Thanks Sebastian.
Will take a note of it.
cheers
Saurabh Thakur,
On Tue, Mar 4, 2014 at 1:20 PM, Sebastian Moeller <
sebastian.moell...@rwth-aachen.de> wrote:
> Hi Saurabh,
>
>
> On Mar 4, 2014, at 07:56 , Saurabh Thakur wrote:
>
> > Hi Markus Gschwind,
> >
> > I am using Matlab 7.12.0.
How to create only Hippocampus segmented file in tkmedit.
aseg.mgz. for Hippocampus file.
Please
cheers
Saurabh Thakur,
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The inform
Hello I m actually looking for to know the way we get stats for the regions
17 and 53 using command
asegstats2table --subjects sam --segno 17 53 --tablefile aseg.vol.table1
Similarly is there any command to get the segmented hippocampus where we
can choose the parameters.
cheers
Saurabh Thakur
Hello,
How can I generate volume for temporal horn, temporal white matter and temporal
gray matter.
Thanks
Rashmi
Sent from my iPhone
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Ye
it is both that, and volumes of label indices (e.g. 17=Left Hippocampus)
and surface models (triangles, edges, points) and scalar and vector fields
over them.
cheers
Bruce
On Mon, 3 Mar 2014, ye tian
wrote:
> Dear Bruce and Doug,
> Thank you very much!
>
> Would you please tell me mo
Hi Saurabh
in general we can't help you unless you give us more information, like
the screen output of the command you ran that failed.
cheers
Bruce
On Tue, 4 Mar 2014,
Saurabh Thakur wrote:
Hello Freesurfer,
I am trying to runs MRIread.m file in matlab.
But it is not reading the brain.m
Hi Rujing
it's tough to tell from a single slice, particularly on an intensity
normalized image. When you compare the brain.mgz and the orig.mgz does it
look like the intensity normalization is too aggressive? Does it change
voxels that look like GM into ones that look like WM
If you upload
you can use mri_extract_label or mri_binarize --match
cheers
Bruce
On Tue, 4 Mar 2014,
Saurabh Thakur wrote:
> How to create only Hippocampus segmented file in tkmedit.
>
> aseg.mgz. for Hippocampus file.
>
> Please
>
> cheers
> Saurabh Thakur,
>
>
>
>
>
>
___
You can create an annotation of the lobels using mri_annoation2label
with the --lobesStrict option. Once you have that you can run
mri_aparc2aseg using the --wmparc option (look in the recon-all.log file
for an example of how the wmparc.mgz is created), then use mri_segstats
to get the volumes
It should come up intensity normalized. Are you sure that there is a
volume to see? Ie, it is not out of the field of view? If you want to
adjust the contrast, you can hit 'i' (toggles inorm), then change the
value in the fmov field
doug
On 03/04/2014 10:00 AM, Borzello, Mia wrote:
> Hi Freesurf
On 03/03/2014 11:25 PM, Xuelong Zhao wrote:
> Hi Doug, thanks for the quick reply. I've been playing around with the
> commands you suggested and managed to get what seemed like a good
> registration by inspecting the green lines in tkregister.
>
> However, I wasn't actually sure if I put the co
Try vol = MRIread('brain.mgz')
On 03/04/2014 01:56 AM, Saurabh Thakur wrote:
> Hi Markus Gschwind,
>
> I am using Matlab 7.12.0.635 (R2011a),
>
> I am not able to read the dicom image neither brain.mgz file nor the
> surface file in matlab.
>
> I have added these file in matlab directory.
>
>
Is there any way to get the volume for the temporal horn using FreeSurfer.
Thanks,
Rashmi
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended
Hi Celine - This command assumes that --intrc is a tracula output
directory, containing all the files that tracula saves in such a
directory. What are you trying to get stats from?
a.y
On Mon, 3 Mar 2014, Celine Louapre wrote:
> Hi Anastasia
> I have finally managed to coregister and resample
actually, you are right, they should have 45. Which one had 66? What was
your command line?
