Doug
The .nii.gz file is completely empty and doesn't come up on any viewer
(fslview, tkmedit, freeview, mricron etc). The .gi files I've generated appear
to be tracking in probtrackx (though slowly on my laptop - probably not
expected given the sizes of the surfaces). I can also generate bina
Thanks Bruce for your answer, as you asked I'm forwarding this
question to the list in case any other can answer this.
We already have the surface generated by mri_preproc, now we are
trying to read it using the matlab function read_mgh. It returns a 4-D
matrix, how can we interpret this data to g
Dear all,
I've a question regarding computing correlations with cortical thicknesses
on the surface; Suppose I have two variables for each subject: (age and
weight) and I want to compute the correlation between cortical thickness
and weight, corrected for age.
Option 1:
Fsgd contains: Variables w
Hi folks!
I would like to use a different subject dirctory (setenv SUBJECTS_DIR ). Does freesurfer still finds the folders which are
located in the default subjects directory of the FS installation? Or are
they simply not needed for the recon-all process ? I refer to cvs_avg35
etc. not to the te
Today Microsoft approved iSurf BrainView version for Windows 8 Tablets and
computers. It's a free App.
http://apps.microsoft.com/windows/en-us/app/brainview/be2623f5-c5e3-4295-a28e-d3f64dc19266
BrainView is a Brain MRI tutor based on the MRI automatic segmentation
produced by FreeSurfer.
FreeSur
Dear Br:
Thanks for your help. I have downloaded Colin 27 subject, and the Surfrend
toolbox. But I still have some questions about the process.
1. You said I need transform the Colin 27 to the latest FS version (v.5.2).
But i don't know how to do this. It is helpful if you can provide some
Hi Fred
the first thing to do is run recon-all on a good T1-weighted anatomical
from each of your subjects. You can then use mri_label2label to map the
labels from one subject onto another.
good luck
Bruce
On Wed, 27 Mar 2013, Fred Lado wrote:
Dear Freesurfers,I'm interested in using FS ide
That makes much more sense than the thing I was looking for.Now I have a problem reading the lh.lh-rh.thickness.mgh with the load_mgh.m function, as I have no idea of how to read it to get the vertex by vertex thickness value of each subject.I tryed as [thick, ~,~,~]=load_mgh('file.mgh',[],[1:nSubj
Hi Anastasia,
I'm attaching the graphic I arrived at with the command:
> freeview -tv /dlabel/diff/aparc+aseg.flt.nii.gz -v
/dmri/dtifit_FA.nii.gz
Here, I used the subject I send you (Sa69845.5) for the subjectID. I could
not detect spill over in these images, mostly because the frontal lobe is
Hi Susie - The -tv (tract volume) option of freeview is designed
specifically to display the merged*.mgz output files of tracula. For a
regular volume, use -v or no option at all. For best displaying the
aparc+aseg, select it in freeview and choose "Lookup Table" from the Color
map menu.
Ho
Sorry, I meant does the left_frontal_lobe.gii overlay properly on the orig
volume?
doug
On 03/27/2013 04:41 AM, Daniel Lumsden wrote:
> Doug
>
> The .nii.gz file is completely empty and doesn't come up on any viewer
> (fslview, tkmedit, freeview, mricron etc). The .gi files I've
> generated app
Hi Luke, people generally use a different SUBJECTS_DIR than the default
FS folder. You can create symbolic links to subjects in the default FS
folder, but recon-all will do this for you.
doug
On 03/27/2013 07:53 AM, lukas.sch...@ukb.uni-bonn.de wrote:
>
> Hi folks!
>
> I would like to use a dif
Hi Anastasia,
Thank you! I can see that the aparc+aseg spilled over badly. I am going
to try bbregister, and then re-betting (Brain Extraction Tool-ing) the
original image, since the dtifit_FA looks to include non-brain near the
frontal lobe. I'll keep you and the FS community updated on the resu
Actually the brain mask used on the diffusion data *is* the aparc+aseg
mapped to diffusion space, so the reason you see that extra non-brain
stuff in the FA map is because the aparc+aseg was not aligned well to it.
