfer] running freesurfer on multi core machine

[Bruce Fischl]

yes, some of our binaries will make use of multiple cores, starting with 
version 5.2. You need to specify how many to use on the recon-all command 
line with -openmp N

On Thu, 14 Feb 2013, Jon Wieser wrote:

> Hi,
> I am runnning fressurfer on a Mac with 23.06 Ghz 6-core intel Xeon 
> processors.  is it possible to run recon-all and trac-all on multiple cores.
> Jon
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Re: [Freesurfer] CORRECTING DEFECT

[Bruce Fischl]

or if the skull is attached or the two hemis. The time it takes to 
correct a defect is quadratic in the size of the (convex hull of) the 
defect, so small ones are fast, and big ones take forever. Anything over 
15K vertices or so usually means there is something dramatically wrong 
with your data. You can look at the ?h.orig.nofix or ?h.inflated.nofix 
surfaces to get an idea

cheers
Bruce
On Thu, 14 Feb 2013, Douglas N Greve wrote:

> Hi Chikku, look at the wm.mgz to see if the cerebellum is still attached
> doug
>
>
> On 02/14/2013 11:22 AM, Varghese Chikku wrote:
>> Dear All,
>>  I have been trying to recon all a patient and unfortunately nothing
>> is  happening after 24 hrs of  processing so far .No error messages
>>  are coming up either .This is the line it  got stuck,CORRECTING
>> DEFECT 10  vertices 67735 convex hull 9509
>>  This is a  rerun after  my initial processing failed for the same
>>  data set ,and patiently  waited 36 hrs at Correcting Defect 10 before
>> logging off .Do you know  why this is  happening.Does it have some
>> thing to do with the  data itself.
>> In Thanks
>> Chikku
>>
>>
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[Freesurfer] running freesurfer on multi core machine

[Jon Wieser]

Hi,
I am runnning fressurfer on a Mac with 23.06 Ghz 6-core intel Xeon 
processors.  is it possible to run recon-all and trac-all on multiple cores.
Jon
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[Freesurfer] talairach transformation troubleshooting problem

[Rongxiang Tang]

Dear All,

When I was checking the talairach transformation output, I noticed that some of 
the white matter was not included inside the green line. Instead of drawing the 
green line to include all of the white matter of the whole brain, it somehow 
only includes the bottom half of the white matter of the brain.

Is there a way to fix that? 

Thanks,
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Re: [Freesurfer] ROI analysis and whitening in fsfast - Percent activity change

[Douglas N Greve]

You can compute the t = ces/sqrt(cesvar) and from that (and the DOF) you 
can compute the p to see if it is  consistent with pValue.
doug
ps. I don't know that your conf interval formula is correct. I don't 
have a reason to think it is wrong, I just don't know, so you might want 
to double check it


