Hi Cassie,
It seems to be a problem with mri_robust_register, when trying to allíen the t1
and t2 scans.
Martin, any ideas?
Sent from my phone, please excuse brevity and typos
From: freesurfer-boun...@nmr.mgh.harvard.edu
Dear Bruce and Douglas,
Thank you for your suggestions. I am trying it and will need your
suggestions on result.
Thank you
Ramesh
On Fri, Jan 19, 2018 at 2:08 AM, Douglas Greve
wrote:
> you can use gcatrain (and jkgcatrain for testing) if you are using v6
>
> On
Hello Doug,
Thanks for responding. I am running a whole brain analysis as result shouldn’t
I build my own MC simulation?
Best,
Paul
Sent from my iPhone
> On Jan 18, 2018, at 5:23 PM, Douglas Greve wrote:
>
> Why are you doing your own MC simulation? You can just
Hi all,
I've been trying to run the hippocampal subfield segmentation with T1 and
T2 images, and haven't had much luck. I had previously run recon-all on all
my scans in v5.3, but testing on one subject I re-ran recon-all with the
additional T2 scan, and that seems to have run fine. However, when
Why are you doing your own MC simulation? You can just use the tables
that we distribute ...
On 1/17/18 6:12 PM, miracle ozzoude wrote:
Hello Experts,
I am running a paired t-test cortical thickness analysis based on the
instruction on the wiki page
It is a little tricky because you don't want to use different masks for
different subjects. I recommend using CVS where I've created a
subcoritcal mask in 2mm space (mri.2mm). So the idea would be that you
map your subcortical MG map to CVS space, then smooth it (mri_fwhm)
specifying the
Dear Dr Greve,
Thank you so much for the quick response.
Just to confirm that I understood the procedure correctly. The analysis is
volume based (i.e. voxel-wise) for the subcortical structures using mask
created by freesurfer's "mri_binarize" for these regions.
Correct?
Original
Is the problem that the surfreg command is failing or that you don't
know how to apply LME?
On 1/17/18 9:55 AM, lanbo Wang wrote:
Hi Martin,
I didn't try to run recon-all, I try to run flipped.
The code I used is:
foreach subject (subj_27_2.long.s27_base)
foreach? surfreg --s $subject --t
It is volume-based for subcortical
On 1/12/18 8:17 AM, John Anderson wrote:
Dear Dr Greeve,
I interestingly read the manuscript "Different partial volume
correction methods lead to different conclusions: An (18)F-FDG-PET
study of aging" Thank you for publishing this data.
I understood from
No, sorry. You have to use mri_vol2vol. Should be pretty simple
On 1/18/18 4:34 PM, John Anderson wrote:
Dear FS developers,
Are there any versions of "mri_coreg" that allows to output the
registered images. I mean flag "--out or -o" similar to spmregister?
Thanks for any guidance
John
Dear FS developers,
Are there any versions of "mri_coreg" that allows to output the registered
images. I mean flag "--out or -o" similar to spmregister?
Thanks for any guidance
John___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
Dear Dr Greeve,
I interestingly read the manuscript "Different partial volume correction
methods lead to different conclusions: An (18)F-FDG-PET study of aging" Thank
you for publishing this data.
I understood from this paper that he recommended stream for PVC is to correct
the PET images
I don't think so, sorry
On 1/18/18 8:58 AM, Carme Uribe Codesal wrote:
Dear all FreeSurfer users,
I was wondering if I can extract any parameter of movement from the
recon-all processing using FreeSurfer 5.1.
Thanks in advance!
Kind regards,
Carme
Why don't you just create a fake directory structure. Should be pretty
easy to script (if you know how to script:)
On 1/15/18 3:44 AM, Stephanos Leandrou wrote:
Dear Freesurfer Developers,
I want to use the asegstats2table and aparcstats2table for my
research. First of all, my subjects
you can use gcatrain (and jkgcatrain for testing) if you are using v6
On 1/12/18 3:27 PM, Bruce Fischl wrote:
Hi Ramesh
if you have segmentations in our aseg format (or edited asegs for that
matter if you find them not accurate enough), you should be able to
use mri_ca_train to genenerate a
That is fine
On 1/12/18 2:26 PM, Ashley Cole wrote:
Dear FreeSurfer Experts,
I have a question about jittering the fixation point and how
Freesurfer handles it.
