Hi Ruth - Glad to hear this is useful to you. The rotation and translation
parameters are extracted from the affine registration of each DWI volume
to the first volume, which in trac-all is performed by eddy_correct.
a.y
On Tue, 10 Dec 2013, Ruth Carper wrote:
Hi Anastasia,
We discussed yo
Hi Emad - The bvecs file that you sent is formatted so that each column is
a gradient vector. The first column is [0, 0, 0] and this corresponds to a
b-value equal to 0 in the bvals file. So that's fine. You'll just have to
download the latest update to tracula to be able to use this column-wis
Dear all,
What I mean is the boundary of pial is incorrect when I check that by this
"tkmedit subject brainmask.mgz -surfs" I want to know how to change the
boundary of the pial.
Thanks.
All the best.
2013-12-11
Rujing Zha
发件人："Rujing Zha"
发送时间：2013-12-10 22:51
主题：[Freesurfer] part of GM
Hi Doug
I'm looking at the effect of MJ usage, the effect of whetherthe subject has
AHDH, and the interaction between MJ usage and ADHD
our threshold is 1.3
i have attahced our qdec.table.dat file
we are also looking at age and gender as covariates
Jon
Jon
- Original Message -
From:
which contrast are you looking at in QDEC? Also, what is the voxel-wise
threshold in QDEC? The value I gave in the command below is 1.3 but I
got that from one of your CSD files.
On 12/10/2013 05:10 PM, Jon Wieser wrote:
> HI doug,
> no, the summary files in the contrasts have the same # o
So one of the contrasts has 40 clusters in the summary file but the
y.ocn.dat file only has a few columns?
On 12/10/2013 04:54 PM, Jon Wieser wrote:
> yes, that is what we want, but the files contain only 1-3 columns
>
> Jon
>
> - Original Message -
> From: "Douglas N Greve"
> To: "Jo
Hi Rito
shortening the TE wouldn't change the overall acquisition. If it's total
brain volume you are interested in, you might consider getting the low
flip FLASH in addition
cheers
Bruce
On Tue, 10 Dec 2013, Ritobrato Datta wrote:
> Hi Bruce,
>
> Thank you for the reply and the suggestions. S
yes, that is what we want, but the files contain only 1-3 columns
Jon
- Original Message -
From: "Douglas N Greve"
To: "Jon Wieser"
Cc: "freesurfer"
Sent: Tuesday, December 10, 2013 3:44:50 PM
Subject: Re: [Freesurfer] qdec analysis with 2 covariates
There should be a column for eac
There should be a column for each cluster in contrast. Is that what you
want?
On 12/10/2013 04:37 PM, Jon Wieser wrote:
> thanks,
> I ran
> mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 1.3 abs
>
> MTA_ADHD_MJ is my project file and has the results from qdec in it
>
>
> it has produced:
>
> lh
thanks,
I ran
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 1.3 abs
MTA_ADHD_MJ is my project file and has the results from qdec in it
it has produced:
lh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat
lh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat
lh-Avg-thickness-Gender-Cor/cache.th13.a
it doesn't create it when it unpacks it - it is a separate series created
on the scanner. If you have the echoes in a single .mgz file named
echoes.mgz you would to:
foreach e (0 1 2 3)
mri_convert -nth $e echoes.mgz echo${e}.mgz
end
mri_average -sqr echo[0123].mgz rms.mgz
cheers
Bruce
Hi Anastasia,
We discussed your paper at our lab meeting yesterday so this was perfect timing
on the release of motion measures in your updated TRACULA. But I wasn't clear
where the numbers are coming from in your new update. Is this from EDDY?
eddy_correct? Some other registration step?