On 02/14/2013 07:25 AM, Clark Fisher wrote:
> Hi Doug and the list,
>
> I think I still have a problem understanding what cesvar.nii contains. 
>  As a sanity check, I tried to create 95% confidence intervals around 
> my CES. I found that in some voxels (or ROIs in my case) that had a 
> p-value of less than 0.05, my 95% confidence interval for my CES 
> included zero.  Here's one example:
>
>
> >> clear
> >> cesNii = MRIread('ces.nii');
> >> cesVol = cesNii.vol;
> >> cesVarNii = MRIread('cesvar.nii');
> >> cesVarVol = cesVarNii.vol;
> >> sigNii = MRIread('sig.nii');
> >> sigVol = sigNii.vol;
> >> pValue = 10^-abs(sigVol(4,1,1))
>
> pValue =
>
> 0.0199
>
> >> ces = cesVol(4,1,1)
>
> ces =
>
>-0.0028
>
> >> cesVar = cesVarVol(4,1,1)
>
> cesVar =
>
>6.4511e-06
>
> >> ces95pctCI = ces + [ -1 +1 ] .* sqrt(cesVar) * 1.96
>
> ces95pctCI =
>
>-0.00780.0022
>
>
> Are the p-values calculated in a way that assumes non-Gaussian error 
> of the ces, or am I otherwise doing something wrong?
>
> Thanks,
> Clark
>
>
>
>> Douglas N Greve 
>> 
>>  
>> Wed, 13 Feb 2013 15:11:27 -0800 
>> 
>>
>> 1). Yes
>> 2) Right, pull the scale outside of the sqrt()
>>
>> doug
>> On 02/13/2013 03:36 PM, Clark Fisher wrote:
>> > Hi Doug,
>> >
>> > Thanks for the help, that seemed to worked great.   I have a few
>> > follow up questions about how to process the resulting statistics.
>> >
>> > I'm still using v4.5 (can't switch to v5 yet), as I mentioned, and
>> > would like to get the % signal change for certain contrasts with error
>> > bars.  Looking through the listserv, I see that the values in
>> > cespct.nii require correction by a scale factor in this version of
>> > fsfast.  The most recent conversation I could find on this comes from
>> > 2010, when you told Thomas Janssens:
>> >> Hi Thomas, you may have found a bug in my scale factor calculation. Can
>> >> you compute the new scale factor as described below? BTW, these issues
>> >> are fixed in version 5.
>> >>
>> >> cd bold/analysis
>> >> x = load('X');
>> >> tirf = x.flac0.ev(3).tirf;
>> >> Xirf = x.flac0.ev(3).Xirf;
>> >> scalefOld = sum(Xirf .* repmat(tirf,[1 size(Xirf,2)]));
>> >> TR = x.flac0.TR;
>> >> dt = tirf(2)-tirf(1);
>> >> scalefNew = sum(Xirf)*TR/dt;
>> > I can't find a follow up to this message. 2 questions.
>> > 1) The results with scalefNew look reasonable to me; do you still think 
>> > that
>> > this is the proper way to adjust cespct.nii in v4.5?
>> > 2) If I want to put error bars on my % signal change, how do I scale the
>> > values in cesvarpct.nii?  I would guess that if I wanted to put a 95% CI on
>> > my % signal change, it would be:
>> >   (cespct * scalefNew) +/- ( sqrt(cesvarpct) * scalefNew * 1.96)  and 
>> > NOT
>> > (cespct * scalefNew) +/- ( sqrt(cesvarpct * scalefNew) * 1.96)
>> > Does this sound right, or am I misinterpreting what cesvarpct.nii contains?
>> > Thanks again,
>> > Clark
>> >
>> >> Hi Clark,
>> >>
>> >> On 02/06/2013 05:55 PM, Clark Fisher wrote:
>> >> > Hi everyone,
>> >> >
>> >> > In a previous discussion on this list
>> >> > (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17681.html),
>> >> > Pablo Polosecki was asking the best way to perform hypothesis testing
>> >> > using functional data within an ROI.  The final opinion was that it
>> >> > was best to average all of the time courses in the ROI, and re-run the
>> >> > analysis from scratch, so that all of the appropriate whitening, etc.
>> >> > occurred.
>> >> >
>> >> > I was considering doing this, creating a small volume (say, 10 voxels
>> >> > total) that had each voxel holding the average time course from one of
>> >> > 10 ROIs.  I would then set up and run a usual fsfast analysis using
>> >> > these tiny volumes.  I am using freesurfer 4.5.  I have a few questions.
>> >> >
>> >> > 1) Is this reasonable?
>> >> In general, it is reasonable. Though I'm curious what you are ultimately
>> >> trying to do. Do you want p-values for each subject in each ROI? Or will
>> >> you be combining the ROI beta values across subject in a group analysis?
>> >> If so, then the whitening will probably make little, if any, difference,
>> >> especially if this is a blocked design. In expectation, the whitening
>> >> does not affect the beta values.
>> >> >
>> >> > 2) One area where I expect to run into problems is with the whitening.
>> >> >  If I set -acfbins to the total number of my dummy voxels, and
>> >> > -acffwhm to 0, will this use the autocorrelation function of the
>> >

Re: [Freesurfer] CORRECTING DEFECT

[Douglas N Greve]