So you just need to switch on bbregister and switch off flirt in your
configu
Doug
When I try to overlay the .gii files on the orig volume I get the following
message:
"Either this surface does not contain valid volume geometry information, or
freeview failed to read the information. This surface may not align with
volumes and other surfaces"
I presume this means th
Hi Anastasia,
I saved out some of the completed trac-all.cmds following each TRACULA
'step', and I see where aparc+aseg is mapped to diffusion space. Thank you
again for all your help - my project is starting to look a lot better!
Sincerely,
Susie Kuo
NIH
On Wed, Mar 27, 2013 at 12:02 PM, Anas
Dear Freesurfistas - This new course, offered at the Martinos Center right
before the OHBM meeting, may be of interest to some of you. There are some
open spots left.
For info on how to register and a tentative schedule, see the web page at
the end of the announcement.
a.y
---
STRUCTURAL
Dear Freesurfers
I will introduce the mean cortial thickness as covariate into my
statistical model, but I'm wonderind which way will be the best.
To get the cortical thickness in individual space, or in AVG space?
Thank you all in advanced,
Rafa.
__
I ran tractstats2table to make a table of my dti tract stats for the
fmajor_PP tract
see the attached script file @tractstats2table and the file list
"fmajor_file_list.txt"
it produced the output file "fmajor_table.txt" (attached)
in the output table all the values for the variables are
I don't think it would make a difference, but I would use the individual
space.
doug
On 03/27/2013 01:12 PM, Rafa X wrote:
> Dear Freesurfers
>
>
> I will introduce the mean cortial thickness as covariate into my
> statistical model, but I'm wonderind which way will be the best.
>
> To get the co
Hello,
I've been having problems with recon-all for only 1 of my 50 subjects.
Recon-all is failing somehow before white matter or surf files are
generated. The T1 and nu.mgz files look fine. Below are the files that my
subject is missing in the 'mri' subdirectory (they are also missing the
entire
Hi Hayley
I think the problem is that the nu.mgz I gave you has a voxel type of
float (3) instead of uchar (0). You will need to figure out which volumes
are float with mri_info, and convert each of them to uchar with:
mri_convert -odt uchar -ns 1 float.mgz uchar.mgz
where the -ns 1 flag tel
Hi Ping - Can you send us your entire trac-all.log? There's some info in
there about your system and the freesurfer build you're using that we'll
need to try to replicate the problem.
Thanks,
a.y
On Tue, 26 Mar 2013, Ping-Hong Yeh wrote:
> Hi Anastasia,
>
> It had the same issue before, but w
Dear. freesurfer users.
I'm trying to make a label for Brodmann area 44.
According to the freesurfer manual, I've run,
recon-all -s subjid -ba-labels
However, it says Flag -ba-labels unrecognized.
I'm using freesurfer version 4.5.0.
By default, recon-all is supposed to create Brodmann areas
you will need to upgrade to a newer version - the BA labeling didn't exist
in 4.5
On Wed, 27 Mar 2013, Ji Won Bang wrote:
> Dear. freesurfer users.
> I'm trying to make a label for Brodmann area 44.
>
> According to the freesurfer manual, I've run,
>
> recon-all -s subjid -ba-labels
>
> How
I am following the wiki page for LME analysis and I have a quick question. The
Mass-univariate example near the bottom of the page proposes an initial model
that contains intercept, linear and quadratic terms as random effects.
However, the examples just below for lme_mass_fit_EM_init(),
lme
if i do the 7 subjects individually, 1 by 1 with the tractstats2table for each
subject, the data in the table are ok,
it's just when I process them all with 1 tractsstat2table command, that the
data is the same in each row of the output
Jon
- Original Message -
From: "Jon Wieser"
To:
Hi Corinna, are you sure that the mri-in-hardi.nii.reg registration is
accurate? the following should look in register:
tkregister2 --reg mri-in-hardi.nii.reg --mov mri-in-hardi.nii --surfs
doug
On 03/25/2013 06:09 PM, Corinna Bauer wrote:
> I am trying to get the V1 label to map onto my HARDI
Hi Yuhong, I put a new version that has a --flat and --patch option here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview
I have not tested it because I don't have any retinotopy handy. Can you
test it and let me know whether it works?
doug
On 03/26/2013 03:00 PM, Y.V. Ji
what is the size of the 4D matrix?
