Dear freeesurfer experts,
I am trying to calculate WMHs of MDD patient populations. I ran the T2FLAIR
separately after processing T1 with recon-all. Presently, I don't have any
dwi data where I can project the WMHs onto the WM tracts. Will you please
tell me how do I project the WMHs of 29 MDD pat
Dear FreeSurfer experts,
I am trying to analyze some single time points of my longitudinal data in QDEC.
I have 3 groups and created a file for the discrete factor "group" with three
levels (1,2 and 3). I have done the same for gender (with 2 levels). The
analysis with gender works just fine b
Hello Bruce,
Thanks for your reply. Brief history of my problem so far is that: as you
noticed before, my images have very low resolution and very less contrast.
My images slice thickness is also about 5mm, voxel size: 0.46x0.46x6.5;
dimension 512x512x20. I do run mri_convert to conform it to 1x1x
Hi Sampada
I don't think it is possible to get reasonable surfaces out of 5 or 6.5mm
slice data. You might get ok asegs.
sorry
Bruce
On Fri, 8 Apr 2016, Dr Sampada Sinha
wrote:
Hello Bruce,
Thanks for your reply. Brief history of my problem so far is that: as you
noticed before, my imag
hi zeke,
i’m following your instructions for getting freesurfer 5.3.0 installed on
debian, though i’m at 7.x as that is what came from ThinkMate on some recently
delivered supermicro machines for our lab.
i’m not successful, and have paused at an error.
1) libtool-bin does not exist for debi
Hi Clara,
I think the message is correct and Qdec can only do 2 levels. Qdec is
rather limited. You need to use mri_glmfit for that.
Best, Martin
On 04/08/2016 08:14 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I am trying to analyze some single time points of my longitudinal data in
>
That's what I feared. But ok, I'll try that.
Thank you!
- Ursprüngliche Mail -
Von: "mreuter"
An: "Freesurfer support list"
Gesendet: Freitag, 8. April 2016 14:55:42
Betreff: Re: [Freesurfer] REPOST: QDEC analysis
Hi Clara,
I think the message is correct and Qdec can only do 2 levels.
Thanks Bruce. Appreciate all your help.
Kind regards,
Sampada
On Friday, April 8, 2016, Bruce Fischl wrote:
> Hi Sampada
>
> I don't think it is possible to get reasonable surfaces out of 5 or 6.5mm
> slice data. You might get ok asegs.
>
> sorry
> Bruce
>
> On Fri, 8 Apr 2016, Dr Sampada Sinh
Dear FS expert and users,We are coming across errors on the WM and Gray
inflated surfaces.When trying to open the surfaces with tksurfer as follows
(tksurfer subid lh inflated -gray) We get only a small part of the cortex
displaying. Also when we try file-label-impor
sure. I wish I had a better answer for you
On Fri, 8 Apr 2016, Dr Sampada
Sinha wrote:
Thanks Bruce. Appreciate all your help.
Kind regards,
Sampada
On Friday, April 8, 2016, Bruce Fischl wrote:
Hi Sampada
I don't think it is possible to get reasonable surfaces out of 5
o
Can you check and see if they look ok with freeview? It might just be a display
problem
> On Apr 8, 2016, at 9:26 AM, pablo najt wrote:
>
> Dear FS expert and users,
> We are coming across errors on the WM and Gray inflated surfaces.
> When trying to open the surfaces with tksurfer as follows (
Dear FreeSurfer experts,
for the analysis in QDEC I created my own Monte Carlo correction.
My questions relate to the threshold option.
1. Would I use neg if I have mostly blue clusters in the QDEC display and pos
if I have mostly red clusters?
2. When do I use abs?
3. I compared the neg optio
2016-04-08 12:09 GMT-03:00 Gamaliel Huerta Urrea :
> Hello Freesurfers
>
> I'm trying to do volumetric reconstruction, i already have done this but.
> i wanted to see if for the same subject, with different directions of
> slices i have the same result, and obviously i had different results of
> v
Hi Gamaliel
many things will change when you change the slice direction - amount of
wrap, possibly your FOV, slab-selection profile if your protocol is
slab-selective, and some types of distortion. These will all change the
image which will change our results. Of course even if you don't chang
Thank you Bruce for the response.Actually the surface works in freeview just
fine. However my second issue about loading annotation continues.In freeview I
clicked on "Annotations" selected inside "label" folder BA1 and everything
Freezes.Terminal shows endless column of the text below. Could t
Hi Pablo
if it has the extension .label then it is a label not an annotation, and
you should load it as such
cheers
Bruce
On Fri, 8 Apr 2016, pablo najt wrote:
Thank you Bruce for the response.Actually the surface works in freeview just
fine. However my second issue about loading annotatio
Use this version of mri_glmfit. For t-tests is will automatically
compute a partial correlation coefficient (pcc.mgh)
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit
On 04/04/2016 12:12 PM, Morenikeji Adebayo wrote:
> Hello Freesurfers,
>
> I'm interested in creating a
Thank you.I confirm, Annotation works fine. However when trying to load label
and select .label file.I get the following message:
reading colortable from annotation file...
colortable with 76 entries read (originally
/autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Sim
label files don't store colortables, so it seems you are still loading
annotations. Make sure you are using label loading. You can also specify
them on the freeview command line with -l
On Fri, 8 Apr 2016, pablo najt
wrote:
Thank you.I confirm, Annotation works fine. However when trying to
Unfortunately, I only programmed it assuming that you would have only
one B0 map per session. There are a couple of work-arounds. One is to
create a different session for each run. This is probably easiest but
makes the group analysis a little trickier.