Hi Chikku, look at the wm.mgz to see if the cerebellum is still attached
doug


On 02/14/2013 11:22 AM, Varghese Chikku wrote:
> Dear All,
>  I have been trying to recon all a patient and unfortunately nothing 
> is  happening after 24 hrs of  processing so far .No error messages 
>  are coming up either .This is the line it  got stuck,CORRECTING 
> DEFECT 10  vertices 67735 convex hull 9509
>  This is a  rerun after  my initial processing failed for the same 
>  data set ,and patiently  waited 36 hrs at Correcting Defect 10 before 
> logging off .Do you know  why this is  happening.Does it have some 
> thing to do with the  data itself.
> In Thanks
> Chikku
>
>
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Fax: 617-726-7422

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[Freesurfer] CORRECTING DEFECT

[Varghese Chikku]

Dear All,
 I have been trying to recon all a patient and unfortunately nothing is
 happening after 24 hrs of  processing so far .No error messages  are
coming up either .This is the line it  got stuck,CORRECTING DEFECT 10
 vertices 67735 convex hull 9509
 This is a  rerun after  my initial processing failed for the same  data
set ,and patiently  waited 36 hrs at Correcting Defect 10 before logging
off .Do you know  why this is  happening.Does it have some thing to do with
the  data itself.
In Thanks
Chikku
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Re: [Freesurfer] longitudinal processing of one timepoint

[Martin Reuter]

Hi Luigi,

1 is the right way of calling it. 2 will have a negative effect in the 
sense that it takes the same image twice and then creates the mid-space 
at the same location, so 2 could be biased.
1 is creating an artifical mid-space and makes sure the image gets 
mapped there.


Best, Martin

On 02/13/2013 08:39 AM, Luigi Angelo Maglanoc wrote:

Dear FreeSurfer experts,

I know that it is possible to submit data with only one timepoint into
the longitudinal stream with FreeSurfer 5.2. My question is, what is 
the exact command?

is it:
1) recon-all -base  -tp  -all
or
2) recon-all -base  -tp  -tp  -all
I have accidently run them with the second command, and I am also 
wondering

whether this will have a negative impact?

Thank you for your time and consideration!

Sincerely
Luigi


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Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
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   reu...@mit.edu
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Re: [Freesurfer] "nu_estimate_np_and_em" error during recon-all

[Nick Schmansky]

Tudor,

Now that there is free space on the virtualbox ubuntu disk, are you able
to complete recon-all's on data that is located on your external disk?  I
ask because although i'm not certain, i think nu_correct uses tmp space on
the ubuntu local drive, which if it was full would cause recon failure on
external data.  Thats my theory anyway.  We no longer have our local
VirtualBox expert that created this to support this issue, so this might
take some struggle.