T
Hi Bruce,
Thank you for the reply and the suggestions. So if I shorten the TE on the
FLASH and lengthen the overall scan time, will that help ? I am specifically
interested in the brain vol (minus CSF) for MS atrophy as well as cortical
thickness analyses so I am keen to explore the possibility
OK, sorry, I thought qdec was running a script called mri_glmfit-sim but
it appears to be running the correction internally. That means that you
will have to run mri_glmfit-sim yourself, something like
mri_glmfit-sim --glmdir glmdir --cache 1.3 abs
doug
On 12/10/2013 02:53 PM, Jon Wieser wro
i have a mri_glmfit.log,(attached) but no cache.mri_glmfit-sim.log in the
qdec output directory
Jon
- Original Message -
From: "Douglas N Greve"
To: "Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, December 10, 2013 1:42:37 PM
Subject: Re: [Freesurfer] qdec analysis with
Thanks Bruce.
I checked, it is multi-echo mprage, it's just when I unpack it, it didn't
automatically generate the RMS.
so can you walk me through when to do the mri-average-sqr?
So I just type the command:
unpacksdcmdir -src
/cluster/archive/304/siemens/Skyra-45407-20130822-092226-174000 -targ
Hello,
I'm using TRACULA to analyze images obtained by a non-Siemens scanner, and
I'm using dcm2niigui app to generate bvec and bval files from DICOMs.
My question is whether or not the attached bvec and bval files match,
because the 0 bval is the first entry while the <0,0,0> bvec is somewhere
i
Hi, yes thank you both. That is exactly what the problem was.
Laura
On Tue, Dec 10, 2013 at 11:12 AM, Douglas N Greve wrote:
> Yep, looks like your annot is out of sync with the surfaces
>
> On 12/10/2013 01:51 PM, Chris Watson wrote:
> > I've seen this happen after making manual edits and th
No, sorry. You might be able to treat two consecutive trials as a single
trial, but then you won't get jitter between them.
doug
On 12/10/2013 02:38 PM, Chris McNorgan wrote:
> Hi all,
>
> I posed a question back in November but got no replies, so I'll try to
> restate it briefly:
>
> Is there
Is there a cache.mri_glmfit-sim.log in the output folder? Can you send
it to me? Also, please remember to post to the list. thanks!
doug
On 12/10/2013 02:30 PM, Jon Wieser wrote:
> FS version 5.3
>
> - Original Message -
> From: "Douglas N Greve"
> To: "Jon Wieser" , Freesurfer@nmr.mgh
Hi all,
I posed a question back in November but got no replies, so I'll try to
restate it briefly:
Is there a means of enforcing at least one set of consecutive trials for
a condition in an optseq schedule (or even consecutive trials with an
intervening NULL event)?
I am trying to produce a s
Yep, looks like your annot is out of sync with the surfaces
On 12/10/2013 01:51 PM, Chris Watson wrote:
> I've seen this happen after making manual edits and then not finishing
> a re-run of recon-all.
> Chris
>
> On 12/10/2013 02:00 PM, Laura Taylor wrote:
>> Hi,
>>
>> I'm trying to load lh.apar
I've seen this happen after making manual edits and then not finishing a
re-run of recon-all.
Chris
On 12/10/2013 02:00 PM, Laura Taylor wrote:
Hi,
I'm trying to load lh.aparc.a2009s.annot onto the lh pial surface of a
subject. When I use the freeview gui and select lh.aparc.a2009s.annot
un
hmmm, it should be there. What version of FS are you using?
On 12/10/2013 12:57 PM, Jon Wieser wrote:
> i was getting the values for the command terminal, when I press the "find
> clusters and GOTo Max" button on the qdec GUI.
> there is no file named cache.th20.abs.y.dat or something similar.
Yes, use the cache files. When "--cache" is used, the csdbase="cache"
On 12/10/2013 12:20 PM, krista kelly wrote:
> Hi again,
>
> I've looked into mri_glmfit-sim --help to figure out which files I
> could overlay in tkurfer after correcting for multiple comparisons
> using the instructions for
Hi Noel
what were the acquisitions? If they were multi-echo mprage than you will
either have to generate the RMS or find the series that is the RMS (since
it should have been generated automatically)
cheers
Bruce
On Tue, 10 Dec 2013, Chan, Noel Yan-Ki,Ph.D.
