[Freesurfer] Maps showing correlations between structural measures

[Martin Juneja]

Hello FreeSurfer experts,

I came across a paper:
http://www.sciencedirect.com/science/article/pii/S0166432815001837
where correlation maps between volume and gyrification are reported.

I am familiar with GLM in FreeSurfer i.e. correlating behavioral measures
with volume and gyrification but I was wondering how to correlate structure
measures with each other e.g. volume and gyrification.

I would really appreciate any help.

Thanks.
___
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.

Re: [Freesurfer] Interaction effects in QDEC

[Heidi Foo]

Great, thank you!

Regards,
Heidi Foo

On Thu, 27 Apr 2017 at 12:17 AM, Douglas N Greve 
wrote:

> Yes
>
>
> On 04/26/2017 09:15 AM, Heidi Foo wrote:
> > Dear Douglas,
> >
> > Thank you for your reply. Does this mean that if I were to have a
> > continuous variable (i.e. Neuroinflammation) and a categorical
> > variable with 2 levels (i.e. gene positive and gene negative),
> > interaction can also be found using QDEC?
> >
> > Thank you.
> >
> > Best Regards,
> > Heidi Foo
> >
> > On Wed, Jan 11, 2017 at 5:20 AM, Douglas N Greve
> > > wrote:
> >
> > This is done automatically when you have two categorical variables
> and
> > two continuous variables. This is equivalent to asking whether the
> two
> > slopes differ across the two categorical variables.
> >
> >
> > On 01/07/2017 09:30 AM, Heidi Foo wrote:
> > > Hi all,
> > >
> > > I was wondering how I could test for interaction effects between a
> > > categorical variable and a continuous variable using QDEC. Is
> > there a
> > > way to do so?
> > >
> > > Thank you.
> > >
> > > Best Regards,
> > > Heidi Foo
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu 
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422 
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > 
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > 
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > 
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > 
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  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 mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
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.

Re: [Freesurfer] Medial Surface Problem

[Bronwyn Overs]

Hi Mailing List,

Still trying to solve the below medial surface problem. Does anyone have any 
ideas?
Kind regards,
Bronwyn Overs
Research Assistant

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265

neura.edu.au  
  
 

> On 28 Mar 2017, at 10:51 pm, Yann Quidé  wrote:
> 
> Dear all,
> 
> I have an equivalent issue with my data. Any idea on how to fix this?
> 
> Thanks.
> 
> Yann
> 
> 
>> Begin forwarded message:
>> 
>> From: Bronwyn Overs >
>> Subject: Re: [Freesurfer] Medial Surface Problem
>> Date: 20 March 2017 10:28:37 am AEDT
>> To: Freesurfer support list > >
>> Reply-To: Freesurfer support list > >
>> 
>> Hello again mailing list,
>> 
>> Can anyone address the possible cause of the medial surface problem shown 
>> below (overestimating of rh medial surface, shows up in the long image and 
>> not the tp or base images). Forgot to mention that I am using freesurfer 
>> v5.3 with an updated mris_make_surfaces binary (sourced from the development 
>> version at 
>> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/
>>  
>> 
>>  ).
>> 
>> Here is the image again:
>> 
>> 
>> Kind regards,
>> Bronwyn Overs
>> Research Assistant
>> 
>> Neuroscience Research Australia
>> Margarete Ainsworth Building
>> Barker Street Randwick Sydney NSW 2031 Australia
>> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
>> 
>> neura.edu.au  
>>   
>>  
>> 
>>> On 6 Mar 2017, at 1:17 pm, Bronwyn Overs >> > wrote:
>>> 
>>> Hi mailing list,
>>> 
>>> I am currently processing a longitudinal image and have come across a 
>>> problem at the medial surface in the long image (step 3). As you can see in 
>>> the attached image, the rh medial surface has been significantly 
>>> overestimated and extends into the lh surface. This error showed up only in 
>>> only 1 of the 2 long images for this subject, and both the time-point 
>>> images and the base are perfectly fine. Do you know why this is happening? 
>>> 
>>> 
>>> 
>>> 
>>> Kind regards,
>>> Bronwyn Overs
>>> Research Assistant
>>> 
>>> Neuroscience Research Australia
>>> Margarete Ainsworth Building
>>> Barker Street Randwick Sydney NSW 2031 Australia
>>> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
>>> 
>>> neura.edu.au  
>>>   
>>>  
>>> 
>>> ___
>>> 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 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 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 

Re: [Freesurfer] FS-Fast's 'subject to fsaverage' registration files?