Nick


> Thanks Nick, it seems disk space is the issue after all, as /dev/sda1 has
> 0KB available space, due to the way the FS/Virtualbox drive was created
> (i.e. size-tailored to the FS installation). My files were in the folder
> that I shared through Virtualbox though (/media/Dell), which has plenty of
> space available, and that's where I ran recon-all from! Shouldn't I have
>>2GB of space in *that* folder? If not, then the issue of making space
> available in the home drive (or whatver it's called), i.e. in /dev/sda1,
> is, as it seems, a very non-trivial issue, which I have unsuccessfully
> tried to seek help with on the Virtualbox forum.
>
> Output of df -h below.
>
> *FreeSurfer:~> df -h
> FilesystemSize  Used Avail Use% Mounted on
> /dev/sda1  11G  9.8G 0 100% /
> tmpfs 755M 0  755M   0% /lib/init/rw
> varrun755M  104K  754M   1% /var/run
> varlock   755M 0  755M   0% /var/lock
> udev  755M  152K  754M   1% /dev
> tmpfs 755M 0  755M   0% /dev/shm
> lrm   755M  2.4M  752M   1%
> /lib/modules/2.6.28-11-generic/volatile
> overflow  1.0M   12K 1012K   2% /tmp
> Dell  173G  106G   68G  62% /media/Dell*
>
> On 13 February 2013 20:47, Nick Schmansky 
> wrote:
>
>> Tudor,
>>
>> I dont have any other suggestions, other than to make sure, as i
>> mentioned before, then you have free space on the disk that appears
>> within Xubuntu.  That is, from a terminal, when you type:
>>
>> df -h
>>
>> you should see that /dev/sda1 has about 2GB of space. the nu_correct
>> tools will fail if there is not enough disk space.
>>
>> Nick
>>
>>
>> On Wed, 2013-02-13 at 18:32 +, Tudor Popescu wrote:
>> > Hi Nick,
>> >
>> > I was wondering if there might be any other solutions left for me to
>> > try, as I am currently stuck in the first (recon-all) stage of my
>> > cortical thickness analysis, not even being able to get the baseline
>> > (bert) command past that nu_correct error.
>> >
>> > In the meantime I installed FreeSurfer on a different computer,
>> > running WinXP 64-bit, and tried the command there, only to obtain the
>> > exact same error, even though the total amount of memory there was
>> > over 3GB, and disk space was plenty. I tried downloading FSL's VMWare
>> > to use on the 64-bit OS, as you suggested, however their website is
>> > down at the moment.
>> >
>> > Many thanks for your help.
>> >
>> > Tudor
>> >
>> >
>> > On 6 February 2013 16:12, Tudor Popescu  wrote:
>> > Hi Nick,
>> > Unfortunately I don't think I can run that version, as my OS
>> > (Win XP) is 32 bit. Is there nothing else I can try? Searching
>> > the list for error messages related to those nu_ components,
>> > it seems that many people have had this problem before. Were
>> > most of these cases related to N3/MNI? In my case, this
>> > doesn't seem to be the cause of the error.
>> > Tudor
>> >
>> >
>> > On 6 February 2013 16:06, Nick Schmansky
>> >  wrote:
>> > Tudor,
>> >
>> > Sorry to hear its not working.  There is a plan B:
>> > scrap our VirtualBox
>> > instance entirely and instead install FSL's VMWare
>> > (from their website).
>> > This has a 64b Centos, so upon successful installation
>> > of it, you would
>> > download our 64b centos freesurfer distribution.
>> >
>> > Nick
>> >
>> >
>> > On Wed, 2013-02-06 at 12:59 +, Tudor Popescu
>> > wrote:
>> > > ..I also did the following in the meantime, to make
>> > sure that the
>> > > problem isn't due to a path error:
>> > > - ran nu_estimate_np_and_em and nu_correct: both
>> > seem to respond fine,
>> > > and they return their version number
>> > > - checked env variables $MNI_PERL5LIB and
>> > $MNI_DATAPATH: both point
>> > > into $FREESURFER_HOME/mni , as they should
>> > >
>> > > Still cannot get recon-all to run because of the
>> > error mentioned
>> > > previously & currently at my wit's end! :(
>> > >
>> > > On 4 February 2013 10:29, Tudor Popescu
>> >  w

Re: [Freesurfer] creating 'Mid' surfaces

[Shantanu Ghosh]

sorry the files are in the surf directory

On Thu, February 14, 2013 9:53 am, Shantanu Ghosh wrote:
> Hi Christine,
> If you cd to the subject directory you can locate the ?h.white surface and
> use mris_expand command to do this.
> Hth,
>  Shantanu
>
> On Thu, February 14, 2013 5:39 am, Ecker, Christine wrote:
>> Dear FreeSurfer Experts,
>>
>> What is the best way of creating surfaces approximating layer IV of the
> cortex or the 'mid' surface (I.e. Surface between grey and white
> matter).
>>
>> Thank you very much for your help.
>>
>> Regards,
>> Christine
>>
>> ___
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>
>
> --
> Shantanu Ghosh, Ph.D.
> Harvard Medical School & Massachusetts General Hospital
> Martinos Center for Biomedical Imaging
>
>
>
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>
>
>


-- 
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Harvard Medical School & Massachusetts General Hospital
Martinos Center for Biomedical Imaging

