[Freesurfer] rewritten: updating the tables and volumes associated with aseg.mgz

[silve...@gmx.com]

Dear Freesurfer Experts,

I'm sorry if I have not been clear with my question so far.
I have completed the cortical analysis on a number of subjects using 5.3, with 
all requiring some editing and re-running.

Now that I have the final surfaces, to update the aseg.mgz, I would like to run:
recon-all -subjid subject -surfsegedit 
before examining the aseg.mgz more closely.

Looking at one aseg.mgz (for example) I can see that edits could be made to 
label more of the cerebellar 
cortex as well as some relabelling of the brainstem. 

After performing edits such as these to aseg.mgz (and possibly to other 
subcortical structures) would I then run:
recon-all -subjid subject -aparc2aseg -segstats -wmparc

to update stats/aseg.stats, aparc+aseg.mgz, aparc.a2009s+aseg.mgz wmparc.mgz, 
and stats/wmparc.stats without changing the cortical stats files such as 
lh.aparc.stats?

Using this approach, I'm hoping that I can begin the group analysis of the 
cortex using lh.aparc.stats (and the like) while the subcortical review is 
underway, without having to re-run this group analysis with subsequent updates 
of lh.aparc.stats that would occur by running -autorecon3 (or similar) to 
update aseg.stats, aparc+aseg.mgz, etc.

Please let me know if this approach is valid, any suggestion would be 
appreciated.

Thanks,

P

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] possible pial surface editing

[Gennan Chen]

Hi! All,

We ran into a few cases which the wm matter surface is pretty decent but pial 
surface did not go far enough to include all gray matter. Is there a way to fix 
this?

Gen


This email message is for the sole use of the intended recipient(s) and may 
contain confidential and privileged information. Any unauthorized review, use, 
disclosure or distribution is prohibited. If you are not the intended 
recipient, please contact the sender by reply email and destroy all copies of 
the original message. If you are the intended recipient, please be advised that 
the content of this message is subject to access, review and disclosure by the 
sender's Email System Administrator
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] "Nuisance factors" in Qdec

[ye tian]

Dear Doug,

Thank you very much!
Sincerely,
Ye


On Tue, Aug 13, 2013 at 11:39 PM, Douglas Greve
wrote:

>
> If x1 and x2 are the same thing, then the equation is non-invertible. If
> they are the not the same variable, then there is no problem. QDEC computes
> all the contrasts for you (but excludes contrasts with nuisance variables)
> doug
>
>
>
>
> On 8/13/13 3:03 PM, ye tian wrote:
>
> Dear Doug,
>
>  I am afraid that I still don't understand why a variable can not be
> "covarying" and "nuisance" simultaneously.
>
>  If variables x1 and x2 are covarying, they both go into the model
> y = b0 + x1*b1 + x2*b2 + err
> Is this correct?
>
>  Nuisance, however, is related to the contrast, i.e., test hypothesis. If
> x2 is nuisance, then
> (1 0) * (x1 x2) = 0
>  Is this correct?
>
>  Otherwise, how does one specify the contrast matrix in Qdec?
>
>  Thank you very much!
>
>  Sincerely,
> Ye
>
>
>
> On Tue, Aug 13, 2013 at 12:03 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> Hi Ye, don't select the same factor as nuisance and covariate. It will
>> result in an error for sure. The difference between a covariate and a
>> "nuisance" factor is purely conceptual. By calling something a nuisance
>> you tell QDEC not to create a contrast related to it.
>> doug
>>
>>
>>
>> On 08/13/2013 02:09 AM, ye tian wrote:
>> > Dear Freesurfers,
>> > I have a question concerning the "nuisance factors" in the qdec
>> > dialogue. Suppose I have two independent variables x1 (discrete) and
>> > x2 (continuous), and only one observable y. I choose "Discrete (Fixed
>> > factor) = x1", "Continuous (covariate) = x2".
>> > If I further chose "Nuisance factor = x2", does that imply that
>> > 1) my contrast matrix is (0 1)
>> > 2) null hypothesis: Y is independent of x2
>> > Thank you very much!
>> > Sincerely,
>> > Ye
>> >
>> >
>>  > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] (no subject)

[Gomar, Jesus]

Hi Doug,
I have run recon-all -s subject -cortparc -parcstats and the process finished 
without errors, but the aparc files do not have the perirhinal cortex on it.
I have noticed that when I recon with 5.3 perirhinal labels are created on the 
label folder, but when I run recon-all -s subject -cortparc -parcstats (to 
update 5.1 to 5.3) no perirhinal labels are created. Do I need to add an 
additional flag to recon-all -s subject -cortparc -parcstats to obtain 
perirhinal measures?
Thanks for your help!
Jesus






The information contained in this electronic e-mail transmission and any 
attachments are intended only for the use of the individual or entity to whom 
or to which it is addressed, and may contain information that is privileged, 
confidential and exempt from disclosure under applicable law. If the reader of 
this communication is not the intended recipient, or the employee or agent 
responsible for delivering this communication to the intended recipient, you 
are hereby notified that any dissemination, distribution, copying or disclosure 
of this communication and any attachment is strictly prohibited. If you have 
received this transmission in error, please notify the sender immediately by 
telephone and electronic mail, and delete the original communication and any 
attachment from any computer, server or other electronic recording or storage 
device or medium. Receipt by anyone other than the intended recipient is not a 
waiver of any attorney-client, physician-patient or other privilege.___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] R: Re: Effect size

[stdp82]

Thank you very much Doug!

