Re: [Freesurfer] Issue downloading FS-FAST fMRI tutorial data {Disarmed}

[fsbuild]

External Email - Use Caution

OK, give it another try.
- R.
I have the same issue for the following command:wget 
ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.tar.gzIf you 
could add that file too, that would be great.RamiOn Mon, Sep 9, 2019 at 4:04 PM 
fsbuild fsbu...@contbay.com 
wrote:External Email - Use 
CautionThere should be a file 
there now, so please try it again.- robOn Sep 9, 2019, at 14:26, Rami Hamati 
rhama...@uottawa.ca 
wrote:External Email - Use 
CautionHello there,When 
attempting to get the analysed functional data using the below command:wget 
ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gzI get 
thefollowing OUTPUT error:--2019-09-09 14:21:20-- 
ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz; 
= 
‘fsfast-functional.tar.gz’Resolvingsurfer.nmr.mgh.harvard.edu(surfer.nmr.mgh.harvard.edu)...
 132.183.240.105Connecting 
tosurfer.nmr.mgh.harvard.edu(surfer.nmr.mgh.harvard.edu)|132.183.240.105|:21...
 connected.Logging in as anonymous ... Logged in!== SYST ... done.  
== PWD ... done..== TYPE I ... done. == CWD (1) 
/pub/data ... done..== SIZE fsfast-functional.tar.gz ... done.== PASV 
... done.  == RETR fsfast-functional.tar.gz ...No such 
file ‘fsfast-functional.tar.gz’.Could you please advise.Thank 
you,Rami___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer--Rami
 Hamati, MSc. Nsc (Candidate)Royal's Institute of Mental Health ResearchMood 
Disorders Research Unit1145 Carling Ave, Ottawa, ON K1Z 7K4T: 613-722-6521 ext. 
6838rhama036@uottawa.ca___Freesurfer
 mailing 
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[Freesurfer] Convert nifti atlas into .annot file

[Dev vasu]

External Email - Use Caution

Dear all,

How can i create .annot files for both left and right hemisphere from nifti
atlases http://www.gin.cnrs.fr/en/tools/aal/

are there any specific guidelines or  commands for surface based
parcellation ?

Thanks
Vasudev
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Re: [Freesurfer] Issue downloading FS-FAST fMRI tutorial data

[Rami Hamati]

External Email - Use Caution

Hey Rob,

I have the same issue for the following command:

wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.tar.gz

If you could add that file too, that would be great.

Rami

On Mon, Sep 9, 2019 at 4:04 PM fsbuild  wrote:

> External Email - Use Caution
>
> There should be a file there now, so please try it again.
>
> - rob
>
> On Sep 9, 2019, at 14:26, Rami Hamati  wrote:
>
> External Email - Use Caution
>
> Hello there,
>
> When attempting to get the analysed functional data using the below
> command:
>
> wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz
>
> I get the following OUTPUT error:
>
> --2019-09-09 14:21:20--
> ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz
>=> ‘fsfast-functional.tar.gz’
> Resolving surfer.nmr.mgh.harvard.edu (surfer.nmr.mgh.harvard.edu)...
> 132.183.240.105
> Connecting to surfer.nmr.mgh.harvard.edu 
> (surfer.nmr.mgh.harvard.edu)|132.183.240.105|:21...
> connected.
> Logging in as anonymous ... Logged in!
> ==> SYST ... done.==> PWD ... done.
> ==> TYPE I ... done.  ==> CWD (1) /pub/data ... done.
> ==> SIZE fsfast-functional.tar.gz ... done.
>
> ==> PASV ... done.==> RETR fsfast-functional.tar.gz ...
> *No such file ‘fsfast-functional.tar.gz’.*
>
> Could you please advise.
>
> Thank you,
>
> Rami
>
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-- 
Rami Hamati, MSc. Nsc (Candidate)
Royal's Institute of Mental Health Research
Mood Disorders Research Unit
1145 Carling Ave, Ottawa, ON K1Z 7K4

T: 613-722-6521 ext. 6838
rhama...@uottawa.ca
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Re: [Freesurfer] Issue downloading FS-FAST fMRI tutorial data

[Rami Hamati]

External Email - Use Caution

Thanks, it worked.

