Hi Arash
Yes. Register the surface to the volume with bbregister, then use mri_vol2surf
to do the sampling
Cheers
Bruce
On Oct 22, 2013, at 12:13 PM, Arash Nazeri wrote:
> Dear all,
>
> I'm new to the freesurfer. I want to project surrounding cortical voxel
> values (intensities) from a giv
I'm not sure it's fixable then. Any idea what they are?
Bruce
On Oct 22, 2013, at 9:30 AM, Jonathan Holt wrote:
> They are bright in orig.mgz. You can see in the pictured attachments
>
>
> On Mon, Oct 21, 2013 at 1:51 PM, Bruce Fischl
> wrote:
> why are they so bright? Are they that way b
Hi Linn,
Sorry for the delay in answering. The path has to be set directly in your
environment variable (the variable $PATH has to point to the correct version).
I need a few more details about what you tried and which OS you are using to be
able to help you.
If you are using mac, here is an
If it's important to you to be able to use wildcards instead of the actual
file name, you can do it from any directory like this:
set dcmlist = (`cd $dcmroot; echo subj238/DTI/i*.MRDC.1`)
On Tue, 22 Oct 2013, Jon Wieser wrote:
it works pnly if the directory that you run the trac-all comman
Thank you for your help! We were able to work out the issue!
Emily
- Original Message -
From: "Anastasia Yendiki"
To: "Jon Wieser"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 22, 2013 2:21:49 PM
Subject: Re: [Freesurfer] Tracula Error
Jon - Thank you for your suggestion.
Jon - Thank you for your suggestion. However, the wiki is correct. The
file names in dcmlist should be relative to the directory name in dcmroot.
The problem is that essentially you are doing this:
set dcmlist = ( )
Because of how you're using the wildcard character *, you end up with an
Hello FreeSurfer experts,
I am trying to run recon all on my data set, but I got following error message.
Please help me understand the message and suggest solution.
Thanks,
Rashmi
#@# Skull Stripping Tue Oct 22 13:57:00 CDT 2013
/home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/ANAL2013/Co
There is no * character in the example on the wiki. What do you think
should change?
On Tue, 22 Oct 2013, Jon Wieser wrote:
> that makes perfect sense, but you should change the instructions in the
> Tracula wiki to reflect this.
> the tracula wiki says:
>
>
>
>
> Step 5: Specify the location
It's the * and its interpretation by the unix shell that does this, so it
has nothing to do with tracula.
When you run this command:
set dcmlist = (i*.MRDC.1)
you're telling unix to find all files that match this pattern and to make
the dcmlist variable equal to the list of files. If it
according to the tracula wiki:
http://freesurfer.net/fswiki/FsTutorial/Tracula
the program should look in the directory specified by "dcmroot" to look for
the dicom list
excerpt from the wiki page:
Step 5: Specify the location of diffusion DICOM files
set dcmroot = $TUTORIAL_DATA/diffus
On 10/22/2013 01:19 PM, Laura M. Tully wrote:
> Thanks for the suggestions Doug, I have a few clarifying questions
> below, to make sure I understand everything.
>
>
> On Tue, Oct 22, 2013 at 8:02 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> The duration of illnessis
The problem is that the command "set dcmlist = (i*.MRDC.1)" is executed as
soon as it is read. So this will end up with an empty dcmlist, because
there are no files named i*.MRDC.1 in the current directory.
On Tue, 22 Oct 2013, Jon Wieser wrote:
>
> Hi anastasia,
> I work with Emily. the wi
Thanks for the suggestions Doug, I have a few clarifying questions below,
to make sure I understand everything.
On Tue, Oct 22, 2013 at 8:02 AM, Douglas N Greve
wrote:
>
> The duration of illnessis always 0 for your healthy controls(which is
> obviously reasonable). The problem is that mri_glmfi
Dear all,
I'm new to the freesurfer. I want to project surrounding cortical voxel values
(intensities) from a given map (e.g. mean diffusivity map in a nifti format) to
a surface file (e.g. mid-cortical surface in a gifti fromat) to generate scalar
maps like ?h.thickness for group-wise statist
Hi anastasia,
I work with Emily. the wild card she used i*.MRDC.1 specifies only the
first dicom image. the dicoms are in the format:
i727056.MRDC.1 i727065.MRDC.10 i727074.MRDC.19 i727083.MRDC.28 i727092.MRDC.37
i727101.MRDC.46 i727110.MRDC.55 i727119.MRDC.64 i727128.MRDC.73 i727137.M
Dear doug:
I overlaped the transformed vol ROI to the original T1 image, both in native
space, then surprisingly found out that lh labeled ROI was on the right
hemisphere but contained the exact lh sulcus or gyrus information. I converted
the spacific label to ROI based on white/grey boundry, s
Hi Emily - You're using "*" to specify all the dicom files in the series.
