[Freesurfer] 答复: ROI

[Jin Bo]

Hi all,


I am a new to Freesurfer.

I am currently useing freeview to get ROI(small lesion) on 7T MRI, but the ROI 
can not display on surface(tksurfer patient lh inflated -overlay 
patient/label/fcd.label ).


The terminal showed the following sentence:


label stat field identically zero - setting to 1


However, it works well on 3T MRI.


Thanks,


Bo



发件人: Jin Bo
发送时间: 2017年9月6日 8:11:40
收件人: freesurfer@nmr.mgh.harvard.edu
主题: ROI


Hi all,


I am a new to Freesurfer.

I am currently useing freeview to get ROI(small lesion) on 7T MRI, but the ROI 
can not display on surface(tksurfer patient lh inflated -overlay 
patient/label/fcd.label ).


The terminal showed the following sentence:


label stat field identically zero - setting to 1


However, it works well on 3T MRI.


Thanks,


Bo
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Re: [Freesurfer] Talairach registration error

[Douglas Greve]

the nifti file does not have the needed information in it. where did you 
get it from?



On 9/5/17 8:42 PM, Ariana Vajdi wrote:

Hello,

Hope this message finds you well.

I was beginning to run recon-all on a dataset and was encountering a 
problem with the talairach registration. I've encountered this error 
before here and there, but I've been receiving the same error for 
every scan that I've been trying to run, and I'm not sure why. It's 
also the first time I've used NIFTI files as the input - not sure if 
that's a contributing factor. I've also tried the -use-mritotal flag 
without any luck.


These are the errors I receive:

WARNING: neither NIfTI-1 qform or sform are valid

WARNING: your volume will probably be incorrectly oriented


ERROR: talairach_afd: Talairach Transform:
transforms/talairach.xfm ***FAILED*** (p=0., pval=0. <
threshold=0.0050)

Manual Talairach alignment may be necessary, or

include the -notal-check flag to skip this test,

making sure the -notal-check flag follows -all

or -autorecon1 in the command string.


I would appreciate your help. Thank you!

Warmly,
Ariana


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Re: [Freesurfer] Ventricle Volumes Decreasing over time?

[Bruce Fischl]

Hi Tamara

have you visualized the multiple time points of a subject whose ventricular 
volume is decreasing? How big a decrease are you seeing?

cheers
Bruce


On Tue, 5 
Sep 2017, Tamara Tavares wrote:

> Hello,
> I used the default longitudinal stream to calculate ventricular volumes over 
> time. When I examined
> the difference score (longitudinal-baseline) I noticed that for some 
> participants ventricular
> volumes decreased. The same site, scanner and scanning protocol was used for 
> both baseline and
> longitudinal scans. I processed the cross, template and longitudinal time 
> points on the same
> computer using the same Freesurfer version (v 5.1). Furthermore, this 
> decrease in ventricular volume
> is evident before and after manual corrects were made to the aseg file. Is it 
> common to see an
> decrease in ventricular volume over time? Can this be due to Freesurfer 
> variability or slight
> differences in the scanner over the two time points?
> 
> Thank you in advance for your help.
> 
> Best,
> Tamara
> 
>
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[Freesurfer] Ventricle Volumes Decreasing over time?

[Tamara Tavares]

Hello,

I used the default longitudinal stream to calculate ventricular volumes
over time. When I examined the difference score (longitudinal-baseline) I
noticed that for some participants ventricular volumes *decreased*. The
same site, scanner and scanning protocol was used for both baseline and
longitudinal scans. I processed the cross, template and longitudinal time
points on the same computer using the same Freesurfer version (v 5.1).
Furthermore, this decrease in ventricular volume is evident before and
after manual corrects were made to the aseg file. Is it common to see
an *decrease
*in ventricular volume over time? Can this be due to Freesurfer variability
or slight differences in the scanner over the two time points?

Thank you in advance for your help.

Best,
Tamara
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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
dispose of the e-mail.

[Freesurfer] Talairach registration error

[Ariana Vajdi]

Hello,

Hope this message finds you well.

I was beginning to run recon-all on a dataset and was encountering a
problem with the talairach registration. I've encountered this error before
here and there, but I've been receiving the same error for every scan that
I've been trying to run, and I'm not sure why. It's also the first time
I've used NIFTI files as the input - not sure if that's a contributing
factor. I've also tried the -use-mritotal flag without any luck.

These are the errors I receive:

WARNING: neither NIfTI-1 qform or sform are valid

WARNING: your volume will probably be incorrectly oriented


ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0., pval=0. < threshold=0.0050)

Manual Talairach alignment may be necessary, or

include the -notal-check flag to skip this test,

making sure the -notal-check flag follows -all

or -autorecon1 in the command string.


I would appreciate your help. Thank you!

Warmly,
Ariana
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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
dispose of the e-mail.

Re: [Freesurfer] controlling for Sex in a model using two continuous variables onto CTh

[Uquillas, Federico D'Oleire]

Thank you so much Doug. We're mainly interested in controlling for Sex so it is 
great to know that it does work for DOSS.

Best,

Fred

> On Sep 5, 2017, at 18:07, Douglas N Greve  wrote:
> 
> For DOSS, It will work, but harder to set up the contrast matrices to 
> look at a sex effect. I would just do it coding males and females as 
> separate classes and not include sex as a variable
> 
> 
>> On 09/05/2017 06:00 PM, Uquillas, Federico D'Oleire wrote:
>> Thank you Doug. Is the one that doesn't fail okay?
>> 
>> Best,
>> 
>> Fred
>> 
>>> On Sep 5, 2017, at 16:57, Douglas N Greve  wrote:
>>> 
>>> in the one that fails you are including the binary gender as a
>>> continuous variable, which will fail in FSGD. All catagorical variables
>>> need to be coded as classes. see
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
>>> 
>>> 
 On 09/05/2017 03:07 PM, Uquillas, Federico D'Oleire wrote:
 Dear Doug,
 
 Sending the FSGD described in our original email as failing due to it 
 being "ill-conditioned or badly scaled" with DOSS [0 1 0 0 0]. It is 
 titled "FAILS_N47_edited_BL_CT_PiB_centAge_fsgd.txt".
 
 The other one is the one that runs and gives expected results with a DOSS 
 contrast [0 1 0 0].
 
 Thanks so much.
 
 Best regards,
 
 Fred
 
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Tuesday, September 05, 2017 12:01 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] controlling for Sex in a model using two 
 continuous variables onto CTh
 
 can you send the fsgd file for the analysis that is failing?
 
 
> On 08/29/2017 02:29 PM, Uquillas, Federico D'Oleire wrote:
> Dear FreeSurfer experts,
> 
> We have run a vertex-wise analysis regressing a continuous variable
> onto cortical thickness on the surface, and would like to verify that
> our contrast that uses Age and Sex as covariates was defined
> correctly, especially since there is probably more than one way to
> control for a binary variable like Sex.
> 
> On the website (https://surfer.nmr.mgh.harvard.edu/fswiki/DodsDoss) it
> suggests to make two regressors, one for Males, and one for Females,
> where for the former a 1 is indicative of the Male category, and a 1
> on the latter is indicative of the Female category. However, using
> that FSGD file and running a DOSS contrast as [0 1 0 0 0], we get the
> error: matrix is ill-condition or badly scaled, condno=2.01889e+07.
> We believe this may be due to the fact that Male and Female categories
> are autocorrelated and Freesurfer likes variables to be de-meaned.
> Running a FSGD file with only Age and our variable of interest via a
> DOSS contrast of [0 1 0] works without any errors.
> 
> We thus created an FSGD file where we have Sex as our third variable
> (in addition to our continuous variable of interest and one demeaned
> continuous covariate), coding 1s for Males and 0s for Females, and we
> used a DOSS contrast of [0 1 0 0]. This provided us with a map that
> makes sense with our expectations.
> 
> We would like to verify if this is doing what we believe it is doing;
> that is, looking at the relationship of our continuous variable or
> interest after accounting for age and sex.
> Any thoughts would be greatly appreciated.
> 
> Thank you so much.
> 
> Best,
> 
> Fred
> 
> 
> 
> 
> 
> ___
> 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
>>> -- 
>>> 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
>>> 

Re: [Freesurfer] controlling for Sex in a model using two continuous variables onto CTh

[Douglas N Greve]

For DOSS, It will work, but harder to set up the contrast matrices to 
look at a sex effect. I would just do it coding males and females as 
separate classes and not include sex as a variable


On 09/05/2017 06:00 PM, Uquillas, Federico D'Oleire wrote:
> Thank you Doug. Is the one that doesn't fail okay?
>
> Best,
>
> Fred
>
>> On Sep 5, 2017, at 16:57, Douglas N Greve  wrote:
>>
>> in the one that fails you are including the binary gender as a
>> continuous variable, which will fail in FSGD. All catagorical variables
>> need to be coded as classes. see
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
>>
>>
>>> On 09/05/2017 03:07 PM, Uquillas, Federico D'Oleire wrote:
>>> Dear Doug,
>>>
>>> Sending the FSGD described in our original email as failing due to it being 
>>> "ill-conditioned or badly scaled" with DOSS [0 1 0 0 0]. It is titled 
>>> "FAILS_N47_edited_BL_CT_PiB_centAge_fsgd.txt".
>>>
>>> The other one is the one that runs and gives expected results with a DOSS 
>>> contrast [0 1 0 0].
>>>
>>> Thanks so much.
>>>
>>> Best regards,
>>>
>>> Fred
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Tuesday, September 05, 2017 12:01 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] controlling for Sex in a model using two 
>>> continuous variables onto CTh
>>>
>>> can you send the fsgd file for the analysis that is failing?
>>>
>>>
 On 08/29/2017 02:29 PM, Uquillas, Federico D'Oleire wrote:
 Dear FreeSurfer experts,

 We have run a vertex-wise analysis regressing a continuous variable
 onto cortical thickness on the surface, and would like to verify that
 our contrast that uses Age and Sex as covariates was defined
 correctly, especially since there is probably more than one way to
 control for a binary variable like Sex.