Cheers,

Rami

On Mon, Sep 9, 2019, 16:04 fsbuild  wrote:

> External Email - Use Caution
>
> There should be a file there now, so please try it again.
>
> - rob
>
> On Sep 9, 2019, at 14:26, Rami Hamati  wrote:
>
> External Email - Use Caution
>
> Hello there,
>
> When attempting to get the analysed functional data using the below
> command:
>
> wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz
>
> I get the following OUTPUT error:
>
> --2019-09-09 14:21:20--
> ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz
>=> ‘fsfast-functional.tar.gz’
> Resolving surfer.nmr.mgh.harvard.edu (surfer.nmr.mgh.harvard.edu)...
> 132.183.240.105
> Connecting to surfer.nmr.mgh.harvard.edu 
> (surfer.nmr.mgh.harvard.edu)|132.183.240.105|:21...
> connected.
> Logging in as anonymous ... Logged in!
> ==> SYST ... done.==> PWD ... done.
> ==> TYPE I ... done.  ==> CWD (1) /pub/data ... done.
> ==> SIZE fsfast-functional.tar.gz ... done.
>
> ==> PASV ... done.==> RETR fsfast-functional.tar.gz ...
> *No such file ‘fsfast-functional.tar.gz’.*
>
> Could you please advise.
>
> Thank you,
>
> Rami
>
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>
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Re: [Freesurfer] Issue downloading FS-FAST fMRI tutorial data

[fsbuild]

External Email - Use Caution

There should be a file there now, so please try it again.
- rob

On Sep 9, 2019, at 14:26, Rami Hamati rhama...@uottawa.ca 
wrote:External Email - Use 
CautionHello there,When 
attempting to get the analysed functional data using the below command:wget 
ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gzI get 
thefollowing OUTPUT error:--2019-09-09 14:21:20-- 
ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz; 
= 
‘fsfast-functional.tar.gz’Resolvingsurfer.nmr.mgh.harvard.edu(surfer.nmr.mgh.harvard.edu)...
 132.183.240.105Connecting 
tosurfer.nmr.mgh..harvard.edu(surfer.nmr.mgh.harvard.edu)|132.183.240.105|:21...
 connected.Logging in as anonymous ... Logged in!== SYST ... done.  
== PWD ... done.== TYPE I ... done. == CWD (1) 
/pub/data ... done.== SIZE fsfast-functional.tar.gz ... done.== PASV 
... done.  == RETR fsfast-functional.tar.gz ...No such 
file ‘fsfast-functional.tar.gz’.Could you please advise.Thank 
you,Rami___Freesurfer mailing 
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Re: [Freesurfer] Extracting contrast data from mri_glmfit to graph

[Greve, Douglas N.,Ph.D.]

It is voodoo to do the same test that you used to generate the cluster 
(or have a graph that implies such a test). If you want to do a post-hoc 
test, that is totally fair. Eg, if you do an unsigned test between the 
two groups, you could then go back and do a signed test on the extraction.


