Hi Doug,
I had not realised that was possible, thanks for that. Will save alot of
time! I am getting an error that the --cache flag is not recognised. This
is the command I am running;
[fitzgeje@lonsdale01 qdec]$ mri_glmfit-sim --glmdir Rh_thickness_15 --cache
2.3 neg --cwp 0.05
ERROR: Flag
Hey Nick.
Good idea. Is there a Centos6 version of Freesurfer 5.1 I can download
somewhere?
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky, MGH
Sent: Monday, April 28, 2014 1:35 PM
To:
Hi list,
Anybody has ever tried to bring Freesurfer pial surfaces for render in 3D
studio max? I would be curious on the procedure to follow, more
specifically on which file to export/import/convert.
Thank you.
Dorian
TJU
___
Freesurfer mailing list
Hi list,
I'd like obtain FS thalami mask (nii.gz) to import in FSL and use it as seed
mask in probtrackx.
Thanks,
Stefano___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The
Hi Stefano
you can use either mri_binarize --match or mri_extract_label with labels
10 and 49 (which I got from FreeSurferColorLUT.txt)
cheers
Bruce
On Tue, 29 Apr 2014,
std...@virgilio.it wrote:
Hi list,
I'd like obtain FS thalami mask (nii.gz) to import in FSL and use it as seed
mask in
My apologies, how can I visualize mri_binarize output? I tried in fslview but
orientation is wrong. Different orientation is a file's feature or swapdim is
request?
Thanks,
Stefano
Messaggio originale
Da: fis...@nmr.mgh.harvard.edu
Data: 29-apr-2014 16.01
A: std...@virgilio.it,
My apologies, how can I visualize mri_binarize output. I tried in fslview but
orientation is wrong. Different orientation is a file's feature or swapdim is
request?
Thanks,
Stefano
Messaggio originale
Da: fis...@nmr.mgh.harvard.edu
Data: 29-apr-2014 16.01
A: std...@virgilio.it,
You could also try the nipy version. works real well with Snow Leopard OS
shantanu
On Mon, April 28, 2014 9:09 pm, Shantanu Ghosh wrote:
Hi Sampada,
Please cc the freesurfer list when answering/asking questions so others
can answer too. And also people with similar issues will benefit from
Research Assistant Positions at Boston Children's Hospital: Pediatric and
Infant (f)MRI/developmental cognitive neuroscience/typical and atypical reading
development
GaabLab at Children's Hospital Boston
Developmental Medicine
Children's Hospital Boston
RESEARCH STUDY ASSISTANTS:
Children's
How do you know the orientation is wrong? Is it right in tkmedit?
On 04/29/2014 10:23 AM, std...@virgilio.it wrote:
My apologies, how can I visualize mri_binarize output? I tried in
fslview but orientation is wrong. Different orientation is a file's
feature or swapdim is request?
Thanks,
what version are you using? There is also help when you run
mri_glmfit-sim --help
On 04/29/2014 08:10 AM, Jacqueline Elaine Fitzgerald wrote:
Hi Doug,
I had not realised that was possible, thanks for that. Will save alot
of time! I am getting an error that the --cache flag is not
The coords in the summary file are for the white surface, not the
inflated. Try freeview again using the white surface
On 04/29/2014 07:50 AM, Rujing Zha wrote:
Hi doug,
Thanks doug.
I saw the sig.mgh in freeview by typing this:
freeview -f
I don't know that it would be preferred or acceptable. You have just
thrown away information about what is left and right, so you might have
inadvertently flipped the brain. Unless your voxel size is 1mm, there
will be some interpolation when conforming. I'm not that worried about
the
If you have an example func of some kind, you can just run bbregister
passing the example func with --mov. This will give you a register.dat
file which can be used in mri_label2vol to map the subcortical seg into
the function space.
doug
On 04/28/2014 06:18 PM, Jones, Richard wrote:
I have
Dear Doug,
I registered with surfreg the hemispheres I would like to analyze. How
should I proceed now for the final statistical vertex-wise analysis?
Should I smooth the surfaces and perform between-group comparison with qdec?
Thank you in advance
Paola
Paola Valsasina, MSc
Research Fellow
OK, you're using an older version that did not copy the volume. You can
just do this
cp subject/surf/lh.volume subject/surf/rh.volume
Note the change from lh to rh!
doug
On 04/28/2014 06:25 PM, Yizhou Ma wrote:
Thanks Doug. I don't see an error message in xhemireg.?h.log files.
Please
Have you tried using dcmunpack? You run it twice, once without any
output to get a list of runs in the folder. The 2nd with how you want
the data converted. Run it with --help to get more info
doug
On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote:
Hello I have only recently started the fmri
You can't use qdec for this, you will have to use mris_preproc,
mri_surf2surf, mri_glmfit, and mri_glmfit-sim. The first step is the
tricky one in that you will have to run mris_preproc twice then merge
the two data sets.
For the subjects that you want the left hemisphere, run mris_preproc as
I'm using version 4.5.0. The --cache does not come up when I type the
command mri_glmfit-sim --help?
Best,
Jackie
On 29 April 2014 16:58, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
what version are you using? There is also help when you run
mri_glmfit-sim --help
On 04/29/2014 08:10
Upgrade! You can run the glm analysis in a new version and keep the old
version for your individual analysis
doug
On 04/29/2014 01:06 PM, Jacqueline Elaine Fitzgerald wrote:
I'm using version 4.5.0. The --cache does not come up when I type the
command mri_glmfit-sim --help?