 On the website (https://surfer.nmr.mgh.harvard.edu/fswiki/DodsDoss) it
 suggests to make two regressors, one for Males, and one for Females,
 where for the former a 1 is indicative of the Male category, and a 1
 on the latter is indicative of the Female category. However, using
 that FSGD file and running a DOSS contrast as [0 1 0 0 0], we get the
 error: matrix is ill-condition or badly scaled, condno=2.01889e+07.
 We believe this may be due to the fact that Male and Female categories
 are autocorrelated and Freesurfer likes variables to be de-meaned.
 Running a FSGD file with only Age and our variable of interest via a
 DOSS contrast of [0 1 0] works without any errors.

 We thus created an FSGD file where we have Sex as our third variable
 (in addition to our continuous variable of interest and one demeaned
 continuous covariate), coding 1s for Males and 0s for Females, and we
 used a DOSS contrast of [0 1 0 0]. This provided us with a map that
 makes sense with our expectations.

 We would like to verify if this is doing what we believe it is doing;
 that is, looking at the relationship of our continuous variable or
 interest after accounting for age and sex.
 Any thoughts would be greatly appreciated.

 Thank you so much.

 Best,

 Fred





 ___
 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
>> -- 
>> 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
> 

Re: [Freesurfer] controlling for Sex in a model using two continuous variables onto CTh

[Uquillas, Federico D'Oleire]

Thank you Doug. Is the one that doesn't fail okay?

Best,

Fred

> On Sep 5, 2017, at 16:57, Douglas N Greve  wrote:
> 
> in the one that fails you are including the binary gender as a 
> continuous variable, which will fail in FSGD. All catagorical variables 
> need to be coded as classes. see 
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
> 
> 
>> On 09/05/2017 03:07 PM, Uquillas, Federico D'Oleire wrote:
>> Dear Doug,
>> 
>> Sending the FSGD described in our original email as failing due to it being 
>> "ill-conditioned or badly scaled" with DOSS [0 1 0 0 0]. It is titled 
>> "FAILS_N47_edited_BL_CT_PiB_centAge_fsgd.txt".
>> 
>> The other one is the one that runs and gives expected results with a DOSS 
>> contrast [0 1 0 0].
>> 
>> Thanks so much.
>> 
>> Best regards,
>> 
>> Fred
>> 
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, September 05, 2017 12:01 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] controlling for Sex in a model using two 
>> continuous variables onto CTh
>> 
>> can you send the fsgd file for the analysis that is failing?
>> 
>> 
>>> On 08/29/2017 02:29 PM, Uquillas, Federico D'Oleire wrote:
>>> Dear FreeSurfer experts,
>>> 
>>> We have run a vertex-wise analysis regressing a continuous variable
>>> onto cortical thickness on the surface, and would like to verify that
>>> our contrast that uses Age and Sex as covariates was defined
>>> correctly, especially since there is probably more than one way to
>>> control for a binary variable like Sex.
>>> 
>>> On the website (https://surfer.nmr.mgh.harvard.edu/fswiki/DodsDoss) it
>>> suggests to make two regressors, one for Males, and one for Females,
>>> where for the former a 1 is indicative of the Male category, and a 1
>>> on the latter is indicative of the Female category. However, using
>>> that FSGD file and running a DOSS contrast as [0 1 0 0 0], we get the
>>> error: matrix is ill-condition or badly scaled, condno=2.01889e+07.
>>> We believe this may be due to the fact that Male and Female categories
>>> are autocorrelated and Freesurfer likes variables to be de-meaned.
>>> Running a FSGD file with only Age and our variable of interest via a
>>> DOSS contrast of [0 1 0] works without any errors.
>>> 
>>> We thus created an FSGD file where we have Sex as our third variable
>>> (in addition to our continuous variable of interest and one demeaned
>>> continuous covariate), coding 1s for Males and 0s for Females, and we
>>> used a DOSS contrast of [0 1 0 0]. This provided us with a map that
>>> makes sense with our expectations.
>>> 
>>> We would like to verify if this is doing what we believe it is doing;
>>> that is, looking at the relationship of our continuous variable or
>>> interest after accounting for age and sex.
>>> Any thoughts would be greatly appreciated.
>>> 
>>> Thank you so much.
>>> 
>>> Best,
>>> 
>>> Fred
>>> 
>>> 
>>> 
>>> 
>>> 
>>> ___
>>> 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
> 
> -- 
> 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

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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

Re: [Freesurfer] controlling for Sex in a model using two continuous variables onto CTh

[Douglas N Greve]

in the one that fails you are including the binary gender as a 
continuous variable, which will fail in FSGD. All catagorical variables 
need to be coded as classes. see 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples


On 09/05/2017 03:07 PM, Uquillas, Federico D'Oleire wrote:
> Dear Doug,
>
> Sending the FSGD described in our original email as failing due to it being 
> "ill-conditioned or badly scaled" with DOSS [0 1 0 0 0]. It is titled 
> "FAILS_N47_edited_BL_CT_PiB_centAge_fsgd.txt".
>
> The other one is the one that runs and gives expected results with a DOSS 
> contrast [0 1 0 0].
>
> Thanks so much.
>
> Best regards,
>
> Fred
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, September 05, 2017 12:01 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] controlling for Sex in a model using two continuous 
> variables onto CTh
>
> can you send the fsgd file for the analysis that is failing?
>
>
> On 08/29/2017 02:29 PM, Uquillas, Federico D'Oleire wrote:
>> Dear FreeSurfer experts,
>>
>> We have run a vertex-wise analysis regressing a continuous variable
>> onto cortical thickness on the surface, and would like to verify that
>> our contrast that uses Age and Sex as covariates was defined
>> correctly, especially since there is probably more than one way to
>> control for a binary variable like Sex.
>>
>> On the website (https://surfer.nmr.mgh.harvard.edu/fswiki/DodsDoss) it
>> suggests to make two regressors, one for Males, and one for Females,
>> where for the former a 1 is indicative of the Male category, and a 1
>> on the latter is indicative of the Female category. However, using
>> that FSGD file and running a DOSS contrast as [0 1 0 0 0], we get the
>> error: matrix is ill-condition or badly scaled, condno=2.01889e+07.
>> We believe this may be due to the fact that Male and Female categories
>> are autocorrelated and Freesurfer likes variables to be de-meaned.
>> Running a FSGD file with only Age and our variable of interest via a
>> DOSS contrast of [0 1 0] works without any errors.
>>
>> We thus created an FSGD file where we have Sex as our third variable
>> (in addition to our continuous variable of interest and one demeaned
>> continuous covariate), coding 1s for Males and 0s for Females, and we
>> used a DOSS contrast of [0 1 0 0]. This provided us with a map that
>> makes sense with our expectations.
>>
>> We would like to verify if this is doing what we believe it is doing;
>> that is, looking at the relationship of our continuous variable or
>> interest after accounting for age and sex.
>> Any thoughts would be greatly appreciated.
>>
>> Thank you so much.
>>
>> Best,
>>
>> Fred
>>
>>
>>
>>
>>
>> ___
>> 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

-- 
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
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Re: [Freesurfer] controlling for Sex in a model using two continuous variables onto CTh

[Uquillas, Federico D'Oleire]

Dear Doug,

Sending the FSGD described in our original email as failing due to it being 
"ill-conditioned or badly scaled" with DOSS [0 1 0 0 0]. It is titled 
"FAILS_N47_edited_BL_CT_PiB_centAge_fsgd.txt".

The other one is the one that runs and gives expected results with a DOSS 
contrast [0 1 0 0].

Thanks so much.

Best regards,

Fred


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, September 05, 2017 12:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] controlling for Sex in a model using two continuous 
variables onto CTh

can you send the fsgd file for the analysis that is failing?


On 08/29/2017 02:29 PM, Uquillas, Federico D'Oleire wrote:
> Dear FreeSurfer experts,
>
> We have run a vertex-wise analysis regressing a continuous variable
> onto cortical thickness on the surface, and would like to verify that
> our contrast that uses Age and Sex as covariates was defined
> correctly, especially since there is probably more than one way to
> control for a binary variable like Sex.
>
> On the website (https://surfer.nmr.mgh.harvard.edu/fswiki/DodsDoss) it
> suggests to make two regressors, one for Males, and one for Females,
> where for the former a 1 is indicative of the Male category, and a 1
> on the latter is indicative of the Female category. However, using
> that FSGD file and running a DOSS contrast as [0 1 0 0 0], we get the
> error: matrix is ill-condition or badly scaled, condno=2.01889e+07.
> We believe this may be due to the fact that Male and Female categories
> are autocorrelated and Freesurfer likes variables to be de-meaned.
> Running a FSGD file with only Age and our variable of interest via a
> DOSS contrast of [0 1 0] works without any errors.
>
> We thus created an FSGD file where we have Sex as our third variable
> (in addition to our continuous variable of interest and one demeaned
> continuous covariate), coding 1s for Males and 0s for Females, and we
> used a DOSS contrast of [0 1 0 0]. This provided us with a map that
> makes sense with our expectations.
>
> We would like to verify if this is doing what we believe it is doing;
> that is, looking at the relationship of our continuous variable or
> interest after accounting for age and sex.
> Any thoughts would be greatly appreciated.
>
> Thank you so much.
>
> Best,
>
> Fred
>
>
>
>
>
> ___
> 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/

___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
GroupDescriptorFile 1
Title N47_edited_BL_CT_PiB_centAge_fsgd.txt 
Measurement thickness 
 