On 9/9/19 1:31 PM, cody samth wrote:
>
> External Email - Use Caution
>
> Hi Douglas,
>
> That's good to know its still a form of voodoo correlation. If 
> researchers wanted to avoid this, when looking for an interaction 
> effect in a DODS model with a continuous variable yet still wanted to 
> know the direction of the relationships how could that be done? As 
> currently if group 1>group 2. That could theoretically be interpreted 
> as 1) both groups are negative 2) both groups are positive 3) one 
> group positive one group negative. Would this be done by looking at 
> the beta values for the slope of that variable?
>
>
>
> Regarding graphing the results I'm not too familiar with matlab 
> however after running the contrast you suggested in matlab and 
> plotting the yhat value for 2 of my clusters the R2 is 1.000 for 
> both which leads me to believe I somehow ended up saving the predicted 
> values. (Rather than the actual values of thickness for each 
> participant) Did I load everything into matlab correctly?
> These were my inputs
>
> X = load('Xg.dat')
> Y = load('ocn.dat')
> beta = inv(X'*X)*(X'*Y)
> beta2 = load('beta2') ; file where I saved the beta values for the 
> mean thickness and slope of my variable of interest; that was computed 
> in the previous step
> X2 = load('X2.dat') ; removed nuisance columns from the Xg.dat file
> yhat = X2*beta2 ' saved these values and plotted them against my 
> variable of interest
>
>
> On Mon, Sep 9, 2019 at 10:37 AM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> Right, the ocn.dat files have data that is uncorrected in that
> sense and might need to nuisance factors removed before plotting.
> There is a design matrix in there (Xg.dat). You can load that into
> matlab along with the ocn.dat, compute beta = inv(X'*X)*(X'*ocn)
> to get the betas. You can then compute yhat = X2*beta2 where X2
> has nuisance columns removed and beta2 has the same nuisance
> coefficients removed, then treat yhat as your data to be plotted.
>
>  Note that plotting the results is still a form a voodoo
> correlations because your eye will compute the correlation even if
> you don't explicitly do so (though it generally does not stop
> anyone:).
>
>
>
> On 9/8/2019 7:37 PM, cody samth wrote:
>>
>> External Email - Use Caution
>>
>> Hi Douglas, thanks for your response.
>>
>> >They should not, but the reason it fairly convoluted. When you
>> get a
>> >cluster after running mri_glmfit-sim, that cluster is on
>> fsaverage which
>> >is an average of 40 subjects. The area of a vertex is computed
>> as the
>> >average of the areas of the vertices from the 40 that mapped
>> into that
>> >vertex. This is the number that is used to compute the surface
>> area of
>> >the cluster in the summary file. Now, when you map your subjects
>> into
>> >the fsaverage space, they may have more or less surface area
>> mapping
>> >into that cluster relative to the 40 (looks like more from #2
>> below).
>> >Also, you probably smoothed the surface area, which could have an
>> >unpredictable effect.
>> Thanks that makes sense.
>>
>> >> 3) ocn.dat files are the input values meaning they're raw and
>> would
>> >> need to be corrected in a statistically (in a similar way that I
>> >> modeled it in freesurfer) before graphing right?
>> >Not sure what you mean by "corrected" here. In general, you need
>> to be
>> >very careful when you extract data from a cluster. It would be
>> circular
>> >to do the same test that you used to generate the cluster,
>> though this
>> >happens a lot (see "VooDoo correlations" by Ed Vul).
>> My apologies corrected wasn't the best way to phrase that question.
>> My interpretation of the ocn.dat file is that the each row
>> contains the
>> average input value for a subject prior to controlling for
>> covariates.
>> Therefore, to graph these results wouldn't these values need to
>> undergo
>> some method to control for covariates such as ICV, sex or age to
>> better
>> reflect the clusters observed from the GLM?
>>
>> Or are the values in the ocn.dat file already reflective of the
>> test/glm
>> used to generate the cluster?
>>
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>
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Re: [Freesurfer] freesurfer 6.0 hires fix

[Greve, Douglas N.,Ph.D.]

You have to rerun from the beginning. (sorry)

On 9/9/19 3:12 PM, Aaron Tanenbaum wrote:
>
> External Email - Use Caution
>
> I noticed that you guys released a fix to improve the -hires option.  
> I have been processing some of our data using the hires flag. if i use 
> this fix do i need to run recon-all from the beginning or can I run 
> over the old folders?
>
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[Freesurfer] freesurfer 6.0 hires fix

[Aaron Tanenbaum]

External Email - Use Caution

I noticed that you guys released a fix to improve the -hires option.  I
have been processing some of our data using the hires flag. if i use this
fix do i need to run recon-all from the beginning or can I run over the old
folders?
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[Freesurfer] Issue downloading FS-FAST fMRI tutorial data

