Dear Bruce,
They look good to me. Should I upload a couple of them, so you can have a look?
They're about 230MB each.
My question is: how serious is the BBR not initializing? Should I run
everything again with FSL installed?
Best wishes,
Veronica
-Original Message-
From: Bruce Fischl
Hi Doug and Bruce,
Doug's comment about vertex spacing and its dependence on the surface
of choice has gotten me thinking:
When I smooth my fMRI data using 6mm kernel, I use the command
mri_surf2surf --hemi lh --s fsaverage6 --sval lh.fmri.nii.gz --cortex
--fwhm-trg 6 --tval rh.fmri.nii.gz
Hello all,
I would just like to know what is the significance of the files that are
produced after a glmfit is done. I was trying to find a write up online but
I was not able to.
They include :
- cnr.mgh
- F.mgh
- gamma.mgh
- gammavar.mgh
- sig.mgh
Thank you
Hi Veronica
thanks for the offer, but I don't need to see them. Glad it seems to be
working. As for BBR, I'll leave that for Doug
Bruce
On Mon, 27 May 2013, Popescu,
Veronica wrote:
Dear Bruce,
They look good to me. Should I upload a couple of them, so you can have a look?
They're about
Hi Laouchedi
if you upload the dataset we'll take a look
Bruce
On Mon, 27 May 2013, LAOUCHEDI
MAKHLOUF wrote:
hi all
i run recon_all on some subjects having 512x512x154 , i noticed
(using tkmedit) that there are no problems with orig.mgz, and rawavg.mgz but
most of them were cropped
I can add that running the -hippo-subfields flag separately did work:
recon-all -s SUBJECTIDENTIFIER -hippo-subfields
Is there a reason the order of processing should matter? Is there a way I
can change my recon-all call (below) so that hippo-subfields will get
processed (so I do not have to
Hi All,
I'm running mris_anatomical_stats with a few manually defined labels. For
a few of my subjects, I am getting the error: Segmentation fault on one
of the labels. However, the other manually defined labels process without
any errors on these same subjects.
For example, I am running
hi
i send you further information of the -nuintensitycor and skullstrip
problem,about three control subjects. after running recon_all -i, i decided
to process my data step by step, i run recon_all -autorecon1 for all of them
and it ended with errors. i picked up three cases of the
Hi Rob,
does the white surface look ok? How about the contents of the
lh.PHC_1.label file? If both seem ok, then feel free to upload the subject
and we'll figure it out
Bruce
On Mon, 27 May 2013, Rob Tennyson
wrote:
Hi All,
I'm running mris_anatomical_stats with a few manually defined
Hi:
I used the following commands to get the cortical volume per each lobe:
mri_annotation2label --subject OAS1_0001_MR1 --hemi rh --lobesStrict
lobulos --seg lobulos --stat lobulos
mri_annotation2label --subject OAS1_0001_MR1 --hemi lh --lobesStrict
lobulos --seg lobulos --stat lobulos
what is your cmd line? What version of FS are you using? What is the
full terminal output?
doug
On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote:
Hi!
I have been running the mri_glmfit-sim command to do the correction for
multiple comparisons for my group analysis and for some voxel-based
Hi Sal, fsvol should be defined. Can you send me your fslregister?
doug
On 5/26/13 12:58 AM, Salil Soman wrote:
Dear Freesurfer experts,
WIth the combination of FS 5.3 and FSL 5.0.2.1, It looks like I am
having some problems with the fslregister script. From what I have
been able to
On 5/26/13 2:11 PM, Salil Soman wrote:
Dear Doug,
Thank you for your email. Following up on our previous discussions:
1) *bbregister fail *- this was happening because of error from
fslregister. The variable fsvol was translating to ERROR. In
fslregister th value for fsvol is set to
yes
On 5/26/13 4:56 PM, Salil Soman wrote:
As I am working with a 3D volume and not an ADC map, should I still
use --seg-erode 1 with mr segstats?
Thank
On Sun, May 26, 2013 at 1:11 PM, Salil Soman salso...@stanford.edu
mailto:salso...@stanford.edu wrote:
Hi - I realize that the --inv
It is based on the white. Notice that since you are using an average
subject (fsaverage6) there is some scaling that happens because an
average subject will have a surface area that is much less than the
average of the subjects that went into. The average of the subjects is
kept when the
Look at mri_glmfit --help. The only one not explained there is cnr.mgh
which is the contrasts (gamma) to residual noise stddev (rstd.mgh in the
glmdir)
doug
On 5/27/13 4:48 AM, Joshua deSouza wrote:
Hello all,
I would just like to know what is the significance of the files that
are
If FSL is not installed, then bbregister should have failed and
recon-all should have stopped. Did that not happen?
To answer your question, it might not make any difference. If the flair
and T1 were acquired at the same time, then it probably just used the
scanner coordinates to do the
you will need to run mri_annotation2label and specify the output to be
an annotation file instead of a segmentation. Then you will have to run
mri_aparc2aseg, specifying your lobes annotation as well as --labelwm
(look in the recon-all.log file for an example of how wmparc.mgz is
created).
Thank you Doug,
I think I initially misinderstood a number of things about this process. I
have a 3D GRE volume (I guessed its contrast is closest to BOLD, bbregister
set to T1 or T2 seemed to work more poorly). It is not a 2D. I would like
to transform the 3D GRE volume into freesurfer space, so
On 5/27/13 10:42 PM, Salil Soman wrote:
Thank you Doug,
I think I initially misinderstood a number of things about this
process. I have a 3D GRE volume (I guessed its contrast is closest to
BOLD, bbregister set to T1 or T2 seemed to work more poorly). It is
not a 2D. I would like to
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