[Bruce Fischl]

glad it worked out :)
On Wed, 26 Apr 2017, Patrycja Naumczyk wrote:


Hi Bruce,

thanks for a quick reply! mri_surf2surf worked fine just with specifying the
target and source subjects, no registration file needed - much appreciated
:)

Best regards,
Patrycja

2017-04-26 22:51 GMT+02:00 Bruce Fischl :
  Hi Patrycja

  the standard transform we use to fsaverage coordinates is
  surface-based (spherical). If you sample your EPI onto the
  surface, I believe you can use mri_surf2surf to transfer it from
  subject to fsaverage

  cheers
  Bruce
  On Wed, 26 Apr 2017, Patrycja Naumczyk wrote:

Hello FS experts,

I have a question regarding FS-Fast processing. I
have performed
(successfully!)  an FS-Fast single subject analysis.
The results look fine
in the fsaverage space, but I'm interested in
viewing them in the subject
space.

Are the registration files used along the processing
pipeline
(EPI->T1->fsaverage) stored anywhere (so far I only
found the EPI->T1 and
T1->talairach files), so I can use them? Or do I
need to create new
registration files (bbregister/tkregister2)?

Best regards,
Patrycja


___
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 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.

Re: [Freesurfer] FS-Fast's 'subject to fsaverage' registration files?

[Patrycja Naumczyk]

Hi Bruce,

thanks for a quick reply! mri_surf2surf worked fine just with specifying
the target and source subjects, no registration file needed - much
appreciated :)

Best regards,
Patrycja

2017-04-26 22:51 GMT+02:00 Bruce Fischl :

> Hi Patrycja
>
> the standard transform we use to fsaverage coordinates is surface-based
> (spherical). If you sample your EPI onto the surface, I believe you can use
> mri_surf2surf to transfer it from subject to fsaverage
>
> cheers
> Bruce
>
> On Wed, 26 Apr 2017, Patrycja Naumczyk wrote:
>
> Hello FS experts,
>>
>> I have a question regarding FS-Fast processing. I have performed
>> (successfully!)  an FS-Fast single subject analysis. The results look fine
>> in the fsaverage space, but I'm interested in viewing them in the subject
>> space.
>>
>> Are the registration files used along the processing pipeline
>> (EPI->T1->fsaverage) stored anywhere (so far I only found the EPI->T1 and
>> T1->talairach files), so I can use them? Or do I need to create new
>> registration files (bbregister/tkregister2)?
>>
>> Best regards,
>> Patrycja
>>
>>
> ___
> 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 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.

Re: [Freesurfer] FS-Fast's 'subject to fsaverage' registration files?

[Bruce Fischl]

Hi Patrycja

the standard transform we use to fsaverage coordinates is surface-based 
(spherical). If you sample your EPI onto the surface, I believe you can 
use mri_surf2surf to transfer it from subject to fsaverage


cheers
Bruce
On Wed, 26 Apr 
2017, Patrycja Naumczyk wrote:



Hello FS experts,

I have a question regarding FS-Fast processing. I have performed
(successfully!)  an FS-Fast single subject analysis. The results look fine
in the fsaverage space, but I'm interested in viewing them in the subject
space.

Are the registration files used along the processing pipeline
(EPI->T1->fsaverage) stored anywhere (so far I only found the EPI->T1 and
T1->talairach files), so I can use them? Or do I need to create new
registration files (bbregister/tkregister2)?