[Rami Hamati]

External Email - Use Caution

Hello there,

When attempting to get the analysed functional data using the below command:

wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz

I get the following OUTPUT error:

--2019-09-09 14:21:20--
ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz
   => ‘fsfast-functional.tar.gz’
Resolving surfer.nmr.mgh.harvard.edu (surfer.nmr.mgh.harvard.edu)...
132.183.240.105
Connecting to surfer.nmr.mgh.harvard.edu
(surfer.nmr.mgh.harvard.edu)|132.183.240.105|:21...
connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/data ... done.
==> SIZE fsfast-functional.tar.gz ... done.

==> PASV ... done.==> RETR fsfast-functional.tar.gz ...
*No such file ‘fsfast-functional.tar.gz’.*

Could you please advise.

Thank you,

Rami
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Re: [Freesurfer] Extracting contrast data from mri_glmfit to graph

[cody samth]

External Email - Use Caution

Hi Douglas,

That's good to know its still a form of voodoo correlation. If researchers
wanted to avoid this, when looking for an interaction effect in a DODS
model with a continuous variable yet still wanted to know the direction of
the relationships how could that be done? As currently if group 1>group 2.
That could theoretically be interpreted as 1) both groups are negative 2)
both groups are positive 3) one group positive one group negative. Would
this be done by looking at the beta values for the slope of that variable?



Regarding graphing the results I'm not too familiar with matlab however
after running the contrast you suggested in matlab and plotting the yhat
value for 2 of my clusters the R2 is 1.000 for both which leads me to
believe I somehow ended up saving the predicted values. (Rather than the
actual values of thickness for each participant) Did I load everything into
matlab correctly?
These were my inputs

X = load('Xg.dat')
Y = load('ocn.dat')
beta = inv(X'*X)*(X'*Y)
beta2 = load('beta2') ; file where I saved the beta values for the mean
thickness and slope of my variable of interest; that was computed in the
previous step
X2 = load('X2.dat') ; removed nuisance columns from the Xg.dat file
yhat = X2*beta2 ' saved these values and plotted them against my variable
of interest


On Mon, Sep 9, 2019 at 10:37 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Right, the ocn.dat files have data that is uncorrected in that sense and
> might need to nuisance factors removed before plotting. There is a design
> matrix in there (Xg.dat). You can load that into matlab along with the
> ocn.dat, compute beta = inv(X'*X)*(X'*ocn) to get the betas. You can then
> compute yhat = X2*beta2 where X2 has nuisance columns removed and beta2 has
> the same nuisance coefficients removed, then treat yhat as your data to be
> plotted.
>
>  Note that plotting the results is still a form a voodoo correlations
> because your eye will compute the correlation even if you don't explicitly
> do so (though it generally does not stop anyone:).
>
>
>
> On 9/8/2019 7:37 PM, cody samth wrote:
>
> External Email - Use Caution
> Hi Douglas, thanks for your response.
>
> >They should not, but the reason it fairly convoluted. When you get a
> >cluster after running mri_glmfit-sim, that cluster is on fsaverage which
> >is an average of 40 subjects. The area of a vertex is computed as the
> >average of the areas of the vertices from the 40 that mapped into that
> >vertex. This is the number that is used to compute the surface area of
> >the cluster in the summary file. Now, when you map your subjects into
> >the fsaverage space, they may have more or less surface area mapping
> >into that cluster relative to the 40 (looks like more from #2 below).
> >Also, you probably smoothed the surface area, which could have an
> >unpredictable effect.
> Thanks that makes sense.
>
> >> 3) ocn.dat files are the input values meaning they're raw and would
> >> need to be corrected in a statistically (in a similar way that I
> >> modeled it in freesurfer) before graphing right?
> >Not sure what you mean by "corrected" here. In general, you need to be
> >very careful when you extract data from a cluster. It would be circular
> >to do the same test that you used to generate the cluster, though this
> >happens a lot (see "VooDoo correlations" by Ed Vul).
> My apologies corrected wasn't the best way to phrase that question.
> My interpretation of the ocn.dat file is that the each row contains the
> average input value for a subject prior to controlling for covariates.
> Therefore, to graph these results wouldn't these values need to undergo
> some method to control for covariates such as ICV, sex or age to better
> reflect the clusters observed from the GLM?
>
> Or are the values in the ocn.dat file already reflective of the test/glm
> used to generate the cluster?
>
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>
>
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[Freesurfer] Opseq2 question

