[Freesurfer] How to set the -retinotopy number in mkanalysis-sess due to different cycle time in the eccen and polar

[yufeng huang]

Dear Doug,
I want you could give me some guidances with my retinotopic analysis.

Eccen run: TR 2 Ncycles 6, 64 sec per cycle, all scan 384 sec.
Polar run:  TR 2,  then follow Ncycles 10, 32 sec per cycle, all scan 320 sec.

 I write the rtopy.par:
 stimtype polar
 diretion neg
 ncycles 10

 and
 stimtype eccen
 diretion pos
 ncycles  6

My question is: How to set the value of -retinotopy in the mkanalysis
as the eccen value should be -retinotopic 64 while the polar value
should be -retinotopic 32 in the mkanalysis-sess
   Thanks a lot!

  Yours Yufeng
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Re: [Freesurfer] QDEC questions

[Douglas N Greve]

Here's part 1. I'll write until I have to catch my shuttle, answer the 
rest tomorrow ...

On 04/18/2013 05:27 PM, Tudor Popescu wrote:
> Apologies for my previous long email; if anyone gets a chance to look 
> over the questions I'd be really grateful!
> Many thanks indeed,
> Tudor
>
> On 16 April 2013 19:40, Tudor Popescu  > wrote:
>
> Thanks Nick, (and thanks Doug too for the answer to question 2.)
>
> It must indeed have been a disk-space issue, as running the
> -qcache again, after clearing up some space, produced all the
> expected .mgh files
>
> If I can follow up on two of my previous questions:
>
> 3) Not sure I understand your answer. So it seems discrete
> variables, such as gender, cannot be taken as covariates or
> nuisance variables, only as factors. But users might want to take
> some discrete variables as covariates, rather than as factors, as
> I might not be interested in their direct effect on the brain
> measure but simply want to parcel out the variance that they
> contribute. Are you suggesting that they should be taken as
> factors even if they aren't of interest?
>
Yes. There is no real distinction between between something that is of 
interest and something that is not. The way the software is set up, the 
continuous factors can be listed as nuisance and get around the 
limitation of only have two covariates.
>
>
> 4) Does the ideal value of FWHM depend on the blob size in the
> sense that if one expects small blobs in the results (how small?),
> then one should use small FWHMs in QDEC, and large FWHMs if
> expecting large blobs?
>
Yes.
>
>
> I apologise for the amount of questions I keep asking, but I have
> a few more:
>
> A) When trying repeated analyses (designs) in QDEC, do I need to
> delete the output files of previous analyses, and/or restart QDEC
> every time? Or are the results of each analysis displayed
> correctly independently of previously-made analyses in the same
> QDEC session? I'm asking because I see that, once the "Set using
> FDR" button is pressed, the corrected t threshold remains in use
> for subsequent analyses, but after restarting QDEC and redoing the
> last analysis, the t threshold is no longer the same
>
Not sure, have to check. I think you can name the output folders 
differently for each analysis. If you do not change the name, then the 
output is totally deleted and recreated.
>
>
> B) Must all QDEC analyses always be done for the two hemispheres
> separately? Is there no analysis that can be done on the whole
> brain, such that the t-value thresholds are FDR-corrected at the
> whole-brain level?
>
There is none.
>
>
> C) I would like to extract the cortical thickness of several
> cortical ROIs including the IPS, IFG and SPL; I didn’t know
> whether the Desikan-Killiany or the Destrieux atlas would be more
> appropriate, but I tried the command given here
> 
> ,
> hoping to obtain a table with the thickness of all ROIs from the
> parcelation corresponding to the Destrieux atlas. However,
> although the command results in the message "
> lh.aparc.a2009.thickness.table", I found no such file anywhere in
> my $SUBJECTS_DIR
>
Did it go into the directory that you ran the command from?
>
>
> D) How should a regression-type analysis be made in QDEC, i.e. one
> where I have a continuous predictor such as behavioural score,
> whose correlation with the brain measure (cortical thickness) I
> want to compare between my two groups? Because of QDEC's
> preference for discrete variables as factors, it seems that only
> ANOVA-type analyses can be done (i.e. effect of discrete factor(s)
> on brain measure), rather than regression-type (i.e. correlation
> between continuous factor and brain measure)
>
Enter it in as a covariate (continuous factor). QDEC will automatically 
produce a contrast testing the difference in thickness/score slopes (ie, 
an interaction between group factor and continuous factor).
>
>
> E) The average brain with inflated cortex that results are
> projected on – is this the same average that is normally used in
> most papers, or does the inflating algorithm differ? And is the
> colour-coding the same (dark gray = sulci, light gray = gyri)?
>
It is mostly the same. Some papers may display on the pial or the white 
or do a custom inflation to keep some of the gyral shape instead of 
having it so smooth. The colors I assume are the same.