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Re: [Freesurfer] creating 'Mid' surfaces

[Shantanu Ghosh]

Hi Christine,
If you cd to the subject directory you can locate the ?h.white surface and
use mris_expand command to do this.
Hth,
 Shantanu

On Thu, February 14, 2013 5:39 am, Ecker, Christine wrote:
> Dear FreeSurfer Experts,
>
> What is the best way of creating surfaces approximating layer IV of the
cortex or the 'mid' surface (I.e. Surface between grey and white
matter).
>
> Thank you very much for your help.
>
> Regards,
> Christine
>
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-- 
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Harvard Medical School & Massachusetts General Hospital
Martinos Center for Biomedical Imaging



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Re: [Freesurfer] creating 'Mid' surfaces

[Bruce Fischl]

Hi Christine

we use mris_expand for this. E.g. from the surf dir

mris_expand -thickness lh.white 0.5 lh.mid

cheers
Bruce


On Thu, 14 Feb 2013, Ecker, Christine wrote:

> Dear FreeSurfer Experts,
> 
> What is the best way of creating surfaces approximating layer IV of the
> cortex or the 'mid' surface (I.e. Surface between grey and white matter).
> 
> Thank you very much for your help.
> 
> Regards,
> Christine
> 
> 
>
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Re: [Freesurfer] ROI analysis and whitening in fsfast - Percent activity change

[Clark Fisher]

Hi Doug and the list,

I think I still have a problem understanding what cesvar.nii contains.  As a 
sanity check, I tried to create 95% confidence intervals around my CES. I found 
that in some voxels (or ROIs in my case) that had a p-value of less than 0.05, 
my 95% confidence interval for my CES included zero.  Here's one example:


>> clear
>> cesNii = MRIread('ces.nii');
>> cesVol = cesNii.vol;
>> cesVarNii = MRIread('cesvar.nii');
>> cesVarVol = cesVarNii.vol;
>> sigNii = MRIread('sig.nii');
>> sigVol = sigNii.vol;
>> pValue = 10^-abs(sigVol(4,1,1))

pValue =

0.0199

>> ces = cesVol(4,1,1)

ces =

   -0.0028

>> cesVar = cesVarVol(4,1,1)

cesVar =

   6.4511e-06

>> ces95pctCI = ces + [ -1 +1 ] .* sqrt(cesVar) * 1.96

ces95pctCI =

   -0.00780.0022


Are the p-values calculated in a way that assumes non-Gaussian error of the 
ces, or am I otherwise doing something wrong?

Thanks,
Clark




Douglas N 
Greve
 Wed, 13 Feb 2013 15:11:27 
-0800

1). Yes
2) Right, pull the scale outside of the sqrt()