[Nasiriavanaki, Zahra]

Hi Freesurfer experts

I have a question about designing an event related task. We are designing a 
task for fear conditioning. Each stimuli presentation lasts 4 seconds. My 
question is if we set the TR to 2 (which is a multiply of 4), will it make the 
paradigm to have more power in signal detection? Or does it not matter if the 
TR and stimuli presentation be a multiply of each other or not?
I appreciate if you give me your comments on that.

Thanks a lot
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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Re: [Freesurfer] fspalm error

[Greve, Douglas N.,Ph.D.]

I think palm itself requires mgh or mgz files. I can't remember why we don't 
convert it. You can run mri_glmfit with --mgz or --mgh (or just without 
--nii.gz) and it should work.


On 9/9/2019 9:24 AM, Barbour, Tracy,M.D. wrote:
Hello Freesurfer community!

I am trying to run fspalm on surface based data. I have installed PALM, fspalm, 
mri_surfcluster, and mri_volcluster.

This is my fspalm command:
fspalm --glmdir TEPSC.glmdir --cft 1.3 --twotail --name palm-twotail-1.3 
--iters 1000 --2spaces --cwp .05

When I run the fspalm command I get the error: "for surface based analysis, 
input cannot be nii or nii.gz"

I thought that fspalm was supposed to convert ces.nii.gz files into something 
that PALM could use.

Please let me know if there is another step I need to run or if I need to 
change the script.

Best,

Tracy



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Re: [Freesurfer] Extracting contrast data from mri_glmfit to graph

[Greve, Douglas N.,Ph.D.]

Right, the ocn.dat files have data that is uncorrected in that sense and might 
need to nuisance factors removed before plotting. There is a design matrix in 
there (Xg.dat). You can load that into matlab along with the ocn.dat, compute 
beta = inv(X'*X)*(X'*ocn) to get the betas. You can then compute yhat = 
X2*beta2 where X2 has nuisance columns removed and beta2 has the same nuisance 
coefficients removed, then treat yhat as your data to be plotted.

 Note that plotting the results is still a form a voodoo correlations because 
your eye will compute the correlation even if you don't explicitly do so 
(though it generally does not stop anyone:).



On 9/8/2019 7:37 PM, cody samth wrote:

External Email - Use Caution

Hi Douglas, thanks for your response.

>They should not, but the reason it fairly convoluted. When you get a
>cluster after running mri_glmfit-sim, that cluster is on fsaverage which
>is an average of 40 subjects. The area of a vertex is computed as the
>average of the areas of the vertices from the 40 that mapped into that
>vertex. This is the number that is used to compute the surface area of
>the cluster in the summary file. Now, when you map your subjects into
>the fsaverage space, they may have more or less surface area mapping
>into that cluster relative to the 40 (looks like more from #2 below).
>Also, you probably smoothed the surface area, which could have an
>unpredictable effect.
Thanks that makes sense.

>> 3) ocn.dat files are the input values meaning they're raw and would
>> need to be corrected in a statistically (in a similar way that I
>> modeled it in freesurfer) before graphing right?
>Not sure what you mean by "corrected" here. In general, you need to be
>very careful when you extract data from a cluster. It would be circular
>to do the same test that you used to generate the cluster, though this
>happens a lot (see "VooDoo correlations" by Ed Vul).
My apologies corrected wasn't the best way to phrase that question.
My interpretation of the ocn.dat file is that the each row contains the
average input value for a subject prior to controlling for covariates.
Therefore, to graph these results wouldn't these values need to undergo
some method to control for covariates such as ICV, sex or age to better
reflect the clusters observed from the GLM?