Best regards,
Patrycja

___
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] FS-Fast's 'subject to fsaverage' registration files?

[Patrycja Naumczyk]

Hello FS experts,

I have a question regarding FS-Fast processing. I have performed
(successfully!)  an FS-Fast single subject analysis. The results look fine
in the fsaverage space, but I'm interested in viewing them in the subject
space.

Are the registration files used along the processing pipeline
(EPI->T1->fsaverage) stored anywhere (so far I only found the EPI->T1 and
T1->talairach files), so I can use them? Or do I need to create new
registration files (bbregister/tkregister2)?

Best regards,
Patrycja
___
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.

Re: [Freesurfer] error with mris_anatomical_stats OR mris_sample_parc

[Bruce Fischl]

Hi Jared

can you send us the full command line and screen output?

cheers
Bruce
On Wed, 26 Apr 
2017, Jared P Zimmerman wrote:



Any chance I could get some help on this?  still having this problem

  On Apr 20, 2017, at 6:26 PM, Jared P Zimmerman
   wrote:

Hi FS Experts,
I’m having trouble getting anatomical stats from a parcellation I made
out of scanner-space volume ROIs.  I have taken the following steps to
do this.

 1. mri_vol2vol --mov myROI.nii.gz --targ orig.mgz --regheader --o
myROI_orig.nii.gz --interp nearest
 2. mris_sample_parc Subj111 lh myROI_orig.nii.gz myROIs.annot -ct
ROI_test_table.txt 
 1. On this step I ALWAYS get an error “could not open translation
file /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt”
even though I specify a CT with -ct, or when I specify a table
with -t, or with both
 2. This seems to work though and I can view this annot on the
surface with tksurfer
 3. mris_anatomical_stats -a /path/to/myROIs.annot -b Subj111 lh


When I run mris_anatomical_stats I get the following error: 
CTABfindAnnotation: ct was NULL
Segmentation fault (core dumped)

I’m guessing this is from the color-table not being embedded in the
annot file, but I’ve tried to get that embedded in many ways.  

My questions are:

 1. What is causing the error with mris_anatomical_stats?
 2. What is the difference between the -t and -ct flags for
mris_sample_parc and which should I use?
 3. Should I use a specific color-table for this?  I made my own which
was just a space delimited file with “index name r g b a” for all
my ROIs, but should I be adding this data to some existing
color-table to make this work?

Thanks,
Jared
___
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 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.

Re: [Freesurfer] error with mris_anatomical_stats OR mris_sample_parc

[Jared P Zimmerman]

Any chance I could get some help on this?  still having this problem

> On Apr 20, 2017, at 6:26 PM, Jared P Zimmerman  
> wrote:
> 
> Hi FS Experts,
> 
> I’m having trouble getting anatomical stats from a parcellation I made out of 
> scanner-space volume ROIs.  I have taken the following steps to do this.
> 
> mri_vol2vol --mov myROI.nii.gz --targ orig.mgz --regheader --o 
> myROI_orig.nii.gz --interp nearest
> mris_sample_parc Subj111 lh myROI_orig.nii.gz myROIs.annot -ct 
> ROI_test_table.txt 
> On this step I ALWAYS get an error “could not open translation file 
> /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt” even though I 
> specify a CT with -ct, or when I specify a table with -t, or with both
> This seems to work though and I can view this annot on the surface with 
> tksurfer
> mris_anatomical_stats -a /path/to/myROIs.annot -b Subj111 lh
> 
> 
> When I run mris_anatomical_stats I get the following error: 
> CTABfindAnnotation: ct was NULL
> Segmentation fault (core dumped)
> 
> I’m guessing this is from the color-table not being embedded in the annot 
> file, but I’ve tried to get that embedded in many ways.  
> 
> My questions are:
> 
> What is causing the error with mris_anatomical_stats?
> What is the difference between the -t and -ct flags for mris_sample_parc and 
> which should I use?
> Should I use a specific color-table for this?  I made my own which was just a 
> space delimited file with “index name r g b a” for all my ROIs, but should I 
> be adding this data to some existing color-table to make this work?
> 
> Thanks,
> Jared
> ___
> 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 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] Extract time courses corresponding to a brain structure from an stc file

[Maria Hakonen]

Dear Freesurfer experts,

I would like to extract time courses of certain brain structures from the
stc file in Matlab. Could someone please let me know how I can determine
the lables of 10242 verices of my stc file? Or is there some matlab
function that gives the time course of a barin structure.

