Dear Rudolph,
thank you very much for your reply. I used the load_mgh command in
matlab for the preprocessed curv.mgh to create the absolute_curvature
_values.mgh, which was successful.
Best regards,
Christoph
>>> Rudolph Pienaar <[EMAIL PROTECTED]> 13.11.08 22.44 Uhr >>>
On Thursday 13 Novembe
Hi Bruce,
thank you very much. That' s what I looked for.
Best regards,
Christoph
>>> Bruce Fischl <[EMAIL PROTECTED]> 13.11.08 14.43 Uhr >>>
Hi Carl,
you could read them into matlab, take the absolute value, and write them
back out again if you want, then run a glm on that. load_mgh and
sav
Hi,
I'm trying to use a TCL script that runs through every time point in a
surface. I'm using the following commands:
set gaLinkedVars(ftimepoint) 0 (or 1, 2, etc)
SendLinkedVarGroup overlay
But tksurfer is always showing point 0 (doesn't advance in time).
Similar TCL commands for fthresh an
dear group,
we acquired a scan of 2 mm.
I know we cannot use FREESURFER to measure cortical thickness.
however, can we use it to measure all the volumes like the Thalamus,
Hippocampus, Amygdala etc..
in addition, in other scan of 1x1x1 we would like to know the whole cortex
thickness and the t
Hi FreeSurfer Expert,
Can I transfer the thickness data into other form, for example, Nifti,
AFNI or SPM?
Thanks a lot!
Xiaochu Zhang PhD
Visiting Research Fellow
Neuroimaging Research Branch
National Institute on Drug Abuse - IRP
Biomedical Research Center
251 Bayview Blvd.
Suite 200 (NID
Asaf,
To get the thickness of each lobe, you will have to add-up the regions
composing a lobe. This wiki page:
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
has a listing of which aparc regions compose a lobe.
Nick
On Fri, 2008-11-14 at 20:57 +0200, asaf achiron wrote:
> dea
Dear Freesurfer users,
We
have made an analysis of 2 groups (i.e. patients, healthy subjects) in
order to see the cortical thickness differencies. We have introduced
these groups into Qdec. The results showed p-values on a
scale from -5 to +5 and the X coordinates of the right hemisphere were
neg
Xiaochu,
You can convert the thickness data to ascii format like this:
mris_convert -c lh.thickness lh.white lh.thickness.asc
where the row data in the .asc file will be vertex_nun, x, y, z,
thickness(mm)
You can convert to Gifti format, which is a new surface data file format
for use in the fr
Hi all,
I am trying to find the atlases in the freesurfer directory. I could not
find the specific atlases sub directory. Is there a sub directory that
contains all the atlases like the MNI, JHU, etc?
Regards,
Sameer Kumar Gottipati
___
Freesurfer mail
Thank you so much for your really quick response, Nick!
I just did it following your advice. However, I found AFNI can not read
the result (".gii").
Actually, my main aim is do a cortical thickness analysis in a ROI. I
just went over the old mails and found one person have same quesiton to
me. One
Hi,
I have a question regarding converting files to mgz format from
siemens (dicom). Per each image I have 144 IMA files (i.e. for one
subject I have files from .001.IMA to .144.IMA) and I am wondering how
to convert those into 1 mgz file. The only way I seem to find is to
use the command
All those commands will do the same thing. When you pass mri_convert a
single dicom file, it looks at all the files in that directory and finds
all the dicoms that have the same series number, and puts them into one
volume.
Alexa Nardelli wrote:
Hi,
I have a question regarding converting fi
Alexandru,
The p-values displayed in qdec are actually -log10(p), so a value of 5
is 0.1, p of 3 would be 0.001, etc.
The coordinates shown are freesurfer 'surface' coordinates, and do not
have much value outside of freesurfer. qdec will be changed to show
talairach coords in the future. You
Hi all,
I am trying to find the sub directory in the Freesurfer directory which
contains all the atlases like MNI, JHU, etc. Can you please help me out...
Thanks,
Regards,
Sameer Kumar Gottipati
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Freesurfer@nmr.mgh.harvard.edu
Hi everybody,
2 quick questions about longitudinal processing.
1) does the longitudinal processing even call the default gca atlas
or does it use something else?
2) when processing say 7 time points should all longitudinal scans
be processed from baseline or should time 3 be processed from
Hello-
I'm running freesurfer-Linux-centos4-stable-pub-v4.0.5 on Suse 11.
I've used the output of FreeSurfer, specifically wmparc.mgz to create a
32-bit volume to which I've applied edits. The two commands I used were:
mri_vol2vol --mov mri/wmparc.mgz --targ mri/rawavg.mgz --o
wmparc-in-native.
Sameer,
The freesurfer atlases are found in the $FREESURFER_HOME/average
directory. The .gcs files are the surface atlases and the .gca files
are the subcortical atlases. These are used by the recon-all script.
I'm not sure what you mean by MNI and JHU atlases. The other files in
the average di
Hi Jared,
1) it uses the same atlas.
2) this is a tough question, and we don't have much experience with
processing multiple time points (yet). I would say you want the analysis
of every one to be the same to prevent the introduction of methodological
artifacts, so for now I would do them all
Hi Xiaochu,
I'm not sure how afni stores its ROIs, but I bet Ziad (ccd) can help. I'll
leave the group statistics in a label for Nick and/or Doug
mris_anatomical_stats -l ... will do it for an individual, so you
can always run it that way, but I bet there is a better/easier way to do
it.
c
Hi, FreeSurfer export,
Thank you very much for response!
Now, under some export's help, I used to the mri_surf2vol to transfer cortex
thickness into nifti.
The below line is what I used.
mri_surf2vol --surfval ../surf/lh.thickness --hemi lh --fillribbon --template
orig.mgz --volregidentity ${su
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