Stefano

Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 17-set-2013 22.25
A: 
Ogg: Re: [Freesurfer] Effect size


what do you mean exactly by "effect size"? gamma.mgh is the contrast 
value (C*beta)
doug


On 9/17/13 8:01 PM, Chung, Yoonho wrote:
> Hi all,
>
> Where can I find the effect size file(.mgh) after running mri_glmfit when 
> doing group analysis (control vs patients adjusting for age and sex)? 
> Somewhere in the wiki said gamma.mgh is the surface overlay for effect size. 
> Is this true? If not, how would I compute one?
>
> Yoon
>
>   
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.




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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Ventriculomegaly causing segmentation issues

[Bruce Fischl]

Hi Victor

have you tried running with the -bigventricles flag?

cheers
Bruce
On Tue, 17 Sep 2013, 
Victor Kovac wrote:



Dear FreeSurfer experts,
There are a number of patients in my study with significant ventricular
dilation, which is causing problems with segmentation of the ventricles and
corpus callosum, in particular, after recon-all (image attached). I am using
v5.3. 

I manually adjusted the talairach, but this did not fix the issue. Is there
anything else I can try? It is very important that I get at least some
volumetric data from these patients, as they are suffering from the worst
neurologic disease.

I appreciate any advice you can provide.

Thanks,
Victor

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] volume of subcortical structure calculation

[Bruce Fischl]

Hi Subha

no, it starts with that then we estimate the partial volume fractions of 
every border voxel by compute the mixture distributions of that label and 
the most likely neighboring label. Not sure if this has been written 
anywhere - maybe in Xiao Han's reliability paper?


cheers
Bruce


On Tue, 17 Sep 2013, Subhabrata Chaudhury 
wrote:



Hello 
 
Where can I get information on how freesurfer calculates volumes of
subcortical structures ? Is there a paper which provides insights into this
method ? Is it that for certain subcortical structures, it just counts the
number of voxels and adds them up since the voxels are 1mm3 ?
 
Thanks
 
Subha

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Maximum significance

[Yang, Daniel]

Hi all,

I performed cluster analyses and obtained several clusters, which are indicated 
by the corresponding maximum significance levels. For example, cluster one -- 
4.00, and cluster two -- 4.00.

Then I did a conjunction analysis to see their overlap, and then did a 
mri_surfcluster to get the clusters from the overlap. 

Then I observed that I have TalX TalY TalZ for each cluster in the overlap -- 
my question is, how does mri_surfcluster determine those coordinates? Since the 
whole cluster might have the same significance level everywhere?

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] TALx coordinates

[Yang, Daniel]

Thanks, Doug!! That sounds good.

I think if FreeSurfer can include MNI152 output option in its next release, 
that would be awesome!

Best,
Daniel

On Sep 15, 2013, at 3:54 PM, "Douglas Greve" 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:

That converts from MNI305 to MNI152 without going through the talairach itself. 
When FS computes Tal coords, it does so nonlinearly.
doug


On 9/11/13 12:08 PM, Yang, Daniel wrote:
Hi Doug,

It's pretty awesome. So accordingly,

MNI152x = (0.9975) MNI305x + (-0.0073) MNI305y + (0.0176) MNI305z + (-0.0429) * 
1
MNI152y = (0.0146) MNI305x + (1.0009) MNI305y + (-0.0024) MNI305z + (1.5496) * 1
MNI152z = (-0.0130) MNI305 + (-0.0093) MNI305y + (0.9971) MNI305z + (1.1840) * 1

The last row of the M (i.e., [-0.0429 1.5496 1.1840]') looks like some sort of 
offset to me, correct?

In other words, we are obtaining MNI305 first, Freesurfer convert that to TAL 
by default (question: is it done linearly or non-linearly?), and then we can 
manually convert it to MNI152 also.

Thanks so much!
Daniel

--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/10/13 6:52 PM, "Douglas N Greve" 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:

Hi Yang, I've computed a matrix that should do the trick. If you are in
matlab, then

M = [0.9975   -0.00730.0176   -0.0429
 0.01461.0009   -0.00241.5496
-0.0130   -0.00930.99711.1840
  0 0 01.]
P305 = [MNI305x MNI305y MNI305z 1]';
P152 = M*P305

Can you give this a shot and see if it makes sense? It will probably be
hard to tell since the matrix is pretty close to identity.

doug




On 09/10/2013 05:17 PM, Yang, Daniel wrote:
Thanks, Doug. I am really hoping to get MNI152 (because I also use
fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates?

Best,
Daniel

--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/10/13 5:14 PM, "Douglas N Greve" 
mailto:gr...@nmr.mgh.harvard.edu>
> wrote:


 It is an estimate of Tal coords from the MNI305. See

 http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach

 If you want MNI305, run mri_surfcluster with --nofixmni

 doug



 On 09/10/2013 05:08 PM, Yang, Daniel wrote:

 Hi all,

 The output of mri_surfcluster --sum shows TalX TalY TalZ. I am
 wondering if they are based on the Talairach system or some
 sort of
 MNI-Talairach system. If the latter, can you tell me something
 more
 about it? Like a webpage that describes its relationship
 between the
 MNI152 or the Talairach system?

 I find it confusing because mri_surfcluster said: "INFO:
 fixing MNI
 talairach coordinates"

 Thanks!
 Daniel

 --
 Yung-Jui "Daniel" Yang, PhD
 Postdoctoral Researcher
 Yale Child Study Center
 New Haven, CT
 (203) 737-5454


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


 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu 

 Phone Number: 617-724-2358
 Fax: 617-726-7422

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

 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu 

 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 The information in this e-mail is intended only for the person to
 whom it is
 addressed. If you believe this e-mail was sent to you in error and
 the e-mail
 contains patient information, please contact the Partners
 Compliance HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to
 you in error
 but does not contain patient information, please contact the
 sender and properly
 dispose of the e-mail.



