, that's odd. Did you do anything outside of FS on any of the
volumes? Try running mri_info on aseg.presurf.mgz, brainmask.mgz and
norm.mgz and send us the output
cheers
Bruce
On Tue, 19 Jul 2016, Uquillas, Federico D'Oleire wrote:
> Dear fellow Freesurfer users,
>
> I ha
Dear FreeSurfer community,
Despite tkmedit being discontinued, I am still using this to make surface edits
to my T1s. The main reason is that when I use Freeview and erase skull/dura,
Freeview creates this blue label wherever I erase outside of the brain surface.
The label is called left (or ri
Dear fellow FreeSurfer users,
I can't get a subject to recon-all all the way through without crashing,
regardless of the FS version used (deleted and started from scratch several
times).
It always fails with a Talairach transform fail error.
Wondering if anybody else has experienced this issue
uce Fischl wrote:
>
> Hi Fred
>
> have you checked the transform to see if it actually failed? If not, you
> can just turn off the checking. If it did, you can manually correct it
> (or run without it)
>
> cheers
> Bruce
>
>> On Wed, 14 Sep 2016, Uquillas, Fede
Dear FreeSurfer community,
We have a cluster that we drew on the surface on the right hemisphere, and
we’re interested in extracting cortical thickness values from the contralateral
hemisphere.
Wondering if there’s a way to transform the dimensions of our cluster from the
right hemisphere to t
ugh the xhemi processing
>stream
>
>https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
>
>There are examples there on mapping a label across hemis
>
>
>On 02/15/2017 03:30 PM, Uquillas, Federico D'Oleire wrote:
>> Dear FreeSurfer community,
>>
>>
Dear FreeSurfer experts,
I ran mri-glmfit-sim using mc-z, for both hemispheres, and the right hemi
finished with the message “mri_glmfit-sim done”.
However, for the left hemi, I got the following:
“ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!”
I believe this is s
ntoArray!"
Can you send the command line and full terminal output?
On 02/16/2017 12:54 PM, Uquillas, Federico D'Oleire wrote:
> Dear FreeSurfer experts,
>
> I ran mri-glmfit-sim using mc-z, for both hemispheres, and the right
> hemi finished with the message “mri_glmfit
Thanks Doug. I did just now.
Best,
Fred
On 2/16/17, 2:05 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N Greve" wrote:
>Can you tar up the glmdir and send it to me on our file drop (see url
>below)?
>
>
>On 02/16/2017 02:01 PM, Uquillas, Feder
ted -aparc
>
>
>does that generate the same errors?
>
>
>On 02/16/2017 02:35 PM, Uquillas, Federico D'Oleire wrote:
>> Thanks Doug. I did just now.
>>
>> Best,
>>
>> Fred
>>
>>
>>
>> On 2/16/17, 2:05 PM, "freesurfer-boun.
Dear FreeSurfer experts,
I’ve been trying to find a way to get a map of the difference between two
independent CTh association maps but can’t seem to find a solution.
I have two maps of independent groups (one is N=15, the other N=20) I would
like to compare. Is there maybe a way to do a sig1.m
Hi Doug,
What do you mean by combining all the data (and how would you suggest we go
about this?)?
And also how does one do a two-group test?
Thank you!
Best,
Fred
> On Mar 22, 2017, at 16:51, Uquillas, Federico D'Oleire
> wrote:
>
> Dear FreeSurfer experts,
>
> I
for group2. You would then combine them into one file, eg
>
> mri_concat group1.mgh group2.mgh --o group1-and2.mgh
>
> you would then create a new FSGD file for both groups, then run
> mri_glmfit --y goup1-and2.mgh ...
>
>
>> On 3/22/17 4:55 PM, Uquillas, Federico D'O
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 cont
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,
>
>
oded 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
>> "
x 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,
>>
y
of subjects but they all crash.
Thank you so much for you help.
All the best,
Fred
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Uquillas, Federico
D'Oleire
Sent: Thursday, December 14, 2017 6:56:56 PM
To: Freesurfer support list [
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