Class MemImpaired 
 
Variables PiB centAge Sex 
 
Input B_02PSWW_2187-09-14 MemImpaired 1.8348 1.48 1
Input B_1IANL2_2252-02-12 MemImpaired 1.7432 2.98 1
Input B_1R4CEV_2016-09-09 MemImpaired 2.0298 7.23 1
Input B_1VUCZY_2281-05-28 MemImpaired 1.769 5.98 1
Input B_3YFK3H_2051-07-15 MemImpaired 1.1154 9.98 1
Input B_48336O_2162-02-05 MemImpaired 1.5667 -1.77 1
Input B_5JSFZF_2092-08-02 MemImpaired 1.0016 -9.77 1
Input B_5M627I_2193-10-16 MemImpaired 1.0857 12.23 1
Input B_6E5T5O_2216-09-07 MemImpaired 1.0997 -6.52 0
Input B_78DARB_2039-12-25 MemImpaired 1.5772 -0.27 1
Input B_792QTC_2048-10-12 MemImpaired 1.8082 2.48 1
Input B_7K01XE_2224-05-15 MemImpaired 1.9029 6.23 1
Input B_7VRF05_2088-03-14 MemImpaired 1.1147 -12.02 0
Input B_8V1H6Z_2211-05-29 MemImpaired 1.6849 10.23 1
Input B_9RW8OT_2270-10-29 MemImpaired 1.1584 -0.77 0
Input B_CR8UTU_2110-09-12 MemImpaired 1.0295 -3.52 1
Input B_D3UERJ_2139-10-05 MemImpaired 1.005 10.48 1
Input B_DDAXH6_2091-04-05 MemImpaired 1.8105 -3.52 1
Input B_DODVA4_2199-08-18 MemImpaired 1.6791 -1.27 0
Input B_ESCGDO_2165-01-29 MemImpaired 1.5164 12.23 1
Input B_FAA8XU_2118-05-15 MemImpaired 1.2742 1.73 1
Input B_FWWU1C_2092-03-28 MemImpaired 1.0554 -0.77 1
Input B_GDX0XO_2234-09-29 MemImpaired 1.3924 7.73 0
Input B_HROZ4V_2164-10-18 MemImpaired 1.5237 9.73 1
Input B_IG2O12_2159-02-10 MemImpaired 1.8466 1.48 0
Input B_J270YT_2130-03-28 MemImpaired 1.7432 6.73 1
Input B_JYY5YY_2147-03-07 MemImpaired 1.7173 -8.52 1
Input B_KBZZYN_2206-12-14 MemImpaired 1.517 2.23 0
Input B_KULIUO_2036-11-15 MemImpaired 1.1925 -7.27 1
Input B_LFQ93G_2186-10-22 MemImpaired 1.5804 -1.27 1
Input B_LNX7V1_2238-02-06 MemImpaired 1.5744 -11.52 1
Input B_N3PE37_2079-03-29 MemImpaired 

[Freesurfer] Error with TRACULA using dcm and nii

[Ferrier, Christopher Q.]

Hi Freesurfer Team!. We are trying to use TRACULA to analyze the structural 
connectivity of PD patients scanned on a 3 tesla Philips Ingenia. We have run 
the tutorial data without any problems but encounter errors when using our own 
data. We ran recon-all on all of our subjects without any problem and follow 
the exact steps that worked for the tutorial data but encounter different 
errors when using the dcm or nii version of the DTI scans. Our nii files go 
from scanner to CD to Osirix to DICOM to dcm2nii which gives us the nii files 
and the bvals and bvecs.  Here is the error for the nii DTI scans (included 
bvals and gradients in the config file for the nii files).
[Christinas-iMac:Freesurfer_temp/PD800/diffusion_recons] christina% trac-all 
-prep -c/Volumes/CFERRIER/Freesurfer_temp/PD800/dmrirc.tutorial
ERROR: flag -c/Volumes/CFERRIER/Freesurfer_temp/PD800/dmrirc.tutorial 
unrecognized
-prep -c/Volumes/CFERRIER/Freesurfer_temp/PD800/dmrirc.tutorial
[Christinas-iMac:Freesurfer_temp/PD800/diffusion_recons] christina% trac-all 
-prep -c /Volumes/CFERRIER/Freesurfer_temp/PD800/dmrirc.tutorial
INFO: SUBJECTS_DIR is /Volumes/CFERRIER/Freesurfer_temp/PD800/diffusion_recons
INFO: Diffusion root is /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT
Actual FREESURFER_HOME /Applications/Freesurfer
trac-preproc -c 
/Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/scripts/dmrirc.local 
-log 
/Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/scripts/trac-all.log 
-cmd 
/Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/scripts/trac-all.cmd
#-
/Applications/Freesurfer/bin/trac-preproc
#-
#@# Image corrections Thu Aug 31 14:45:46 CDT 2017
mri_convert --bvec-voxel 
/Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI_combined.nii 
/Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel 
/Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI_combined.nii 
/Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 
/Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI_combined.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999339, -0.0363145, -0.00163044)
j_ras = (-0.0363101, 0.99508, 0.0921851)
k_ras = (0.00172524, -0.0921834, 0.995741)
writing to 
/Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz...
cp /Volumes/CFERRIER/Freesurfer_temp/PD800/bvecs/PD800_bvecs.txt 
/Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvecs
cp /Volumes/CFERRIER/Freesurfer_temp/PD800/bvals/PD800_bvals.txt 
/Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvals
mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvecs.tmp 
/Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvecs
mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvals.tmp 
/Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvals
orientLAS 
/Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz 
/Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -9.1875
mri_convert -oni 128 -onj 128 -onk 50 -oid -0.999339 -0.0363145 -0.00163044 
-ojd -0.0363101 0.99508 0.0921851 -okd 0.00172524 -0.0921834 0.995741 -oc 
7.38609 19.7949 1.17333 -rt nearest 
/Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz 
/Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.nii.gz
mri_convert.bin -oni 128 -onj 128 -onk 50 -oid -0.999339 -0.0363145 -0.00163044 
-ojd -0.0363101 0.99508 0.0921851 -okd 0.00172524 -0.0921834 0.995741 -oc 
7.38609 19.7949 1.17333 -rt nearest 
/Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz 
/Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.nii.gz
normalizing out_i_direction: (-0.999339, -0.0363145, -0.00163044) -> 
(-0.999339, -0.0363145, -0.00163044)
normalizing out_j_direction: (-0.0363101, 0.99508, 0.0921851) -> (-0.0363101, 
0.99508, 0.0921851)
normalizing out_k_direction: (0.00172524, -0.0921834, 0.995741) -> (0.00172524, 
-0.0921834, 0.995741)
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 
/Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999339, -0.0363145, -0.00163044)
j_ras = (-0.0363101, 0.99508, 0.0921851)
k_ras = (0.00172524, -0.0921834, 0.995741)
Reslicing using nearest
writing to 
/Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.nii.gz...
INFO: found 
/Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvals, 
copying
INFO: found 

Re: [Freesurfer] sub-cortical analysis

[Douglas N Greve]

I've added a voxel-based analysis to the wiki page
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer

Note that I'm recommending using permutation instead of GRF for 
correction of multiple comparisons

On 08/29/2017 10:03 AM, John Anderson wrote:
>
> Hi Dr Greve,
>
> I am using pet surfer to analyze suv images. I followed all the steps 
> in wiki, I used the option mgx then I fed the 
> imagesmgx.{ctxgm,subctxgm,gm} into surface based analysis for left and 
> right hemispheres. I want to inquire about the sub cortical analysis.
>
> 1. I assume the analysis for sub cortical gray matter (i.e. using the 
> imagessubctxgm) is volumetric. Is this correct?
>
Yes. This is on the wiki page.
>
> 2. Are the following steps correct for sub cortical gray matter analysis
>
> mri_vol2vol --movsubctxgm.nii.gz --reg reg.dat --tal --talres 2 
> --talxfm talairach.xfm --nearest --no-save-reg --osubctxgm.tal2mm.nii.gz
>
> mri_masksubctxgm.tal2mm.nii.gz 
> $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgzsubctxgm.tal2mm_subc.nii.gz
>  
> &
>
> Concatenate all subjects together using mri_concat
>
> smooth using mri_fwhm (what is the recommended smoothing for suv)?
>
>  Then Group analysis:
>
> mri_glmfit --y all.suvr.tal2mm.subc.sm10.nii --fsgd fsgd.dat --C 
> contrast.mtx --glmdir dir
>
> mri_glmfit-sim --glmdir dir --grf 1.3 pos --cwpvalthresh 0.0166
>
>  for "mri_glmfit-sim"  in subcortical structure is the flag grf 
>  correct or cache?
>
>
> Thanks in advance!
> John
>
>
>
>
>
> ___
> 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/

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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] controlling for Sex in a model using two continuous variables onto CTh

[Douglas N Greve]

can you send the fsgd file for the analysis that is failing?


On 08/29/2017 02:29 PM, Uquillas, Federico D'Oleire wrote:
> Dear FreeSurfer experts,
>
> We have run a vertex-wise analysis regressing a continuous variable 
> onto cortical thickness on the surface, and would like to verify that 
> our contrast that uses Age and Sex as covariates was defined 
> correctly, especially since there is probably more than one way to 
> control for a binary variable like Sex.
>
> On the website (https://surfer.nmr.mgh.harvard.edu/fswiki/DodsDoss) it 
> suggests to make two regressors, one for Males, and one for Females, 
> where for the former a 1 is indicative of the Male category, and a 1 
> on the latter is indicative of the Female category. However, using 
> that FSGD file and running a DOSS contrast as [0 1 0 0 0], we get the 
> error: matrix is ill-condition or badly scaled, condno=2.01889e+07.
> We believe this may be due to the fact that Male and Female categories 
> are autocorrelated and Freesurfer likes variables to be de-meaned. 
> Running a FSGD file with only Age and our variable of interest via a 
> DOSS contrast of [0 1 0] works without any errors.
>
> We thus created an FSGD file where we have Sex as our third variable 
> (in addition to our continuous variable of interest and one demeaned 
> continuous covariate), coding 1s for Males and 0s for Females, and we 
> used a DOSS contrast of [0 1 0 0]. This provided us with a map that 
> makes sense with our expectations.
>
> We would like to verify if this is doing what we believe it is doing; 
> that is, looking at the relationship of our continuous variable or 
> interest after accounting for age and sex.
> Any thoughts would be greatly appreciated.
>
> Thank you so much.
>
> Best,
>
> Fred
>
>
>
>
>
> ___
> 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/

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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] Cortical thickness

[Douglas N Greve]

You need to map them into the same space. You can use mris_apply_reg to 
map one subject into the other or you can use mris_preproc to put them 
both into fsaverage space


On 09/01/2017 10:29 AM, Esteban, Eva(GE Healthcare) wrote:
>
> Hello everyone,
>
> I am trying to compare the difference in cortical thickness between 
> two subjects by overlaying the surfaces (lh.thickness and r 
> rh.thickness) but -diff doesn’t seem to be doing the work. Does anyone 
> know of any other commands which could be useful for this?
>
> Thank you!
>
> Eva
>
>
>
> ___
> 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/

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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] R: Re: Map of covariance

