Hello Freesurfer expert,
I have done Hippo campus segmentation using Freesurfer.
Can u tell me how to extract the only Hippo campus volume from nu.mgz
Why only nu.mgz is used for the main volume--is there some specific reason
to use?
Thanks in advance ,
Saurabh Thakur,
sure, you can load them into matlab with read_surf.m and do whatever you
want, or convert to ascii with for example:
mris_convert lh.orig lh.orig.asc
cheers
Bruce
On Thu, 27 Feb 2014, ye tian
wrote:
> Dear Freesurfers,
> I would like to do some customized model fitting for cortical thickness.
Hi Saurabh
I'm not sure what you mean by "the main volume", but the hippocampus is
segmented in the aseg.mgz. You can extract it from there using
mri_extract_label or mri_binarize --match
cheers
Bruce
On Fri, 28 Feb 2014, Saurabh
Thakur wrote:
> Hello Freesurfer expert,
>
> I have done Hippo
Thanks for such quick reply Bruce,
I am saying i am using these file , referring to feesurfer website.
cd $SUBJECTS_DIR/bert/mri freeview nu.mgz -p-labels posterior_left_*
posterior_Left-Hippocampus.mgz -p-labels posterior_right_*
posterior_Right-Hippocampus.mgz -p-prefix posterior_ -p-lut
$FRE
Hi!
I want to know how to clone from T1.mgz to brainmask.mgz in freeview (to amend
a skullstript that has removed too much). I couldn’t find the tool in freeview.
Thank you very much,
Emad
Emad Ahmadi, MD
---
Postdoc Research Fellow
Department of Ra
Hi Eric,
I just came across your old email, have you ever figured it out?
You don't need to compute ni beforehand, it is computed in sortData.
This is what it says in the help:
ni: Vector (mx1, m # of subjects in the study) whose entries are the
number of repeated measures for each subject (ord
In general you should use a registration file when viewing your results.
In many cases, it may look like it is in registration with out a
registration file. This can happen if you acquired your anatomical and
DTI data in the same session. For this subject, were they acquired in
different sessi
Hi Bruce,
I had a follow up question. In the training videos they seem to indicate that
the CVS registration improves accuracy for subcortical and cortical structural
analysis. Can you clarify for me what the best use of CVS is if not for
improving the subcortical and cortical alignment for gr
I concur. If this is the lowb.nii.gz from trac-all and brainmask.mgz from
recon-all, they will be in their respective native spaces, and thus I
wouldn't expect them to be registered to each other.
On the other hand, any brain masks that trac-all saves under dlabel/diff/
are in diffusion space,
There appears to be something wrong with
rh.38sb_score.10.mgh. Try running this
mri_convert rh.38sb_score.10.mgh junk.mgh
If that fails, then regenerate rh.38sb_score.10.mgh
On 02/27/2014 08:12 PM, charujing123 wrote:
> Hi doug,
> Thanks doug.
> I try to ftp by this manu,so I think server is
>
Can you be more specific about what you mean by "freesurfer data"? Each
subject has 300MB of "data"
doug
On 02/27/2014 10:48 PM, ye tian wrote:
> Dear Freesurfers,
>
> I would like to do some customized model fitting for cortical
> thickness. Is there a way to export freesurfer data into R or s
Hi Emad,
Which version of FS are you using? The freeview in the 5.3 release has
the clone tool within the voxel edit mode, but it's not in 5.1 or earlier.
It's represented by an icon with a blue and gray rectangle.
Take a look at the 5th section on this page:
https://surfer.nmr.mgh.harvard.ed
Hi Freesurfers,
I get an error when using spmregister saying "Maximum variable size allowed by
the program is exceeded"- is that a problem with the number of dicoms?
I can attach a screenshot of the error if that helps.
Thanks,
Mia
___
Freesurfer maili
never seen that. can you send your command line and the log file?
On 02/28/2014 11:43 AM, Borzello, Mia wrote:
> Hi Freesurfers,
>
> I get an error when using spmregister saying "Maximum variable size
> allowed by the program is exceeded"- is that a problem with the number
> of dicoms?
> I can at
the last line of "error_spm" is the command line, and the errors for that
command are above.
Thanks,
m
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: F
Hi Saurabh
I didn't realize you meant the subfields. For that you'll need Koen or
Eugenio to answer.
You are probably seeing the cc in freeview because that is the default
slice it shows, but you should be able to scroll around and see other stuff
cheers
Bruce
On Fri, 28 Feb 2014, Saurabh T
Hi Jennifer
Lilla might want to chime in. They do improve the accuracy of alignment, so
if you were looking at average fMRI results or something it would be a good
thing to do. But once the structure volumes have been computed the
alignment is no longer needed - you can just look at bar charts
Hello all,
I have 2 subjects that failed autorecon-all at the same Talairach step.
Both subjects successfully completed autorecon-all in version 5.2. Here is
the output from one of the subjects.
Any suggestions?
Corinna
#
#@# Talairach Fri Feb 28 12:39
Hi Saurabh,
the volume of the hippocampal subfields can be computed with:
cd $SUBJECTS_DIR/bert/mri
kvlQuantifyPosteriorProbabilityImages \
$FREESURFER_HOME/data/GEMS/compressionLookupTable.txt \
posterior_right_* posterior_Right-Hippocampus.mgz
and the whole hippocampal volume is just the a
Hi Marie,
The ?h.pial_lgi.fwhm?.fsaverage.mgh files in the surf folder are there. Here
is the output when I run more ~/.Qdecrc:
# This file is automatically generated by the application
# If you change any lines or add new lines, note that all
# coments and empty lines will be deleted. Every line
Thnak you very much for clarifying this.
So recon-all and trac-all outputs are all in their own native space.
Now if I need to sample surfaces on the diffusion images based on recons
surface, I need to provide the /dmri/xfms/anatorig2diff registration
matrix right?
But it is not completely clear t
Hi Krista,
You need to add the following line in your .Qdecrc:
MEASURE1 = pial_lgi
and save the change.
I don't think it matters where you add it, I have it before all the Qdec lines.
Then start qdec again, it should work. If not, check again the .Qdecrc file,
and look whether starting qdec er
Hi Freesurfers,
In general when aligning an MR and a CT, is a 32 slices CT sufficient? I've
done a coregistration and am looking at it in tkmedit and the quality of the
image isn't so good.
Thanks,
Mia
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Freesurfer@nmr.mgh.ha
It is a registration file that goes from the anat to the orig space, but
freeview (and mri_vol2surf) knows this and knows which direction to
apply it to
doug
On 02/28/2014 04:12 PM, Celine Louapre wrote:
> Thnak you very much for clarifying this.
> So recon-all and trac-all outputs are all in
32 at what slice thickness? The quality of what is not good?
On 02/28/2014 04:20 PM, Borzello, Mia wrote:
> Hi Freesurfers,
>
> In general when aligning an MR and a CT, is a 32 slices CT sufficient?
> I've done a coregistration and am looking at it in tkmedit and the
> quality of the image is
looks like there is something going wrong in your matlab setup
Warning: Executing startup failed in matlabrc.
This indicates a potentially serious problem in your MATLAB setup,
which should be resolved as soon as possible. Error detected was:
MATLAB:UndefinedFunction
Undefined function or variabl
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