--
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

Re: [Freesurfer] (no subject)

[Douglas Greve]

That should have done it. You are looking at the ?h.aparc.annot, right? 
Send me the recon-all.log file

doug


On 9/17/13 10:34 PM, Gomar, Jesus wrote:

Hi Doug,
I have run recon-all -s subject -cortparc -parcstats and the process 
finished without errors, but the aparc files do not have the 
perirhinal cortex on it.
I have noticed that when I recon with 5.3 perirhinal labels are 
created on the label folder, but when I run recon-all -s subject 
-cortparc -parcstats (to update 5.1 to 5.3) no perirhinal labels are 
created. Do I need to add an additional flag to recon-all -s subject 
-cortparc -parcstats to obtain perirhinal measures?

Thanks for your help!
Jesus

The information contained in this electronic e-mail transmission and 
any attachments are intended only for the use of the individual or 
entity to whom or to which it is addressed, and may contain 
information that is privileged, confidential and exempt from 
disclosure under applicable law. If the reader of this communication 
is not the intended recipient, or the employee or agent responsible 
for delivering this communication to the intended recipient, you are 
hereby notified that any dissemination, distribution, copying or 
disclosure of this communication and any attachment is strictly 
prohibited. If you have received this transmission in error, please 
notify the sender immediately by telephone and electronic mail, and 
delete the original communication and any attachment from any 
computer, server or other electronic recording or storage device or 
medium. Receipt by anyone other than the intended recipient is not a 
waiver of any attorney-client, physician-patient or other privilege.



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


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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] volume of subcortical structure calculation

[Subhabrata Chaudhury]

Hello 

Where can I get information on how freesurfer calculates volumes of subcortical 
structures ? Is there a paper which provides insights into this method ? Is it 
that for certain subcortical structures, it just counts the number of voxels 
and adds them up since the voxels are 1mm3 ?

Thanks

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Effect size

[Douglas Greve]

what do you mean exactly by "effect size"? gamma.mgh is the contrast 
value (C*beta)
doug


On 9/17/13 8:01 PM, Chung, Yoonho wrote:
> Hi all,
>
> Where can I find the effect size file(.mgh) after running mri_glmfit when 
> doing group analysis (control vs patients adjusting for age and sex)? 
> Somewhere in the wiki said gamma.mgh is the surface overlay for effect size. 
> Is this true? If not, how would I compute one?
>
> Yoon
>
>   
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] covariates in cortical thickness analysis

[Douglas Greve]

yes, you may exclude the mean cortical thickness

On 9/17/13 7:51 PM, std...@virgilio.it wrote:

Hi list,

I'm performing cortical thickness analysis on 3 groups. One of these 
is a control groups.


Mean cortical thickness in right and left hemispheres do not show any 
significativity among groups.


I'd like to not use mean cortical thickness as covariate becouse it 
worsens and make difficult to explain results. May I do it?


Thank you very much.


Stefano



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


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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Mac OS X 10.8.5 breaks recon-all

[Peter J. Molfese]

I have dependencies for AFNI and the fBIRN QC tools.  The dependencies get 
installed to /usr/local and I can disable the path extension to those binaries. 
 

-Peter

On Sep 17, 2013, at 3:01 PM, Z K  wrote:

> Ok. Thanks for the info. But what dependancies were required to be installed 
> (using homebrew)? Other than installing XQuartz, freesurfer should run on a 
> clean system.
> 
> -Zeke
> 
> On 09/17/2013 02:53 PM, Peter J. Molfese wrote:
>> The DYLD message does not appear on the 10.8.4 system.  Both systems have 
>> homebrew (http://brew.sh) installed for handling linux dependencies, but 
>> that message only appears on the 10.8.5 system.  Disabling homebrew does not 
>> resolve the error for me.
>> 
>> Best,
>> Peter
>> 
>> On Sep 17, 2013, at 2:40 PM, Z K  wrote:
>> 
>>> Hello,
>>> 
>>> Do you know if the following line:
>>> 
>>> "dyld: DYLD_ environment variables being ignored because main executable 
>>> (/usr/bin/top) is setuid or setgid"
>>> 
>>> from the log file you you've attached, also exists when you run the same 
>>> case on the machine running 10.8.4? I will update my Mac tonight to the 
>>> most recent version of OSX and attempt to duplicate the issue. I will keep 
>>> you updated.
>>> 
>>> -Zeke
>>> 
>>> On 09/17/2013 12:57 PM, Peter J. Molfese wrote:
 I updated my Mac OS X install  to 10.8.5 late yesterday and now recon-all 
 (FS 5.3) fails early in the processing pipeline (Talairach).  I've 
 attempted running the process with both my own data that works on 
 Freesurfer 5.3 with 10.8.4 and receive the same error message.  I have two 
 identical computers, with only one updated to 10.8.5, which will make 
 further testing straightforward.  I attached the log below of the attempt 
 to run the "bert" data with just one MRI.  The error message is the same 
 for other data.
 
 bugr output:
 -
 
 FREESURFER_HOME: /usr/local/freesurfer
 
 Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
 
 Kernel info: Darwin 12.5.0 x86_64
 
 -
 Please include the following additional information in your report:
 
   1) subject name - bert (and any other subject)
   2) the entire command-line executed - recon-all -s bert -i 
 /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz -all -3T
   3) the error message generated - see below
   4) optionally include the subject's /script/recon-all.log
 