[Douglas N Greve]

you would need to create a contrast to look for the interaction. If you 
have four gruops and 1 covariate, then it would be

0 0 0 0 1 -1 0 0

0 0 0 0 1 0 -1 0

0 0 0 0 1 0 0 -1



On 09/05/2017 04:32 PM, std...@virgilio.it wrote:
> Hi,
> e.g., by considering two or more groups, I would like to map the clusters
> reporting the covariance between the functional connectivity or cortical
> thickness (dependent variable) and age, tacking in account the group
> differences.
> Instead, I'm not interested to map the group differences, taking in account
> the nuisance factors.
> Thanks,
> Stefano
>
>> Messaggio originale
>> Da: "Douglas N Greve" 
>> Data: 5-set-2017 18.12
>> A: 
>> Ogg: Re: [Freesurfer] Map of covariance
>>
>> I don't understand what you are asking. can you elaborate?
>>
>>
>> On 08/30/2017 12:50 PM, std...@virgilio.it wrote:
>>> Hi list,
>>> by applying a design e.g. 4GV1 in fsgd I could assess the dependence
>>> of group differences taking in account the effect of covariate.
>>> Anyway, where I should look if I want assess the the map showing the
>>> clusters in which the dependent variable is associated to covariate,
>>> tacking in account the group difference? Please could you suggest my
>>> the path?
>>> Thanks
>>>
>>> Stefano
>>>
>>>
>>> ___
>>> 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
>>
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Re: [Freesurfer] MNI average brain in Freesurfer space

[Douglas N Greve]

not sure what you mean, but check out the use cases here

https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems


On 09/05/2017 03:35 PM, Anna Kasdan wrote:
> Hi everyone,
>
> Is there a freesurfer file/file format for the /average/ MNI brain (as 
> opposed to fsaverage which is just based on different subjects)? Or is 
> there a way to turn MNI coordinates into freesurfer space? Thanks so much!
>
> Anna
> Research Assistant, NYU
>
>
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[Freesurfer] R: Re: Map of covariance

[stdp82]

Hi, 
e.g., by considering two or more groups, I would like to map the clusters 
reporting the covariance between the functional connectivity or cortical 
thickness (dependent variable) and age, tacking in account the group 
differences.
Instead, I'm not interested to map the group differences, taking in account 
the nuisance factors.
Thanks,
Stefano

>Messaggio originale
>Da: "Douglas N Greve" 
>Data: 5-set-2017 18.12
>A: 
>Ogg: Re: [Freesurfer] Map of covariance
>
>I don't understand what you are asking. can you elaborate?
>
>
>On 08/30/2017 12:50 PM, std...@virgilio.it wrote:
>> Hi list,
>> by applying a design e.g. 4GV1 in fsgd I could assess the dependence 
>> of group differences taking in account the effect of covariate.
>> Anyway, where I should look if I want assess the the map showing the 
>> clusters in which the dependent variable is associated to covariate, 
>> tacking in account the group difference? Please could you suggest my 
>> the path?
>> Thanks
>>
>> Stefano
>>
>>
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[Freesurfer] MNI average brain in Freesurfer space

[Anna Kasdan]

Hi everyone,

Is there a freesurfer file/file format for the *average* MNI brain (as
opposed to fsaverage which is just based on different subjects)? Or is
there a way to turn MNI coordinates into freesurfer space? Thanks so much!

Anna
Research Assistant, NYU
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Re: [Freesurfer] Problem with ambiguous voxels?

[Bruce Fischl]

really? I've never seen that. If you upload one of the subjects to our 
ftp site (the entire subject dir tarred and gzipped) I will take a look


cheers
Bruce
On 
Tue, 5 Sep 2017, Del Re, Elisabetta wrote:




Dear FS Team,

We are running recon-all for a large dataset and 5 of the cases keep getting 
stuck at the exact same spot. It is the point at which the following has
just been displayed on the screen:

#@# WM Segmentation Wed Aug 30 17:34:40 EDT 2017

 mri_segment brain.mgz wm.seg.mgz 

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (107.0): 105.5 +- 6.4 [91.0 --> 125.0]
GM (78.0) : 81.0 +- 6.1 [56.0 --> 94.0]
setting bottom of white matter range to 87.1
setting top of gray matter range to 93.2
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...



For these 5 cases it will sit at this step apparently still running for over a 
week without any change before I cancel the job. There does not seem to
be anything special about these 5 cases either in terms of their header 
information or visually. We have not found any artifacts in the images except
for some minor ringing which is present in many images in the dataset, not just 
these. The rest of the cases of the dataset all ran to completion and
produced all of the files we were expecting, but a subset of them seem to have 
a related issue where most of the wmparc.mgz labelmap is unsegmented
white matter. Only the very edges and the very center are getting designated as something 
other than this label. The rest of the files in the "mri"
directory such as aparc+aseg.mgz and so on are equally as affected by this. Do 
you know what could be going on here? I would be happy to give you any
more information that could be helpful.

Best,
Elisabetta and Nate



Elisabetta C. del Re, Ph.D.
Assistant Professor of Psychiatry,
Department of Psychiatry
Harvard Medical School
phone 617 9675569
mail elisabetta_de...@hms.harvard.edu




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Re: [Freesurfer] Reliability of labeling procedure in the same scan

[Mike Schmidt]

I've run many hundreds of scans repeatedly and found variance between
versions of FreeSurfer, but identical output within a version. Something
must have changed between runs. Perhaps you could try comparing the log
files and see where the deviations begin.

Mike Schmidt


On Sep 5, 2017 10:54 AM, "Phoolan Devi"  wrote:

I mean the hippocampal volume in the aseg... so, it's not normal?


Bruce Fischl

 Sat, 26 Aug 2017 11:24:44 -0700


do you mean the hippocampal volume in the aseg or in the subfields?

On Sat, 26 Aug 2017, anonymous anonymous wrote:

Hi all,
Without noticing I run recon-all twice on the same scan of the same subject and
we noticed there are
some differences, at least in the hippocampal volume estimation.

Is it normal? If it is, why is it so?


Thank you so much for your help

This is a great community!


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Re: [Freesurfer] Fixed Effects Analysis on Single Subject's Brain

[Douglas N Greve]

Do you mean in the native fMRI space or the native subject surface space?


On 09/05/2017 12:15 PM, Taylor, Johnmark wrote:
> Hello,
>
> Quick question. If I scanned a single subject across several sessions 
> and want to do a fixed effects analysis on that subject's brain 
> (without registering to MNI or Talairach space), how do I go about 
> doing this? I am trying to us isxconcat-sess and then mri_glmfit, but 
> I am not seeing an option to simply do the analysis in native space 
> instead of registering to a standard brain. Is there a way to do this 
> besides taking the end result of the analysis and doing the reverse 
> registration back to the subject's brain?
>
> JohnMark
>
>
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Re: [Freesurfer] individual mri_segstats waveforms for vertices or face in label

[Douglas N Greve]

You could do it in matlab, something like

waveforms = fast_vol2mat(MRIread('waveform.nii.gz'));

% this will be a matrix ntimepoints by nvertices

You can then load the label with read_label.m and then pull out the 
columns from waveforms that you want. Make sure to account for the fact 
that the label indices are 0-based but  matlab uses 1-based


On 08/31/2017 02:27 PM, Mcnorgan, Christopher wrote:
> Though one workaround might be to subdivide a label many, many times 
> using mris_divide_parcellation, I was wondering if it is possible to 
> obtain a per-vertex (or even per-face) fMRI waveform for a label. In 
> other words, rather than compute the average waveform across all 
> vertices, as with mri_segstats --label subject semi /path/to/label 
> --avgwf avgwave.txt, which yields a single value that averages across, 
> say, 5000 vertices, I would like to obtain each of the 5000 waveforms 
> averaged over. I assume this would be more comparable to the scale of 
> analysis used by those looking at voxel populations (e.g., as in MVPA).
>
> Thanks, Chris
>
> /**
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> * http://ccnlab.buffalo.edu/
> * Office: 716.645.0236
> * Lab: 716.645.0222
> **/
>
>
>
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Re: [Freesurfer] Combining Echo Frames Error

[Douglas N Greve]

the first question is whether this is multi-echo data? Assuming it is, 
you can

mv 001.mgz multiecho.mgz

mri_concat --rms multiecho.mgz --o 001.mgz


On 08/31/2017 09:16 AM, Maksimovskiy, Arkadiy wrote:
>
> Dear Freesurfer experts,
>
> Here are the commands I entered, and errors I received:
>
> recon-all -subjid Test01 -i  /Testing/T1_MEMPRAGE_4/IM-0002-0206.dcm 
> -autorecon1
>
> #@# MotionCor Thu Aug 31 09:00:15 EDT 2017
>
> Found 1 runs
>
> /Users/amaksimovskiy/Desktop/Testing/Test01/mri/orig/001.mgz
>
> Checking for (invalid) multi-frame inputs...
>
> ERROR: input(s) cannot have multiple frames!
>
> /Users/amaksimovskiy/Desktop/Testing/Test01/mri/orig/001.mgz has 4 frames
>
> If this is a multi-frame MEMPRAGE image,
>
> use mri_concat --rms to combine echo frames.
>
> Could you please advice on how I can run the mri_concat --rms to 
> combine echo frames? Also, would this have to be done before the 
> autorecon1, and then reference the output (dicom or mgz?) into the 
> recon-all command?
>
> Thank you for your help and information.
>
> - Arkadiy
>
> -- 
>
> Arkadiy L. Maksimovskiy, Ph.D.
>
> Postdoctoral Research Fellow
> McLean Imaging Center, McLean Hospital
> Department of Psychiatry, Harvard Medical School
>
>
>
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Re: [Freesurfer] How to estimate the Intracranial area?

[Douglas N Greve]

do you mean the surface area of the inside of the skull? We do not 
segment the skull, so no such area measure is possible.