On 04/05/2016 04:48 PM, Shea, Conor wrote
I don't know what you mean, can you just send the header of the fsgd
file and the contrast matrix?
On 04/04/2016 11:20 AM, Afzal, Afsana wrote:
> Hi,
>
> I want to perform a linear regression for a task with 3 different risk
> conditions (low, medium, high) with the following linear trend: low =
Yes, if the contrast matrix is correct, then everything should be fine.
Also check the design matrix (but I'm pretty sure that will be correct).
On 04/05/2016 04:07 AM, tom parker wrote:
> Hi Freesurfers,
>
> I posted this question a few days ago but didn't get any replies.
> Would you mind answe
ps, you may want to smooth the wmh volumes, eg,
mri_fwhm --smooth-only --i all.wmh.mgh --fwhm 5 --o all.wmh.sm05.mgh
then use all.wmh.sm05.mgh as input to glmfit
On 04/08/2016 12:27 PM, Douglas N Greve wrote:
> You can binarize each WMH volume, ie,
> mri_binarize --i aseg.mgz --match 77 --o wmh.mg
You can binarize each WMH volume, ie,
mri_binarize --i aseg.mgz --match 77 --o wmh.mgz
Convert to mni305 space with
mri_convert wmh.mgz wmh.mni305.mgz --apply_transform
transforms/talairach.xfm -oc 0 0 0
View to check (only need to do for one subject):
tkmedit fsaverage orig.mgz -ov wmh.mni305.mg
can you show a pic? What were your matlab commands to read in and write
out the volume?
On 04/04/2016 07:36 AM, Francesca Strappini wrote:
> Dear Freesurfers,
>
> I run the preprocessing step of some functional data with
> preproc-sess, then the Fourier analysis with matlab. Now, I'm trying
> t
On 04/01/2016 04:44 PM, Jennifer Legault wrote:
> Hi Doug,
>
> Thanks for your quick response! When running the LME mass univariate
> analysis, I am assuming this also includes subcortical structures,
> correct?
Which processing are you doing? It should be obvious if you are doing
surface-bas
Can you send subjlist.csv? Do you get the same error if you run
ls -d PD* > subjlist.txt
and use that file instead?
On 04/03/2016 05:16 AM, Lars M. Rimol wrote:
>
>
> Hi,
>
> I'm trying to run asegstats2table
>
> asegstats2table --subjects subjlist.csv --skip --delimiter comma
> --common-segs --
On 04/07/2016 03:50 PM, Trisanna Sprung-Much wrote:
> thanks, Doug. I am still extremely confused, however. *Am I meant to
> run recon-all first? *I was told in a previous email that I should do
> this first, however, I thought that Freesurfer takes the volumes and
> does a linear registration
You can use mri_binarize with the --match option using the aseg.mgz or
aparc+aseg.mgz (the latter probably better but harder). You would
specify the indices for all the GM segments (or WM or CSF). You can also
try some of the predefined options, eg,
--ctx-wm : set match vals to 2, 41, 77, 25
Look at http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
if you want to compare all subjects, then you'll need to do this for all
subjects not just the ones you want to flip
On 03/28/2016 02:30 PM, Ajay Kurani wrote:
> Hello Freesurfer Experts,
>
>I processed all of my brains through freesurfer
Hi Doug,
I'm currently running the LME mass-univariate analysis (I've
previously conducted the LME univariate analyses with ROIs with little
to no problems) and, thanks to your help, have run my data through
this analysis and done the cluster-thresholding for the aparc data but
not the aseg data (
This is what I don't understand: "done the cluster-thresholding for the aparc
data"
The aparc data is an ROI and so you should not have (could not have)
done clusterwise thresholding (?)
On 04/08/2016 12:57 PM, Jennifer Legault wrote:
> Hi Doug,
>
> I'm currently running the LME mass-univariate
Apologies for likely using the wrong term. I meant to say that I've
done the cluster-thresholding for the surface data, using the
mri_surfcluster command with annot -aparc as an argument.
On Fri, Apr 8, 2016 at 1:03 PM, Douglas N Greve
wrote:
> This is what I don't understand: "done the cluster-
And now you want to do an ROI analysis or a map-based analysis of the
subcortical structures? We don't do the latter as that is a VBM analysis.
On 04/08/2016 01:07 PM, Jennifer Legault wrote:
> Apologies for likely using the wrong term. I meant to say that I've
> done the cluster-thresholding fo
thanks, Doug. I'll get started on running all brains using recon-all.
The MNI has several ICBM templates now:
ICBM152 linear
ICBM152 nonlinear symmetric VI
ICBM152 nonlinear 2009
Do you know which one mni152reg is using?
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuro
not sure, mni152reg uses $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz
You can always just run the following command directly
fslregister --mov icbm.nii.gz --s $subject --reg
$SUBJECTS_DIR/subject/transforms/icbm.reg.dat --dof 12
--lta $SUBJECTS_DIR/subject/transforms/icbm.reg.lta
This will use
I¹d add that SNR may also change if you don¹t acquire as much data axially
as you did sagittally. Really it¹s better to acquire your 3D
T1w/T2w/FLAIR scans sagittally as this is most efficient.
Peace,
Matt.
On 4/8/16, 10:23 AM, "Bruce Fischl"
wrote:
>Hi Gamaliel
>
>many things will change whe
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