Best,
Maria
___
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.

Re: [Freesurfer] Interaction effects in QDEC

[Douglas N Greve]

Yes


On 04/26/2017 09:15 AM, Heidi Foo wrote:
> Dear Douglas,
>
> Thank you for your reply. Does this mean that if I were to have a 
> continuous variable (i.e. Neuroinflammation) and a categorical 
> variable with 2 levels (i.e. gene positive and gene negative), 
> interaction can also be found using QDEC?
>
> Thank you.
>
> Best Regards,
> Heidi Foo
>
> On Wed, Jan 11, 2017 at 5:20 AM, Douglas N Greve 
> > wrote:
>
> This is done automatically when you have two categorical variables and
> two continuous variables. This is equivalent to asking whether the two
> slopes differ across the two categorical variables.
>
>
> On 01/07/2017 09:30 AM, Heidi Foo wrote:
> > Hi all,
> >
> > I was wondering how I could test for interaction effects between a
> > categorical variable and a continuous variable using QDEC. Is
> there a
> > way to do so?
> >
> > Thank you.
> >
> > Best Regards,
> > Heidi Foo
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> 
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
>
> ___
> 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 mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Error when transforming aal.nii to lh.aal.label

[Douglas N Greve]

In the mri_label2label command you have lh.aal.label as the input and 
output. Are you overwriting the input and so now it does not match the 
original subject?


On 04/25/2017 09:23 PM, haidong wang wrote:
> Hello FS experts,
>  I want to get the thickness of 90 ROIs of AAL using freesurfer. I 
> use the following commands to transform aal.nii to lh.aal.label.
> 1.bbregister --s sub_con_sub01 --mov ch2.nii --t1 --init-fsl --reg 
> register_vol2surf.dat
> 2.mri_vol2surf --mov aal.nii --reg register_vol2surf.dat --hemi lh 
> --out_type mgh --o lh.aal.mgh --interp nearest
> 3.mri_cor2label --i lh.aal.mgh --id 1 --l ./lh.aal.label --surf 
> sub_con_sub01
> 4.mri_label2label --srclabel lh.aal.label --srcsubject fsaverage 
> --trgsubject sub_con_sub01 --trglabel lh.aal.label --regmethod surface 
> --hemi lh
> 5.mris_anatomical_stats -l lh.aal.label -t lh.thickness -b -f 
> sub_con_sub01/stats/lh.aal.stats sub_con_sub01 lh
> 6.aparcstats2table --hemi lh --subjects sub_con_sub01 --parc aal 
> --meas thickness -t ./aal_thickness.txt
>The result is that there is no measurement in the produced 
> document named lh.aal.stats.
> I am also confused about how to set id in mri_cor2label.Could you 
> please give me some suggestions?
> I am looking forwad for your prompt reply.
>Yours,
> Haidong
>
> The attachment is the screenshot of my working directory.
> Here is the error:
> mri_cor2label --i lh.aal.mgh --id 1 --l ./lh.aal.label --surf 
> sub_con_sub01
> $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $
> Loading mri lh.aal.mgh
> --- Vox2RAS of input volume ---
> -1.000   0.000   0.000   75659.000;
>  0.000   0.000   1.000  -0.500;
>  0.000  -1.000   0.000   0.500;
>  0.000   0.000   0.000   1.000;
> Scanning the volume
> Found 6451 label voxels
> Writing label file ./lh.aal.label
> LabelWrite: saving to ./lh.aal.label
> Centroid: -9707.33   -0.500.50
> mri_cor2label completed SUCCESSFULLY
> admi@admi:~/Desktop/freesurfer_thickness$ mri_label2label --srclabel 
> lh.aal.label --srcsubject fsaverage --trgsubject 
> sub_con_sub01 --trglabel lh.aal.label --regmethod surface --hemi lh
>
> srclabel = lh.aal.label
> srcsubject = fsaverage
> trgsubject = sub_con_sub01
> trglabel = lh.aal.label
> regmethod = surface
>
> srchemi = lh
> trghemi = lh
> trgsurface = white
> srcsurfreg = sphere.reg
> trgsurfreg = sphere.reg
> usehash = 1
> Use ProjAbs  = 0, 0
> Use ProjFrac = 0, 0
> DoPaint 0
>
> SUBJECTS_DIR/home/admi/Desktop/freesurfer_thickness
> FREESURFER_HOME /usr/local/freesurfer
> Loading source label.
> Found 6451 points in source label.
> Starting surface-based mapping
> Reading source registration
>  /home/admi/Desktop/freesurfer_thickness/fsaverage/surf/lh.sphere.reg
> Rescaling ...  original radius = 100
> Reading target surface
>  /home/admi/Desktop/freesurfer_thickness/sub_con_sub01/surf/lh.white
> Reading target registration
>  /home/admi/Desktop/freesurfer_thickness/sub_con_sub01/surf/lh.sphere.reg
> Rescaling ...  original radius = 100
> Building target registration hash (res=16).
> Building source registration hash (res=16).
> ERROR: there is a vertex in the label that cannot be
> matched to the surface. This usually occurs when
> the label and surface are from different subjects or
> hemispheres or the surface has been changed since
> the label was created.
> Label point 0: vno = -1, max = 163842
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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.