On 03/27/2013 05:41 AM, Rafa X wrote:
> Thanks Bruce for your answer, as you asked I'm forwarding this
> question to the list in case any other can answer this.
>
> We already have the surface generated by mri_preproc, now we are
> trying to read it using the ma
In the 2nd option, age and weight (and other variables) are
simultaneously fit to the data. Most people refer to this as "regressing
out" the effect of one variable when looking at the other. But it is not
regressing out age and then looking at the correlation of age with the
residual.
doug
Here is a link describing the difference in the methods:
http://onlinelibrary.wiley.com/store/10.1046/j.1365-2656.2002.00618.x/asset/j.1365-2656.2002.00618.x.pdf?v=1&t=heswinwb&s=dce1a222e16e861d105340fd919c65fb43dc39ac
Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fe
If you use
thick = fast_vol2mat(MRIread('file.mgh'));
thick will be a matrix of nsubjects-by-nvertices.
Note that the vertex indices from labels are 0-based whereas matlab
expects 1-based.
doug
On 03/27/2013 09:08 AM, Gabriel Gonzalez Escamilla wrote:
> That makes much more sense than the th
it sounds like the problem is in label2surf. Where did that come from?
On 03/27/2013 12:09 PM, Daniel Lumsden wrote:
> Doug
>
> When I try to overlay the .gii files on the orig volume I get the
> following message:
>
> "Either this surface does not contain valid volume geometry
> information, or
Hi Doug,
It worked very well, thank you so much!
For future references, these are the commands I put in with this new
version of rtview (under the folder bold):
Polar angle:
rtview --lh --polar --real rtopy.self.lh/polar/real.nii.gz --imag
rtopy.self.lh/polar/imag.nii.gz --fsig rtopy.self.lh/pol
Hi all,
I have been trying to take an SPM volume and extract FS thickness measurements.
I think I successfully took my spm volume from mni152 to fsaverage space
(mni305) via the command line:
mri_vol2vol --mov $FREESURFER_HOME/subjects/fsaverage/mri.2mm/mni305.cor.mgz
--targ RTPJ_9mm_001_10_64
Ping,
According to line 9 of the log file you sent to Anastasia, are running
freesurfer version v5.1. Not version 5.2.
-Zeke
Original Message
Subject: Re: [Freesurfer] memory allocation errors on Snow Leopard
running dmri_train (fwd)
Date: Wed, 27 Mar 2013 15:17:34 -0400 (ED
Hi Francois
If you want to test the model with
three random effects including intercept, time, and time*time as the
random effects then you should use [1 2 3] (these are the columns
corresponding to those covariates in X). Actually, for the example in
the wiki page we first tested [1 2 3] but the
Hello Admin,
Please unsubscribe this email address.
Regards,
Manish
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The information in this e-mail is intended only for the person
Hi Maish,
You can just go to
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
and unsubscribe your email address.
Lilla
On Wed, 27 Mar 2013, Dalwani, Manish wrote:
> Hello Admin,
>
> Please unsubscribe this email address.
>
> Regards,
> Manish
>
attached is the dmrirc config file
- Original Message -
From: "Jon Wieser"
To: "freesurfer"
Sent: Wednesday, March 27, 2013 3:33:03 PM
Subject: [Freesurfer] error during trac-all -prep
i ran
trac-all -prep -c dmrirc_single_subject
and got the error :
fslmaths
/BrainLabDocs/Studies/
Ping,
Yes, I see. We are looking into it now and will try and replicate the
issue.
-Zeke
On 03/27/2013 05:21 PM, Ping-Hong Yeh wrote:
> Hi Zeke,
>
> That specific subject had v5.1 recon-all run by Leopard with FS v5.1
> (another computer), but v5.2 trac-all run by Snow Leopard with FS v5.2
>
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