 See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 
 
 === BEGIN ERROR REPORT ===
 
 recon-all -s bert -i /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz 
 -all -3T
 Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
 INFO: SUBJECTS_DIR is /Volumes/MRIData/srtt/freesurfer
 Actual FREESURFER_HOME /usr/local/freesurfer
 Darwin frankie.haskins.lab 12.5.0 Darwin Kernel Version 12.5.0: Mon Jul 29 
 16:33:49 PDT 2013; root:xnu-2050.48.11~1/RELEASE_X86_64 x86_64
 dyld: DYLD_ environment variables being ignored because main executable 
 (/usr/bin/top) is setuid or setgid
 /Volumes/MRIData/srtt/freesurfer/bert
 \n mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz 
 /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz \n
 mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz 
 /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz
 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
 reading from /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz...
 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
 i_ras = (-1, 0, 0)
 j_ras = (0, 0, -1)
 k_ras = (0, 1, 0)
 writing to /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz...
 #
 #@# MotionCor Tue Sep 17 12:49:59 EDT 2013
 Found 1 runs
 /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz
 Checking for (invalid) multi-frame inputs...
 WARNING: only one run found. This is OK, but motion
 correction cannot be performed on one run, so I'll
 copy the run to rawavg and continue.
 \n cp /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz 
 /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz \n
 /Volumes/MRIData/srtt/freesurfer/bert
 \n mri_convert /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz 
 /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz --conform \n
 mri_convert /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz 
 /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz --conform
 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
 reading from /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz...
 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>

Re: [Freesurfer] Mac OS X 10.8.5 breaks recon-all

[Peter J. Molfese]

The DYLD message does not appear on the 10.8.4 system.  Both systems have 
homebrew (http://brew.sh) installed for handling linux dependencies, but that 
message only appears on the 10.8.5 system.  Disabling homebrew does not resolve 
the error for me.  

Best,
Peter

On Sep 17, 2013, at 2:40 PM, Z K  wrote:

> Hello,
> 
> Do you know if the following line:
> 
> "dyld: DYLD_ environment variables being ignored because main executable 
> (/usr/bin/top) is setuid or setgid"
> 
> from the log file you you've attached, also exists when you run the same case 
> on the machine running 10.8.4? I will update my Mac tonight to the most 
> recent version of OSX and attempt to duplicate the issue. I will keep you 
> updated.
> 
> -Zeke
> 
> On 09/17/2013 12:57 PM, Peter J. Molfese wrote:
>> I updated my Mac OS X install  to 10.8.5 late yesterday and now recon-all 
>> (FS 5.3) fails early in the processing pipeline (Talairach).  I've attempted 
>> running the process with both my own data that works on Freesurfer 5.3 with 
>> 10.8.4 and receive the same error message.  I have two identical computers, 
>> with only one updated to 10.8.5, which will make further testing 
>> straightforward.  I attached the log below of the attempt to run the "bert" 
>> data with just one MRI.  The error message is the same for other data.
>> 
>> bugr output:
>> -
>> 
>> FREESURFER_HOME: /usr/local/freesurfer
>> 
>> Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>> 
>> Kernel info: Darwin 12.5.0 x86_64
>> 
>> -
>> Please include the following additional information in your report:
>> 
>>   1) subject name - bert (and any other subject)
>>   2) the entire command-line executed - recon-all -s bert -i 
>> /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz -all -3T
>>   3) the error message generated - see below
>>   4) optionally include the subject's /script/recon-all.log
>> 
>> See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> 
>> 
>> === BEGIN ERROR REPORT ===
>> 
>> recon-all -s bert -i /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz 
>> -all -3T
>> Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>> Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>> INFO: SUBJECTS_DIR is /Volumes/MRIData/srtt/freesurfer
>> Actual FREESURFER_HOME /usr/local/freesurfer
>> Darwin frankie.haskins.lab 12.5.0 Darwin Kernel Version 12.5.0: Mon Jul 29 
>> 16:33:49 PDT 2013; root:xnu-2050.48.11~1/RELEASE_X86_64 x86_64
>> dyld: DYLD_ environment variables being ignored because main executable 
>> (/usr/bin/top) is setuid or setgid
>> /Volumes/MRIData/srtt/freesurfer/bert
>> \n mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz 
>> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz \n
>> mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz 
>> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz
>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>> reading from /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz...
>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-1, 0, 0)
>> j_ras = (0, 0, -1)
>> k_ras = (0, 1, 0)
>> writing to /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz...
>> #
>> #@# MotionCor Tue Sep 17 12:49:59 EDT 2013
>> Found 1 runs
>> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz
>> Checking for (invalid) multi-frame inputs...
>> WARNING: only one run found. This is OK, but motion
>> correction cannot be performed on one run, so I'll
>> copy the run to rawavg and continue.
>> \n cp /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz 
>> /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz \n
>> /Volumes/MRIData/srtt/freesurfer/bert
>> \n mri_convert /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz 
>> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz --conform \n
>> mri_convert /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz 
>> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz --conform
>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>> reading from /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz...
>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-1, 0, 0)
>> j_ras = (0, 0, -1)
>> k_ras = (0, 1, 0)
>> Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels.
>> Data is conformed to 1 mm size and 256 voxels for all directions
>> changing data type from float to uchar (noscale = 0)...
>> MRIchangeType: Building histogram
>> writing to /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz...
>> \n mri_add_xform_to_header -c 
>> /Volumes/MRIData/srtt/freesurfer/bert/mri/transforms/talairach.xfm 
>> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz 
>> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz \n
>> INFO: extension is mgz
>> #

Re: [Freesurfer] Mac OS X 10.8.5 breaks recon-all

[Z K]

Ok. Thanks for the info. But what dependancies were required to be 
installed (using homebrew)? Other than installing XQuartz, freesurfer 
should run on a clean system.