On 03/03/2014 04:22 PM, sabin khadka wrote:
> All aseg.stats seems to have volume of 45 ROIs with some
> hypointensities value =0. Also, I checked aseg.mgz and looks fine with
> these subjects. I extracte
Hi Mia, these types of general descriptions are hard to debug. Please
remember to send your command line and terminal output and/or log file.
doug
On 03/03/2014 03:42 PM, Borzello, Mia wrote:
> So I'm running spmregister from a new computer now, and I'm still not getting
> a successful output.
The wmparc is off because the surfaces are incorrect. The aseg does not
have to follow the surfaces, but wmparc does
doug
On 03/03/2014 03:10 PM, Victor Kovac wrote:
> Hi Bruce and Doug,
>
> "cp aseg.auto.mgz aseg.mgz" was my last step before running
> -autorecon2-cp -autorecon3, as suggested
Hi,
we have a longitudinal data set and have processed all of the baseline data
using FS v5.1.0. We are now about to start preprocessing follow-up brains.
Can you please give your opinion on whether we had better stick with v5.1.0 for
the follow-up data as well or whether it would be safe to
Hi guys, just wondering what you'd say is the best measure for whole brain
volume? Cortex volume.. Cortical white matter volume.. Total gray volume..
Intracranial volume.. etc.
Cheers!
Hugh
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https
Hi everybody,
I'd like to know if it's possible and if yes how to add new paths to the
tracula pathlist? Otherwise how can I add a new path after the entire
trac-all process?
Francesco Baldacchini
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.e
oh yes I see, I have renamed the dpath/${TRACT[$num_tract]} directories to
have a backup, so the name is not correct anymore. Actually I didn't need
to do that, I can just set a different name for the outputs
pathpathstats.byvoxel.txt and pathstats.overall.txt
Thanks
Celine
>
> Hi Celine - This co
Hi Francesco - The pathways that tracula reconstructs are only the ones
included in its atlas. To add a new pathway to this atlas, it would have
to be labeled manually in a set of subjects, just as we have done with
the other 18 pathways.
Hope this helps,
a.y
On Tue, 4 Mar 2014, Francesco Bal
Ok, thanks. And if I want to add a new pathway which is the file I've to
modify and where can I find it?
Francesco Baldacchini
2014-03-04 17:28 GMT+01:00 Anastasia Yendiki :
>
> Hi Francesco - The pathways that tracula reconstructs are only the ones
> included in its atlas. To add a new pathway
Hi Rashmi
the temporal horn of the lateral ventricles you mean? We segment that
explicitly although it is called "inferior lateral ventricle" I believe
cheers
Bruce
On
Tue, 4 Mar 2014, Rashmi Singh wrote:
> Is there any way to get the volume for the temporal horn using FreeSurfer.
> Thanks,
>
Hi Francesco - It's not a single file that needs to be modified. The new
pathway would have to be labeled manually in several subjects. You can
look at our paper to get a better idea of what this involves:
http://journal.frontiersin.org/Journal/10.3389/fninf.2011.00023/abstract
a.y
On Tue, 4
Thank you Bruce, This is what I had thought but wanted to be sure about
the anatomy before I used its measurements.
Also, this is again an anatomy question but the parcellation files have
temporal lobe measurement as lh/rh superior, medial and inferior regions .
There is another measurement lh/rh
Hello Michael,
Use the Freesurfer Centos4 build for your Centos5 platform. People who
want to take advantage of of multiple cores typically use the "-openmp
" flag when running recon-all. Theoretically the more cores
you use the faster the runtime, but we have found that that there is
little g
Hello,
I am re-posting this since I haven't got an answer yet.
Thanks!
Mihaela
On Fri, Feb 21, 2014 at 3:55 PM, Mihaela Stefan wrote:
> Hi freesurfers,
>
> I get this error when I load qdec.table.dat. Is it something wrong or
> should I ignore it?
