Hi list,
I have download the files of Yeo parcellation from
ftp://surfer.nmr.mgh.harvard.edu/pub/data/Yeo_JNeurophysiol11_MNI152.zip.
I have two questions, please.
A- Which is the directory where I should put these files?B-I have already run
by recon-all -all all my subjects. How can I added to t
I use the Yeo parcellations often for more functionally defined regions.
You should perhaps check out those.
http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011
Cheers
On Thu, Feb 6, 2014 at 7:14 PM, Estephan Moana wrote:
> Dear Freesurfer experts,
>
> Is it a fair assumpti
Hi Doug,
I have a followup question on this topic. I understand the two command you
mentioned in this thread to warp a segmentation to the MNI152 space.
In the subjects dir, I see there is an average subject "cvs_avg35_inMNI152"
which is already in MNI space (and the volume size is 256^3). I want
Mehul, I'm not sure what you are trying to do? Just get a version of the
aparc+aseg into mni152 space? If so, what is the application? In most
applications (eg, linear intersubject registration), this is not very
useful because the cortical labels are quite small (tailored to
surface-based an
Hi Estephan
I actually don't know what the FSL masks correspond to. If they are
volumetric labels then they are unlikley to perfectly correspond to
anything in FreeSufer. If you really want correspondence you are
probably best off taking their maps and mapping them to our surfaces.
Note that
Dear Freesurfer experts,
Is it a fair assumption that the Desikan-Killiany parcellations of the
postcentral gyrus is roughly equivalent to SI+SII, and that the
supramarginal gyrus ≈ inferior parietal lobule? I used SI, SII and IPL
ROI masks in some FSL analyses, and would like to use similar RO
We've generally seen better results with BBR, which is why it became the
default setting.
On Thu, 6 Feb 2014, Jon Wieser wrote:
> HI Anastasia,
>
> I ran it again with the flirt registration and it finished ok.
> We did not have a specific reason for running it both ways. we are using the
> de
That's entirely up to you, and whether you had a specific reason for
running it both ways.
If you want to fix the bbr registration manually, check the trac-all.log
file for a command at the end of bbregister, where it says "To check
results, run".
On Thu, 6 Feb 2014, Jon Wieser wrote:
> Hi A
So in other words, there is not a tool in Freesurfer similar to mris_label_calc
but that works with labels defined in the volume rather than on the surface,
correct?
I am simply double checking that there is not a simple single step tool before
I write a matlab script or start transforming labe
This may be a bug that I fixed. Try this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/optseq2
On 02/06/2014 02:11 PM, Wei-chun Wang wrote:
> Hi, I am trying to set up a design using optseq2, but the tnullmax
> command doesn't seem to be functioning. the script runs and ou
Thank you for your email. I have been using the command:
freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz
-p-labels posterior_right_* posterior_Right-Hippocampus.mgz -p-prefix
posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt
to visualize the hippocampal subfield
Hi, I am trying to set up a design using optseq2, but the tnullmax command
doesn't seem to be functioning. the script runs and outputs files, but they
exceed the tnullmax which i specify. is anyone familiar with this issue?
this is what i am inputting:
--tr 2 --psdwin 0 20 1 --ev easy 4 36 --ev ha
'mris_calc' accepts as inputs volumes or "curvature" files. Calculations
on labels don't make sense in the context for which "mris_calc" was
written -- what would an operation like "label1 multiply-by label2" even
mean?
Having said that, 'mris_calc' does support labels in as much as using a
la
Hi Salil,
You should be able to apply an isosurface to each subfield label in
freeview. You can set the color for each isosurface as well, since the
default is gray. You need to be in the 3D view in order to display
isosurfaces.
-Louis
On Thu, 6 Feb 2014, Salil Soman wrote:
Hi,
I generate
As far as I can tell - and I may very well be using incorrect syntax -
mris_calc needs volumes as inputs and does not accept labels. Does
mris_calc accept label files as inputs, for instance in a command like:
"mris_calc roi2.label and roi3.label"? If so, could someone point me at
the correct synt
I'm not sure what is going on with that dicom file (we usually have
dicoms from MRI machines). I ran this command
mri_convert CT00.dcm ct.mgh -iks 5 -it dicom -iid 1 0 0 -ijd 0
0.1153970063 -0.9933194518 -ikd 0 -.9933 .1154
and it starts to look ok. The problem appears to be that the slice
Hi Anastasia,
We used both flirt and bbr registration in the dmrirc file, the Aparc+seg I
just showedd you was from the BBR resitration. I looked at the flirt
registration. it looks OK.
should I rerun tracula using only the flirt registration?
Jon
- Original Message -
From: "Anastas
On 02/06/2014 11:56 AM, Rotem Saar wrote:
> Dear Doug,
>
> Sorry - I'm probably missing something, as trying to write what u
> suggested (see below email history) didn't work (not sure what am I
> doing wrong).
> I'm copying here what I did to get the average FA value to each
> region. Can u
yes, mri_surf2surf. You can spec --s subject to set both src and trg
subject to the same thing.
On 02/06/2014 11:42 AM, Caspar M. Schwiedrzik wrote:
> Hi!
> I need to export results from a surface-based analysis in FSFAST
> (v5.1) to another program (Caret) that accepts .w files. I was
> wonde
So there's your culprit. You need to fix the intra-subject
(diffusion-to-T1) registration. Did you use flirt or bbregister for that?
