Hi,
I have run recon-al longitudinal process on abel cluster with this command
recon-all -base @filename@_template -tp @filename@ -tp @filename@v2 -all
-debug. However, it crashed or is killed when it ran mri_ca_register.
I have looked through the log, and I have not found a reason for it being
The error would indicate that the number of elements in 'lh.area' and
'lh.area.pial' are not the same. You can check this also with mris_calc:
mris_calc lh.area stats
mris_calc lh.area.pial stats
which will provide some basic statistical output, including the size
(i.e. number of elements) of
Hi FreeSurfers,
I'm doing an analysis with two groups: patients and controls. When I look
at "Does the average thickness differ between 1 (patients) and 2
(controls)?", I can see blue (negative) and red (positive) correlations. I
know that it means that in some cases, the patients have a higher co
Hello,
I have a question about using mri_convert on diffusion *.dcm files.
When extracted, the gradient table is different than that given by
either MRIConvert (from the UCLA-LCNI webpage) or than dcm2nii of
MRICron; NB: the latter give the *same* results. The differences in
gradient are also not
Hello Freesurfer People,
Below is the error that I have been receiving after running a recon-all.
There seems to be a problem in the normalization stage.
I checked the orig.mgz and the transform.xfm, and both seem to be
reasonable.
I was hoping for some guidance/expert advice for how to precede fr
Well, I was using Freesurfer for some other things, and was thinking
that everything would be more consistent if using Freesurfer for all,
but perhaps yes, dcm2nii will be the way to go for this instead.
Thanks,
pt
On Thu, Sep 12, 2013 at 5:18 PM, Harms, Michael wrote:
>
> The gradient direction
Hi All,
I am trying to compare my VBM results from FSL with cortical thickness changes
using freesurfer.
I would like to perform permutation based FWER correction to see cortical
thickness changes. The reason to do FWER correction is I used randomise in FSL
with FWER correction so I want to ke
Hi Erica
if you upload this subject dir we will take a look
cheers
Bruce
On Thu, 12 Sep 2013,
Erica Tatham wrote:
Hello Freesurfer People,
Below is the error that I have been receiving after running a recon-all.
There seems to be a problem in the normalization stage.
I checked the orig.mgz an
The gradient directions, at least as reported in Siemen's DICOMs, are NOT
rotated into the imaging axes. Rather, they are reported in the
coordinate frame of the gradient system. So the conversion tool has to
account for this. Doug will have to comment as to whether mri_convert has
an option to
Hi all - I'm trying to design my first event related experiment, and I'm
having trouble figuring out how to best optimize the design...wondering if
you have any insights:
I have two conditions (milkshake and water).
Each condition has several events in order: Participants get a squirt of
milksha
Thanks.
These are the output[iMac-di-Stefano:Con28/SUBJECTS_DIR/surf] Stefano%
mris_calc lh.area stats Size
[ 126850 ] Min@(index)
[ -0.322716 (56402) ]
Hello,
Oddly it seems that 'nu_correct' is not in your PATH, which is supposed
to be set after you source the SetUpFreeSurfer.csh file. Can you please
provide me with the following information:
-Do you have the file $FREESURFER_HOME/mni/bin/nu_correct?
-Can you respond with the output of the te
Just my two cents:
I think the age should be mean-centered; otherwise, the meaning of the other
variables need to be interpreted as age = 0 (rather than mean age = 0).
In general, I believe in qdec or mri_glmfit, the effects of Class variable are
interpreted as 0 on the continuous/nuisance vari
When I run recon-all -base 1_template -tp 1_first -tp 1_secon -all
-debug. It crash during CA Reg Thu Sep 12 19:59:01 CEST 2013. I can send
the rest of the log.
Knut J
#--
#@# CA Reg Thu Sep 12 19:59:01 CEST 2013
/cluster/home/kjbjuland/freesurfer/long/NTN
Hmmm... I'm sorry, but I can't really help/comment on why your specific
run of recon-all resulted in those two files having different sizes.
On 9/12/13 16:00 , std...@virgilio.it wrote:
> OK. But, I have run a simple command (recon-all) for cortical
> parcellation.
> I have already used this c
Hello Freesurfer experts,
I am doing volumetrics study. During the scan we get 2-3 mprage per scan for a
subject.