-Zeke

On 09/17/2013 02:53 PM, Peter J. Molfese wrote:
> The DYLD message does not appear on the 10.8.4 system.  Both systems have 
> homebrew (http://brew.sh) installed for handling linux dependencies, but that 
> message only appears on the 10.8.5 system.  Disabling homebrew does not 
> resolve the error for me.
>
> Best,
> Peter
>
> On Sep 17, 2013, at 2:40 PM, Z K  wrote:
>
>> Hello,
>>
>> Do you know if the following line:
>>
>> "dyld: DYLD_ environment variables being ignored because main executable 
>> (/usr/bin/top) is setuid or setgid"
>>
>> from the log file you you've attached, also exists when you run the same 
>> case on the machine running 10.8.4? I will update my Mac tonight to the most 
>> recent version of OSX and attempt to duplicate the issue. I will keep you 
>> updated.
>>
>> -Zeke
>>
>> On 09/17/2013 12:57 PM, Peter J. Molfese wrote:
>>> I updated my Mac OS X install  to 10.8.5 late yesterday and now recon-all 
>>> (FS 5.3) fails early in the processing pipeline (Talairach).  I've 
>>> attempted running the process with both my own data that works on 
>>> Freesurfer 5.3 with 10.8.4 and receive the same error message.  I have two 
>>> identical computers, with only one updated to 10.8.5, which will make 
>>> further testing straightforward.  I attached the log below of the attempt 
>>> to run the "bert" data with just one MRI.  The error message is the same 
>>> for other data.
>>>
>>> bugr output:
>>> -
>>>
>>> FREESURFER_HOME: /usr/local/freesurfer
>>>
>>> Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>>>
>>> Kernel info: Darwin 12.5.0 x86_64
>>>
>>> -
>>> Please include the following additional information in your report:
>>>
>>>1) subject name - bert (and any other subject)
>>>2) the entire command-line executed - recon-all -s bert -i 
>>> /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz -all -3T
>>>3) the error message generated - see below
>>>4) optionally include the subject's /script/recon-all.log
>>>
>>> See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>
>>>
>>> === BEGIN ERROR REPORT ===
>>>
>>> recon-all -s bert -i /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz 
>>> -all -3T
>>> Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>>> Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>>> INFO: SUBJECTS_DIR is /Volumes/MRIData/srtt/freesurfer
>>> Actual FREESURFER_HOME /usr/local/freesurfer
>>> Darwin frankie.haskins.lab 12.5.0 Darwin Kernel Version 12.5.0: Mon Jul 29 
>>> 16:33:49 PDT 2013; root:xnu-2050.48.11~1/RELEASE_X86_64 x86_64
>>> dyld: DYLD_ environment variables being ignored because main executable 
>>> (/usr/bin/top) is setuid or setgid
>>> /Volumes/MRIData/srtt/freesurfer/bert
>>> \n mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz 
>>> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz \n
>>> mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz 
>>> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz
>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>>> reading from /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz...
>>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>>> i_ras = (-1, 0, 0)
>>> j_ras = (0, 0, -1)
>>> k_ras = (0, 1, 0)
>>> writing to /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz...
>>> #
>>> #@# MotionCor Tue Sep 17 12:49:59 EDT 2013
>>> Found 1 runs
>>> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz
>>> Checking for (invalid) multi-frame inputs...
>>> WARNING: only one run found. This is OK, but motion
>>> correction cannot be performed on one run, so I'll
>>> copy the run to rawavg and continue.
>>> \n cp /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz 
>>> /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz \n
>>> /Volumes/MRIData/srtt/freesurfer/bert
>>> \n mri_convert /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz 
>>> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz --conform \n
>>> mri_convert /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz 
>>> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz --conform
>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>>> reading from /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz...
>>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>>> i_ras = (-1, 0, 0)
>>> j_ras = (0, 0, -1)
>>> k_ras = (0, 1, 0)
>>> Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels.
>>> Data is conformed to 1 mm size and 256 voxels for all directions
>>> changing data type from float to uchar (noscale = 0)...
>>> MRIchangeType: Building histogram
>>> writing to /Volumes/MRIData/s

Re: [Freesurfer] Mac OS X 10.8.5 breaks recon-all

[Z K]

Hello,

Do you know if the following line:

"dyld: DYLD_ environment variables being ignored because main executable 
(/usr/bin/top) is setuid or setgid"

from the log file you you've attached, also exists when you run the same 
case on the machine running 10.8.4? I will update my Mac tonight to the 
most recent version of OSX and attempt to duplicate the issue. I will 
keep you updated.

-Zeke

On 09/17/2013 12:57 PM, Peter J. Molfese wrote:
> I updated my Mac OS X install  to 10.8.5 late yesterday and now recon-all (FS 
> 5.3) fails early in the processing pipeline (Talairach).  I've attempted 
> running the process with both my own data that works on Freesurfer 5.3 with 
> 10.8.4 and receive the same error message.  I have two identical computers, 
> with only one updated to 10.8.5, which will make further testing 
> straightforward.  I attached the log below of the attempt to run the "bert" 
> data with just one MRI.  The error message is the same for other data.
>
> bugr output:
> -
>
> FREESURFER_HOME: /usr/local/freesurfer
>
> Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>
> Kernel info: Darwin 12.5.0 x86_64
>
> -
> Please include the following additional information in your report:
>
>1) subject name - bert (and any other subject)
>2) the entire command-line executed - recon-all -s bert -i 
> /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz -all -3T
>3) the error message generated - see below
>4) optionally include the subject's /script/recon-all.log
>
> See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
> === BEGIN ERROR REPORT ===
>
> recon-all -s bert -i /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz 
> -all -3T
> Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> INFO: SUBJECTS_DIR is /Volumes/MRIData/srtt/freesurfer
> Actual FREESURFER_HOME /usr/local/freesurfer
> Darwin frankie.haskins.lab 12.5.0 Darwin Kernel Version 12.5.0: Mon Jul 29 
> 16:33:49 PDT 2013; root:xnu-2050.48.11~1/RELEASE_X86_64 x86_64
> dyld: DYLD_ environment variables being ignored because main executable 
> (/usr/bin/top) is setuid or setgid
> /Volumes/MRIData/srtt/freesurfer/bert
> \n mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz 
> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz \n
> mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz 
> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 0, -1)
> k_ras = (0, 1, 0)
> writing to /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz...
> #
> #@# MotionCor Tue Sep 17 12:49:59 EDT 2013
> Found 1 runs
> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz
> Checking for (invalid) multi-frame inputs...
> WARNING: only one run found. This is OK, but motion
> correction cannot be performed on one run, so I'll
> copy the run to rawavg and continue.
> \n cp /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz 
> /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz \n
> /Volumes/MRIData/srtt/freesurfer/bert
> \n mri_convert /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz 
> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz --conform \n
> mri_convert /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz 
> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz --conform
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 0, -1)
> k_ras = (0, 1, 0)
> Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels.
> Data is conformed to 1 mm size and 256 voxels for all directions
> changing data type from float to uchar (noscale = 0)...
> MRIchangeType: Building histogram
> writing to /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz...
> \n mri_add_xform_to_header -c 
> /Volumes/MRIData/srtt/freesurfer/bert/mri/transforms/talairach.xfm 
> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz 
> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz \n
> INFO: extension is mgz
> #
> #@# Talairach Tue Sep 17 12:50:13 EDT 2013
> /Volumes/MRIData/srtt/freesurfer/bert/mri
> \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
> orig.mgz --o orig_nu.mgz \n
> Darwin frankie.haskins.lab 12.5.0 Darwin Kernel Version 12.5.0: Mon Jul 29 
> 16:33:49 PDT 2013; root:xnu-2050.48.11~1/RELEASE_X86_64 x86_64
>
> recon-all -s bert exited with ERRORS at Tue Sep 17 12:50:20 EDT 2013
>
> For more det