Re: [Freesurfer] FS6.0 mri_surf2surf failure

[Douglas N Greve]

I just tried it, and there was not a problem. Are you sure that 
hem.fsaverage.nii.gz has non-zeros in it? Can you send it to me? What 
platform are you using?


On 04/26/2017 11:55 AM, dongnandi1 wrote:
>
> Dear FS experts,
>
> I’m trying to transform some files from fsaverage space to fsaverage5 
> space using mri_surf2surf(FS version: 6.0), however, it is weird that 
> the results turn out to be all zeros on the fsaverage5 surface, the 
> command line I used is :
>  mri_surf2surf –srcsubject fsaverage –sval ${hemi}.fsaverage.nii.gz 
> –hemi ${hemi}  --cortex –trgsubject fsaverage5 –tval 
> ${hemi}.fsaverage5.nii.gz –surfreg sphere.reg.
> There is no error reported.
>
> The strange thing is that it works well using FS5.3, it failed after I 
> update to FS 6.0. Any suggestion of solving this?
>
> Many thanks!
> Best!
> Dong
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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.

Re: [Freesurfer] Fixing a left/right flip

[Dan Grupe]

I took a look at the xhemireg script and I feel like editing this to serve my 
purposes might be too tall of an order.

However, I think I have a processing stream that will work — I want to make 
sure there’s nothing problematic about it.

1. Run recon-all on the properly oriented T1 images through -segmentation
2. Take the old hand-edited wm.mgz file [containing extensive hand-edits] and 
left/right flip this file (using mri_convert to change LIA to RIA)
3. Visually confirm alignment of this hand-edited, flipped wm.mgz file. It 
turns out this brain was shifted by 1 voxel in the left/right direction; I 
manually adjusted this after converting the file to COR-format, and then 
converted back to .mgz and visually confirmed proper alignment.
4. Drop this hand-edited, L/R flipped and 1-voxel-shifted wm.mgz file into the 
subject/mri directory from running recon-all in (#1), then proceed with 
recon-all -autorecon2-wm -autorecon3

Is there anything inherently flawed about this approach? Are there any other 
files that I also need to flip (i.e., wm.seg.mgz or anything else?)

thanks,
Dan


On 4/17/17 6:48 PM, Douglas Greve wrote:

you can try xhemireg. it is kind of meant to do this kind of thing, but
not to the extent that you need it. If you know a little programming,
you can try to edit the script so that it does everything.


