Dear FS Experts,
I have one group to compare the difference between their preoperative and
postoperative after one month. I followed
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial to
process data. I run these command in number 2.* Longitudinal Image
Processing*：
1. recon
Hi Bronwyn,
to shorten equations, lets set t = years_form_baseline
a = age
g = group
s = sex
so your model is
Y_ij = b0 + b1 t_ij + b2 a_i + b3 g_i + b4 s_i + b5 t_ij a_i + b6 t_ij g_i + b7
a_i g_i + b8 t_ij a_i g_i
(as a fist step, I would consider simplifying it, by dropping the age
interact
Hi, I am using Freesurfer to estimate cortical thickness.
Is there any way to get all the details of the thickness distribution?
I used mri_segstats but it only provided mean and standard deviation.
Thank you.
___
Freesurfer mailing list
Freesurfer@nmr.m
not sure exactly what you mean, but you can use read_curv.m to load the
entire spatial map of thickness into matlab for each subject. If you tell
us what you want to do we can give you more detailed advice
cheers
Bruce
On Tue, 7 Mar
2017, Chih-Yang Hsu wrote:
> Hi, I am using Freesurfer to est
Dear Dr. Fischl,
Thank you for the fast response.
We would like to obtain the entire distribution of the cortical thickness
so we can calculate more statistical, such as the first and third quartile.
I tried read_cuv.m and it works perfect.
Thank you again.
Best regards,
Chih-Yang Hsu
On Tue,
Perfect! Thanks so much Douglas! Any idea how long that will take?
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Thursday, March 02, 2017 11:20 AM
To: freesurfer@nmr.mgh.harvard.edu
Subj
There are no more moments you can get from it. You're best bet is to
load the thickness (read_curv.m) and aparc (read_annotation) maps into
matlab and then do what you want with them.
On 3/7/17 9:14 AM, Chih-Yang Hsu wrote:
Hi, I am using Freesurfer to estimate cortical thickness.
Is there an
Not sure, but probably on the order of 30min/subject
On 3/7/17 10:27 AM, West, John D. wrote:
> Perfect! Thanks so much Douglas! Any idea how long that will take?
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On
Dear Dr. Greve,
Thank you for the response.
I will definitely try those.
Best regards,
Chih-Yang Hsu
On Tue, Mar 7, 2017 at 9:34 AM, Douglas Greve
wrote:
> There are no more moments you can get from it. You're best bet is to load
> the thickness (read_curv.m) and aparc (read_annotation) maps
answers below
On 3/7/17 7:54 AM, 刘丽 wrote:
Dear FS Experts,
I have one group to compare the difference between their preoperative
and postoperative after one month. I followed
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial
to process data. I run these command in n
sorry for the delayed response. it makes sense *if* the ?h.orig.nofix
surface contains those voxels
cheers
Bruce
On Tue, 28 Feb 2017, Melanie Ganz wrote:
> Hi Doug,
>
> the orig looks fine and we cannot see a file orig.nofix in the subject dirs.
> We still use v5.3.
>
> But what we tried now
Hello all,
Again, I tried to modify the white matter surface by adding voxels to
the wm.mgz file, and performed the reconstruction by doing the
following.
-Opened brainmask.mgz for reference
-Opened wm.mgz on top of that
-Click the voxel edit button
-Check the recon editing checkbox
-Fill in voxe
You can try this one
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_convert.v53
On 03/06/2017 06:51 PM, Dhaval Shah wrote:
> Could i get a solution for the earlier version than 6.0? I can't use
> the new one unfortunately.
>
> On Mon, Mar 6, 2017 at 4:19 PM, Douglas N Greve
> mailto:gr.
Hi Antonin,
Thanks a lot for your reply.
Somehow, in the link you sent, I could not find any response to your email.
But I can see your email to Anderson and command line parameters.
As I am not an expert in using FreeSurfer, so would it be possible for you
to share detailed step-by-step guide a
Dear Eli,
did you read my response to your previous thread?
I recommended you to try adding control points to the white matter.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51959.html
Regards,
Antonin
Hello all,
Again, I tried to modify the white matter surface by adding vox
Hi Antonin,
As you suggested in discussion forum, I tried to run following command
after mri_glmfit:
palm -s fsaverage/surf/lh.white -n 1 -m mask.mgh -Cstat extent -C
1.974975 -pmethodp none -pmethodr none -twotail -d Design_MEQ.txt -t
Contrast_MEQ.txt
Running PALM alpha104 using MATLAB 9.0.
