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Thanks.
I have sent you the tar by FileDrop.
Stefano
>
> Il 7 maggio 2018 alle 22.23 "Douglas N. Greve"
> ha scritto:
>
> It should not have taken that long. If you want me to look, you can tar
> up the glmdir and send it to me on our
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I ran 'recon-all -all -hires -qcache' on several datasets. I made numerous
edits of the brainmansk.mgz (for dura removal) and added control points and
want to rerun with the changes.
I thought I could rerun with changes using;
'recon-all -make all'
D
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Eugenio,
Not sure if there is any interest in this, but here is our code for converting
the data into T1 NIFTI space.
Thanks for the help,
Mark
Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albe
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Hello,
I am working on T1 images from multi-sites. One site in particular is
producing T1s that have small to large areas of temporal cortex being
excluded from segmentation. It seems that there may be an issue with
inhomogeneity of the bias field an
It should not have taken that long. If you want me to look, you can tar
up the glmdir and send it to me on our filedrop (below). You can also
use PALM. I've created a tool to assist in the interface
http://freesurfer.net/fswiki/FsPalm
On 05/07/2018 04:20 PM, std...@virgilio.it wrote:
>
>
> Tha
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Thanks.
I have about 40 subjects. The last run went ahead for five days. I have killed
it.
What's do you think about the use of PALM in my study (details are listed in
previous mails)?
Best regards,
Stefano
>
> Il 7 maggio 2018 alle 19.48
Use mri_coreg instead of bbregister. Make sure to use 12 DOF. You could
use CVS as well since that is non-linear
On 05/07/2018 04:11 PM, David Beeler wrote:
>
>
> Hi Doug,
> Ok so if I am understanding correctly, SPM or FSL will be better at
> registering functional data to CVS or MNI space for
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Hi Doug,
Ok so if I am understanding correctly, SPM or FSL will be better at registering
functional data to CVS or MNI space for group analyses than freesurfer will be
because they have the capability of doing nonlinear registrations. If that's
the
to follow up - you could use your manual labelings to create a new atlas
using mri_ca_train (assuming you mean subcortical regions). There is some
intelligence in it that you can only take advantage of if you use our
numbering/lut (i.e. left hippocampus is 17, etc...)
cheers
Bruce
On Mon, 7
Do you mean you want the xyz displacment of each vertex at each time
point? I don't think we have anything that does it explicitly, though
you could put something together
On 04/28/2018 11:19 AM, Pfannmoeller, Joerg Peter wrote:
>
> Dear all,
>
>
> in fMRI analyses the translation of the the br
You can do it in matlab with read_curv.m (to read in the thickness) and
read_annotation.m (to read in, eg, lh.aparc.annot), then pull out the
vertices you want (make sure to account for the 1-based in matlab)
On 04/27/2018 02:35 PM, Bruce Fischl wrote:
> oh sorry, I misunderstood. Hmm, that's a
Yes sorry. I meant without resampling. In that case, I will just re-run as you
suggested. Thanks for your help!
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Monday, May 7, 2018 1:44:55 PM
To: freesurfer@nmr.mgh.harvard.edu
S
Use mni152reg to register to the MNI 152 space. Then use mri_label2vol
with --seg wmparc.mgz to convert it into mni space
On 04/28/2018 09:28 PM, Rongxiang Tang wrote:
>
>
> Dear All,
>
> I would like to transform individual wmparc.mgz into MNI space for
> each of my subjects. I have tried usin
It will always apply it. If your data are 256 anyway, it will not have
an effect. If your data are <256, then it will have some small effects
On 05/03/2018 04:30 AM, JAVIER ROJO MUÑOZ wrote:
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>
> Hello FreeSufer developers,
>
> We're trying to have a small
Not that I know of. For our atlases, the prob information is
incorporated during trying
On 05/03/2018 05:38 AM, Mageshwar Selvakumar wrote:
>
>
> Dear Doug,
>
> Thank you for your help. On the query on atlas, We have a atlas that
> was built at our institute comprising of 183 regions and these
We don't currently segment sulcal CSF (it is coming!). Try using SPM --
it can segment all CSF
On 05/03/2018 11:22 AM, M Janani wrote:
>
>
> Hi Team,
>
> We would like to compute the CSF value from the MRI
> data. We have both T1 and T2 weighted images.
>
> Have
It looks right. How many subjects do you have? You can also check on the
progress by looking at the csd files in the glmdir/csd folder
On 05/03/2018 11:30 AM, std...@virgilio.it wrote:
>
> Hi list,
>
> I'm running the follow command lines:
>
> 1) mri_glmfit --y ces.nii.gz --cortex --surf fsavera
The two covariates (in theory) will account for some of the variance by
themselves. You could get some bias if you don't includ ethem
On 05/03/2018 03:33 PM, David S Lee wrote:
>
>
> Dear Douglas,
> Thank you for your guidance.
> I am following-up on your response with regards to setting up DODS
I'm not sure what you mean to apply the tal without a registration. Do
you mean without resampling? We don't have anything that will do that
for a 12dof registration.
On 05/04/2018 05:11 PM, Boggess, Matthew Jozsef wrote:
>
> Hello,
>
>
> I just wanted to follow up on this again. Is there any w
You cannot have empty classes. You should adjust the weights so that all
the positives add up to 1 and all the negatives add up to -1
On 05/04/2018 04:49 AM, C.P.E. Rollins wrote:
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>
> Hi,
>
> Sorry for coming back to this, but I'm still confused about the
As I mentioned in the previous email, you should not use bbregister for
this. If you are ok with a linear registration to MNI space (not very
good in general), then you should work using the commands I gave in the
link you presented. If you have version 6, don't use --init-fsl
On 05/04/2018 09
If that is really what you want to do, you should use a tool appropriate
for this type of analysis (eg, SPM and FSL have non-linear intersubject
registration)
On 05/04/2018 01:13 PM, David Beeler wrote:
>
>
> Hi Doug,
>
> funcVol is an individual functional resting state scan. We are doing
> s
Something like
mri_segcentroid --i aseg.mgz --o centroids.dat --ctab-default
On 05/05/2018 01:06 PM, Lucia Billeci wrote:
>
> Sorry Douglas,
>
> hereafter you can find previous emails
>
> Regards
> Lucia
>
>
>
>
>
>
>
> Dear Douglas,
> thanks a lot. This can solve my problem. Could you please gi
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Ûghrf7f77f7f7ef
On Thu, May 3, 2018, 19:32 Matthew Grecsek wrote:
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>
> I'm using the following flags on my recon -all: -mprage -time -multistrip
> -subcortseg
>
> and getting the following errors at this section
Hi Matt, this issue should be fixed in the freesurfer development version, but
as a temporary fix to get things working in v6, I would suggest disabling SIP
and rerunning:
http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/
best
Andrew
From: on behalf of Matth
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