> Verifying subject data.sh: 1: Syntax error: B
Are those subjects in your SUBJECTS_DIR?
What is the output of
ls $SUBJECTS_DIR
?
On Tue, Mar 4, 2014 at 1:10 PM, Mihaela Stefan wrote:
> Hello,
> I am re-posting this since I haven't got an answer yet.
>
> Thanks!
> Mihaela
>
>
> On Fri, Feb 21, 2014 at 3:55 PM, Mihaela Stefan
> wrote:
>>
>> H
Hi Rashmi
the regions are disjoint, so if you want all temporal lobe you need to add
them together.
cheers
Bruce
On Tue, 4 Mar 2014, Rashmi Singh wrote:
> Thank you Bruce, This is what I had thought but wanted to be sure about
> the anatomy before I used its measurements.
>
> Also, this is aga
Please be sure to 'reply all' so everyone may participate.
Yes, You need to set the SUBJECTS_DIR before using freesurfer tools.
HTH
D
On Tue, Mar 4, 2014 at 2:02 PM, Mihaela Stefan wrote:
> It says "No such file or directory"
> The environment for SUBJECTS_DIR was set as /usr/local/freesurfer/s
Thank you Bruce!
Rashmi
On 3/4/14 12:43 PM, "Bruce Fischl" wrote:
>Hi Rashmi
>
>the regions are disjoint, so if you want all temporal lobe you need to
>add
>them together.
>
>cheers
>Bruce
>
>On Tue, 4 Mar 2014, Rashmi Singh wrote:
>
>> Thank you Bruce, This is what I had thought but wanted to
Sorry..
We had Louis Vinke come here to train our lab last year. He helped us set
the environment for FS
He taught us to cd to the working directory and then use the command sd to
set the directory.
I thought that was enough to use freesurfer tools.
On Tue, Mar 4, 2014 at 2:09 PM, dgw wrote:
>
Hello Freesurfer experts,
I have a question about how to determine if a covariate is important in a
mixed effects model
for example:
Y1 = B1 + B2(time) + B3(rand_effect1) + B4(rand_effect*time) +
B5(covariate_1) +B6(covariate_2)
Y2 = B1 + B2(time) + B3(rand_effect1) + B4(rand_effect*time) +
B5(cov
Sorry!
I made a mistake with my example. I meant to say group_effect instead of
rand_effect.
It should read as follows:
Y1 = B1 + B2(time) + B3(group_effect1) + B4(group_effect*time) +
B5(covariate_1) +B6(covariate_2)
Y2 = B1 + B2(time) + B3(group_effect1) + B4(group_effect*time) +
B5(covariate_1
Dear Doug,
I've managed to get functional information onto the cortical surface following
your instructions.
But, there's a few issues that are still not resolved:
1/ wrt to registration I believe the supplied anatomical template (in tailarach
coords) is already aligned with the ica maps (whi
Hi Marie,
Thanks for the the response. I've done that a few times and still, the lgi
option does not come up in qdec as a measure. Could it be that I'm using an
outdated version of Qdec? My freesurfer v is 5.3 so unless I need to update
qdec on its own, I don't think that this is the problem. Any
Hi Krista,
Did you verify that your changes to .Qdecrc were properly saved? As long as the
command more ~/.Qdecrc doesn't give you a line with MEASURE1 = pial_lgi, then
you'll not have it in qdec menu. And version should not be an issue. How do you
edit the .Qdecrc file? Did you check to see w
Hi Eric
The longitudinal lme model is no
different from cross-sectional models when it comes to testing the
significance of a covariate. You just simply use an F-test with the
contrast [0 0 0 0 0 1] to test the last covariate in the first model. You can
then drop the last covariate if the test
is
On 3/4/14 7:18 PM, Xuelong Zhao wrote:
Dear Doug,
I've managed to get functional information onto the cortical surface
following your instructions.
But, there's a few issues that are still not resolved:
1/ wrt to registration I believe the supplied anatomical template (in
tailarach coords)
40 matches
Mail list logo