On 08/30/2017 11:14 PM, Zhiliang Long wrote:
> Dear FS experts:
>
>  I'am writting to ask for help about intracranial area. I can find 
> the information of intracranial volume in aseg.stats file. But i did 
> not find the information of intracranial area or is there any way to 
> estimate the intracranial area ?
>
> Looking forward to any suggestions.
>
> best
> Zhiliang Long
>
>
>
>
>
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Re: [Freesurfer] Occipital Cortex Segmentation

[Douglas N Greve]

On 08/30/2017 03:57 PM, Torrado Carvajal, Angel wrote:
> Hello,
>
> I need to get the segmentation of the occipital cortex. I am 
> attempting to generate the corresponding ROI, using the 
> mri_annotation2label command and then running mris_anatomical_stats to 
> merge the labels and get the actual volume. I am calling 
> mri_annotation2label as follows:
>
> mri_annotation2label --subject  --hemi lh --lobesStrict
> lobefile --outdir 'TEMP'
>
> However, I have a couple of questions:
>
>  1. Is there any way to generate both lh and rh together? Or should I
> generate separate volumes and then merge them?
>
For a surface-based segmentation, the hemispheres must be done separately
>
> 1.
>
>
>  2. What is the structure of the lobefile? I cannot find any example
> on the wiki.
>
This is the output annotation file (like lh.aparc.annot)
>
> 1.
>
> Thank you very much for your help!
> -- 
> *Angel Torrado-Carvajal*
> Postdoctoral Research Fellow
> Pain Neuroimaging Laboratory
> MGH/HST Athinoula A. Martinos Center for Biomedical Imaging
> Building 149, Room 1101, 13th Street, Charlestown, MA 02129 USA
> atorradocarva...@mgh.harvard.edu | www.nmr.mgh.harvard.edu 
>  | @MGHMartinos
>
>
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Re: [Freesurfer] Freesurfer Preliminary Questions

[Douglas N Greve]

you have to create the directory before you can cd to it. If you don't 
know how to create a directory in unix, then you should take some time 
to learn unix before trying to run FS.


On 08/31/2017 12:22 PM, Ledesma, Jason wrote:
>
> Hi Bruce,
>
>
> Do you have any suggestions as to how to determine the correct 
> directory and pathway to use?
>
>
> Sincerely,
>
> Jason Ledesma
> Staff Research Associate
> Phone: 1(424)571-7755
> E-mail: jason.lede...@labiomed.org 
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Ledesma, Jason 
> 
> *Sent:* Wednesday, August 30, 2017 1:39:30 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Freesurfer Preliminary Questions
>
> Bruce,
>
>
> It appears that the directory does not exist. See the following:
>
>
> fsuser@xubuntu-VirtualBox:~$ ls C:\tutorial data
> ls: cannot access C:tutorial: No such file or directory
> ls: cannot access data: No such file or directory
>
> fsuser@xubuntu-VirtualBox:~$ ls tutorial data
> ls: cannot access tutorial: No such file or directory
> ls: cannot access data: No such file or directory
>
> Here is what happens when doing a general ls command:
>
>
> fsuser@xubuntu-VirtualBox:~$ ls
> buckner_data-tutorial_subs  error.log  Pictures  surfer.log Videos
> Desktop export Publictar
> Documents   matlab setenv  Templates
> Downloads   Music  source  tutorial_data
> fsuser@xubuntu-VirtualBox:~$ ^C
> fsuser@xubuntu-VirtualBox:~$ ^C
> fsuser@xubuntu-VirtualBox:~$
>
>
> Sincerely,
>
> Jason Ledesma
> Staff Research Associate
> Phone: 1(424)571-7755
> E-mail: jason.lede...@labiomed.org 
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Bruce Fischl 
> 
> *Sent:* Wednesday, August 30, 2017 1:35:49 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Freesurfer Preliminary Questions
> thanks Jason
>
> does that directory exist? What happens if you try to ls it?
>
> Bruce
> On Wed, 30 Aug
> 2017, Ledesma, Jason wrote:
>
> >
> > Hi Bruce,
> >
> >
> > Here is the command that I tried and the resulting output/error message:
> >
> >
> > fsuser@xubuntu-VirtualBox:~$ export TUTORIAL_DATA=C:\tutorial data
> > fsuser@xubuntu-VirtualBox:~$ export 
> SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs
> > fsuser@xubuntu-VirtualBox:~$ cd $SUBJECTS_DIR
> > bash: cd: C:tutorial/buckner_data/tutorial_subjs: No such file or 
> directory
> > fsuser@xubuntu-VirtualBox:~$ ^C
> > fsuser@xubuntu-VirtualBox:~$
> >
> >
> > Sincerely,
> >
> > Jason Ledesma
> > Staff Research Associate
> > Phone: 1(424)571-7755
> > E-mail: jason.lede...@labiomed.org
> >
> > 
> 
> > From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of
> > Bruce Fischl 
> > Sent: Wednesday, August 30, 2017 1:24:12 PM
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] Freesurfer Preliminary Questions
> > Hi Jason
> >
> > in general it is much easier for us if you can cut and paste text into
> > the email. Pictures are useful for showing things in the data and such
> >
> > cheers
> > Bruce
> > On
> > Wed, 30 Aug 2017, Ledesma, Jason wrote:
> >
> > >
> > > Hi Bruce,
> > >
> > >
> > > Thank you for your quick response. Attached are photos in number 
> order which should help to
> > explain my situation. The first three photos depict the tutorial data as
> > > they are downloaded into my computer. Photo 4 illustrates the 
> version of Freesurfer that I am
> > using. Photos 5 and 6 express how the downloaded tutorial data 
> folder has
> > > been shared to Freesurfer.  Photo 7 illustrates an example of the 
> commands I have used. I have
> > tried other pathways as well but am still unsure which the proper 
> command
> > > should be. Unix is in fact new to me. Let me know if you require 
> any other details. Looking
> > forward to hearing your thoughts.
> > >
> > >
> > > Sincerely,
> > >
> > > Jason Ledesma
> > > Staff Research Associate
> > > Phone: 1(424)571-7755
> > > E-mail: jason.lede...@labiomed.org
> > >
> > 
> >___
> > _
> > > From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of
> > Bruce Fischl 
> > > Sent: Wednesday, August 30, 2017 12:10:24 PM
> > > To: Freesurfer support list
> > > Subject: Re: 

[Freesurfer] Fixed Effects Analysis on Single Subject's Brain

[Taylor, Johnmark]

Hello,

Quick question. If I scanned a single subject across several sessions and
want to do a fixed effects analysis on that subject's brain (without
registering to MNI or Talairach space), how do I go about doing this? I am
trying to us isxconcat-sess and then mri_glmfit, but I am not seeing an
option to simply do the analysis in native space instead of registering to
a standard brain. Is there a way to do this besides taking the end result
of the analysis and doing the reverse registration back to the subject's
brain?

JohnMark
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Re: [Freesurfer] Map of covariance

[Douglas N Greve]

I don't understand what you are asking. can you elaborate?


On 08/30/2017 12:50 PM, std...@virgilio.it wrote:
> Hi list,
> by applying a design e.g. 4GV1 in fsgd I could assess the dependence 
> of group differences taking in account the effect of covariate.
> Anyway, where I should look if I want assess the the map showing the 
> clusters in which the dependent variable is associated to covariate, 
> tacking in account the group difference? Please could you suggest my 
> the path?
> Thanks
>
> Stefano
>
>
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Re: [Freesurfer] upsampling ?h.curv

[Douglas N Greve]

You can also run

mris_apply_reg --src lh.curv --streg lh.white lh.white.upsampled --trg 
lh.curv.upsampled.mgh


On 08/30/2017 01:17 PM, Bruce Fischl wrote:
> ?h.curv is just the spatially smoothed ?h.white.H. If you specify -a 10
> (average 10 times) it should be pretty close th ?h.curv
>
> On Wed, 30 Aug 2017,
> sha...@nmr.mgh.harvard.edu wrote:
>
>> Hi Bruce,
>> Would you be more specific.  The command that you suggested generates
>> ?h.white.K and ?h.white.H. I am trying to generate ?h.curv.
>>
>>> try running
>>>
>>> mris_curvature -w  ...
>>> On Wed, 30 Aug 2017,
>>> sha...@nmr.mgh.harvard.edu wrote:
>>>
 Dear Freesurfers,
 I want to project a map on up-sampled inflated brain.  Up-sampled
 inflated brain has been generated using mris_mesh_subdivide command
 (without any problem).  But when I apply the same command to ?h.cuv I
 get an error message that:

 ERROR: MRISread: file 'surf/rh.curv' has many more faces than vertices!
 Probably trying to use a scalar data file as a surface!

 I even tried to regenerate ?h.curv files using mris_make_surfaces as
 below:

 mris_make_surfaces -c -white rh.white_upsampled subjid ?h

 But this command automatically down-sample rh.curv after
 down-sampling
 rh.white.

 Regards
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>>>
>>>
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>>
>>
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Re: [Freesurfer] patch for ribbon mgz failure

[Douglas N Greve]

Use the mri_segstats from this URL that is appropriate for your system 
(eg, if you're running centos6, the download that patch and copy it to 
mri_segstats)

https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/

On 08/30/2017 06:32 AM, Maria Gloria Rossetti wrote:
> Hi freesurfer team,
>
> I got the same error described here: 
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45983.html 
> and, as suggested, I tried to copy in $FREESURFER_HOME/bin/  the patch 
> from 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats 
> but I cannot find the URL.
> I also found some patches here : 
> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/ 
> but I don't know which one I'm supposed to use.
>
> Any advice?
>
> Thanks!
> Gloria
>
>
>
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[Freesurfer] Problem with ambiguous voxels?

[Del Re, Elisabetta]

Dear FS Team,

We are running recon-all for a large dataset and 5 of the cases keep getting 
stuck at the exact same spot. It is the point at which the following has just 
been displayed on the screen:

#@# WM Segmentation Wed Aug 30 17:34:40 EDT 2017

 mri_segment brain.mgz wm.seg.mgz

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (107.0): 105.5 +- 6.4 [91.0 --> 125.0]
GM (78.0) : 81.0 +- 6.1 [56.0 --> 94.0]
setting bottom of white matter range to 87.1
setting top of gray matter range to 93.2
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...



