Hello Peter,
I understand your dilemma, its unfortunate the updated version of perl
causes the MNI tools to fail. If you MUST use freesurfer 5.3 on an Ubuntu
16 machine there is only one way that I can think of to make it work:
You need to install perlbrew and use that to install perl version 5.
Hi Aung
that means that the input type is "rgb". Are you sure it is a T1-weighted
MRI and not something derived from a diffusion scan (which is the typical
use of RGB data)?
cheers
Bruce
On Tue, 29 Nov 2016, Htet, Aung Thu wrote:
Hi Everybody,
I am trying to use an nii file in recon-all
Hi Everybody,
I am trying to use an nii file in recon-all, where subject_dir does not exist
yet.
recon-all -subject -i -all
But I am having this error:
niiRead(): unsupported datatype 128 (with scl_slope != 0) in
/home/fsuser/aung/18991230_00s001a000A.nii
Any help in understan
Awesome. Thank you very much Bruce.
Sent from my BlackBerry 10 smartphone.
Original Message
From: Bruce Fischl
Sent: Monday, November 28, 2016 5:14 PM
To: Freesurfer support list
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all -autorecon2 error.
-rl is for "reslice like"
No idea, I did not program it:). I've put the help file here. Hopefully
that is up-to-date
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_pmake.help.xml
On 11/28/2016 06:50 PM, Garikoitz Lerma-Usabiaga wrote:
> Thanks Doug!
> I am using the following command, which is working in the old v
Thanks Doug!
I am using the following command, which is working in the old version:
mris_pmake --subject fsaverage --hemi lh --surface0 smoothwm --curv0 sulc
--curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs
startVertex:46986,endVertex:162197
In the new version it gives errors sayi
I was able to figure out my design matrix issue. I had not originally
appreciated that there were no data sets from a particular class.
Thanks!
-Tim
FreeSurfer experts,
I am attempting to use the two stage model for longitudinal analysis,
however I keep receiving an error message that my d
here's a linux version
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_pmake
On 11/28/2016 05:22 PM, Garikoitz Lerma-Usabiaga wrote:
> Hi,
> I am using the 2011 of mris_pmake and I've seen in the list that there
> are newer versions.
> I am using both linux and mac.
> It's giving severa
Hi,
I am using the 2011 of mris_pmake and I've seen in the list that there are
newer versions.
I am using both linux and mac.
It's giving several errors when computing distances in fsaverage (just in
some of the pairs), so I hope that the new version will be able to solve
them.
Thank you very much
-rl is for "reslice like" and you include it in the mri_convert command
line with orig.mgz as the template volume. Run mri_convert --help and it
should be clear
Bruce
On Mon, 28
Nov 2016, miracoo...@gmail.com wrote:
Thanks a lot Bruce. What do you mean by -rl and how do I incorporate it t
Thanks a lot Bruce. What do you mean by -rl and how do I incorporate it to
mri_convert?
Best,
Paul
Sent from my BlackBerry 10 smartphone.
Original Message
From: Bruce Fischl
Sent: Monday, November 28, 2016 4:57 PM
To: Freesurfer support list
Reply To: Freesurfer support list
Subject: Re: [
I think this is your problem - the brainmask is not in the same voxel
coords as the other volumes. YOu probably need to -rl orig.mgz in your
conversion, then make sure that the volumes look aligned in freeview (and
that mri_info gives the same ras2vox and such for them)
On Mon, 28 Nov 2016,
mir
Oh. Thanks bruce.* For mri_info for my orig.mgz is*
Volume information for orig.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.00, 1.00, 1.00
type: UCHAR (0)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystar
Hi Paul
if you run mri_info on the orig.mgz and your new brainmask.mgz they
should give you the same thing in terms of ras2vox and such
cheers
Bruce
On Mon, 28 Nov
2016, miracle ozzoude wrote:
This was the info from mri_convert when i converted my skull stripped volume
to mgz
before repla
This was the info from mri_convert when i converted my skull stripped
volume to mgz before replacing it with the brainmask from FS
mri_convert --in_type analyze --in_orientation LAS --out_type mgz
--out_orientation LAS brainmask.img brainmask.mgz
cp foldername/subjid/brainmask.mgz foldername/subjd
Hi Doug,
This is my main objective.
1. PET in Group 1 vs Group 2
2. Thickness in the same sample, Group 1 vs Group 2
3. ASL in the same sample of Group 1 vs Group 2
4. Create a binary mask of the overlapping corrected sig voxels from 1-3.
5. This mask is therefore a site of co-localised atrophy,
On 11/28/2016 03:45 PM, Elijah Mak wrote:
> Dear Doug,
>
> Thanks.
>
> Do you mean use ROI averages as the samples and then test across
> ROIs?