whew! made it through all of them before my shuttle.
doug

>
>
>
> On 15 April 2013 23:52, Nick Schmansky  > wrote:
>
> Tudor,
>
> In the recon-all.log, it has this line:
> ER

Re: [Freesurfer] QDEC questions

[Tudor Popescu]

Apologies for my previous long email; if anyone gets a chance to look over
the questions I'd be really grateful!
Many thanks indeed,
Tudor

On 16 April 2013 19:40, Tudor Popescu  wrote:

> Thanks Nick, (and thanks Doug too for the answer to question 2.)
>
> It must indeed have been a disk-space issue, as running the -qcache again,
> after clearing up some space, produced all the expected .mgh files
>
> If I can follow up on two of my previous questions:
>
> 3) Not sure I understand your answer. So it seems discrete variables, such
> as gender, cannot be taken as covariates or nuisance variables, only as
> factors. But users might want to take some discrete variables as
> covariates, rather than as factors, as I might not be interested in their
> direct effect on the brain measure but simply want to parcel out the
> variance that they contribute. Are you suggesting that they should be taken
> as factors even if they aren't of interest?
>
> 4) Does the ideal value of FWHM depend on the blob size in the sense that
> if one expects small blobs in the results (how small?), then one should use
> small FWHMs in QDEC, and large FWHMs if expecting large blobs?
>
> I apologise for the amount of questions I keep asking, but I have a few
> more:
>
> A) When trying repeated analyses (designs) in QDEC, do I need to delete
> the output files of previous analyses, and/or restart QDEC every time? Or
> are the results of each analysis displayed correctly independently of
> previously-made analyses in the same QDEC session? I'm asking because I see
> that, once the "Set using FDR" button is pressed, the corrected t threshold
> remains in use for subsequent analyses, but after restarting QDEC and
> redoing the last analysis, the t threshold is no longer the same
>
> B) Must all QDEC analyses always be done for the two hemispheres
> separately? Is there no analysis that can be done on the whole brain, such
> that the t-value thresholds are FDR-corrected at the whole-brain level?
>
> C) I would like to extract the cortical thickness of several cortical ROIs
> including the IPS, IFG and SPL; I didn’t know whether the Desikan-Killiany
> or the Destrieux atlas would be more appropriate, but I tried the command
> given 
> here,
> hoping to obtain a table with the thickness of all ROIs from the
> parcelation corresponding to the Destrieux atlas. However, although the
> command results in the message " lh.aparc.a2009.thickness.table", I found
> no such file anywhere in my $SUBJECTS_DIR
>
> D) How should a regression-type analysis be made in QDEC, i.e. one where I
> have a continuous predictor such as behavioural score, whose correlation
> with the brain measure (cortical thickness) I want to compare between my
> two groups? Because of QDEC's preference for discrete variables as factors,
> it seems that only ANOVA-type analyses can be done (i.e. effect of discrete
> factor(s) on brain measure), rather than regression-type (i.e. correlation
> between continuous factor and brain measure)
>
> E) The average brain with inflated cortex that results are projected on –
> is this the same average that is normally used in most papers, or does the
> inflating algorithm differ? And is the colour-coding the same (dark gray =
> sulci, light gray = gyri)?
>
>
>
> On 15 April 2013 23:52, Nick Schmansky  wrote:
>
>> Tudor,
>>
>> In the recon-all.log, it has this line:
>> ERROR: writing lh.jacobian_white.fwhm15.fsaverage.mgh
>>
>> but earlier in the log it saved lh.jacobian_white.fwhm10.fsaverage.mgh
>> correctly, so this indicates to me that it might have run out of disk
>> space.  is that the case?
>>
>> to answer the others:
>> 2. not sure
>> 3. you can select discrete can a regular variate along with your main
>> variate.  'nuisance' variates are like any other.
>> 4. depends on the expected 'blob' size
>> 5. the selection of fwhm in qdec corresponds directly with the values
>> selected by qcache (they are one-to-one related, ie the 10mm fwhm values
>> created by qcache are used by the 10mm fwhm selection in qdec).
>>
>> Nick
>>
>>
>>
>> On Mon, 2013-04-15 at 18:38 +0200, Tudor Popescu wrote:
>> > Dear experts,
>> >
>> > Upgrading to 5.2.0 stopped QDEC (specifically, mri_concat) from
>> > misbehaving, and so after running a first whole-brain group cortical
>> > thickness analysis on my structural data, I have some questions:
>> >
>> > 1. After running recon-all with the –qcache flag (i.e. presmoothing),
>> > files of the type lh.thickness.*.mgh were created for all 38 subjects
>> > (19 in each group), however files of the type rh.thickness.*.mgh were
>> > not created for 5 out of the 19 subjects of the first group. Log files
>> > recon-all-status.log and recon-all.log (attached, for one of those 5
>> > subjects) both mention that the process ran on Mar22nd ended with
>> > errors, although I can't quite see what