For these 5 cases it will sit at this step apparently still running for over a 
week without any change before I cancel the job. There does not seem to be 
anything special about these 5 cases either in terms of their header 
information or visually. We have not found any artifacts in the images except 
for some minor ringing which is present in many images in the dataset, not just 
these. The rest of the cases of the dataset all ran to completion and produced 
all of the files we were expecting, but a subset of them seem to have a related 
issue where most of the wmparc.mgz labelmap is unsegmented white matter. Only 
the very edges and the very center are getting designated as something other 
than this label. The rest of the files in the "mri" directory such as 
aparc+aseg.mgz and so on are equally as affected by this. Do you know what 
could be going on here? I would be happy to give you any more information that 
could be helpful.

Best,
Elisabetta and Nate




Elisabetta C. del Re, Ph.D.
Assistant Professor of Psychiatry,
Department of Psychiatry
Harvard Medical School
phone 617 9675569
mail elisabetta_de...@hms.harvard.edu



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Re: [Freesurfer] Interpretting Brain Segmentation Volume to eTIV ratio

[Douglas N Greve]

I put that in there mainly as a quality check to automatically flag 
something that has gone wrong. I think something went wrong if the value 
is 0.65 (unless you have very atrophied subjects). You will have to take 
a look to see what might have gone wrong.



On 08/29/2017 09:03 PM, Mehta, Chintan wrote:
>
> Dear FreeSurfer community,
>
>
> I wanted to interpret the BrainSegVol.to.eTIV ratio that is outputted 
> from FreeSurfer version 5.2.0. In my sample of normally developing 
> adolescents of ages 8 to 21, this ratio is between 0.65 and 0.85 for 
> 98% of subjects. However, the value is less than 0.65 for 2% of subjects.
>
>
> Could this reflect actual feature of brain volume to eTIV?
>
>
> Or is this a reflection of poor scans, poor overall FreeSurfer 
> processing, or inaccurate eTIV estimates for these subjects? Subjects 
> with BrainSegVol.to.eTIV ratios less than 0.65 tended to all be 
> females. They had Brain Segmentation volumes falling in normal ranges 
> of females in the full sample. However, their eTIV was on the 
> upper-end among eTIVs of females in the sample. If the eTIVs for these 
> subjects were over-inflated, then it makes sense the ratios are 
> especially low.
>
> Thank you.
>
> Best,
> Chintan
>
>
>
>
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Re: [Freesurfer] group interaction with one continuous covariate and three nuisance variables (two continuous, one dichotomous)

[Douglas N Greve]

try looking at the FSGD examples for a case that you can generalize

https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples


On 08/29/2017 08:59 PM, Ines Mürner-Lavanchy wrote:
>
> Dear FS experts,
>
> I would like to test if the correlations between thickness/area and 
> cognition differ between two groups, while age, socioeconomic status 
> (continuous) and gender (dichotomous) should be nuisance variables.
>
> To look at the effect of cognition in one group only, I made a model 
> with 8 regressors:
>
> - sex male
> - sex female
> - age male
> - age female
> - cognition male
> - cognition female
> - ses male
> - ses female
>
> With the contrast 0 0 0 0 0.5 0.5 0 0: how does cognition correlate 
> with Cth/CSA, controlled for age, sex, and ses.
>
> Now how do I model this, if I have *two* groups and want to look at 
> the interaction of group*cognition? I have trouble setting up the fsgd 
> and design matrix.
>
> Any help is appreciated,
>
> Thanks in advance,
>
> Ines
>
>
>
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Re: [Freesurfer] Multi-Subject Comparison in FreeSurfer

[Douglas N Greve]

You will need to run 500 different recon-all jobs. Obviously, if you run 
them on a single computer, it will take a long time, so you will need 
access to a cluster. Or you can buy time on a cloud service.


On 08/29/2017 02:54 PM, Sherrill, John T wrote:
>
> I am a new grad student and have been assigned a project in our Brain 
> Imaging Research Center. I would be taking the time to push through 
> and find these answers on my own but our program gives us 5 weeks of 
> half days in a lab for a trial. So I am in a bit of a time crunch.
>
> I have been given a database of about 500 .nii files and been asked to 
> find duplicates or likely duplicates. (Some subjects were 
> duel-consented so they may have multiple scans.) What is the best way 
> to recon-all all of the files? Individually, in small groups, or in 
> one larger group? If I do it in groups do I need to list each file or 
> can I just recon-all the entire directory? And if a recon-all on 1 
> file takes 6-20hr, will doing a recon-all on the entire data set take 
> 500*(6-20hr)=3000-10,000hr?  Any help is greatly appreciated.
>
> John Sherrill
> jtsherr...@uams.edu
> john_sherr...@me.com
> (870) 761-0580
> 
> Confidentiality Notice: This e-mail message, including any 
> attachments, is for the sole use of the intended recipient(s) and may 
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> destroy all copies of the original message.
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Re: [Freesurfer] mris_anatomical_stats error: missing ", " in "Measure Cortex, CortexVol Total cortical gray matter volume, ..."

[Douglas N Greve]

what is this causing an error in?


On 08/29/2017 06:50 AM, Ernst Schwartz wrote:
> Hi!
>
> It seems that in FreeSurfer 6, the comma between “CortexVol” and 
> “Total cortical gray matter volume” is missing
>
> here’s the relevant part of one of my stats-files:
>
> # Table of FreeSurfer cortical parcellation anatomical statistics
> #
> # CreationTime 2017/08/23-20:19:44-GMT
> # generating_program 
> /software/easybuild/software/FreeSurfer/6.0.0-centos6_x86_64/bin/mris_anatomical_stats
> # cvs_version $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 
> greve Exp $
> # mrisurf.c-cvs_version $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 
> zkaufman Exp $
> # cmdline 
> /software/easybuild/software/FreeSurfer/6.0.0-centos6_x86_64/bin/mris_anatomical_stats
>  
> -mgz -cortex 
> /data/datasets/pediatric/CLG//sub-A00057725_ses-CLG2/label/lh.cortex.label 
> -a 
> /data/datasets/pediatric/CLG//sub-A00057725_ses-CLG2/label/lh.aparc.a2009s.annot
>  
> -b -f 
> /data/datasets/pediatric/CLG//sub-A00057725_ses-CLG2/stats/lh.aparc.a2009s.pial.stats
>  
> sub-A00057725_ses-CLG2 lh pial
> # sysname  Linux
> # hostname cn4.cir.meduniwien.ac.at 
> # machine x86_64
> # user ernst
> #
> # SUBJECTS_DIR /data/datasets/pediatric/CLG/
> # anatomy_type surface
> # subjectname sub-A00057725_ses-CLG2
> # hemi lh
> # AnnotationFile 
> /data/datasets/pediatric/CLG//sub-A00057725_ses-CLG2/label/lh.aparc.a2009s.annot
> # AnnotationFileTimeStamp 2017/08/23 22:18:44
> # Measure Cortex, NumVert, Number of Vertices, 121790, unitless
> # Measure Cortex, PialSurfArea, Pial Surface Total Area, 105158, mm^2
> # Measure Cortex, MeanThickness, Mean Thickness, 2.80672, mm
> # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 
> 1051285.00, mm^3
> # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation 
> Volume Without Ventricles, 1040194.00, mm^3
> # Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain 
> Segmentation Volume Without Ventricles from Surf, 1039128.584538, mm^3
> # Measure Cortex, *CortexVol Total* cortical gray matter volume, 
> 532907.136355, mm^3
> # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 
> 926570.584538, mm^3
> # Measure SupraTentorialNotVent, SupraTentorialVolNotVent, 
> Supratentorial volume, 918874.584538, mm^3
> # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total 
> Intracranial Volume, 1254280.104289, mm^3
>
>
> cheers,
> Ernst
>
>
> ~
>
> Ernst Schwartz
> Computational Image Research (CIR) Lab
> Department of Biomedical Imaging and Image-guided Therapy
> Medical University Vienna, Austria
>
> --
>
>
>
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Re: [Freesurfer] time.dat file in Kinetic Modelling MRTM1 step - Petsurfer processing

[Douglas N Greve]

It is just a text file with the time at the middle of the frame. I've 
attached an example. The time units should be in seconds.



On 08/27/2017 11:28 AM, M Janani wrote:


Hi team,

Could anyone please tell how to create the time.dat 
file in the Kinetic Modelling MRTM1 step


mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o 
mrtm1 --no-est-fwhm --nii.gz


Regards,

Janani



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23.0
33.0
43.0
53.0
63.0
73.0
88.0
108.0
128.0
153.0
183.0
213.0
243.0
273.0
303.0
348.0
408.0
468.0
528.0
588.0
678.0
798.0
918.0
1038.0
1158.0
1368.0
1668.0
1968.0
2268.0
2568.0
2868.0
3168.0
3468.0
3918.0
4518.0
5118.0
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Re: [Freesurfer] Freesurfer PIB PET image processing

[Douglas N Greve]

the explanation is on this page

http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer


On 08/27/2017 05:22 AM, M Janani wrote:
> Thanks for your reply Douglas.
>
> Below is the data I have in my gtm.stats.dat file.
>
>12 Left-Cerebral-White-Matter  wm138789
> 65391.6480.858   0.1584
>27 Left-Cerebellum-White-Matterwm  9431   5373.205 
>  0.976   0.2046
>38 Left-Cerebellum-Cortex  subcort_gm 27648 15818.709  
>0.390   0.1331
>
> Could you please tell me which is intensity value here?
>
> Regards,
> Janani
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: 15 August 2017 00:12
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Freesurfer PIB PET image processing
>
> If you use mri_gtmpvc, then the gtm.stats file will have the intensity values.
>
>
> On 08/11/2017 02:37 AM, M Janani wrote:
>> Thanks for your support Douglas.
>>
>> I have processed my PIB PET images using PETSURFER. It works fine.
>>
>> I have one more query. Could you please help in computing the PiB mean value 
>> and intensity value for the ROIs.
>>
>> Regards,
>> Janani
>>
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
>> Sent: 10 August 2017 20:06
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Freesurfer PIB PET image processing
>>
>> do you mean to run the anatomical analysis on them? No.
>>
>>
>> On 08/10/2017 05:23 AM, M Janani wrote:
>>> Is it correct to process the PiB images using Freesurfer ?
>>>
>>>
>>> -Original Message-
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N
>>> Greve
>>> Sent: 10 August 2017 03:41
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Freesurfer PIB PET image processing
>>>
>>> We do not have any thing to specifically analyze PiB. You can look at
>>> the PETsurfer page for more general instructions
>>>
>>>
>>> On 08/09/2017 02:15 AM, M Janani wrote:
 Hi Team,

 I apologize, I am new to Freesurfer.