>
> This would be unusual as the interpretation is problematic. I would
>
> probably compute a single number per subject that is a weight
Yes, it was arbitrary. A linear trajectory was a sufficiently good model for
the mean response over time for most of the cortex points in my analyses. Also
if you only have at most three time points per user then you can only have at
most two random effects in your mixed-model (intercept and tim
I mean after you have converted it
On Mon, 28 Nov 2016, miracle ozzoude
wrote:
Thanks Bruce for the response. mri_info? do you mean when i converted it from
analyze to
mgz or when I ran recon-all autorecon2 after inserting it to freesurfer.
On Mon, Nov 28, 2016 at 3:09 PM, Bruce Fischl
wr
Dear Doug,
Thanks.
Do you mean use ROI averages as the samples and then test across ROIs?
This would be unusual as the interpretation is problematic. I would
probably compute a single number per subject that is a weighted
sum/difference of the ROI values, then test whether this one number is
d
It is ok to use the PET analysis stream from v6 with anatomical analysis
from v5.3. Assuming the PET stream itself does not change after the beta
release, you should be ok.
On 11/24/2016 02:38 AM, Lee Subin Kristine wrote:
>
> Hi Freesurfer team,
>
>
> I have currently used version 5.3. for al
Thanks Bruce for the response. mri_info? do you mean when i converted it
from analyze to mgz or when I ran recon-all autorecon2 after inserting it
to freesurfer.
On Mon, Nov 28, 2016 at 3:09 PM, Bruce Fischl
wrote:
> what is the output of mri_info on your new brainmask.mgz and on say the
> orig.
Try using the data in the csdbase.y.ocn.dat file rather than
transferring the clusters back into the individual space. What are you
using to do the ROI-based analysis? You have to make sure that the
design matrix and contrasts are exactly the same. You can do this in
matlab with FS commmands, e
But before you do, you should note that you cannot use fMRI data as
input to FS.
On 11/24/2016 01:11 PM, Bruce Fischl wrote:
> Hi James
>
> you need to send us the full command line that you ran and the entire
> screen output.
>
> cheers
> Bruce
> On Wed, 23 Nov 2016, James Wilks wrote:
>
>> He
Hi Marine, these are two different analyses. In the first analysis, you
have used a voxel-wise analysis, and in the second you've done an ROI
analysis. They are not guaranteed to give the same results. Also, it is
possible that the actual GLM design matrices are different. QDEC will
create a fi
what is the output of mri_info on your new brainmask.mgz and on say the
orig.mgz? You may need to conform you brainmask
On Mon, 28 Nov 2016, miracle ozzoude wrote:
Hello Freesurfer, I ran recon-all -autorecon 1 -s subjID on T1 (T1_nii) image
and after
that, I replaced the skull stripped volu
On 11/21/2016 08:59 PM, Elijah Mak wrote:
> Apologies, please ignore the other email response. I believe this
> should be tagged to the right thread (hopefully!)
> -
>
>
> Many thanks for the information, Doug! I will give it a go.
>
> Actually, I would like to carry out the following analys
On 11/26/2016 09:31 PM, Elijah Mak wrote:
> Hi there,
>
> What is the correct way to plot, at each vertex, the Cohen's /D/ after
> a /mri_glmfit/ comparison? I've seen a few variations posted on the
> mailing list.
>
> Is gamma.mgh / rstd.mgh is the correct formula?
Yes
> Does rstd.mgh represen
Dear Bruce,
thanks a lot for your answer. I am still a bit confused. I followed your
suggestion to use msris_curvature to compute the curvature on the white surface
(unsmoothed) instead of on smoothwm:
mris_curvature -w -a 10 $subj/surf/lh.white
mris_preproc -s $subj --target fsaverage --hemi l
Hi Jordi
You have implicitlyincluded the reference group in your statistical model by
includingan intercept term and a time variable:
group0 intercept: ß1group0 time: ß2group1 intercept:ß1+ß3group1 time:
ß2+ß4group2 intercept:ß1+ß5group2 time: ß2+ß6
>From here you canquickly see that your prop
Hi Doug,
I have one additional question regarding surface based analyses:
Let's say that we have two types of brain lesions:
1. The first one is located in the cortical parcellates ( the labels in freesurfer atlas (wmparc.mgz) are named ctx-lh-? and ctx-rh-?).
2. The second lesion is located in
One postdoctoral position is available within the Laboratory of Psychiatric
Neuroimaging (LIM21) (www.neuroimagem.org.br/) at the University of São
Paulo Medical School, Brazil, directed by Geraldo F. Busatto, Ph.D.
Candidates should send a message to neuroimagem@hc.fm.usp.br with
his/her CV
Hello,
I made an analysis thanks to the QDEC tool :
I tested a correlation between an inhibition score and cortical thickness,
corrected for age
(continuous = inhibition score ; nuisance = age ; smoothing = 25 and FDR
corrected)
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