Re: [Freesurfer] Hippo-subfields

[Juan Eugenio Iglesias]

I agree with Bruce. You can use MRIread.m to read in the data.

Regarding the other question: first you need to combine the posteriors
of all the subfields into a single posterior for the whole hippocampus.
You can do that like this:

mri_concat posterior_fimbria.mgz posterior_CA1.mgz ... --sum --o
posteriorWholeHippocampus.mgz

Then you can threshold the posterior at probability 0.5 to obtain a
binary hippocampal mask:

mri_binarize --i posteriorWholeHippocampus.mgz --min 127 --o
binaryHippocampalMask.mgz

Finally, you can generate a surface by tesselating the mask:

mri_tesselate binaryHippocampalMask.mgz 1 surfaceFile

You can visualize the output with

freeview -v posteriorWholeHippocampus.mgz -f surfaceFile

Cheers,

/Eugenio







On Thu, 2013-04-18 at 11:22 -0400, Bruce Fischl wrote:
> Hi Marcos
> 
> I would do it in matlab. Compute the spatial eigenvectors then divide the 
> hippocampus up along the primary eigenvector
> 
> cheers
> Bruce
> On Thu, 18 Apr 2013, Marcos 
> Martins da Silva wrote:
> 
> > Thank you for your answer, Juan.
> > 
> >  Yes, I want a surface of the whole hippocampus and I thought I had just 
> > obtained that using
> > freeview and adding all hippo-subfield files. That resulted in the 
> > screenshot I previously
> > attached. I just do not know how I can save the resultant surface.
> > 
> > After I checked "show as isosurface in 3D view" the low and high threshold 
> > controls appeared.
> > The default threshold values on Freeview for low was 127.5 and high was 
> > 255. When I played
> > with these controls, the size of the surfaces changed on 3D view. That is 
> > why I made the
> > second question. I was trying to select the correct values for low and high 
> > threshoulds so I
> > get an image consistent with the volume values we get after running
> > kvlQuantifyPosteriorProbabilityImages. After setting the correct values I 
> > would like to save
> > the work as a surface so I could load the whole surface instead of loading 
> > each individual
> > subfield file. But I did not find a "save as surface" option. So I used the 
> > screenshot tool to
> > "save" the work. This way I could at least show you what I got but I 
> > thought it was not the
> > best way to do it.
> > 
> > Relating to the last question about generating a new segmentation 
> > (anterior, body and
> > posterior), you said I could use simple geometric rules to get it. Could 
> > you tell me where I
> > can find instructions about how to do it?
> > 
> > Sorry, I am afraid I am a novice here and my questions are the best proof 
> > of this, so I would
> > like to thank you for all your patience.
> > 
> > Em Qua, 2013-04-17 às 21:19 -0400, Juan Eugenio Iglesias escreveu:
> > Dear Marcos,
> > >
> > > > 1- How do I save the combined 3D view I got as a surface?
> > >
> > > Do you want a surface of the whole hippocampus? In that case I would
> > > suggest adding up the probability volumes from all the subfields and
> > > thresholding the resulting volume.
> > >
> > >
> > > > 2-I know the hippo-subifields .mgz files are probability maps and if I
> > > > guess right kvlQuantifyPosteriorProbabilityImages read these files to