 Currently we are processing PIB PET images.

When we compare the SPM data along with FREESURFER
 outputs. We were able to see a large variation in the values.

Could you please guide us in processing PIB PET
 images in Freesurfer?

Since the signal of a PET image is very weak, we
 used MRI image as a guide to map it to Standard brain.

How does Freesurfer process in this case?

Your help would be grateful.

 Regards,

 Janani



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

Re: [Freesurfer] preproc-sess

[Douglas N Greve]

On 08/31/2017 11:47 AM, Jiahe Zhang wrote:
> Dear Freesurfer experts,
>
> I have two questions regarding preproc-sess:
>
> 1) What is the default algorithm that does the functional-anatomical 
> registration? And is there any way to change the default to other 
> types of registration methods?
it uses bbregister. There is no easy way to change it
>
> 2) If I do not want to normalize to template, i.e. I want to keep the 
> image in native space, should I be using -noreg or -noinorm?
Use the -per-session option and dont specify a hemisphere or mni305

>
> Thanks,
> Jiahe
>
>
> -- 
> Jiahe Zhang
> Ph.D. Candidate
> Department of Psychology
> Northeastern University
> 617-373-4789
>
>
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Re: [Freesurfer] aparc.DKTatlas+aseg.mgz

[Douglas N Greve]

Right, I think this is a new file with version 6.


On 08/31/2017 04:32 PM, John Anderson wrote:
> Thank you Dr Bruce,
> It seems that FS5.3 doesn't output this file. I just checked many 
> recons processed using FS5.3 without FLAIR and the file 
> "aparc.DKTatlas+aseg.mgz" is missing in all these recons.
> I see aseg.mgz, aseg+aparc.mgz and wmparc.mgz
>
>
>>  Original Message 
>> Subject: Re: [Freesurfer] aparc.DKTatlas+aseg.mgz
>> Local Time: August 31, 2017 4:04 PM
>> UTC Time: August 31, 2017 8:04 PM
>> From: fis...@nmr.mgh.harvard.edu
>> To: John Anderson , Freesurfer support 
>> list 
>> "Boyd, Emma" 
>>
>> Hi John
>>
>> the atlas isn"t flair-based (and is done before the flair processing). I
>> thought we always generated both (plus Christophe"s for 3 total), so I"m
>> a bit confused
>> cheers
>> Bruce
>> On Thu, 31 Aug 2017, John Anderson wrote:
>>
>> > Hi Emma,
>> > Thank you for your response.
>> > I am running my recons using V5.3 and V6.0
>> > In the data base I have ~200  T1 images and for some I have FLAIR 
>> images.
>> > When I run recon all with the flag FLAIR I get the file 
>> "aparc.DKTatlas+aseg.mgz" in FS5.3 and FS6.0
>> > If I run recon-all without the flag FLAIR i don"t see the 
>> file aparc.DKTatlas+aseg.mgz
>> > as an output of FS5.3 or FS6.0
>> >
>> > I am a bit confused about this!! Is this atlas FALIR-based or I am 
>> doing something wrong?!
>> >
>> >
>> >
>> >
>> >  Original Message 
>> > Subject: Re: [Freesurfer] aparc.DKTatlas+aseg.mgz
>> > Local Time: August 31, 2017 3:11 PM
>> > UTC Time: August 31, 2017 7:11 PM
>> > From: ebo...@mgh.harvard.edu
>> > To: Freesurfer support list , John 
>> Anderson
>> > 
>> >
>> >
>> > Hi John,
>> >
>> > Which version of FreeSurfer are you running?
>> >
>> >
>> > Emma
>> >
>> >
>> > -
>> >
>> > Emma Boyd
>> >
>> > Research Technician II
>> >
>> > Laboratory for Computational Neuroimaging
>> >
>> > Martinos Center for Biomedical Imaging
>> >
>> > 
>> 
>> >
>> > From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on
>> > behalf of John Anderson 
>> > Sent: Thursday, August 31, 2017 12:17 PM
>> > To: Freesurfer support list
>> > Subject: Re: [Freesurfer] aparc.DKTatlas+aseg.mgz
>> >
>> > Dear experts,
>> > looking into the output of Freesurfer in this
>> > page https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles
>> > I see that there should be a file named "aparc.DKTatlas+aseg.mgz". 
>> Is this atlas can be
>> > generated with the presence of FLAIR images.
>> >
>> > When i run recon-all without FLAIR or T2 I don"t see this atlas!! 
>> Is this atlas FLAIR -based?
>> >
>> > thank you for any clarification
>> > John
>> >
>> >  Original Message 
>> > Subject: aparc.DKTatlas+aseg.mgz
>> > Local Time: August 30, 2017 7:49 PM
>> > UTC Time: August 30, 2017 11:49 PM
>> > From: john.ande...@protonmail.com
>> > To: Freesurfer support list 
>> >
>> > Dear experts,
>> > looking into the output of Freesurfer in this
>> > page https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles
>> > I see that there should be a file named "aparc.DKTatlas+aseg.mgz". 
>> Do I need FLAIR
>> > images to get this file.
>> >
>> > I ran the command recon-all --s subj --all and I can";t find this file
>> >
>> >
>> > thank you for any clarification
>> > John
>> >
>> >
>> >
>> > The information in this e-mail is intended only for the person to 
>> whom it is
>> > addressed. If you believe this e-mail was sent to you in error and 
>> the e-mail
>> > contains patient information, please contact the Partners 
>> Compliance HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to 
>> you in error
>> > but does not contain patient information, please contact the sender 
>> and properly
>> > dispose of the e-mail.
>> >
>> >
>> >
>> >
>
>
>
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Re: [Freesurfer] Contrast matrix for PVR

[Douglas N Greve]

On 08/31/2017 02:30 PM, Martin Juneja wrote:
> Hi experts,
>
> I have a follow up question:
> In case I wanted to add another covariate in contrast matrix e.g. in 
> addition to age and gender if I want to add BMI as another covariate 
> in calculating correlation between volume and LGI (as mentioned in 
> previous email), could you please confirm if following contrast matrix 
> is correct:
>
> *0 0 0 0 0 0 1*
>
that is correct
> for FSGD:
>
> GroupDescriptorFile 1
>
> Class Male
>
> Class Female
>
> Variables Age BMI
>
> Inputzerek1 Male 21 17
>
> Input zerek2 Male 25 19
>
> etc.
>
> If that's the correct matrix, could you please briefly explain how 
> this matrix explains the effect of age, sex and BMI i.e. how does each 
> zero and 1 explain the correlation between volume and LGI and removes 
> the effect of age, sex and BMI?
This is a contrast matrix, so it does not explain anything. It is the 
columns in the design matrix that will explain effects. Each column 
means something and each column gets a regression coefficient. By 
setting the corresponding value in the contrast mat to 0 you tell 
mri_glmfit to to fit/account for that column in the design but do not  
include it in the contrast
>
> Thanks.
>
> On Tue, May 16, 2017 at 8:31 AM, Douglas Greve 
> > wrote:
>
> The 2nd is the correct matrix
>
>
> On 5/15/17 12:36 PM, Sahil Bajaj wrote:
>>
>> Hi everyone,
>>
>> From FreeSurfer manual and discussion forum, I found that volume
>> and LGI can be correlated using mri_glmfit command with -pvr flag.
>>
>> For that, my fsgd file has age, gender as covariates and the file
>> is as following:
>>
>> GroupDescriptorFile 1
>>
>> Class Male
>>
>> Class Female
>>
>> Variables Age
>>
>> Inputzerek1 Male 21
>>
>> Input zerek2 Male 25
>>
>> etc.
>>
>> My concern is:
>>
>> To run mri_glmfit command, I am not sure how to define my
>> contrast matrixif I am interested in removing the effect of age
>> and sex.
>>
>> 1st option I tried is: 0 0.5 0.5 0 1
>>
>> Here, I think first 0 regresses out age, 0.5 0.5 should be
>> averaging over males and females and last 0 1 correlates between
>> volume and LGI. But this looks like it is not giving me correct
>> correlations maps, although there is no error.
>>
>> 2nd option I tried is: 0 0 0 0 1
>>
>> This looks like its working and maps look correct to me
>> but I want to make sure this is the correct contrast matrix and
>> I am not sure how this matrix is regressing out age and gender or
>> 1st option is correct contrast matrix?
>>
>> Thank you so much !
>>
>> Best,
>>
>> Sahil
>>
>>
>>
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Re: [Freesurfer] Reliability of labeling procedure in the same scan

[Bruce Fischl]

no, I don't think so. There is some randomness in the algorithm (e.g. 
sampling paths through the volume), but I thought we used the same random 
seed each time to ensure repeatability. Was it on the same machine? What 
was your command line? And How big were the differences?


On Tue, 5 
Sep 2017, Phoolan Devi wrote:




I mean the hippocampal volume in the aseg... so, it's not normal?


Bruce Fischl Sat, 26 Aug 2017 11:24:44 -0700

do you mean the hippocampal volume in the aseg or in the subfields?
On Sat, 26 Aug 2017, anonymous anonymous wrote:

Hi all,
Without noticing I run recon-all twice on the same scan of the same subject and 
we noticed there are

some differences, at least in the hippocampal volume estimation.

Is it normal? If it is, why is it so? 


Thank you so much for your help

This is a great community!

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Re: [Freesurfer] Reliability of labeling procedure in the same scan

[Phoolan Devi]

I mean the hippocampal volume in the aseg... so, it's not normal?


Bruce Fischl

 Sat, 26 Aug 2017 11:24:44 -0700


do you mean the hippocampal volume in the aseg or in the subfields?

On Sat, 26 Aug 2017, anonymous anonymous wrote:

Hi all,
Without noticing I run recon-all twice on the same scan of the same subject and
we noticed there are
some differences, at least in the hippocampal volume estimation.

Is it normal? If it is, why is it so?


Thank you so much for your help

This is a great community!


