Greetings,
We would like to downsample surfaces (e.g. using mris_decimate) but we want to
duplicate the way it was done with fsaverage (namely, find out how
fsaverage3/4/5 were created from the original fsaverage). Also, we wish to be
able to project using mri_surf2surf but we don’t have
Hi,
I tried to use mne_make_movie but got the following error:
Movie production selected (from data)...
Scanning /Applications/MNE-2.7.3-3268-MacOSX-i386/lib for plugins
Found lqt_mjpeg.so...Getting codec info from module
Trying to load
Hello Bruce,
I am referring to link
http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
to calculate the cortical thickness of particular area such as Left
hippocampus for our own data set.
But i am looking for forward to generate lh.thickness file in freesurfer
for own data
On Wed, Mar 26, 2014 at 2:39 PM, Saurabh Thakur srbht...@gmail.com wrote:
Hello Bruce,
I am referring to link
http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
to calculate the cortical thickness of particular area such as Left
hippocampus for our own data set.
But i am
Dear Doug and Bruce,
I have three more questions concerning 'pctsurfcon'.
1) The inner sampling distance is set to 1mm by default, but the outer
sampling is done at a 30% of the cortical thickness. I saw that I could
easily change the parameters or modify the script, but I wonder why this
has
Hi Itamar,
fsaverage3/4 are just different icosahedral supersamplings. They were
actually used to create fsaverage (which you can think of as fsaverage7).
That is, fsaverage1 has 12 vertices, fsaverage2 42, etc..., and the first
12 of fsaverage[234567] are the ones from fsaverage1, the first
Hi Saurabh
I'm not sure I understand. This is the purpose of recon-all - to generate
morphomological models, including the thickness estimates in lh.thickness.
Is that would you mean? BTW: I wouldn't look at thickness in the
hippocampus, the results will be unreliable due to all the internal
Hi list,
we would like to perform cortical thickness analysis on fetal brain.
We have a single shot T2 image (good quality) and T1 image (poor quality). All
images are in 2D with overlapping and they are acquired by using 1.5 tesla.
We have some questions:
1. Do you know a post-processing way to
Greetings,
I am working with pediatric data and have some early evidence that running
recon-all with the flag -norm2-b 20 -norm2-n 5 improves the anterior
temporal lobe segmention as suggested in the v5.2 release notes (I am
running this with v5.3). I'd like to experiment more with this parameters
Hi,
The analysis necessary to my study is to run some analysis on the raw time
course data. Before working on the raw time course data, it is necessary to
remove linear drifting, mean, and head motion. Can I just specify those
parameters without having
Hi Bruce,
Thanks for your response. It is B0 normalization scan. What it does is to get
an homogeneity image, which could be used to normalize the MRRAGE image by
dividing it. Is there an build in function in freesurfer to do this operation?
Thanks,Xiaomin
Date: Mon, 24 Mar 2014 12:42:52
On 3/26/14 8:24 AM, Markus Gschwind wrote:
Dear Doug and Bruce,
I have three more questions concerning 'pctsurfcon'.
1) The inner sampling distance is set to 1mm by default, but the outer
sampling is done at a 30% of the cortical thickness. I saw that I
could easily change the parameters or
thank you. But if the lnog process has already been done and these
induviduals already have long directories so to speak, I would just put the
lgi flag on as normal but just replace the subject name with the long
subject name eg ?
recon-all -s _long -localGI
Thank you
On Sat, Mar 15, 2014
Sorry, I don't follow what you are asking. FSFAST does not do any drift
removal from the raw data, all of that is in the design matrix
doug
On 03/26/2014 10:45 AM, Xiaomin Yue wrote:
Hi,
The analysis necessary to my study is to run some analysis on the raw
time course data. Before working
Hello list,
I'm trying to get aparc surface area from the pial surface in a table
using aparcstats2table but I'm not being able to...
I've already created the file aparc_pial.stats inside the stats dir
running the following command line from the subjects's label dir:
mris_anatomical_stats
Hi Jason
the only documentation is in mri_normalize --help (and the code). Try
running it directly on your data (you can get the command line syntax from
the recon-all.log). It only take a couple of min/call so you should be able
to try a bunch of the options pretty quickly, then set them for
Hi Xiaomin
do you mean dividing by the Jacobian of the B0 unwarping field? Are you
sure it's not B1? That is by far the more common intensity normalization
for an mprage. The B0 effects are small due to the high bandwidth of the
mprage.
I think Rudolph and/or Doug have tools for multiplying
You can use fscalc, something like
fscalc file1.mgz div file2.mgz -o file1-div-file2.nii
On 03/26/2014 11:54 AM, Bruce Fischl wrote:
Hi Xiaomin
do you mean dividing by the Jacobian of the B0 unwarping field? Are
you sure it's not B1? That is by far the more common intensity
Dear Freesurfers,
To obtain an accurate volume-surface alignment of Freesurfer surfaces
in Caret, it is advised that oblique sforms should be removed from the
header of the t1w images. I tried to remove the sform (using
sform_code='0' and qform='1') and changed the nii header using
Hi Anna,
no, you would still do:
recon-all -long tpid baseid -localGI
just not use the '-all'.