> > > > count how many voxels you have in each subfield. I also guess it count
> > > > only the voxels with reasonable high probability to be part of each
> > > > subfield. If so, what is the minimum value between 1 and 255 the
> > > > program use to decide if a particular voxel is valid?
> > >
> > > The estimates of the volumes are based on soft probabilities, so all
> > > voxels with non-zero probability contribute towards the estimate. For
> > > instance, a voxel with value 255 contributes to the volume 255 times as
> > > much as a voxel with a value of 1.
> > >
> > >
> > > > 3- Is it possible to merge hippo-subfield .mgz files data and to
> > > > generate a different segmentation like anterior (anterior quarter),
> > > > body (the2 intermediate quarters) and posterior (posterior quarter).
> > >
> > > There are currently no scripts in FreeSurfer to generate such a
> > > partition. But you could always take a mask of the whole hippocampus
> > > (either from aseg.mgz of from the combination of all the subfields, like
> > > I mentioned in 1) and define some simple geometric rules to create it.
> > >
> > > Kind regards,
> > >
> > > Eugenio
> > >
> > >
> > >
> > >
> > > >
> > > > TY in advance
> > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
> > 
> >

-- 
-
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
Department of Radiology, MGH, Harvard Medical School
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.


___

Re: [Freesurfer] Hippo-subfields

[Bruce Fischl]

Hi Marcos

I would do it in matlab. Compute the spatial eigenvectors then divide the 
hippocampus up along the primary eigenvector


cheers
Bruce
On Thu, 18 Apr 2013, Marcos 
Martins da Silva wrote:



Thank you for your answer, Juan.

 Yes, I want a surface of the whole hippocampus and I thought I had just 
obtained that using
freeview and adding all hippo-subfield files. That resulted in the screenshot I 
previously
attached. I just do not know how I can save the resultant surface.

After I checked "show as isosurface in 3D view" the low and high threshold 
controls appeared.
The default threshold values on Freeview for low was 127.5 and high was 255. 
When I played
with these controls, the size of the surfaces changed on 3D view. That is why I 
made the
second question. I was trying to select the correct values for low and high 
threshoulds so I
get an image consistent with the volume values we get after running
kvlQuantifyPosteriorProbabilityImages. After setting the correct values I would 
like to save
the work as a surface so I could load the whole surface instead of loading each 
individual
subfield file. But I did not find a "save as surface" option. So I used the 
screenshot tool to
"save" the work. This way I could at least show you what I got but I thought it 
was not the
best way to do it.

Relating to the last question about generating a new segmentation (anterior, 
body and
posterior), you said I could use simple geometric rules to get it. Could you 
tell me where I
can find instructions about how to do it?

Sorry, I am afraid I am a novice here and my questions are the best proof of 
this, so I would
like to thank you for all your patience.