You should specify just one file.
BTW, do you have the latest version of freesurfer and the tutorials? This
dmrirc looks like it might have been adapted from an older version of the
tutorials. If so, I highly recommend d
Hi Mike - I'll need to see the configuration file and trac-all.log.
Thanks,
a.y
On Mon, 21 Oct 2013, Michael Datko wrote:
Hello,I am running into a tracula error very early in the preprocessing steps.
I have data that was already somewhat preprocessed (reconstruction, eddy
correction and mag
How are you determining that they are lr flipped?
On 10/21/2013 11:18 PM, wen.zhang55 wrote:
> Dear Freesurfer：
> I am now working in converting cortical labels from freesurfer to
> volumetric masks. First i gained the registration matrix by
> bbregister, then applied those matrix to tranform RO
Thank you Doug. I did compute the mean from all the ages.
Crystal
On 10/22/13 9:51 AM, "Douglas N Greve" wrote:
>
>Hi Crystal, that is ok. When you demean the ages, make sure you compute
>the mean from all the ages, not separate means for each group
>
>doug
>
>
>
>
>On 10/21/2013 05:30 PM, Fra
The duration of illnessis always 0 for your healthy controls(which is
obviously reasonable). The problem is that mri_glmfit is creating a
regressor of all 0s to model this duration and this is causing the
ill-conditionedness. There are several things you can do:
1. Create your own design matri
Hi Crystal, that is ok. When you demean the ages, make sure you compute
the mean from all the ages, not separate means for each group
doug
On 10/21/2013 05:30 PM, Franklin, Crystal G wrote:
> Freesurfer,
>
> I want to make sure I am setting up my group analysis correctly. I
> have 2 groups
-- Forwarded message --
From: Todd Constable
Date: Thu, Oct 17, 2013 at 9:25 AM
Subject: 2nd Whistler Scientific Workshop on Brain Function, March 9-12, 2014
To: Todd Constable
Cc: Todd Constable
The 2nd Whistler Scientific Workshop on Brain Functional Organization,
Connectivi
No, the individual subjects processed by recon-all -all are all OK (not cut
off superiorly), only the average produced by make_average_subject is cut
off superiorly.
Thanks
Cheers
Jürgen
On [DATE], "Bruce Fischl" <[ADDRESS]> wrote:
> Does it happen with just one subject? If so, can you upload i
Does it happen with just one subject? If so, can you upload it?
Thanks
Bruce
> On Oct 22, 2013, at 5:21 AM, Jürgen Hänggi
> wrote:
>
> Hi Bruce
>
> I am running FS 5.3.0 on Mac OSX and both versions
>
> Lion OX X 10.7 (64b Intel) and
> SnowLeopard OS X 10.6 (32b Intel)
>
> are affected. Howe
Hi,
I am trying to compute lgi measures, and I think my problem lies in the
fact that the matlab path is not set correctly; it is calling an older
version of matlab however I need it to point to matlab2013b. I have tried
numerous things like changing the startup.m file, the .bashrc file and
export
Hi Bruce
I am running FS 5.3.0 on Mac OSX and both versions
Lion OX X 10.7 (64b Intel) and
SnowLeopard OS X 10.6 (32b Intel)
are affected. However, the average surface model looks fine.
Cheers
Jürgen
On [DATE], "Bruce Fischl" <[ADDRESS]> wrote:
> what version are you running?
> On Tue, 22 Oct
what version are you running?
On Tue, 22 Oct 2013, J?rgen H?nggi wrote:
> Dear FS experts
>
> When using make_average_subject the resulting volume files (T1.mgz,
> orig.mgz, brain.mgz, etc.) are cut off superiorly (see attachment).
>
> Any idea?
>
> Thanks in advance
> Regards
> J?rgen
>
> ---
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