On 4/17/17 6:43 PM, Dan Grupe wrote:
> Hi all,
>
> After running a bunch of subjects through FreeSurfer and making
> extensive manual edits to the white matter masks, we discovered that
> the data were left/right flipped during the dicom-to-nifti conversion
> process. I hope to maintain these manual edits while processing data
> in the proper orientation and running them through the rest of the
> pipeline. Is this possible to do?
>
> An old thread from 10 years ago directed me to this page:
> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal that
> offered some tips on how to go about this. However, after confirming
> that the volume was reversed running recon-all -autorecon1 in a new
> directory, I encountered an error message:
>
> > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
> ***FAILED*** (p=0., pval=0. < threshold=0.0050)
>
> This problem does not arise when running the same command on a copy of
> this subject’s non-flipped data.
>
> Are there different steps that I should be following to rectify the
> problem? Or can you help me troubleshoot this error?
>
> Best,
> Dan


___
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] FS6.0 mri_surf2surf failure

[dongnandi1]

Dear FS experts,

I’m trying to transform some files from fsaverage space to fsaverage5 space 
using mri_surf2surf(FS version: 6.0), however, it is weird that the results 
turn out to be all zeros on the fsaverage5 surface, the command line I used is :
 mri_surf2surf –srcsubject fsaverage –sval ${hemi}.fsaverage.nii.gz –hemi 
${hemi}  --cortex –trgsubject fsaverage5 –tval ${hemi}.fsaverage5.nii.gz 
–surfreg sphere.reg. 
There is no error reported.


The strange thing is that it works well using FS5.3, it failed after I update 
to FS 6.0. Any suggestion of solving this?


Many thanks!
Best!
Dong___
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.

Re: [Freesurfer] Filling in missing ventricles in WM

[Bruce Fischl]

Hi Shane

I can't really tell from the image. YOu can try setting some of the 
intensity bounds in mris_make_surfaces and mri_segment (eg. wlo, ghi and 
such). If you upload the subject I'll take a look


cheers
Bruce


On Wed, 26 Apr 2017, Shane Schofield wrote:


Hi Bruce,

Thanks!

The -bigventricles flag worked like a charm! But I have now run into other
cases with fuzzy data and thin cortex that are not captured, such as the
picture below:


Inline image

Any tips on filing them out?

Thank you.



On Sunday, April 23, 2017 3:41 PM, Bruce Fischl 
wrote:


yes, that is correct. An alternative would be editing the aseg directly.
Editing the wm will help the surfaces but not correct the aseg.

But as Antonin suggests, try running with -bigventricles and see if that
fixes your problems

cheers
Bruce


On Sun, 23 Apr 2017, Shane Schofield wrote:

> Thank you. I will try that. Do I run that command after editing the wm.mgz
> to fill in the ventricles? I noticed that the voxels (value = 255) are
still
> 255 in the new WM.mgz after autorecon2-wm. Is this correct?
>
>
> On Sunday, April 23, 2017 1:33 PM, Antonin Skoch  wrote:
>
>
> Dear Shane,
>
> I would suggest to run:
>
> recon-all -bigventricles -s subject -autorecon2 -autorecon3 (-T2pial or
> -FLAIRpial if you have 3D T2 or 3D FLAIR). This should help to correct
aseg
> in case of such large ventricles.
>
> Antonin Skoch
>
>
> From: Shane Schofield 
> To: Freesurfer Support List , Antonin
Skoch
> 
> Sent: 4/22/2017 11:30 PM
> Subject: Filling in missing ventricles in WM
>
>      Hi Freesurfer Experts and Antonin,
>
> About an earlier question on XL Defects
>
> I have used your suggestions to check the orig.nofix surfaces and I
> think the skull and missing ventricle voxels are causing the problem.
> Picture pasted.
>
> Inline image
> I have  removed the WM voxels in the skull, filled in the ventricles
> by adding WM voxels (brush value = 255 ), and ran the command
> recon-all -s subject -autorecon2-wm -autorecon3
> Recon-all was completed successfully and the surfaces look good.
> However, the aseg volume in the lateral ventricles are still wrong.
> Inline image
> At the crosshair, the WM value is 255 and the ASEG value is 0. Should
> I be editing the aseg now? Or should I be doing something else to the
> wm.mgz?
> Appreciate your tips!
> Best Wishes,
> Shane
>
>
>
>
>
___
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 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.