Em Qua, 2013-04-17 às 21:19 -0400, Juan Eugenio Iglesias escreveu:
Dear Marcos,
>
> > 1- How do I save the combined 3D view I got as a surface?
>
> Do you want a surface of the whole hippocampus? In that case I would
> suggest adding up the probability volumes from all the subfields and
> thresholding the resulting volume.
>
>
> > 2-I know the hippo-subifields .mgz files are probability maps and if I
> > guess right kvlQuantifyPosteriorProbabilityImages read these files to
> > count how many voxels you have in each subfield. I also guess it count
> > only the voxels with reasonable high probability to be part of each
> > subfield. If so, what is the minimum value between 1 and 255 the
> > program use to decide if a particular voxel is valid?
>
> The estimates of the volumes are based on soft probabilities, so all
> voxels with non-zero probability contribute towards the estimate. For
> instance, a voxel with value 255 contributes to the volume 255 times as
> much as a voxel with a value of 1.
>
>
> > 3- Is it possible to merge hippo-subfield .mgz files data and to
> > generate a different segmentation like anterior (anterior quarter),
> > body (the2 intermediate quarters) and posterior (posterior quarter).
>
> There are currently no scripts in FreeSurfer to generate such a
> partition. But you could always take a mask of the whole hippocampus
> (either from aseg.mgz of from the combination of all the subfields, like
> I mentioned in 1) and define some simple geometric rules to create it.
>
> Kind regards,
>
> Eugenio
>
>
>
>
> >
> > TY in advance
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Hippo-subfields

[Marcos Martins da Silva]

Thank you for your answer, Juan.

 Yes, I want a surface of the whole hippocampus and I thought I had just
obtained that using freeview and adding all hippo-subfield files. That
resulted in the screenshot I previously attached. I just do not know how I
can save the resultant surface.

After I checked "show as isosurface in 3D view" the low and high threshold
controls appeared. The default threshold values on Freeview for low was
127.5 and high was 255. When I played with these controls, the size of the
surfaces changed on 3D view. That is why I made the second question. I was
trying to select the correct values for low and high threshoulds so I get
an image consistent with the volume values we get after running
kvlQuantifyPosteriorProbabilityImages. After setting the correct values I
would like to save the work as a surface so I could load the whole surface
instead of loading each individual subfield file. But I did not find a
"save as surface" option. So I used the screenshot tool to "save" the work.
This way I could at least show you what I got but I thought it was not the
best way to do it.

Relating to the last question about generating a new segmentation
(anterior, body and posterior), you said I could use simple geometric rules
to get it. Could you tell me where I can find instructions about how to do
it?

Sorry, I am afraid I am a novice here and my questions are the best proof
of this, so I would like to thank you for all your patience.

Em Qua, 2013-04-17 às 21:19 -0400, Juan Eugenio Iglesias escreveu:
Dear Marcos,
>
> > 1- How do I save the combined 3D view I got as a surface?
>
> Do you want a surface of the whole hippocampus? In that case I would
> suggest adding up the probability volumes from all the subfields and
> thresholding the resulting volume.
>
>
> > 2-I know the hippo-subifields .mgz files are probability maps and if I
> > guess right kvlQuantifyPosteriorProbabilityImages read these files to
> > count how many voxels you have in each subfield. I also guess it count
> > only the voxels with reasonable high probability to be part of each
> > subfield. If so, what is the minimum value between 1 and 255 the
> > program use to decide if a particular voxel is valid?
>
> The estimates of the volumes are based on soft probabilities, so all
> voxels with non-zero probability contribute towards the estimate. For
> instance, a voxel with value 255 contributes to the volume 255 times as
> much as a voxel with a value of 1.
>
>
> > 3- Is it possible to merge hippo-subfield .mgz files data and to
> > generate a different segmentation like anterior (anterior quarter),
> > body (the2 intermediate quarters) and posterior (posterior quarter).
>
> There are currently no scripts in FreeSurfer to generate such a
> partition. But you could always take a mask of the whole hippocampus
> (either from aseg.mgz of from the combination of all the subfields, like
> I mentioned in 1) and define some simple geometric rules to create it.
>
> Kind regards,
>
> Eugenio
>
>
>
>
> >
> > TY in advance
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
___
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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.