Or are the values in the ocn.dat file already reflective of the test/glm
used to generate the cluster?



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[Freesurfer] fspalm error

[Barbour, Tracy,M.D.]

Hello Freesurfer community!

I am trying to run fspalm on surface based data. I have installed PALM, fspalm, 
mri_surfcluster, and mri_volcluster.

This is my fspalm command:
fspalm --glmdir TEPSC.glmdir --cft 1.3 --twotail --name palm-twotail-1.3 
--iters 1000 --2spaces --cwp .05

When I run the fspalm command I get the error: "for surface based analysis, 
input cannot be nii or nii.gz"

I thought that fspalm was supposed to convert ces.nii.gz files into something 
that PALM could use.

Please let me know if there is another step I need to run or if I need to 
change the script.

Best,

Tracy
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Re: [Freesurfer] Morphological Features, Description & References

[Bruce Fischl]

for the continuous curvature you can just cite the FreeSurfer paper, or 
recon1/2). For the discrete curvature I think Rudolph Pienaar 
published something on it. Some of the curvature indices are from David Van 
Essen's papers, and the volume/area calculation is Anderson M. Winkler's 
paper


cheers
Bruce


On Mon, 9 Sep 2019, Loske, Philipp wrote:



External Email - Use Caution

Hi you two,

thank you very much for your quick reply! Just two short followup questions:

@Bruce: Is this published in any paper or documentation so I can cite it?

@Doug: Has this method been implemented with the last release of FS in 6.0.0
or already before in 5.3.0 (I'm still using this version)?

Cheers
Philipp

  For cortical volume we compute  vertex-wise volume based on
  dividing each obliquely truncated   trilateral pyramid into
  three tetrahedra. Based on Anderson M. Winkler's   srf2vol
  matlab script.
On 9/6/2019 10:22 AM, Bruce Fischl wrote:
Hi Philipp

I'll leave the volume question to Doug. The curvatures are estimated
by fitting a second order polynomial to the local height function in
the tangent bundle then computing the Hessian using the white
(gray/white boundary) surface. We also have some discrete measures of
curvature that uses the Gauss-Bonnet theorem, but those aren't run by
default.

cheers
Bruce
On Fri, 6 Sep 2019, Loske, Philipp wrote:


    External Email - Use Caution

Hello FreeSurfer Developers,


I have a question about references and descriptions to all the
morphological
features available in aparc.stats, extracted from structural MRI. I am
using
all the different features (SurfArea, GrayVol, ThickAvg, ThickStd,
MeanCurv,
GausCurv, FoldInd, CurvInd) for the 68 cortical regions available from
the
Desikan Kiliany atlas. I have been trying to find references to how
these
features are measured or derived, but couldn't find a proper list of
references to each of the features. I a lot of references
here
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation,
with detailed descriptions on surface reconstruction and how cortical
thickness is measured, but couldn't find a detailed explanation on the
other
features, especially curvature values.

I think I have been able to find out what each of the measurements
mean and
how they are calculated in principle, through searching the internet a
lot,
but with no direct link to FreeSurfer. For instance, I know you can
calculate
the curvature values from the principle curvatures, but how does FS
estimate
those form the reconstructed Surface? And which one of the two
surfaces does
it use? White-pial or pial-csf surface? I found https://brainder.org/
really
helpful, but it says for example that a new way of measuring cortical
volume
was implemented in FS 6.0.0, so does that mean for previous versions
FS uses
the Thickness x SurfaceArea method? Would be great if you can help me
with
this, or point me to the correct website I might just have missed
during my
search.


Best wishes

Philipp




The University of Aberdeen is a charity registered in Scotland, No
SC013683.
Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba,
?ir.
SC013683.