Hi experts,
I try to convert my volumetric nifti file to surface files.
My nifti volumetric file looks like : 1. screenshot
I have first registered the volumetric file using bbregister with this
command line :
*bbregister --s fsaverage --mov segment_7.nii --reg segment_7.dat --t1
--init-coreg*
t
Hi FreeSurfer,
I have analyzed my diffusion data using Tracula and combined the voxelwise
diffusion measures across all subjects in one file (following the guidelines
online).
In this text file, I saw that on some of these voxels some people have NAs, so
their tract is most likely shorter there
Hi Andrew
wow, that's pretty strange. The only thing I can think of that might
recover this is to put pairs of control points in the white matter, one
on either side of the boundary of your artifact. Or maybe it always affects
the same slices and you can scale them up? I guess it depends on h
Dear Martin,
input -i input file is
lh.MEQ_LGI.10.mgh file in your glmdir directory (for left hemisphere).
As you could read in following messages in the referenced thread in FSL
discussion forum, cluster-forming threshold need to be specified in z, not in t.
Therefore, you would have to sele
Hi Antonin,
Thank you so much for this detailed explanation, that's really useful.
Following your instructions, I ran:
palm -i lh.MEQ_LGI.10.mgh -s fsaverage/surf/lh.white.avg.area.mgh -d
check.csv -t Contrast_MEQ.csv -n 5000 -m lh.MEQ_LGI.glmdir/mask.mgh -o
myresults -Cstat extent -C 3.719016
Dear Martin,
after -s option, there have to be 2 arguments, as I specified in my previous
mail:
-s fsaverage/surf/lh.white fsaverage/surf/lh.white.avg.area.mgh
And beware that -C has to have negative sign, if your hypothesis is one-tailed
negative.
Antonin
Hi Antonin,
Thank you so much for
Dear Freesurfer Experts,
I was running qdec, and encountered an error while I was running the analyze
button on the qdec. Subsequently, if you can help with the following error
would greatly appreciate it.
Continuous Variable Means (all subjects)
0 Intracranial_volume 1.53095e+06 157812
1 Gend
The error message says that it cannot find a file. Does that file exist?
Do you have fsaverage in your $SUBJECTS_DIR?
On 03/07/2017 06:19 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote:
>
> Dear Freesurfer Experts,
>
> I was running qdec, and encountered an error while I was running the
> analyze
Hello Martin and Antonin,
I was following this conversation very closely to understand how to use
PALM in FreeSurfer.
Can any of you please confirm in case I am interested in checking
correlation between gyrification index (LGI) and behavioral measure using
two tailed, p < 0.05:
Step 1: I used --
Dear Martin,
thinking of that further, my advice for negative cluster-forming threshold was
probably wrong in this context. Instead, I think that you can achieve negative
one-side hypothesis by specifying positive cluster-forming threshold and
inverting the sign of your contrast vector.
Antoni
Dear Sahil,
I suppose, for qcache 1.3 the equivalent cluster-forming threshold z-value is
two-tailed test:
qnorm(1-10^-1.3/2)=1.958949
for one-tailed test:
qnorm(1-10^-1.3)=1.643704
(qnorm is R function call for quantile function of normal distribution, you can
compute this by using other met
Hi Doug，
I am also interested in seed to seed resting state analysis.
It seems no fcseedcor command in Freesurfer v5.3.? Is it command in v6.0?
Thanks and best,
Jinsong
On Mon, Mar 6, 2017 at 10:13 AM, Douglas N Greve
wrote:
> Try fcseedcor. Run with -help to get docs
>
>
> On 03/06/201
yes, v6
On 3/7/17 8:18 PM, Jinsong Tang wrote:
Hi Doug，
I am also interested in seed to seed resting state analysis.
It seems no fcseedcor command in Freesurfer v5.3.? Is it command in v6.0?
Thanks and best,
Jinsong
On Mon, Mar 6, 2017 at 10:13 AM, Douglas N Greve
mailto:gr...@nmr.mg
In the volume
Thanks
Julie
On 3/03/2017 3:33 am, "Douglas N Greve" wrote:
>so are these on the surface or in the volume?
>
>
>On 03/01/2017 07:03 PM, Julie Hall wrote:
>> Hi Doug
>>
>> Thanks for your quick reply. It??s a resting state FC data driven
>> parcellation atlas (see
>> https://acad
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