Best, Martin
On 03/26/2014 11:12 AM, Anna Jonsson wrote:
thank you. But if the lnog process has already been done and these
induviduals already have long directories so to speak, I would just
Hello,
I am visually checking wm.mgz after running recon-all. There seems to be a
pattern where I'm seeing white matter bleed past the (correct) white
matter surface and into gray matter or appear in the sagittal sinus/dura.
However, when I look at wmparc.mgz, the problem is no longer there and
nope, that's why we usually trust the surfaces more than the volume
segmentations.
cheers
Bruce
On Wed, 26 Mar 2014, Eleanor Stahura wrote:
Hello,
I am visually checking wm.mgz after running recon-all. There seems to be a
pattern where I'm seeing white matter bleed past the (correct) white
I get the correlation result between two condition of the functional data
by using AFNI( I do not know how to do correlation by using freesurfer)
And then I use the bbregister to aline the correlation result (produce by
Afni) to the anatomical result produced by using freesurfer.
Next I using
Are the AFNI results already in talairach space? If so, then there is no
point in going to surface space.
doug
On 03/26/2014 01:22 PM, Linda Xu wrote:
I get the correlation result between two condition of the functional
data by using AFNI( I do not know how to do correlation by using
No, sorry
On 03/26/2014 01:54 PM, Xiaomin Yue wrote:
I like to regress out the linear drift, mean, and head motion
generated by the motion correction step of fsfast from the raw time
course only. Is it possible using fsfast?
Xiaomin
Date: Wed, 26 Mar 2014 11:28:57 -0400
From:
thanks.
Xiaomin Yue
Date: Wed, 26 Mar 2014 11:54:58 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] B1 correction
Hi Xiaomin
do you mean dividing by the Jacobian of the B0 unwarping field? Are you
sure it's not B1? That is by far the more
Hi Andreia,
If you remove the underscore from aparc_pial for the --parc flag in the
aparcstats2table command, that should do the trick.
-Louis
On Wed, 26 Mar 2014, _andre...@sapo.pt wrote:
Hello list,
I'm trying to get aparc surface area from the pial surface in a table
using
I like to regress out the linear drift, mean, and head motion generated by the
motion correction step of fsfast from the raw time course only. Is it possible
using fsfast?
Xiaomin
Date: Wed, 26 Mar 2014 11:28:57 -0400
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
that might work. You'd have to make sure that you specified native space
in mkanalysis-sess
doug
On 03/26/2014 02:56 PM, Caspar M. Schwiedrzik wrote:
you could try to run mkanalysis-sess with -notask and your nuisance
regressors specified as -nuisreg, then run selxavg3-sess with
-no-con-ok
you should probably apply it before giving the data to recon-all
cheers
Bruce
On Wed, 26
Mar 2014, Xiaomin Yue wrote:
Hi Bruce,
You are correct that it is B1. How could I incorporate this data into the
reconstruction stream?
Thanks,
Xiaomin
Dear FS experts,
I've been dealing with the conversion to MNI152 of some volumetric labels of my
subjects extracted with mris_extract_label in FS v.5.1 but, I've been unable to
succeed.
I've tried bbregister and mni152reg commands, both of them give me an example
to check at the
Thanks very much, i will try it.
Xiaomin
From: cschwie...@mail.rockefeller.edu
Date: Wed, 26 Mar 2014 14:56:26 -0400
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fsfast question
you could try to run mkanalysis-sess with -notask and your nuisance regressors
specified as
Hi,
I got this error while running recon: 'imgreg_4dfp
/opt/freesurfer-530/average/711-2C_as_mni_average_305
/opt/freesurfer-530/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none
talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254ERROR:
mpr2mni305 execution aborted
We are using Freesurfer v5.3 with the recent Jacobian area correction, but
there may be a subtle bug that affects longitudinal studies. In a pediatric
population, we see area growth on top of gyrii, and area loss in the base of
sulci. This effect may be a true morphological change, but it may
What is your vol2vol command line?
On 3/26/14 3:58 PM, Gabriel Gonzalez Escamilla wrote:
Dear FS experts,
I've been dealing with the conversion to MNI152 of some volumetric
labels of my subjects extracted with mris_extract_label in FS v.5.1
but, I've been unable to succeed.
I've tried
Thanks for reply bruce.
I got my mistake.Actually i am learning Cortical thickness using
freesurfer.In which ROI5.nii n *TT_avg152T1.nii*. image is required which i
took from our own data set,but didnt have thickness file for surface to
surface mapping.Now i will do recon all on my data set to
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