While running the FreeSurfer, if I want to use the three mprages for that
subject as an input file, may I just keep the three mgz files (001.mgz, 002
.mgz and 003.mgz) in the
OK. But, I have run a simple command (recon-all) for cortical parcellation.
I have already used this command for other structural images.This is the image
features:data_type FLOAT32dim1 212dim2 320dim3
320dim4 1datatype 16pixdim10.80
you can refer to this post:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg31297.html
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
On 9/12/13 9:04 AM, "Anita van Loenhoud"
mailto:acvanloenh...@gmail.com>> wrote:
Hi F
Dear freesurfer
I am looking for old segmentation of Colin27 that you have replaced with
new version.
Is there anywhere that I can find archive of colin27 segmentations. I think
it might be segmented with freesurfer 3 or 4.
Because I have some labels from the old version. But I dont have the
segme
Dear freesurfers,
If I were to do it through a fsgd file, with one categorical and one
continuous factors, is the following format correct?
GroupDescriptorFile 1
Title title
Class level1
Class level2
Class level3
Variables Year
Input subjid1 level1 0
Input subjid2 level2 15
.
Thank you very
try running recon-all -make all
On Thu, 12 Sep 2013, Rudolph Pienaar wrote:
> Hmmm... I'm sorry, but I can't really help/comment on why your specific
> run of recon-all resulted in those two files having different sizes.
>
>
>
> On 9/12/13 16:00 , std...@virgilio.it wrote:
>> OK. But, I have run a
Hi Rashmi
putting them in the orig folder with those numbers will get recon-all to
do motion correction and averaging.
cheers
Bruce
On Thu, 12 Sep 2013, Rashmi Singh wrote:
Hello Freesurfer experts,
I am doing volumetrics study. During the scan we get 2-3 mprage per
scan for a subject.
Dear freesurfers,
One of my categorical factors have three levels, and I would like to
specify my own design matrix. What is a command line argument that I can
use?
Thank you very much!
Sincerely,
Ye
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harva
Just specify --X X.mtx on the mri_glmfit command line instead of using
--fsgd
doug
On 9/13/13 12:06 AM, ye tian wrote:
Dear freesurfers,
One of my categorical factors have three levels, and I would like to
specify my own design matrix. What is a command line argument that I
can use?
Thank
yes, that looks right
On 9/13/13 12:26 AM, ye tian wrote:
Dear freesurfers,
If I were to do it through a fsgd file, with one categorical and one
continuous factors, is the following format correct?
GroupDescriptorFile 1
Title title
Class level1
Class level2
Class level3
Variables Year
Input
Hi (and thanks for the speedy reply!),
There may be some obliquity (from 3dinfo of the created nifti file):
Data Axes Tilt: Oblique (1.770 deg. from plumb)
I guess if the data were oblique, shouldn't that tilt be included in
the gradients? Or am I missing something?
And assuming that that inf
The 4th handles any translation. The 3x3 handles rotation and any scale.
On 9/11/13 10:21 AM, Garikoitz Lerma-Usabiaga wrote:
Hi Doug,
just a very naive question about coordinate change: why do we need the
fourth component? I mean, shouldn't be the transformation matrix 3x3
instead of 4x4 fo
Dear Doug,
Thank you very much!
Sincerely,
Ye
On Thu, Sep 12, 2013 at 5:50 PM, Douglas Greve wrote:
> yes, that looks right
>
>
>
> On 9/13/13 12:26 AM, ye tian wrote:
>
> Dear freesurfers,
>
> If I were to do it through a fsgd file, with one categorical and one
> continuous factors, is the
Try
recon-all -make all
On Sep 12, 2013, at 4:00 PM, wrote:
> OK. But, I have run a simple command (recon-all) for cortical parcellation.
> I have already used this command for other structural images.
> This is the image features:
> data_type FLOAT32
> dim1 212
> dim2
Were these oblique acquisitions?
By default, dcm2nii and MRIConvert rotate the bvecs according to the
orientation info for oblique acquisitions, whereas it sounds like
mri_convert might not be doing that.
cheers,
-MH
--
Michael Harms, Ph.D.
--
The file 'lh.area' contains 126850 elements. The file 'lh.area.pial'
contains 126355 elements.
You cannot add them together since they have different sizes.
On 9/12/13 11:14 , std...@virgilio.it wrote:
> Thanks.
>
> These are the output
> [iMac-di-Stefano:Con28/SUBJECTS_DIR/surf] Stefano% mris_c
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