Use aparc.a2009s+aseg.mgz
On 05/11/2015 02:01 PM, Alshikho, Mohamad J. wrote:
Hi Doug,
I want to use the command fcseed-config to configure the segment 1126 (in
aparc+aseg) as a seed to pass it to connectivity analysis. I ran the command
line:
fcseed-config -segid 1126 -fcname
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From: i...@humanbrainmapping.org
Reply-To: i...@humanbrainmapping.org
To: gr...@nmr.mgh.harvard.edu
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Greetings Freesurfer experts,
I've looked over the FS mailing list, as well as other resources (such as
Mumford's page on demeaning and fMRI data), but I was still a bit confused,
so apologizes in advance.
I have a datatset that consists of only 1 group (an expert trained group),
and I'd like to
Hi Sarah
the unfolding tries very hard to preserve exactly this - the metric
properties. If you cut off the occipital third of cortex and flatten it
(after introducing some cut along the axis of the cone) you should be
able to get to around 10% distortion or below, which I assume is good
Hi Doug,
I want to use the command fcseed-config to configure the segment 1126 (in
aparc+aseg) as a seed to pass it to connectivity analysis. I ran the command
line:
fcseed-config -segid 1126 -fcname L_G_Precentralgyrus.dat -fsd bold -mean -cfg
mean.L_G_Precentralgyrus.config
Then I ran
oh, the 1126 is for the 2005 atlas, try 11129 (ctx_lh_G_precentral) instead
On 05/11/2015 03:00 PM, Alshikho, Mohamad J. wrote:
Hi Doug,
Here is the output:
cmdline mri_binarize --i aparc.a2009s+aseg.mgz --binval 1 --o
L_G_Precentralgyrus.mgz --match 1126
sysname Linux
hostname glia
Fabulous!!! It worked
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Monday, May 11, 2015 5:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fcseed-sess
oh, the 1126 is
You only need to make it once for mni305. The analysis is not lateralized.
doug
On 05/04/2015 05:19 PM, Alshikho, Mohamad J. wrote:
Hi Doug,
I wanted to run FSFAST without using the paradigm file in the analysis
using the following command lines:
1.preproc-sess -s ${i} -fwhm 5 -surface
On 05/04/2015 09:29 PM, Alena Piovar wrote:
Hello,
I am trying to establish contrast for direct statistical analysis in FS.
if I have for example three subject and I want to correlate thickness
with age
the fsgd file is set
GroupDescriptorFile 1
Title G1V2
Class Patient
Variables
You can try mri_segstats with the label or annotation option
doug
On 05/05/2015 09:21 AM, Corinna Bauer wrote:
Hi all,
What command would I use to apply the aparc labels to a different
surface (e.g. to $h.ratio.mgh)??
The ratio file was created as follows:
mri_vol2surf --src ${nu_mgz}
Hi Doug,
Here is the output:
cmdline mri_binarize --i aparc.a2009s+aseg.mgz --binval 1 --o
L_G_Precentralgyrus.mgz --match 1126
sysname Linux
hostname glia
machine x86_64
user malshikh
input aparc.a2009s+aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output
Hi Bruce,
Is there some way to know when cuts have been made correctly so that
distortion can be minimized? (Or conversely, some way to know when a given
patch has or will undergo too much distortion during flattening?
Thanks!
Michael
On Mon, May 11, 2015 at 12:24 PM, Bruce Fischl
Use --lh instead of --hemi lh
On 05/10/2015 03:32 PM, Derek James Dean wrote:
Dear Freesurfer community,
I am trying to complete the final iteration described in the Xhemi
wiki page to compare left-right hemisphere symmetry between a patient
and control group but I get an error when I run
This is an example where the method was used in a study (but it did not
try to verify it)
Greve, Douglas N., Lise Van der Haegen, Qing Cai, Steven Stufflebeam,
Mert R. Sabuncu, Bruce Fischl, and Marc Bysbaert. A surface-based
analysis of language lateralization and cortical asymmetry. (2013).
It sounds like you did the right thing.
On 05/10/2015 02:41 PM, Pedro Rosa - GMail wrote:
Dear developers,
I am running an analysis with dt_recon, and it seems that my DWI files
are organized into three series (one larger, and two smaller, that I
believe are ADC and Trace). Inputing a DICOM
what is the error?
On 05/04/2015 01:56 PM, Xiaomin Yue wrote:
I am having another problem with mkanalysis-sess, here is my command:
mkanalysis-sess -funcstem fmc.so.sm2 -analysis volanalysis -native
-paradigm human_curv.par -event-related -gammafit 2.25 1.25
-refeventdur 16 -polyfit 2 -TR
There is no one place you can get it from. You can go to
cache.th30.abs.y.ocn.dat. this will have a column for each cluster. Each
row is an input/subject. If you compute the mean of the rows, you'll get
the mean effect in each cluster.
On 05/04/2015 03:03 PM, Hirsch, Gabriella wrote:
Hi FS
Dear Freesurfer Users,I am trying to update the freeview file. However, I cannot find the folder$FREESURFER_HOME/Freeview.app/Contents/MacOS/FreeviewWhen I go into my Freesurfer folder, I cannot find Freeview.app.Any help would be greatly appreciated.Thanks,Isabelle
Dear all,
I am looking to take two measures within the visual cortex.
1) A measure of width and length for each activation cluster overlaid onto the
flattened cortical surface.
2) A measure of spacing between each cluster
I can find how to take measures of area but I specifically want to know
Hello,
I wanted to inquire about when you think that this new package for
freesurfer 6.0 will be complete? I am interested in pursuing hippocampal
segmentation, but it seems that I should not use the segmentation from your
older program and I should wait, would you agree?
Thank you,
Josh
--
Hello, I'm looking for some help to generate connectivity matrices using
Freesurfer segmented volumes and my DTI data.
Firstly, the output from Freesurfer required for network analysis in
ExploreDTI needs a label volume file in .nii format. Then, I need a
coordinate .txt file and two column label
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