Re: [Freesurfer] autorecon2-cp error

[Bruce Fischl]

Hi Claudia

that defect is bigger than more cortical surfaces so something is 
dramatically wrong. Did you check any of the outputs (wm.mgz, filled.mgz, 
lh.orig, etc...)?


cheers
Bruce
On Thu, 18 Apr 2013, Claudia Dacquino wrote:


Hi freesurfer, 
my autorecon2-cp after ctrl pts edits exited with this error message: 

CORRECTING DEFECT 0 (vertices=176788, convex hull=8149)
Excessive topologic defect encountered: could not allocate -776253752 edges for 
retessellation
Cannot allocate memory

Could anyone help me with this, please?

Thanks to all.

Cheers
Claudia

___
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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.

Re: [Freesurfer] error while performing recon-all for multiple datasets

[Bruce Fischl]

Hi Anupa

you need to specify each input volume with -i if there are more than one. 
In your example you would need an inner loop of the form


set inputs = ()
foreach vol (SZ*.nii)
set input = ($inputs -i $vol)
end
recon-all $inputs ...

cheers
Bruce

On Wed, 17 Apr 2013, Anupa AV wrote:


Dear All,

I want to run recon-all for multiple subjects.
I named my sbjects as SZ01.nii, SZ02.nii etc.

After setting the cd and environmanet variable, I ran using following for loop:

>for x in *
> do
>recon-all -i SZ*.nii -s $x -all
>done

I got the following error: WHAT MIGHT BE THE REASON FOR THE ERROR???


WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

ERROR: Flag SZ02.nii unrecognized.
-i SZ01.nii SZ02.nii SZ03.nii SZ04.nii -s SZ01.nii -all
Linux mbial-HP-Z210-Workstation 3.2.0-40-generic-pae #64-Ubuntu SMP Mon Mar 25 
21:44:41 UTC
2013 i686 i686 i386 GNU/Linux

recon-all -s  exited with ERRORS at Fri Apr 19 11:43:24 IST 2013

For more details, see the log file
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

ERROR: Flag SZ02.nii unrecognized.
-i SZ01.nii SZ02.nii SZ03.nii SZ04.nii -s SZ02.nii -all
Linux mbial-HP-Z210-Workstation 3.2.0-40-generic-pae #64-Ubuntu SMP Mon Mar 25 
21:44:41 UTC
2013 i686 i686 i386 GNU/Linux

recon-all -s  exited with ERRORS at Fri Apr 19 11:43:24 IST 2013

For more details, see the log file
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

ERROR: Flag SZ02.nii unrecognized.
-i SZ01.nii SZ02.nii SZ03.nii SZ04.nii -s SZ03.nii -all
Linux mbial-HP-Z210-Workstation 3.2.0-40-generic-pae #64-Ubuntu SMP Mon Mar 25 
21:44:41 UTC
2013 i686 i686 i386 GNU/Linux

recon-all -s  exited with ERRORS at Fri Apr 19 11:43:24 IST 2013

For more details, see the log file
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

ERROR: Flag SZ02.nii unrecognized.
-i SZ01.nii SZ02.nii SZ03.nii SZ04.nii -s SZ04.nii -all
Linux mbial-HP-Z210-Workstation 3.2.0-40-generic-pae #64-Ubuntu SMP Mon Mar 25 
21:44:41 UTC
2013 i686 i686 i386 GNU/Linux

recon-all -s  exited with ERRORS at Fri Apr 19 11:43:24 IST 2013

For more details, see the log file
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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[Freesurfer] autorecon2-cp error

[Claudia Dacquino]

Hi freesurfer,
my autorecon2-cp after ctrl pts edits exited with this error message:

CORRECTING DEFECT 0 (vertices=176788, convex hull=8149)
Excessive topologic defect encountered: could not allocate -776253752 edges
for retessellation
Cannot allocate memory

Could anyone help me with this, please?

Thanks to all.