Best,
Jackie
It sounds like you are doing the right thing with the right equation.
Can you elaborate on what is going wrong?
On 04/28/2014 05:10 PM, ISAAC PEDISICH wrote:
Sorry - I meant just the matrix.
I'm trying to map from CRS in the CT to tkrRAS in the anatomical, I
believe. I'm a little unclear
Hi Bruce,
in tkmedit the orientation is ok. Is wrong in fslview. Now, I'm running
probtrackx. I'll update you on results.
Thanks,
Stefano
Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 29-apr-2014 17.52
A: freesurfer@nmr.mgh.harvard.edu
Ogg: Re: [Freesurfer] R: Re: thalami
John,
I just noticed that you are looking for v5.1, and that we don't have a
centos6 build of that (we started those with v5.2). Can you try v5.3?
N.
On Tue, 2014-04-29 at 12:20 +, West, John D. wrote:
Hey Nick.
Good idea. Is there a Centos6 version of Freesurfer 5.1 I can download
Is the brain merely shown sideways in FSLview? What matters is that the A/P/S/I/L/R labels are correct in FSLview, in which case the orientation info is read just fine, and it is solely a matter of how FSLview choses to display data that doesn't have
an RAS/LAS orientation.
cheers,
-MH
I'm trying to do it. But I have an error. It shoud be due to difference in
size? In freeviewer the files are shown in fslview no.
fslinfo T1_STRUCT.nii.gz (T1 used for recon-all)data_type FLOAT32dim1
212dim2 320dim3 320dim4 1datatype
16pixdim1
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.
Tel: 314-747-6173
St. Louis, MO 63110
Email:
Yes, they need to be the same dimensions to overlay in FSLview.
Run 'mri_convert' on orig.mgz, and you should be able to underlay the orig.
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Hello all,
Is there a way to read ?h.smoothwm.nofix using freesurfer_fread3() command in
matlab? The question that I want to ask really is ?h.smoothwm.nofix should
essentially have the same file format as ?h.pial (but I may be wrong) because
?h.*.pial.asc and ?h.*.nofix.asc both have vertices
Hi Virendra
I think you can use read_surf.m for any of the binary (not named *.asc)
surfaces.
cheers
Bruce
On Tue, 29 Apr 2014, Virendra Mishra wrote:
Hello all,
Is there a way to read ?h.smoothwm.nofix using freesurfer_fread3() command
in matlab? The question that I want to ask
Hello Bruce,
Thank you for the quick reply. Essentially, I want to use
find_corresponding_center_FSformat matlab command with ?h.smoothwm.nofix
surface file which I believe calls freesurfer_fread3() file and throws an error
Unknown magic number in surface file ?h.smoothwm.nofix. How do I get
Hi again!
I tried read_surf() with ?h.smoothwm.nofix surface file and it throws an
error..essentially still to do with magic number. Any help is greatly
appreciated.
Thank you.
Sincerely,
Virendra.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
Yes, the S/I/A/P labels are all correct. (Can never tell with R/L).
So, FSLview is reading the orientation info correctly. Orientation, as coded in the NIFTI, is a completely separate issue from how a given viewing tool chooses to display the data. You may not like the manner in which
-- Forwarded message --
Hello Doug et al.,
I was wondering if anyone could give me some information about whether a p
value can be associated with t maps generated in individual subjects
(across one or two runs) for fMRI data. When doing group contrasts an
uncorrected p value can
Is this the same question posted yesterday on martinos-tech? I answered
it as below
Yes, those are in the sig.nii.gz file (these are -log10(p)). The DOF is
related to the number of TRs
doug
On 04/29/2014 04:49 PM, jaco...@nmr.mgh.harvard.edu wrote:
-- Forwarded message --
Thank you very much Michael.
Now I'm running probtrackx, I will update you.
Stefano
Messaggio originale
Da: mha...@wustl.edu
Data: 29-apr-2014 22.25
A: std...@virgilio.itstd...@virgilio.it,
freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu, Harms,
Thank you, much appreciated!
Is this the same question posted yesterday on martinos-tech? I answered
it as below
Yes, those are in the sig.nii.gz file (these are -log10(p)). The DOF is
related to the number of TRs
doug
On 04/29/2014 04:49 PM, jaco...@nmr.mgh.harvard.edu wrote:
Other than orientation, (which could be deduced from visual inspection of
fiducial markers or other) are there any other concerns with this approach?Paul
On Tue, 29 Apr 2014 09:04:00 -0700 Douglas N Greve
lt;gr...@nmr.mgh.harvard.edugt; wrote
I don't know that it would be
No, once you've got the orientation correct, then it should be fine
On 04/29/2014 08:03 PM, prasser wrote:
Other than orientation, (which could be deduced from visual inspection
of fiducial markers or other) are there any other concerns with this
approach?
Paul
On Tue, 29 Apr 2014
Hi Virendra
Is that our function? I haven't heard of it. Have you tris read_surf?
Bruce
On Apr 29, 2014, at 4:16 PM, Virendra Mishra
virendra.mis...@utsouthwestern.edu wrote:
Hello Bruce,
Thank you for the quick reply. Essentially, I want to use
find_corresponding_center_FSformat
Hi Bruce,
I tried read_surf. There is a line in read_surf.m magic =
freesurfer_fread3(name of the surface_file) The number returned into magic
does not match any of the predefined numbers for quad or tri type of file and
hence it throws an error for vertices because vertices get assigned
40 matches
Mail list logo