[Freesurfer] Effect size

[Chung, Yoonho]

Hi all,

Where can I find the effect size file(.mgh) after running mri_glmfit when doing 
group analysis (control vs patients adjusting for age and sex)? Somewhere in 
the wiki said gamma.mgh is the surface overlay for effect size. Is this true? 
If not, how would I compute one? 

Yoon

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] covariates in cortical thickness analysis

[stdp82]

Hi list,
I'm performing cortical thickness analysis on 3 groups. One of these is a 
control groups. 
Mean cortical thickness in right and left hemispheres do not show any 
significativity among groups.
I'd like to not use mean cortical thickness as covariate becouse it worsens and 
make difficult to explain results. May I do it?
Thank you very much.

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Mac OS X 10.8.5 breaks recon-all

[Peter J. Molfese]

I updated my Mac OS X install  to 10.8.5 late yesterday and now recon-all (FS 
5.3) fails early in the processing pipeline (Talairach).  I've attempted 
running the process with both my own data that works on Freesurfer 5.3 with 
10.8.4 and receive the same error message.  I have two identical computers, 
with only one updated to 10.8.5, which will make further testing 
straightforward.  I attached the log below of the attempt to run the "bert" 
data with just one MRI.  The error message is the same for other data.  

bugr output:
-

FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

Kernel info: Darwin 12.5.0 x86_64

-
Please include the following additional information in your report:

  1) subject name - bert (and any other subject)
  2) the entire command-line executed - recon-all -s bert -i 
/usr/local/freesurfer/subjects/bert/mri/orig/001.mgz -all -3T
  3) the error message generated - see below
  4) optionally include the subject's /script/recon-all.log

See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


=== BEGIN ERROR REPORT ===

recon-all -s bert -i /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz -all 
-3T
Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /Volumes/MRIData/srtt/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
Darwin frankie.haskins.lab 12.5.0 Darwin Kernel Version 12.5.0: Mon Jul 29 
16:33:49 PDT 2013; root:xnu-2050.48.11~1/RELEASE_X86_64 x86_64
dyld: DYLD_ environment variables being ignored because main executable 
(/usr/bin/top) is setuid or setgid
/Volumes/MRIData/srtt/freesurfer/bert
\n mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz 
/Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz \n
mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz 
/Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz...
#
#@# MotionCor Tue Sep 17 12:49:59 EDT 2013
Found 1 runs
/Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.
\n cp /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz 
/Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz \n
/Volumes/MRIData/srtt/freesurfer/bert
\n mri_convert /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz 
/Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz --conform \n
mri_convert /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz 
/Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz --conform 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
writing to /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz...
\n mri_add_xform_to_header -c 
/Volumes/MRIData/srtt/freesurfer/bert/mri/transforms/talairach.xfm 
/Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz 
/Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz \n
INFO: extension is mgz
#
#@# Talairach Tue Sep 17 12:50:13 EDT 2013
/Volumes/MRIData/srtt/freesurfer/bert/mri
\n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz \n
Darwin frankie.haskins.lab 12.5.0 Darwin Kernel Version 12.5.0: Mon Jul 29 
16:33:49 PDT 2013; root:xnu-2050.48.11~1/RELEASE_X86_64 x86_64

recon-all -s bert exited with ERRORS at Tue Sep 17 12:50:20 EDT 2013

For more details, see the log file 
/Volumes/MRIData/srtt/freesurfer/bert/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was 

Re: [Freesurfer] Significant clusters before and after Monte Carlo

[Anita van Loenhoud]

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mris_anatomical_stats

[Douglas Greve]

If you have 5.3, you run

recon-all -s subject -cortparc -parcstats

will update just the aparc annotation and the corresponding stats files

doug





On 9/17/13 4:49 PM, Gomar, Jesus wrote:

Dear Freesurfer experts,
I hope someone can help me with a couple of questions regarding the 
use of mris_anatomical_stats command:


1. I am using mris_anatomical_stats to compute perirhinal thickness 
but with subjects I had previously recon through v5.1.0, and of course 
the mris_anatomical_stas failed because there is no perirhinal label. 
Is there a shorcut to compute perirhinal thickness without re-runnig 
recon-all again with v5.2.0/5.3.0?