The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir.
SC013683.
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Re: [Freesurfer] error while running "-hippocampal-subfields-T1" with Freesurfer 6.0

[Bruce Fischl]

Hi Shahrazd

can you try:

chmod -R a+rx  $FREESURFER_HOME/bin

and see if that fixes your problem?

Bruce


On Mon, 9 Sep 2019, shahrzad kharabian wrote:



External Email - Use Caution

Hi, 
I have already run recon-all with default options on a large set of
T1-weighted images, using Freesurfer v 6.0. 
Now we want to extract the hippocmpal subfields from these already processed
images. 
Apparently our installation was missing Matlab Compiler Runtime (MCR) for
Matlab 2012b.
We followed the instructions and downloaded it and placed it in the
$FREESURFER_HOME. 

Yet now when running the "recon-all -s subj_id -hippocampal-subfields-T1"
command, I get the following error:

$FREESURFER_HOME/bin: Permission denied.

and the error occurs in the step:

$FREESURFER_HOME/bin/segmentSF_T1.sh

--- 
I am using a bash shell. But also temporarily changing the shell to tcsh and
adding the Freesurfer to the path, did not solve the problem. 

How can the error be avoided?

Thanks a lot for your help in advance,
Shahrazd

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Re: [Freesurfer] Correcting defect problem after checking skull stripped and editing wm.mgz

[Bruce Fischl]

Hi Jiun-Wei

have you looked at the ?h.defect_labels overlaid on the inflated.nofix 
and orig.nofix surfaces? That will tell you where the defect is that is 
causing you trouble. If you have lesions they may be the source of the 
issue. If you can't sort it out you can tar and gzip the entire subject 
directory and put it on our ftp site for us to have a look

cheers
Bruce
On Mon, 9 Sep 
2019, Jiun Wei Chen wrote:




External Email - Use Caution

Dear freesurfer experts,
When executing recon-all in two subjects with brain lesions, the recon-all
process stopped at CORRECTING DEFECT 13 (vertices=49319, convex hull=12973,
v0=65403) and 
CORRECTING DEFECT 6 (vertices=23529, convex hull=6740, v0=16029),
respectively.

After reading the relevant problem from freesufer mailing list, I had
checked the skull and cerebellum not attached to the surface, two
hemispheres are separated using freeview. In addition, I also load
the brain.mgz, wm.mgz, ?h.orig.nofix and ?h.inflated.nofix and separately
overlap the ?h.defect_label onto ?h.orig.nofix  , ?h.inflated.nofix to edit
wm.mgz to solve this problem.

However, after editing wm.mgz in two subjects, the recon-all process still
stopped at CORRECTING DEFECT 0 (vertices=32853, convex hull=7926) and
CORRECTING DEFECT 6 (vertices=16533, convex hull= 4510) , respectively.

Although I try to erase the non-white matter and label voxels as white
matter as much as possible, there are too many voxels I think I need to
label, which may cause the failure. 

I can't figure out how to continue to solve this problem. I use freesurfer
version 6.0.0.

I really appreciate your help. Thanks a lot.

Best regards,

Jiun-Wei





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Re: [Freesurfer] Morphological Features, Description & References

[Loske, Philipp]

External Email - Use Caution

Hi you two,

thank you very much for your quick reply! Just two short followup questions:

@Bruce: Is this published in any paper or documentation so I can cite it?

@Doug: Has this method been implemented with the last release of FS in 6.0.0 or 
already before in 5.3.0 (I'm still using this version)?