wrote:
Hi,
I'm trying to do r
Hi Ri
the sequence looks reasonable, although your TE of 5ms is somewhat long
and will reduce CNR and SNR. Can you shorten it? I would think you should
be able to. We looked at this for a while, and in the end the mprage
outperformed FLASH in terms of cortical gray matter/cerebral white matter
Hi,
I'm trying to do recon-all for a file, and it gave me this multiple frame error
message:
#@# MotionCor Mon Nov 25 13:11:40 EST 2013
Found 1 runs
/autofs/cluster/lazar/projects/Noel/SUBJECTS_DIR/BHI_BJU-345_pre_lazar/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s)
Hi again,
I've looked into mri_glmfit-sim --help to figure out which files I could
overlay in tkurfer after correcting for multiple comparisons using the
instructions for xhemi on the freesurfer wiki. However, I do not see any of
these files (csd.base...) in the glmdir/osgm folder. I only see ones
Hi All,
I have collected T1 3D FLASH on a subject and here are some details of the
sequence,
Manufacturer = SIEMENS
StudyDescription = Neuro_3T^brain_3t
SeriesDescription = Axial Global FLASH FA27
ManufacturersModelName = Verio
ReferencedImageSequence =
1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5
your interpretation is correct. Here's the matlab code
cd glmdir/yourcontrast
X = load('../Xg.dat');
C = load('C.dat');
y = load('cache.th20.abs.y.ocn.dat');
[beta rvar] = fast_glmfit(y,X);
[F pvalues] = fast_fratio(beta,X,rvar,C);
pvalues will be an array with the pvalue for each cluster
make s
Dear all,
In tkmedit brainmask.mgz -surfs, there are a bit of GM part missing. I want to
know how to paint the voxels to lable it as GM. And then run recon-all in a
specific style to reconstruct the surfs.
Thanks.
All the best.
2013-12-10
Rujing Zha
School of Life Science
University of Scien
Dear Bruce,
Thanks. I see.
All the best.
2013-12-10
Rujing Zha
发件人：Bruce Fischl
发送时间：2013-12-10 21:29
主题：Re: [Freesurfer] after PialEdit_tktools
收件人："Rujing Zha"
抄送："freesurfer"
sorry, looking at the script, I think:
recon-all -autorecon-pial -s
should be all you need, but perhaps som
sorry, looking at the script, I think:
recon-all -autorecon-pial -s
should be all you need, but perhaps someone else can confirm.
Bruce
On Tue, 10 Dec 2013, Rujing Zha wrote:
Dear Bruce,
In PialEdit_tktools
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_tktools, it
say this:
Dear Bruce,
In PialEdit_tktools
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_tktools, it say
this:
recon-all -autorecon-pial -subjid pial_edits_before
.So I didnot know whether the "-autorecon-pial" option "-autorecon2-pial"
option I can run.
Would you please tell me which one I
yes, with "-s subjects" replaced with "-s "
On Tue, 10 Dec 2013, Rujing Zha wrote:
Dear all,
Can I just type "recon-all -autorecon-pial -autorecon3 -s subjects" after
editing the pial by PialEdit_tktools?
All the best
2013-12-10
___
Hi Megha
looking at your images it's not clear to me where the gray/white boundary
is. Do you think it should be further out? One thing you can try is (if the
occipital white matter intensity in brain.mgz is <110) putting some control
points in the interior of the white matter. Or as Matt sugg
Hi Rujing,
yes, you should run -autorecon2-pial -autorecon3
cheers
Bruce
On Tue, 10 Dec 2013, Rujing
Zha wrote:
Dear all,
I run "recon-all -autorecon-pial -s subjects" after editing the pial by
PialEdit_tktools. However I only find "-autorecon2-pial" option in recon-all
manual. So I donot kn
Dear all,
Can I just type "recon-all -autorecon-pial -autorecon3 -s subjects" after
editing the pial by PialEdit_tktools?
All the best
2013-12-10
Rujing Zha
School of Life Science
University of Science and Technology of China
E-mail:
zh...@mail.ustc.edu.cn
charuj...@gmail.com
charujing...@163
39 matches
Mail list logo