Re: [Freesurfer] Filling in missing ventricles in WM

[Shane Schofield]

Hi Bruce,
Thanks!
The -bigventricles flag worked like a charm! But I have now run into other 
cases with fuzzy data and thin cortex that are not captured, such as the 
picture below:



Any tips on filing them out?
Thank you.

 

On Sunday, April 23, 2017 3:41 PM, Bruce Fischl 
 wrote:
 

 yes, that is correct. An alternative would be editing the aseg directly. 
Editing the wm will help the surfaces but not correct the aseg.

But as Antonin suggests, try running with -bigventricles and see if that 
fixes your problems

cheers
Bruce


On Sun, 23 Apr 2017, Shane Schofield wrote:

> Thank you. I will try that. Do I run that command after editing the wm.mgz
> to fill in the ventricles? I noticed that the voxels (value = 255) are still
> 255 in the new WM.mgz after autorecon2-wm. Is this correct?
> 
> 
> On Sunday, April 23, 2017 1:33 PM, Antonin Skoch  wrote:
> 
> 
> Dear Shane,
> 
> I would suggest to run:
> 
> recon-all -bigventricles -s subject -autorecon2 -autorecon3 (-T2pial or
> -FLAIRpial if you have 3D T2 or 3D FLAIR). This should help to correct aseg
> in case of such large ventricles.
> 
> Antonin Skoch
> 
> 
> From: Shane Schofield 
> To: Freesurfer Support List , Antonin Skoch
> 
> Sent: 4/22/2017 11:30 PM
> Subject: Filling in missing ventricles in WM
>
>      Hi Freesurfer Experts and Antonin,
> 
> About an earlier question on XL Defects
> 
> I have used your suggestions to check the orig.nofix surfaces and I
> think the skull and missing ventricle voxels are causing the problem.
> Picture pasted.
> 
> Inline image
> I have  removed the WM voxels in the skull, filled in the ventricles
> by adding WM voxels (brush value = 255 ), and ran the command
> recon-all -s subject -autorecon2-wm -autorecon3
> Recon-all was completed successfully and the surfaces look good.
> However, the aseg volume in the lateral ventricles are still wrong.
> Inline image
> At the crosshair, the WM value is 255 and the ASEG value is 0. Should
> I be editing the aseg now? Or should I be doing something else to the
> wm.mgz?
> Appreciate your tips!
> Best Wishes,
> Shane
> 
> 
> 
> 
>___
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 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.

Re: [Freesurfer] Interaction effects in QDEC

[Heidi Foo]

Dear Douglas,

Thank you for your reply. Does this mean that if I were to have a
continuous variable (i.e. Neuroinflammation) and a categorical variable
with 2 levels (i.e. gene positive and gene negative), interaction can also
be found using QDEC?

Thank you.

Best Regards,
Heidi Foo

On Wed, Jan 11, 2017 at 5:20 AM, Douglas N Greve 
wrote:

> This is done automatically when you have two categorical variables and
> two continuous variables. This is equivalent to asking whether the two
> slopes differ across the two categorical variables.
>
>
> On 01/07/2017 09:30 AM, Heidi Foo wrote:
> > Hi all,
> >
> > I was wondering how I could test for interaction effects between a
> > categorical variable and a continuous variable using QDEC. Is there a
> > way to do so?
> >
> > Thank you.
> >
> > Best Regards,
> > Heidi Foo
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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 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.