Cheers
Claudia
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[Freesurfer] Thank you

[Valtina Pouegue]

Hi everyone, 
I would just say you thank you for the help you give to Freesurfer users. I use 
Freesurfer for my school project and I ended yesterday. I didn't know anything 
about Linux before and before segmentation software of cortical surface.  I 
don't think I would did an so great job without your help. 
Again, Thank you! And Good Luck !!!
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Re: [Freesurfer] Autoreg-sess and mri_surf2vol

[Lucille Deroche]

Hi, 

Sorry for the answer too late. 
I tried the command to evaluate the RMS distance but I just get the difference 
between the 2 surfaces in terms of faces and vertices. 
But I would compare my 2 surfaces by calculating the euler characteristic ( 
vertices-edges+ faces) . 

Thank you so much for your help!!!

Lucille




 De : Bruce Fischl 
À : Michael Harms  
Cc : Lucille Deroche ; Douglas N Greve 
; "freesurfer@nmr.mgh.harvard.edu" 
 
Envoyé le : Jeudi 11 avril 2013 16h02
Objet : Re: [Freesurfer] Autoreg-sess and mri_surf2vol
 

yes, I agree. Two surfaces could be extremely close and have 0 dice. I 
don't think it would be as informative as Hausdorff or RMS as Mike 
suggests

Bruce
On Thu, 11 Apr 2013, Michael Harms wrote:

> 
> Try:
> mri_surf2vol --surf pial --mkmask --hemi lh --identity  --template 
> /mri/norm.mgz --o
> /mri/pial_in_vol.mgz
> 
> FWIW, I'm not sure if sampling two surfaces to the volume, and then computing 
> a dice coefficient is
> really the best way to "compare" two surfaces.  I would instead compare the 
> two surfaces directly --
> e.g., the rms distance between matched vertices.
> 
> cheers,
> -MH
> 
> -- 
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO  63110 Email: mha...@wustl.edu
> 
> From: Lucille Deroche 
> Reply-To: Lucille Deroche 
> Date: Thursday, April 11, 2013 2:39 PM
> To: Doug Greve , "freesurfer@nmr.mgh.harvard.edu"
> 
> Subject: Re: [Freesurfer] Autoreg-sess and mri_surf2vol
> 
> Hi, 
> 
> I did the command: 
> mri_surf2vol --surfval $SUBJECTS_DIR/Patient1/surf/rh.pial --hemi rh 
> --identity Patient1. 
> ERROR: cannot recognize the type of
> /home/lucille/Freesurfer/freesurfer/subjects/Patient1/surf/rh.pial
> The name of my subject is ' Patient1'. 
> Did I do a wrong entery at the --surfval argument ? 
> 
> 
> Cheers
> Lucille
> 
> _
> De : Douglas N Greve 
> À : freesurfer@nmr.mgh.harvard.edu
> Envoyé le : Jeudi 11 avril 2013 12h49
> Objet : Re: [Freesurfer] Autoreg-sess and mri_surf2vol
> 
> 
> Hi Lucile, don't use autoreg-sess (that is an old program and was for
> fMRI). Use mri_surf2vol with --identity subjectname instead of --reg
> doug
> 
> On 04/11/2013 11:45 AM, Lucille Deroche wrote:
> > Hi Bruce,
> >
> >  In fact, have 2 differents  surfaces  of pial surface. I would like
> > to save my surfaces in volume to be able to calculate the dice score
> > between the two.
> >
> > Cheers
> >
> > Lucille
> > 
> > *De :* Bruce Fischl 
> > *À :* Lucille Deroche 
> > *Cc :* "freesurfer@nmr.mgh.harvard.edu" 
> > *Envoyé le :* Jeudi 11 avril 2013 11h18
> > *Objet :* Re: [Freesurfer] Autoreg-sess and mri_surf2vol
> >
> > Hi Lucille
> >
> > what do you mean by converting a surface to the volume? What do you want
> > to do with it? What volume would you like to convert it to?
> >
> > cheers
> > Bruce
> > On Thu, 11 Apr
> > 2013, Lucille Deroche wrote:
> >
> > > Hi,
> > > My name is Lucille and I'm really new  with Freesurfer : My
> > questions are very basic, sorry.
> > > I just start a project in segmentation of cerebrum.
> > >  For converting a surface in volume. I would like to use
> > mri_surf2vol but for that I need a
> > >  volume registration file . For creating that file, I would use
> > autoreg-sess.
> > > In documentation, it is said that : 'The volume registration file
> > contains the matrix that
> > > maps XYZ in the reference anatomical to XYZ in the functional volume'
> > > My question is : what here, represent the anatomical reference ? The
> > functionnal volume ?
> > > Secondly, for autoreg-sess, the arguments are the subject name and
> > the subject directory. I
> > > think the registration I need to create must be between my 2
> > volumes, so should I use the
> > > subject name and subject directory for my 2 subjects ?
> > >
> > > Sorry,I am really messed...
> > >
> > > Cheers
> > > Lucille
> > >
> > >
> > ___
> > 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.
> >
> >
> >
> >
> > 