doug

On 02/13/2013 03:36 PM, Clark Fisher wrote:
> Hi Doug,
>
> Thanks for the help, that seemed to worked great.   I have a few
> follow up questions about how to process the resulting statistics.
>
> I'm still using v4.5 (can't switch to v5 yet), as I mentioned, and
> would like to get the % signal change for certain contrasts with error
> bars.  Looking through the listserv, I see that the values in
> cespct.nii require correction by a scale factor in this version of
> fsfast.  The most recent conversation I could find on this comes from
> 2010, when you told Thomas Janssens:
>> Hi Thomas, you may have found a bug in my scale factor calculation. Can
>> you compute the new scale factor as described below? BTW, these issues
>> are fixed in version 5.
>>
>> cd bold/analysis
>> x = load('X');
>> tirf = x.flac0.ev(3).tirf;
>> Xirf = x.flac0.ev(3).Xirf;
>> scalefOld = sum(Xirf .* repmat(tirf,[1 size(Xirf,2)]));
>> TR = x.flac0.TR;
>> dt = tirf(2)-tirf(1);
>> scalefNew = sum(Xirf)*TR/dt;
> I can't find a follow up to this message. 2 questions.
> 1) The results with scalefNew look reasonable to me; do you still think that
> this is the proper way to adjust cespct.nii in v4.5?
> 2) If I want to put error bars on my % signal change, how do I scale the
> values in cesvarpct.nii?  I would guess that if I wanted to put a 95% CI on
> my % signal change, it would be:
>   (cespct * scalefNew) +/- ( sqrt(cesvarpct) * scalefNew * 1.96)  and NOT
> (cespct * scalefNew) +/- ( sqrt(cesvarpct * scalefNew) * 1.96)
> Does this sound right, or am I misinterpreting what cesvarpct.nii contains?
> Thanks again,
> Clark
>
>> Hi Clark,
>>
>> On 02/06/2013 05:55 PM, Clark Fisher wrote:
>> > Hi everyone,
>> >
>> > In a previous discussion on this list
>> > (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17681.html),
>> > Pablo Polosecki was asking the best way to perform hypothesis testing
>> > using functional data within an ROI.  The final opinion was that it
>> > was best to average all of the time courses in the ROI, and re-run the
>> > analysis from scratch, so that all of the appropriate whitening, etc.
>> > occurred.
>> >
>> > I was considering doing this, creating a small volume (say, 10 voxels
>> > total) that had each voxel holding the average time course from one of
>> > 10 ROIs.  I would then set up and run a usual fsfast analysis using
>> > these tiny volumes.  I am using freesurfer 4.5.  I have a few questions.
>> >
>> > 1) Is this reasonable?
>> In general, it is reasonable. Though I'm curious what you are ultimately
>> trying to do. Do you want p-values for each subject in each ROI? Or will
>> you be combining the ROI beta values across subject in a group analysis?
>> If so, then the whitening will probably make little, if any, difference,
>> especially if this is a blocked design. In expectation, the whitening
>> does not affect the beta values.
>> >
>> > 2) One area where I expect to run into problems is with the whitening.
>> >  If I set -acfbins to the total number of my dummy voxels, and
>> > -acffwhm to 0, will this use the autocorrelation function of the
>> > average timecourse within each individual ROI?  Is that an appropriate
>> > approach? How sensitive will this be to the number of actual voxels
>> > averaged to get each ROI (for instance, would this bias me to finding
>> > more significant results in ROIs containing fewer voxels?).
>> That might work, but no promises! It is an appropriate approach. It
>> might be sensitive to the number of voxels if the number is small (say,
>> less than 100).
>> >
>> > 3) Are there other steps that depend upon the spatial arrangement of
>> > voxels that I am forgetting, and will these steps choke on these small
>> > volumes (or worse, fail in silent but pernicious way

[Freesurfer] creating 'Mid' surfaces

[Ecker, Christine]

Dear FreeSurfer Experts,

What is the best way of creating surfaces approximating layer IV of the cortex 
or the 'mid' surface (I.e. Surface between grey and white matter).

Thank you very much for your help.

Regards,
Christine

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[Freesurfer] re error when making average subject

[Catherine Bois]

Hi all,

I was trying to create an average subject however received this error  
message. I temporarily removed that subject however I was wondering  
what a possible cause for this error is?

Applying LTAtransformInterp (resample_type 1)
writing to  
/sdata/images/projects/EHRS/2/Freesurfer_EHRS/READYFORANALYSIS/avgsubject/tmp/make_average_vol-tmp-10132/T1-EHRS_0764_1.mgh...
mri_convert  
/sdata/images/projects/EHRS/2/Freesurfer_EHRS/READYFORANALYSIS/EHRS_0774_1/mri/T1.mgz
 
/sdata/images/projects/EHRS/2/Freesurfer_EHRS/READYFORANALYSIS/avgsubject/tmp/make_average_vol-tmp-10132/T1-EHRS_0774_1.mgh
 --apply_transform 
/sdata/images/projects/EHRS/2/Freesurfer_EHRS/READYFORANALYSIS/EHRS_0774_1/mri/transforms/talairach.xfm
 -oc 0 0  
Segmentation fault
/home/orkney_01/cbois
ERROR: mri_convert failed.
ERROR: make_average_volume
[cbois@poplar ~]$


Thank you very much for your help

Cathy


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