Sure, here it is:
# Cluster Growing Summary (mri_volcluster)
# $Id: mri_volcluster.c,v 1.38.2.3 2009/01/16 02:26:36 greve Exp $
# cwd
/autofs/cluster/maury/users/gcoombs/College_Risk/ObjectLooming/allSBQ_061213/st4-obj_ns-4runs/face_v_car
# cmdline mri_volcluster --in tal.sm.wls.pct.rfx//group/si
This raises an interesting question.
Given that the longitudinal process is more reliable, if we collect 2 scans
on the same day, should we average those scans and then submit to
Freesurfer or apply Freesurfer first and then create an average of the
metrics from the longitudinal pipeline?
Best Re
Dear FreeSurfers,
I would like to get the tracts in Corpus Callosum body, not just the forceps
major and forceps minor given by tracula. Is there a way to get that with
Tracula?
Thank you.
Roxana.
---
Rox
Hi Roxana - How tracula works is decribed in detail here:
http://www.frontiersin.org/Journal/DownloadFile.ashx?pdf=1&FileId=8155&articleId=10815&Version=1&ContentTypeId=21&FileName=fninf-05-00023.pdf
To add a new tract to the tracula atlas that is not currently part of it,
the tract would first
You should take the better of the two images (the one without motion
artifacts).
Cheers, Martin
On 06/26/2013 11:06 AM, MCLAREN, Donald wrote:
This raises an interesting question.
Given that the longitudinal process is more reliable, if we collect 2
scans on the same day, should we average
Hello Dear Freesurfers,
is there a possibility, a way, to visualize the substantia nigra in Freesurfer
like using 3DSlicer!?
Thanks
Ata ___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.
Hi Ata
it's not a visualization issue - it's a segmentation one, and we don't
yet segment the SN, although it is on our list
sorry
Bruce
On Wed, 26 Jun 2013, Ata Akh wrote:
> Hello Dear Freesurfers,
> is there a possibility, a way, to visualize the substantia nigra in
> Freesurfer like using 3D
Hi all,
Any update on this issue? At present, I'm not able to use mri_cvs_register as
a result of the problem (several other programs also require this library).
Best,
Matt
From: Hoptman, Matthew
Sent: Tuesday, June 18, 2013 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: libboost_program_op
Hi Doug,
This is the complete terminal output:
cwd /SA
cmdline mri_glmfit --y /FREESURFER/lh.thickness.15.mgh --fsgd SA_base.fsgd --C
/FREESURFER/con4.mtx --surf fsaverage lh --cortex --glmdir
/FREESURFER/lh.pair-thick-T1-00.glmdir --pvr
/FREESURFER/lh.paired-cope1.psc.00.mgh
sysname Linux
ho
Hi Ye
you need to give recon-all a T1-weighted anatomical (e.g. mprage,
SPGR/FLASH, etc...), not the fMRI data.
cheers
Bruce
On Wed, 26 Jun 2013, ye tian wrote:
Dear Bruce,
Recon-all exits with the following error
ERROR: input(s) cannot have multiple frames!
$SUBJECTS_DIR/Barba50527_2/mri/
Hello Bruce,
Sorry! The first email was too big and the mailing list rejected me. My
image was already in Jpeg though.
Sincerely,
Ye
On Wed, Jun 26, 2013 at 5:17 PM, Bruce Fischl wrote:
> Hi Ye,
>
> can you cc the list so that others can help you? 787 would usually be too
> many files for an a
Dear FreeSurfers,
Sorry I accidentally clicked "send" before I finished. I will send a new
link. Would the moderator please delete the previous link?
Sorry!
Ye
On Wed, Jun 26, 2013 at 5:34 PM, ye tian wrote:
> Dear FreeSurfers,
>
> Recon-all exits with the following error
>
> *ERROR: input(s
Hi Folks,
I am trying to create an entorhinal cortex volume from
?h.entorhinal_exvivo.label using mri_label2vol
I cd to the subject dir ($SUBJECTS_DIR/bert) and the command I use is:
*mri_label2vol --label label/lh.entorhinal_exvivo.label --temp
mri/nu.mgz --identity --o mri/lh-new-erc.mgz *
not necessarily. That is a very small structure, and getting a few edge
voxels wrong will mess things up a lot. Can you load lh-new-erc.mgz in
tkmedit and load the surfaces too and see how good it did?
doug
On 06/26/2013 06:49 PM, Mehul Sampat wrote:
> Hi Folks,
>
>
> I am trying to create an en
won't the anatomical_stats one multiply thickness by surface area, where
the label2vol will only fill voxels on the gray/white boundary, not all
the way through the ribbon? Mehul: if you visualize the one from label2vol
does it fill the ribbon or just hug the white boundary?
On Wed, 26 Jun 2013
Oh, right. Mehul, you'll need to tell it to fill the ribbon with
something like --proj frac 0 1 .1
doug
On 06/26/2013 06:55 PM, Bruce Fischl wrote:
> won't the anatomical_stats one multiply thickness by surface area,
> where the label2vol will only fill voxels on the gray/white boundary,
> not
Hi Freesurfer experts,
I was wondering how exactly time point exclude files are used by FSFAST.
Are the time points removed from the time series before the GLM, or is
the time point exclude file used to build a nuisance predictor (as in
FSL's motion outliers routine,
http://fsl.fmrib.ox.ac.uk/fsl/f
They are accounted for as nuisance predictors in the GLM. They are not
removed from the time series.
doug
On 06/26/2013 06:59 PM, Caspar M. Schwiedrzik wrote:
> Hi Freesurfer experts,
> I was wondering how exactly time point exclude files are used by FSFAST.
> Are the time points removed from t
Your last column is all 0s. You probably declared a class but don't have
any subjects of that class.
doug
On 06/26/2013 04:29 PM, Gautam, Prapti wrote:
> Hi Doug,
>
> This is the complete terminal output:
>
> cwd /SA
> cmdline mri_glmfit --y /FREESURFER/lh.thickness.15.mgh --fsgd
> SA_base.fsgd
Hi Bruce,
Yes, the one from label2vol "just hugs the white boundary"
Doug, I will try with the --proj frac 0 1 .1 option and let you all know.
Thanks
Mehul
On Wed, Jun 26, 2013 at 3:58 PM, Douglas N Greve
wrote:
> Oh, right. Mehul, you'll need to tell it to fill the ribbon with
> something lik
Dear freesurfers,
I have a general question concerning *recon-all -i*.
Suppose under the subject *Beth*, there are 256 files:
Beth1.1.ima, Beth1.2.ima, Beth1.3.ima, ..., Beth1.128.ima
Beth2.1.ima, Beth2.2.ima, Beth2.3.ima, ..., Beth2.128.ima
I understand that I can use the following command to
Hi Mehul
the surfaces don't follow voxel boundaries and mris_anatomical_stats is
computed from them so they won't necessarily match
cheers
Bruce
On Wed, 26 Jun 2013,
Mehul Sampat wrote:
Hi Doug and Bruce,
Adding the option "-proj frac 0 1 .0 " to mri_label2vol helps a lot;
Just in case a
Thanks, Doug!
Caspar
On Wednesday, June 26, 2013, Douglas N Greve wrote:
>
> They are accounted for as nuisance predictors in the GLM. They are not
> removed from the time series.
> doug
>
>
> On 06/26/2013 06:59 PM, Caspar M. Schwiedrzik wrote:
> > Hi Freesurfer experts,
> > I was wondering how
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