2. When using mris_anatomical_stats, Can I compute measures for a list 
of subjects using something similar to --subjectsfile? It doesn't say 
so in the --help, but I thought perhaps there might be a way.


Thank you very much!
Jesus

The information contained in this electronic e-mail transmission and 
any attachments are intended only for the use of the individual or 
entity to whom or to which it is addressed, and may contain 
information that is privileged, confidential and exempt from 
disclosure under applicable law. If the reader of this communication 
is not the intended recipient, or the employee or agent responsible 
for delivering this communication to the intended recipient, you are 
hereby notified that any dissemination, distribution, copying or 
disclosure of this communication and any attachment is strictly 
prohibited. If you have received this transmission in error, please 
notify the sender immediately by telephone and electronic mail, and 
delete the original communication and any attachment from any 
computer, server or other electronic recording or storage device or 
medium. Receipt by anyone other than the intended recipient is not a 
waiver of any attorney-client, physician-patient or other privilege.



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


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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] mris_anatomical_stats

[Gomar, Jesus]

Dear Freesurfer experts,

I hope someone can help me with a couple of questions regarding the use of 
mris_anatomical_stats command:

1. I am using mris_anatomical_stats to compute perirhinal thickness but with 
subjects I had previously recon through v5.1.0, and of course the 
mris_anatomical_stas failed because there is no perirhinal label. Is there a 
shorcut to compute perirhinal thickness without re-runnig recon-all again with 
v5.2.0/5.3.0?

2. When using mris_anatomical_stats, Can I compute measures for a list of 
subjects using something similar to --subjectsfile? It doesn't say so in the 
--help, but I thought perhaps there might be a way.

Thank you very much!


Jesus





The information contained in this electronic e-mail transmission and any 
attachments are intended only for the use of the individual or entity to whom 
or to which it is addressed, and may contain information that is privileged, 
confidential and exempt from disclosure under applicable law. If the reader of 
this communication is not the intended recipient, or the employee or agent 
responsible for delivering this communication to the intended recipient, you 
are hereby notified that any dissemination, distribution, copying or disclosure 
of this communication and any attachment is strictly prohibited. If you have 
received this transmission in error, please notify the sender immediately by 
telephone and electronic mail, and delete the original communication and any 
attachment from any computer, server or other electronic recording or storage 
device or medium. Receipt by anyone other than the intended recipient is not a 
waiver of any attorney-client, physician-patient or other privilege.___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Significant clusters before and after Monte Carlo

[Douglas Greve]

I think that the simulation will run at whatever the visualization 
threshold is set to. Before and after you run it, you can change it to 
anything you want. You are correct on your other statements.

doug


On 9/17/13 3:24 PM, Anita van Loenhoud wrote:
> Hi Doug,
>
> It is finally starting to make sense to me. It was indeed the case
> that before Monte Carlo, within a cluster there were different values
> for each vertex, and after Monte Carlo, each vertex had the same
> value. I had difficulty understanding the different functions of the
> color scale min/max threshold and the vertexwise threshold. Is the
> following correct:
>
> The min/max threshold is nothing more than a visualisation threshold;
> it does not change anything in subsequent analyses that are performed
> (such as Monte Carlo), it just decides which results are significant
> enough to be colored or opaque.
>
> The vertexwise threshold (the one that is next to Monte Carlo) is the
> one that decides which vertices should be considered in the
> simulation. So a vertexwise threshold of 2 only takes vertices into
> account that have a p value < 0.01.
>
> After Monte Carlo, the min/max (visualisation) threshold now decides
> which cluster wise p-values (cwp's) should be shown in color. So,
> compared to before Monte Carlo, it now has a slightly different
> function: it does not decide which individual vertices, but which
> clusters should be colored/opaque.
>
> One last question (if the above is correct): could one decide to set
> the vertex wise threshold at 1.3 for example, and the visualisation
> threshold at 2? Or do both threshold always have to be the same?
>
> Thanks a lot for your help,
>
> Anita
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Significant clusters before and after Monte Carlo

[Anita van Loenhoud]

Hi Doug,

It is finally starting to make sense to me. It was indeed the case
that before Monte Carlo, within a cluster there were different values
for each vertex, and after Monte Carlo, each vertex had the same
value. I had difficulty understanding the different functions of the
color scale min/max threshold and the vertexwise threshold. Is the
following correct:

The min/max threshold is nothing more than a visualisation threshold;
it does not change anything in subsequent analyses that are performed
(such as Monte Carlo), it just decides which results are significant
enough to be colored or opaque.

The vertexwise threshold (the one that is next to Monte Carlo) is the
one that decides which vertices should be considered in the
simulation. So a vertexwise threshold of 2 only takes vertices into
account that have a p value < 0.01.

After Monte Carlo, the min/max (visualisation) threshold now decides
which cluster wise p-values (cwp's) should be shown in color. So,
compared to before Monte Carlo, it now has a slightly different
function: it does not decide which individual vertices, but which
clusters should be colored/opaque.

One last question (if the above is correct): could one decide to set
the vertex wise threshold at 1.3 for example, and the visualisation
threshold at 2? Or do both threshold always have to be the same?

Thanks a lot for your help,

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Mappin lesions labels to Talairach space

[Lisa Prilop]

I created the label by first opening the patient's image (tkmedit pat3 brainmask.mgz), using tools -> Configure Brush Info -> Shape: Square & 3D and then marking the lesion. Then I saved it via File -> Label -> save label as.

Should I create it another way to avoid the problem?

Lisa

 

 

Gesendet: Montag, 16. September 2013 um 17:11 Uhr
Von: "Douglas Greve" 
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Mappin lesions labels to Talairach space



The problem is probably that each label represents a finite amount of space. If the space between your label points is much more than 1mm, then you will get the pattern you show. How did you create the label in the first place?

doug

 
On 9/16/13 4:43 PM, Lisa Prilop wrote:




Hi Bruce!