Cheers
Philipp

For cortical volume we compute  vertex-wise volume based on dividing each 
obliquely truncated   trilateral pyramid into three tetrahedra. Based on 
Anderson M. Winkler's   srf2vol matlab script.
On 9/6/2019 10:22 AM, Bruce Fischl wrote:
Hi Philipp

I'll leave the volume question to Doug. The curvatures are estimated by fitting 
a second order polynomial to the local height function in the tangent bundle 
then computing the Hessian using the white (gray/white boundary) surface. We 
also have some discrete measures of curvature that uses the Gauss-Bonnet 
theorem, but those aren't run by default.

cheers
Bruce
On Fri, 6 Sep 2019, Loske, Philipp wrote:


External Email - Use Caution

Hello FreeSurfer Developers,


I have a question about references and descriptions to all the morphological
features available in aparc.stats, extracted from structural MRI. I am using
all the different features (SurfArea, GrayVol, ThickAvg, ThickStd, MeanCurv,
GausCurv, FoldInd, CurvInd) for the 68 cortical regions available from the
Desikan Kiliany atlas. I have been trying to find references to how these
features are measured or derived, but couldn't find a proper list of
references to each of the features. I a lot of references
here https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation,
with detailed descriptions on surface reconstruction and how cortical
thickness is measured, but couldn't find a detailed explanation on the other
features, especially curvature values.

I think I have been able to find out what each of the measurements mean and
how they are calculated in principle, through searching the internet a lot,
but with no direct link to FreeSurfer. For instance, I know you can calculate
the curvature values from the principle curvatures, but how does FS estimate
those form the reconstructed Surface? And which one of the two surfaces does
it use? White-pial or pial-csf surface? I found https://brainder.org/ really
helpful, but it says for example that a new way of measuring cortical volume
was implemented in FS 6.0.0, so does that mean for previous versions FS uses
the Thickness x SurfaceArea method? Would be great if you can help me with
this, or point me to the correct website I might just have missed during my
search.


Best wishes

Philipp




The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir.
SC013683.



The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. 
SC013683.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] error while running "-hippocampal-subfields-T1" with Freesurfer 6.0

[shahrzad kharabian]

External Email - Use Caution

Hi, I have already run recon-all with default options on a large set of 
T1-weighted images, using Freesurfer v 6.0. Now we want to extract the 
hippocmpal subfields from these already processed images. Apparently our 
installation was missing Matlab Compiler Runtime (MCR) for Matlab 2012b.We 
followed the instructions and downloaded it and placed it in the 
$FREESURFER_HOME. 
Yet now when running the "recon-all -s subj_id -hippocampal-subfields-T1" 
command, I get the following error:
$FREESURFER_HOME/bin: Permission denied.
and the error occurs in the step:
$FREESURFER_HOME/bin/segmentSF_T1.sh

--- I am using a bash shell. But also temporarily changing the shell to tcsh 
and adding the Freesurfer to the path, did not solve the problem. 
How can the error be avoided?
Thanks a lot for your help in advance,
Shahrazd___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Correcting defect problem after checking skull stripped and editing wm.mgz

[Jiun Wei Chen]

External Email - Use Caution

Dear freesurfer experts,

When executing recon-all in two subjects with brain lesions, the recon-all
process stopped at CORRECTING DEFECT 13 (vertices=49319, convex hull=12973,
v0=65403) and
CORRECTING DEFECT 6 (vertices=23529, convex hull=6740, v0=16029),
respectively.

After reading the relevant problem from freesufer mailing list, I had
checked the skull and cerebellum not attached to the surface, two
hemispheres are separated using freeview. In addition, I also load
the brain.mgz, wm.mgz, ?h.orig.nofix and ?h.inflated.nofix and separately
overlap the ?h.defect_label onto ?h.orig.nofix  , ?h.inflated.nofix to edit
wm.mgz to solve this problem.

However, after editing wm.mgz in two subjects, the recon-all process still
stopped at CORRECTING DEFECT 0 (vertices=32853, convex hull=7926) and
CORRECTING DEFECT 6 (vertices=16533, convex hull= 4510) , respectively.

Although I try to erase the non-white matter and label voxels as white
matter as much as possible, there are too many voxels I think I need to
label, which may cause the failure.

I can't figure out how to continue to solve this problem. I use freesurfer
version 6.0.0.

I really appreciate your help. Thanks a lot.

Best regards,

Jiun-Wei
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