yes!
On Wed, 15 Jun 2016, kojima_masaki_m...@yahoo.co.jp wrote:
Hi Bruce
Thank you for useful advice.
I referred to FreesurfuerWiki and tried to use tkmedit to check whether
recon is accurate or not.
Now I am trying to use freeview.
Is it possible to do these procedure with freeview instead of
Hi Bruce
Thank you for useful advice.
I referred to FreesurfuerWiki and tried to use tkmedit to check whether recon
is accurate or not.
Now I am trying to use freeview.
Is it possible to do these procedure with freeview instead of tkmedit?
Regards,
Kojima
- Original Message -
>From: B
Hi there
is there a way to convert .mesh (BrainVisa) to the Freesurfer surface
format? mri_convert doesn't seem to do it.
best wishes
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
___
Freesurfer mailing li
Hi William,
either way is fine, as long as you don't mix results from cross and long
processing in your analysis. Since all images need to go through the
cross sectional stream anyway, I think actually (2) will be less
processing (and potentially less QC and editing).
Best, Martin
On 06/10/2
Hello Hari,
In order to use mri_coreg on Mac, you will need to download the
"Development Version" of freesurfer. See the following page under
Development Version:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
Once downloaded, uncompress the .tar.gz file to some directory on your
machi
When you run that command, are you in a folder where you have write
permission?
On 6/8/16 10:05 AM, Hao wen wrote:
tkregister2 --mov template.nii --s fbirn-anat-101.v4 \
--regheader --reg myregister.dat --surf
ok, here it is
On 6/8/16 9:51 AM, Yu Sun Chung wrote:
Hi, all,
While working on gyrification data using Freesurfer, I have a question
to confirm one of output files.
First, I did run mri_glmfit using age x IQ itneraction. fsgd file in
which I included intracranial volume and gender to covary out. then, I
When passed to mris_preproc, the fsgd file is only to specify the
subjects. Using the fsgd file for both mris_preproc and mri_glmfit
assure that the order of the subjects is the same
On 6/14/16 6:10 AM, Hao wen wrote:
Hello:
To make it more clear!
I thought from FSGD file in mris_preproc,
remove the 1st column and it will be ok
On 6/14/16 6:24 AM, Hao wen wrote:
It turned out this is not possible, I got this error:
ERROR: matrix is ill-conditioned or badly scaled, condno = 1.34551e+07
here is my design matrix:
1 AD CN age male female
1.000 0.0
Hello Christopher,
Perhaps you could upload a data set for which mri_convert is segfaulting
so that we can take a closer look?
http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
-Zeke
On 06/13/2016 02:19 PM, Christopher Finuf wrote:
> I'm trying to convert the dicom to the original 00
Go to the indicated by the link, fill out the form, and license key will
be emailed to you.
-Zeke
On 06/13/2016 06:56 PM, shi yao wang wrote:
> Dear Experts:
> I set up FS development version.
> And now it shows error message:
>
> -
Hi Ruopeng,
I am very sorry since I think you would like to figure out why freeview did
not take my DICOM's, but due to privacy issues I have deleted the DICOM's
after the recon -all (on the niftis) was completed without any errors.
Basically when I selected the files, nothing happened, while when
Would it be possible to send us a file?
Best,
Ruopeng
> On Jun 14, 2016, at 8:52 AM, Marja Caverlé wrote:
>
> Hi Bruce,
>
> I did not get any error message, the page just remained empty after selecting
> the files. Maybe my files were the reason why it didn't work.
>
> Best,
>
> Marja
>
>
Hi Bruce,
I did not get any error message, the page just remained empty after
selecting the files. Maybe my files were the reason why it didn't work.
Best,
Marja
On Tue, Jun 14, 2016 at 10:50 PM, Bruce Fischl
wrote:
> freeview works fine with most dicoms. Do you get an error message?
>
> On T
Hi Kojima
tkmedit has been deprecated. Can you try using freeview instead?
cheers
Bruce
On Tue, 14
Jun 2016, kojima_masaki_m...@yahoo.co.jp wrote:
Hi.
I have this error, when I was doing tkmedit
PSY1001fs/Users/MRI/Desktop/fsurfer_test_kojima/Surf_data_main/PSY1001fs/mri/brainma
sk.mgz -a
freeview works fine with most dicoms. Do you get an error message?
On Tue,
14 Jun 2016, Marja Caverlé wrote:
Hi Bruce,
When I wanted to view them in freeview, simply nothing happened. Freeview
did not load the files, so I assumed it did not work with dicoms, that's why
I converted them.
Best
It turned out this is not possible, I got this error:
ERROR: matrix is ill-conditioned or badly scaled, condno = 1.34551e+07
here is my design matrix:
1 AD CN age male female
1.000 0.000 1.000 74.300 0.000 1.000;
1.000 0.000 1.000 73.700 0.00
Dear FS experts,
Could you explained me how to interpret results from the QA tools. Please
find attached the recon_checker summary log.
1) How to know there is a problem according to results below:
*checking subcortical label: Left-Cerebral-Exterior, 0 +/-*
*checking subcortical label: Left-Cere
Hello:
To make it more clear!
I thought from FSGD file in mris_preproc, it will regard the group and gender
as class, so in the X.dat will be gender*group; will not be possible to have
the seperate columns for gender and group? do I understand it correctly?
Or the FSGD file used in mris-prepr
Dear FS experts,
I tried to run the QA Tools on a subject with the following command:
*${QA_TOOLS}/recon_checker -s 207043_M0_2010-10-07 -outputFOF
${SUBJECTS_DIR}/FOF -gen-outputFOF -gen-asegLUT
${SUBJECTS_DIR}/AsegOutliers*
But I got all errors concerning the detection of Aseg outliers:
*Making
Thank you for quick reply.
I finished preprocessing and tried to check imagies, but tkmedit does not work.
Please let me know how to do.
Kojima
- Original Message -
>From: "kojima_masaki_m...@yahoo.co.jp"
>To: "freesurfer@nmr.mgh.harvard.edu"
>Date: 2016/6/14, Tue 17:53
>Subject: [Fr
Hi.
I have this error, when I was doing tkmedit PSY1001fs
/Users/MRI/Desktop/fsurfer_test_kojima/Surf_data_main/PSY1001fs/mri/brainmask.mgz
-aux
/Users/MRI/Desktop/fsurfer_test_kojima/Surf_data_main/PSY1001fs/mri/wm.mgz
-surfs
ERROR:
Assertion failed: (!c->out.queue_len), function write_vec,
Yes, actually, I just want to know what does that mean when we use *, for
example Gender*Group, does this mean group and gender has a interaction? So
what i want to know, if we can create design matrix like this:
X = 1 + age + gender + group,
I dont want the interact between group and gender
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