Is it ok to have different rest times in the paradigm file for FS-FAST
pipeline? In the paradigm file, I am giving it an actual
I don't think we have anything. You can do it in matlab, eg
aseg = MRIread('aseg.mgz');
vol = MRIread('vol.nii.gz');
ind = find(aseg.vol==17); % left hippo
median(vol.vol(ind))
On 1/12/18 10:42 AM, Helen Beaumont wrote:
> I can use mri_segstats to get mean and std dev for values within a
>
Use aparc+aseg.mgz
On 1/12/18 5:14 AM, Vidhu Agrawal wrote:
Does freesurfer segments frontal cortex?
If yes the how we can do that
I have tried to do it by using the command :mri_binarize --i aseg.mgz
--o ctx-lh-s_frontal_superior.nii --match 1156
mri_binarize --i aseg.mgz --o
Hi Ahmad, you can use mris_left_right_register to register the left and
right hemis, then mris_apply_reg to map the left annot to the right (or
other way around).
ps. please remember to post to the FS list. Thanks!
On 1/17/18 9:13 AM, Ahmad Mheich wrote:
/Hello, /
//
/Is it possible to
I've uploaded the data. Just want to confirm you received it.
Thanks,
Carissa
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Saturday, January 13, 2018 3:49 PM
To: Freesurfer support list
I see. Thank you very much!
Cheers,
Ruy
> On Jan 18, 2018, at 1:24 PM, Bruce Fischl wrote:
>
> Hi Ruy
>
> they both register to a .gca atlas that is quite a bit more accurate than
> the MNI. The details are in the 2002 and 2004 papers.
>
> cheers
> Bruce
> On Thu,
Hi Ruy
they both register to a .gca atlas that is quite a bit more accurate than
the MNI. The details are in the 2002 and 2004 papers.
cheers
Bruce
On Thu, 18 Jan 2018,
Ricardo Valle wrote:
> Dear Freesurfer community,
>
> I would like to get a better sense of how mri_em_register and
Hi Andrew
Thank you for your response. I gave it a go and still no luck, unless I am
missing something completely obvious here
trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp
surfer.nmr.mgh.harvard.edu
Connected to surfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center
Dear Freesurfer community,
I would like to get a better sense of how mri_em_register and mri_ca_register
work. I understand the former is a linear registration and the latter is
nonlinear, and that they are both meant to register an individual to a template
space (MNI152?).
Would it be
Hi Mohamed
if you tar, gzip and ftp this subject to our ftp site we will take a look
cheers
Bruce
On
Thu, 18 Jan 2018, m.ba...@uliege.be wrote:
Dear Bruce,
Attached is the screen shot of the results of the segmentation of the
perirhinal Roi with Freesurfer V6. Unfortunately, as with V5 the
Dear all FreeSurfer users,
I was wondering if I can extract any parameter of movement from the
recon-all processing using FreeSurfer 5.1.
Thanks in advance!
Kind regards,
Carme
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
Hello:
I run the command to open freeview -v…(the installation guide example in Bert)
and I get the error in I point out in the subject of this email. Thanks for the
help in advance!
Sincerely,
Rene Andrade.
___
Freesurfer mailing list
Dear experts,
I run FreeSurfer 6.0 longitudinal pipeline on a set of scans acquired with
identical protocol (ADNI) but 2 different Philips 3T scanners (all time 1 with
Achieva, all time 2 with Ingenia). Unfortunately ~ 50% of the within-subjects
templates completely failed. Is there anything
Hi Andrew,
My test in December with last version of make_average_surface worked correctly.
However, now I am trying to make another average subject and medial_wall.label
is not created. I am using the last patch as last time. It is unusual because
last time label folder was correctly created.
29 matches
Mail list logo