On Thu, 6 Feb 2014, Jon Wieser wrote:
> Hi Anastasia,
> I looked at the dlabel/diff/Aparc+aseg overlayed on the dmri/dtifit_FA.nii.gz
> the alignemenst is way off
On 02/05/2014 05:07 PM, Natasha Haris wrote:
> Dear Freesurfers,
>
> My measure is thickness and I want to be able to get a list of all the
> maximum thickness values at the centers of each significant cluster -
> is there any simple way to do that on QDEC?
Do you want the maximum across the clu
Dear Doug,
Sorry - I'm probably missing something, as trying to write what u suggested
(see below email history) didn't work (not sure what am I doing wrong).
I'm copying here what I did to get the average FA value to each region. Can
u PLEASE write what do I need to change in order to get the MD
Hi!
I need to export results from a surface-based analysis in FSFAST (v5.1) to
another program (Caret) that accepts .w files. I was wondering what the
recommended way of doing this is.
It seems that mri_surf2surf will do the trick?
Do I set the source and the target to be the same?
Thanks, Caspar
_
mris_calc should work for this purpose. Run mris_calc -h to see the
options
On Thu, 6 Feb 2014, Kami Koldewyn
wrote:
Hi All,
I was thinking that there was a freesurfer tool that performed simple math
operations on volumetric labels (similar to
those that mris_label_calc performs for surf
Hi All,
I was thinking that there was a freesurfer tool that performed simple math
operations on volumetric labels (similar to those that mris_label_calc performs
for surface labels) but I can't seem to find one. Is there such a tool that I
am simply missing? I am hoping to easily create non-o
Bruce, Thanks a lot!
Would you explain more on how to run recon-all in parallel? By run the
script it did not automatically took the advantage of multiple cores (by
checking CPU usage). Is their somewhere I can change the preference or I
shall add some parameters in my code?
On Thu, Feb 6, 2014 a
orig.mgz is not converted to Talairach. The computed Talairach xfm is
used internally by some stages of recon-all, but none of the volumes are
ever converted to Talairach/MNI space.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for
Hi Harm,
Thanks for the trick. Will this, however, give not rise to conversion to
Talairach
coordinates?
Cheers,
Ed
On 6 Feb 2014, at 15:38, Harms, Michael wrote:
>
> Hi Ed,
> If you want to avoid the rotation (e.g., to avoid an interpolation at the
> conform step) then you need to manually
Hi Ed,
If you want to avoid the rotation (e.g., to avoid an interpolation at the
conform step) then you need to manually alter the input so as to remove
the off-diagonal elements. That is in fact what we do as part of our
DICOM2NIFTI conversion in the HCP.
cheers,
-MH
--
Michael Harms, Ph.D.
-
Hi Bruce,
Yes, I do understand that is coronal, but there is an actual rotation apart
from an orientation to coronal.
You can read it from the off-diagonal matrix elements.
Cheers,
Ed
On 6 Feb 2014, at 14:36, Bruce Fischl wrote:
> yes, we reorient it to be coronal as part of the "conform" proc
Sorry seems like my reply didn't go through to the list. Still trying to figure
this out if anyone has some ideas on what to do / recommend trying to calculate
manually.
Best,
Jeremy
-Original Message-
From: Jeremy Young
Sent: Tuesday, February 04, 2014 4:30 PM
To: 'Douglas N Greve'
S
Hi Peng
the recon-all instances should be able to be run in parallel. The first
time you run one it will see that fsaverage does not exist, and will
symlink it to $FREESURFER_HOME/subjects/fsaverage (which is our existing
coordinate system, NOT an average of your subjects - to make your own
a
yes, we reorient it to be coronal as part of the "conform" process
cheers
Bruce
On Thu, 6
Feb 2014, Ed Gronenschild wrote:
> Hi,
>
> Using recon-all (freesurfer v5.1.0, MacOSX10.6) I noticed a rotation
> of the T1 data early in the pipeline, i.e., converting rawavg.mgz to
> orig.mgz., see excerp
Hi everyone,
I just re-checked the folder [fsaverage], their modified date was quite
old, probably they are just copies from freesurfer installation folder
rather than results of my scripts. Then my question 2 become void...
best!
Peng
-- Forwarded message --
From: peng
Date:
Hi everyone,
I am a new user of freesurfer. As a first step, I wrote a script (see
below between ---) to run recon-all on the anatomical data. Since I found
it very slow, and our server has multi-cores, I run this script manually
several times, thus it appeared to be parallel.Then I have severa
Hi anastasia,
Thanks for your answer!
I've already find where is my bug.
I've downloaded other tracula update (Centos4). After I download Centos6,
tracula runs without problems with the files used before.
Thanks again
No dia 6 de Fev de 2014 00:56, "Anastasia Yendiki" <
ayend...@nmr.mgh.harvard.e
Hi,
Using recon-all (freesurfer v5.1.0, MacOSX10.6) I noticed a rotation
of the T1 data early in the pipeline, i.e., converting rawavg.mgz to
orig.mgz., see excerpt of output of mri_info below
rawavg.mgz:
xform info: x_r = 0.0081, y_r = -0.0913, z_r = 0.9958, c_r = 0.0813
Hi,
I generated hippocampal subfield segmentations, can generate statistics,
but was wondering if there was a way to visualized the subfield
segmentations as a 3D structure? (e.g. like the figure in this paper:
http://niacal.northwestern.edu/projects/17)
Thank you for your consideration.
Best wi
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