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[Freesurfer] Fwd: Postdoctoral Position Available at Cincinnati Children’s Hospital Medical Center

[Lili He]

Postdoctoral Position Available at Cincinnati Children’s Hospital Medical
Center, Perinatal Institute

The multidisciplinary team in the laboratory of Nehal Parikh, DO, MS is
seeking a creative and highly motivated individual with solid training in
image processing, computer science, and/or neuroscience to conduct research
to develop advanced MRI (diffusion, functional) biomarkers in high-risk
neonates and infants. The lab’s research goals are to: 1) develop
prognostic biomarkers of neurodevelopmental impairments (e.g., intellectual
impairments, learning disabilities, autism) using advanced statistical
approaches (e.g. machine learning); and 2) develop neuroprotective
therapies in high-risk newborns. Programming expertise in Matlab, C/C++ and
in UNIX environment preferred. The work promises to be challenging and
presents a highly exciting opportunity to work on two NIH R01 projects.

*Website: **https://www.cincinnatichildrens.org/bio/p/nehal-parikh*



*Qualifications: *Qualified applicants will have a PhD with high-quality
peer-reviewed research publications, a developing expertise and strong
interest in image processing, biomedical engineering, machine learning,
and/or neuroscience, and highly motivated to develop an independent
research program in the areas of neuroimaging, or computational sciences as
it relates to newborns and infants.

Please submit your application to Dr. Sivaprasad with the following
information: A cover letter, a statement of interest, and a CV with contact
details for 3 referees.

Contact: Uma Sivaprasad, PhD; Scientist Recruiter, HR
Email: siv...@cchmc.org


Cincinnati Children’s Research Foundation
Cincinnati Children’s Hospital Medical Center (CCHMC) is a premier
pediatric research institution with over 900 diverse and productive faculty
members. Here, researchers work collaboratively across specialties and
divisions to address some of the biggest challenges we face today in
improving child health. A strong network of research support services and
facilities, along with institutional commitment to research, push our team
of faculty, postdocs and support staff to explore the boundaries of what is
possible, leading to significant breakthroughs. We are driven by our
mission to improve child health and transform the delivery of care through
fully integrated, globally recognized research, education and innovation.


Post-doctoral research fellows at Cincinnati Children’s are valued for
their unique interests and strengths, and are supported by our
institution’s strong programming for post-docs through the Office of
Postdoctoral Affairs and the Office of Academic Affairs and Career
Development. Mentoring, support for international students and an emphasis
on crafting high-quality grant proposals are only a few of the features
that set our program apart. Cincinnati Children’s is a respected part of
the broader, and very vibrant, Cincinnati community. With a thriving arts
scene, numerous festivals celebrating music and food, a passionate fan
following for our college and professional sports teams, and a variety of
opportunities for outdoor activities, our region is truly a great place to
work and live.
Please visit our website for more information about Postdoctoral Research
at CCHMC: http://www.cincinnatichildrens.org/education/research/postdo
ctoral/default/

*To apply online go to:
**http://www.cincinnatichildrens.org/careers/apply/default.htm
* *and search
for job (requisition) number 93065.*
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[Freesurfer] Fwd: Research Associate Position Available at Cincinnati Children’s Hospital

[Lili He]

Research Associate Position Available at Cincinnati Children’s Hospital
Medical Center, Perinatal Institute

The multidisciplinary team in the laboratory of Nehal Parikh, DO, MS is
seeking a creative and highly motivated individual with solid training in
image processing, computer science, and/or neuroscience to conduct research
to develop advanced MRI (diffusion, functional) biomarkers in high-risk
neonates and infants. The lab’s research goals are to: 1) develop
prognostic biomarkers of neurodevelopmental impairments (e.g., intellectual
impairments, learning disabilities, autism) using advanced statistical
approaches (e.g. machine learning); and 2) develop neuroprotective
therapies in high-risk newborns. Programming expertise in Matlab, C/C++ and
in UNIX environment preferred. The work promises to be challenging and
presents a highly exciting opportunity to work on two NIH R01 projects.

*Website: **https://www.cincinnatichildrens.org/bio/p/nehal-parikh*


*Qualifications: *Qualified applicants will have a PhD and post-doctoral
experience with peer-reviewed research publications and expertise in image
processing, biomedical engineering, machine learning, and/or neuroscience,
and highly motivated to work in the areas of neuroimaging, brain
development, and/or computational sciences as it relates to newborns and
infants.

Please submit your application to Dr. Sivaprasad with the following
information: A cover letter, a statement of interest, and a CV with contact
details for 3 referees.

Contact: Uma Sivaprasad, PhD; Scientist Recruiter, HR
Email: siv...@cchmc.org


Cincinnati Children’s Research Foundation
Cincinnati Children’s Hospital Medical Center (CCHMC) is a premier
pediatric research institution with over 900 diverse and productive faculty
members. Here, researchers work collaboratively across specialties and
divisions to address some of the biggest challenges we face today in
improving child health. A strong network of research support services and
facilities, along with institutional commitment to research, push our team
of faculty, postdocs and support staff to explore the boundaries of what is
possible, leading to significant breakthroughs. We are driven by our
mission to improve child health and transform the delivery of care through
fully integrated, globally recognized research, education and innovation.


Post-doctoral research fellows at Cincinnati Children’s are valued for
their unique interests and strengths, and are supported by our
institution’s strong programming for post-docs through the Office of
Postdoctoral Affairs and the Office of Academic Affairs and Career
Development. Mentoring, support for international students and an emphasis
on crafting high-quality grant proposals are only a few of the features
that set our program apart. Cincinnati Children’s is a respected part of
the broader, and very vibrant, Cincinnati community. With a thriving arts
scene, numerous festivals celebrating music and food, a passionate fan
following for our college and professional sports teams, and a variety of
opportunities for outdoor activities, our region is truly a great place to
work and live.
Please visit our website for more information about Postdoctoral Research
at CCHMC: http://www.cincinnatichildrens.org/education/research/
postdoctoral/default/
To apply online go to: http://www.cincinnatichildrens.org/
careers/apply/default.htm and search for job (requisition) number 93066.
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Re: [Freesurfer] Question on surface-based analysis

[Bruce Fischl]

Hi Chintan

(a) yes, I would think fsaverage would be fine in this age range

(b)  we do *not* resample into talairach coords, so volumes and surface 
areas should include eIV or something equivalent as a covariate. Thickness 
shouldn't require it.


cheers
Bruce


On Tue, 5 
Sep 2017, Mehta, Chintan wrote:




Dear FreeSurfer users,


I am new to surface based analysis in FreeSurfer (version 6.0). My data 
consists of T1-weighted scan
from normally developing youth of 8 to 21 years of age. I have two questions on 
assumptions of this
analysis for pediatric data:


(a) Is "fsaverage" an appropriate common template for all subjects of ages 8 to 
21? Online tutorials
suggest that fsaverage is the most commonly used template in FreeSurfer 
analyses and, furthermore,
imply that FreeSurfer can be used on scans of normally developing children as 
young as five years
old.


I am running analyses separately over different age groups (like ages 8 to 12,  
13 to 16, 17 to 21)
to ensure robustness. However, would combining results be inaccurate? 


(b) Previous posts in this forum and FreeSurfer documentation strongly 
recommend somehow normalizing
for head size or total brain volume in models of ROI area/volume. Would the 
eTIV covariate also be
appropriate for surface-based analysis of scans registered to fsaverage when 
using mri_glmfit? 

To me, it appears that scans registered to fsaverage have been warped to 
Talairach space, so the
whole brain adjustment has been implicitly made.


Thank you in advance for your great insights!

 

Best,

Chintan


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Re: [Freesurfer] Question on surface-based analysis

[Douglas Greve]

On 9/5/17 9:09 AM, Mehta, Chintan wrote:


Dear FreeSurfer users,


I am new to surface based analysis in FreeSurfer (version 6.0). My 
data consists of T1-weighted scan from normally developing youth of 8 
to 21 years of age. I have two questions on assumptions of this 
analysis for pediatric data:



(a) Is "fsaverage" an appropriate common template for all subjects of 
ages 8 to 21? Online tutorials suggest that fsaverage is the most 
commonly used template in FreeSurfer analyses and, furthermore, imply 
that FreeSurfer can be used on scans of normally developing 
children as young as five years old.



fsaverage is appropriate


I am running analyses separately over different age groups (like ages 
8 to 12,  13 to 16, 17 to 21) to ensure robustness. However, would 
combining results be inaccurate?

Not sure what you mean here



(b) Previous posts in this forum and FreeSurfer documentation strongly 
recommend somehow normalizing for head size or total brain volume in 
models of ROI area/volume. Would the eTIV covariate also be 
appropriate for surface-based analysis of scans registered to 
fsaverage when using mri_glmfit?


Yes, for surface area and volume analysis. Such an adjustment is not 
needed for thickness analysis


To me, it appears that scans registered to fsaverage have been warped 
to Talairach space, so the whole brain adjustment has been implicitly 
made.


All FS analysis is done in native space, so no adjustments are done. 
Surface-based warping to fsaverage does not account for changes in volume.



Thank you in advance for your great insights!

Best,

Chintan



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[Freesurfer] Question on surface-based analysis

[Mehta, Chintan]

Dear FreeSurfer users,


I am new to surface based analysis in FreeSurfer (version 6.0). My data 
consists of T1-weighted scan from normally developing youth of 8 to 21 years of 
age. I have two questions on assumptions of this analysis for pediatric data:


(a) Is "fsaverage" an appropriate common template for all subjects of ages 8 to 
21? Online tutorials suggest that fsaverage is the most commonly used template 
in FreeSurfer analyses and, furthermore, imply that FreeSurfer can be used on 
scans of normally developing children as young as five years old.

I am running analyses separately over different age groups (like ages 8 to 12,  
13 to 16, 17 to 21) to ensure robustness. However, would combining results be 
inaccurate?


(b) Previous posts in this forum and FreeSurfer documentation strongly 
recommend somehow normalizing for head size or total brain volume in models of 
ROI area/volume. Would the eTIV covariate also be appropriate for surface-based 
analysis of scans registered to fsaverage when using mri_glmfit?

To me, it appears that scans registered to fsaverage have been warped to 
Talairach space, so the whole brain adjustment has been implicitly made.


Thank you in advance for your great insights!



Best,

Chintan
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