The command line I used was: mri_label2label --srcsubject pat3 --srclabel /home/lisap/CIMT/fscal/pat3/label/testsept9 --trgsubject fsaverage --trglabel /home/lisap/CIMT/fscal/pat3/label/talairach --regmethod volume . The testsept9 -label looks perfectly normal (but corresponds to the original patient - on fsaverage it is wrongly placed), the new talairach-label is the grid i attached as an jpg-file - the location on fsaverage is correct (but not anymore so on the individual patient).

Lisa

 

Gesendet: Montag, 16. September 2013 um 14:52 Uhr
Von: "Bruce Fischl" 
An: "Lisa Prilop" 
Cc: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Mappin lesions labels to Talairach space

Hi Lisa what you are seeing is probably the effects of resampling. What did the labels look like before mapping? And you need to send us your full mri_label2label command line so that we (Doug?) can help. cheers Bruce On Mon, 16 Sep 2013, Lisa Prilop wrote: > Hi, > I have the following problem: I'm trying to map lesions from different > patients into talairach space. I hand-drew the lesions and saved them as > labels, then opened them on fsaverage. I didn't get an error-message, but in > the direct comparison between the native label (of the individual patient) > to the transformed label on fsaverage I could see that the lesions were > wrongly placed. I tried that with different flags on mri_label2label. Once > the place was roughly correct but then the label itself looked different (it > was a grid). What can I do to put that right? I attached a jpg-file > demonstrating what i mean. >   > Thanks for your help! >   > Lisa Prilop > > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.




 

 
 

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






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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Significant clusters before and after Monte Carlo

[Douglas Greve]

Can you check whether all vertices are the same value? If so, then it is 
showing the clusterwise p-value (not the uncorrected vertexwise p-value)
doug



On 9/17/13 10:44 AM, Anita van Loenhoud wrote:
> Hi Doug,
>
> I mean that before doing any correction, I can press 'Find Clusters
> and Goto Max', which will show me clusters based on my visualisation
> threshold. As far as I understood, it will go to the most significant
> vertex within each cluster and display that value. So before Monte
> Carlo, I found a cluster in the RMF, and the most significant vertex
> in there was -4.42.
>
> After Monte Carlo, I again see a cluster in the RMF. Now, when I again
> press 'Find Clusters and Goto Max' it gives me a new value of -2.19.
>
> I guess I have a difficulty with interpreting these 'new values' after
> Monte Carlo. Do I understand correctly from your previous comment that
> after this correction, they don't correspond to single vertices
> anymore? If my question is too elaborate for this mailinglist, could
> you recomment me some literature that might help me?
>
> Thanks so much!
>
> Anita
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Significant clusters before and after Monte Carlo

[Anita van Loenhoud]

Hi Doug,

I mean that before doing any correction, I can press 'Find Clusters
and Goto Max', which will show me clusters based on my visualisation
threshold. As far as I understood, it will go to the most significant
vertex within each cluster and display that value. So before Monte
Carlo, I found a cluster in the RMF, and the most significant vertex
in there was -4.42.

After Monte Carlo, I again see a cluster in the RMF. Now, when I again
press 'Find Clusters and Goto Max' it gives me a new value of -2.19.

I guess I have a difficulty with interpreting these 'new values' after
Monte Carlo. Do I understand correctly from your previous comment that
after this correction, they don't correspond to single vertices
anymore? If my question is too elaborate for this mailinglist, could
you recomment me some literature that might help me?

Thanks so much!

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] MNI coordinates

[Douglas Greve]

It was not in version 5.1, try 5.3 or let me know what platform you are 
using and I can send it to you.

doug

ps. Please remember to post to the list and not to us personally. thanks!




On 9/17/13 2:09 AM, Simon Baker wrote:

Hi Doug,

There are several posts in which you mention the mri_surfcluster 
--centroid option as a method for obtaining MNI coordinates of the 
centroid of each parcellation label. When I type the below command, I 
get and error saying "ERROR: Option --centroid unknown". What am I 
doing wrong?


mri_surfcluster --in lh.thickness --clabel lh.G_and_S_cingul-Ant.label 
--sum sum.lh.G_and_S_cingul-Ant --centroid --thmin 0 --hemi lh 
--subject ###


I am using Freesurfer version 5.1 and the Destrieux parcellation.

Thank you,

Simon



On 24 July 2013 13:59, Douglas Greve > wrote:



We don't have those number available, but you can generate them
with something like:

#1 Convert the annotation to a set of labels. This is for the
Desikan atlas, but you can spec the destrieux instead
mri_annotation2label --subject fsaverage --hemi lh --outdir
~/tmp/aparc

# For each label, run mri_surfcluster to get the centroid
mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness
--clabel lh.pericalcarine.label --sum sum.lh.pericalcarine
--centroid --thmin 0 --hemi lh --subject fsaverage

This will actually be weighted by the thickness, but that should
not matter much

The centroid coordinates will be in MNI305 space

doug




On 7/23/13 11:57 AM, LAOUCHEDI MAKHLOUF wrote:

Hi
i am using corticals parcels (destrieux) as nodes in a
connectivity study using the NBS (Network Based Statistics) tool;
i want to assign MNI coordinates for these nodes. is there any
MNI coordinates in freesurfer for each component of this
parcellation (not for every vertex in those components) or any
other strategy to assign coordinates for these components ?

otherwise, i intend to non-linearily register the freesurfer's
labels for a healthy subject in MNI and for each label i will use
coordinates of one of its points to represent that label

thanks for help


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



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


The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.




--

Simon Baker
PhD Candidate
Faculty of Medicine, Nursing and Health Sciences
Monash University


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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.