nope — that are not compressed.
(I’ve sent out a sample DICOM in a separate email).
Thanks!
Noam
On Dec 17, 2014, at 11:39 PM, Bruce Fischl wrote:
> Hi Noam
>
> do you know if they are compressed? If so, you can try decompressing them and
> converting them (dcmdrle dcmdjpls). I thought we d
Hi Doug,
The problem is with the "int_genderXgroup" contrast (between .05 & .01
cluster forming thresholds).
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Aus
Hi Noam
do you know if they are compressed? If so, you can try decompressing them
and converting them (dcmdrle dcmdjpls). I thought we detected the
compression and wrote out a message, so that might not be the problem, but
it's easy enough to try
Bruce
On Wed, 17 Dec 2014, Ben Eliezer,
No
Hi Emad
it actually did better than I would have though. Yes, you can clone back
into the brainmask.mgz from the T1.mgz. Not sure how accurate a cortical
model you will ever get near the injury though - would you be able to draw
the gray/white boundary if you had to?
cheers
Bruce
On Wed, 1
Can you try this version of mri_convert? Make a copy of the original one
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert
If that does not work, can you upload the dicoms to our file drop?
doug
On 12/17/2014 04:09 PM, Ben Eliezer, Noam wrote:
> Hi —
>
> I’m having troub
Pradeep,
If you have a Sandy-Bridge or Ivy-Bridge based system, and it has at
least eight cores, and those cores run at 3.4GHz, and you use the
'-openmp 8' flag (available in v5.3) and you arrange recon-all to run
the hemi stages in parallel, then recon-all completes in about 3.5
hours. In the up
Hi —
I’m having trouble using the commands mri_convert and recon-all, both of which
produce the same error:
test.dcm does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header
I’ve read through the forum and did find similar problem
Hello,
We're running into a bit of a hiccup in trying to do an analysis of subcortical
volume differences between groups using mri_glmfit instead of the tables
generated by asegstats2table. The error occurs at the end of our pipeline when
running mri_glmfit-sim: "ERROR: Input volume voxel dime
Hi Gabe
we try very hard to support a wide range of contrast types and different
sequences, but sometimes that means that a particular sequence and/or
pathology doesn't work that well. Setting parameters like wlo is
perfectly reasonable - you are giving us more information about what to
expec
Hello freesurfers,
I wanted to get your opinion on altering the white matter low limit in the
mri_segment command through attaching the "-seg-wlo" flag onto -autorecon2. I
am working on a Frontotemporal Dementia cohort. In patients with severe
atrophy, there always tends to be a great deal of b
Dear Freesurfers,
I ran the following commands to read in mass-univariate data into matlab in
prep for LME analysis:
>> [Y,mri] = fs_read_Y('lh.thickness_sm10.mgh');
>> lhsphere = fs_read_surf('avgsubject/surf/lh.sphere');
>> lhcortex = fs_read_label('avgsubject/label/lh.cortex.label');
Next, I w
There are a bunch of contrasts there. Which one had the discrepancy?
doug
On 12/15/2014 07:43 PM, Bronwyn Overs wrote:
> Hi Douglas,
>
> I uploaded my glmdir to you on the 3/12/14 (named
> site-gender-group-prothaplotype.area.lh.glmdir.zip). Can you see what
> the problem is?
>
> Kind regards,
p { margin-bottom: 0.1in; line-height: 120%; }Hi Lars
I'm not sure whetheryou are talking about comparing different statistical
models with thesame model for the mean but different models for the covariance
orcomparing models with different models for the mean itself. In order touse
the lreml/c
Hi Jon
We recommend toorder the columns of your design matrix in the following way:
First,the intercept term (which is a column of ones); second, the
timecovariate; third, any time-varying covariates (eg. cannabis use);fourth,
the group covariates of interest (eg. a binary variableindicating whe
Ok I try this out using MATLAB.
Thanks Bruce,
On Wed, Dec 17, 2014 at 7:32 PM, Bruce Fischl
wrote:
>
> Hi Gunjan
>
> I can't help you preserve it in minc and using someone else's tools to
> convert slices to nifti. Can you work in matlb instead? If so, you can
> convert the minc to .mgz with mri
Hi Gunjan
I can't help you preserve it in minc and using someone else's tools to
convert slices to nifti. Can you work in matlb instead? If so, you can
convert the minc to .mgz with mri_convert, then load the mgz into matlab
using either MRIread or load_mgh (which will both return the directi
Hi Bruce!
I am working on a Mac, OS 10.10.1, FS version:
freesurfer-Darwin-lion-stable-pub-v5.3.0
Many thanks in advance!
Lukas
> Hi Luke
>
> what software/hardware version do you need?
> Bruce
> On Wed, 17 Dec 2014, lukas.sch...@ukb.uni-bonn.de wrote:
>
> Hi Bruce!
>
> I just would like to
Hi Bruce,
I am sorry that you could not get me properly.
My query is, how can I preserve direction cosine information. As I am new
to this issue, any help would really be appreciated.
Thanks,
Gunjan
On Wed, Dec 17, 2014 at 7:08 PM, Bruce Fischl
wrote:
>
> Hi Gunjan
>
> our coordinate systems ar
Hi Luke
what software/hardware version do you need?
Bruce
On Wed, 17 Dec 2014,
lukas.sch...@ukb.uni-bonn.de wrote:
Hi Bruce!
I just would like to come back to your offer to post the current version of
mri_tessellate.
Would you mind to send me the file?
Sincerely yours,
Luke
> Hi Bruce!
Hi Gunjan
our coordinate systems are extensively documented here:
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFile&do=get&target=fscoordinates.ppt
cheers
Bruce
On
Wed, 17 Dec 2014,
Gunjan Gautam wrote:
Hi Bruce,
I can view the file using "freeview -v file.mnc"
Dear experts,
Sorry for emailing you again. Can you please help me with the question in
the email below?
Kind regards,
Las
2014-12-11 10:54 GMT+01:00 Las Blawimo :
>
> Dear experts,
>
> I had a question regarding the output of my Qdec analyses. When I run a
> Monte Carlo Z simulation on my resul
Hi Bruce!
I just would like to come back to your offer to post the current version of
mri_tessellate.
Would you mind to send me the file?
Sincerely yours,
Luke
> Hi Bruce!
> I am working on a Mac, OS 10.10.1, FS version:
> freesurfer-Darwin-lion-stable-pub-v5.3.0
>
> All the best,
>
> Luke
Hi Nick,
Can you tell me what would be best processing time to do recon-all process
on one brain mri image using a high end machine ( Servers ) or using GPU
based machine.
We have more than 1000 of brain mri images, processing all these images is
the bottleneck now.
Pradeep
On Tue, Dec 16, 2014
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