[Freesurfer] mri_segstats SNR calculation

[Jordi Delgado]

Dear Freesurfers,

After running the first tests of freesurfer 5.2, I found a file named
$hemi.w-g.pct.stats on the stats folder. The last column of the file is a
SNR calculation, i found on the help manual, that is required to add --snr
to perform this calculation.

I'm interested to know how this SNR is calculated. Is there any method or
paper  related?

Thank you in advance,

-- 
Jordi Delgado Mengual
PIC (Port d'Informació Científica)
Campus UAB, Edifici D
E-08193 Bellaterra, Barcelona
Tel: +34 93 586 82 32 Fax: +34 93 581 41 10
http://www.pic.es
Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html
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[Freesurfer] Problems with Saving Segmentation

[iripp]

Hello,

I have troubles with saving my files, after I did some segmentation  
changes. I think this could be related to a problem, which I have,  
when I load the brainmask:

libGL error: failed to load driver: nouveau
libGL error: Try again with LIBGL_DEBUG=verbose for more details.

This is shown, but it would still be loading and open the brainmask (aseg).

Can anyone help me with this problem?

Thanks a lot,

Isabelle Ripp

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Re: [Freesurfer] How to calcutate Brain volume?

[Anupa AV]

Dear All,
 
I went thru the link suggested by Mr. 
Cedric.https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009600.html
From that mail I understood how to create the label for multiple subjects.

I already created a DLPFC for one individual.
I want to know how to measure the corticla volume (mm3) of that created DLPFC.

Any helps'll be greatly appreciated.





 From: Anupa AV 
To: "Koolschijn, Cédric" ; Freesurfer 
 
Sent: Monday, April 15, 2013 2:50 PM
Subject: Re: [Freesurfer] How to calcutate Brain volume?
 


Dear Cedric,

Thanks a bunch.
I'll try with mri_label2label.



 From: "Koolschijn, Cédric" 
To: Anupa AV  
Sent: Monday, April 15, 2013 1:07 PM
Subject: Re: [Freesurfer] How to calcutate Brain volume?
 


 
Dear Anupa,

The DLPFC is not a standard label in FS. So you need to create it yourself by 
merging the following labels:
DLPFC:  middle frontal gyrus, and inferior and middle frontal sulci 
See also: 
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009600.html

Best,
Cédric



  P.C.M.P. Koolschijn (Cédric), PhD 
  Dutch Autism & ADHD Research Center
  Brain and Cognition
  Weesperplein 4; Room 3.07
  1018 XA Amsterdam
  The Netherlands
  E  p.c.m.p.koolsch...@uva.nl  W http://www.dutcharc.nl//
On 4/15/13 7:34 AM, "Anupa AV"  wrote:

Dear FreeSurfer Experts,
>
>
>I'd like to know how to measure the volume of a brain region using freesurfer.
>I know to obtain the volumes after runnin recon-all command. But I don't find 
>the brain volume of my interest which is DLPFC.
>How can I get the brain volume of my interest.?
>
>
>
>
>Thanks for your response in advance.
>
>
>
>
> ___
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