Hello Doug and Freesurfers,We are having trouble unpacking DTI data collected in Bay7. Data are here: cd /autofs/eris/marco/tmp/seunThe error I get is this one, which prevents the nii file from being created:ERROR: mri_convertchild killed: segmentation violationIt looks like the problem doesn’t
Good morning Doug and all,
I am running epidewarp.fsl (using the dev version since I need it to be
compatible with the recent versions of FSL;
/usr/local/freesurfer/dev/bin/epidewarp.fsl).
However, for the first time I see that it complains that it can no longer find
Hi Doug,
I just noticed that when I run epidewarp, it gives me a strange 'if:
Expression Syntax' error message, even if I have no if-statements in my
script (see below for an example of usage). Note that I use the full path for
epidewarp because I am using FSL 5.0.7.
Is this a bug?
Thanks,
Hi all,
If I wanted to find out what was the 'current' FSL version at the Martinos
Center on May 1, 2012, how would i do it?
Thanks!
Marco
__
Marco L. Loggia, PhD
Assistant Professor of Radiology
Harvard Medical School
Massachusetts General Hospital
149
Hello Doug,
I am encountering the error below when running spmregister. Where do you
think is the issue? Thanks!
Best,
Marco
bash-4.1$ spmregister --mov $file.nii --s PBR_$subj --reg tmp.dat
--fsvol merged.lrrev
Log file is ./spmregister.log
Fri Jul 26 10:52:49 EDT 2013
--mov
Hi again,
interestingly, if I run the same command using the full fsvol path I get
the 'Disk quota exceeded' message... I wonder if even the message I wrote
you about in my previous email has something to do with disk space.
I will try free up some room and try spmregister again!
Marco
Hi Doug and Freesurfer team,
I am trying to coregister some PET maps with their relative high resolution
MEMPRAGE files.
I was thinking that bbregister might be my best option but the results are
still not satisfactory, likely due to the intrinsic features of my radioligand
(the resulting
column is the mean in your ROI.
Cheers,
Michael
On Wed, Feb 29, 2012 at 10:56 AM, Marco Loggia ma...@nmr.mgh.harvard.edu
wrote:
Dear all,
Given a series of fsaverage-registered rCBF maps, I am trying to extract
the average rCBF value from one specific region. This region, which
the results for things inside your mask.
doug
Marco Loggia, PhD wrote:
Thank you so much Michael for clarifying this.
Final, related question: is there a way to retrieve the name/paths of the
files concatenated with mris_preproc to create the .mgh file mentioned
below? I usually have
Dear all,
Given a series of fsaverage-registered rCBF maps, I am trying to extract
the average rCBF value from one specific region. This region, which was a
significant cluster from a volumetric (fsl) analysis, was binarized and
then converted to surface.
When I run mri_segstats with the --avgwf
Dear Surfers,
In the past couple of days epidewarp.fsl has been failing, reporting
vsm-smooth: Command not found (see below). Epidewarp was run using the same
parameters, and within the same script that I have been using with no problems
for many months... Has there been a software update
Dear Freesurfers,
I have noticed a slight incongruity between the coordinates outputted by
sig.cluster.summary and those in tksurfer.
For instance, in the .summary file one of my maxima (VtxMax=92221) has the
following Tal coordinates: -14.9, -62.2, 57.5.
Now, if I open the fsaverage
Dear all,
In mris_anatomical_stats, the average cortical thickness value comes with
a measure of dispersion around the mean. Is this Standard Deviation? If so,
is there a way to plot the 95% confidence intervals instead?
Thanks,
Marco
_
Marco L. Loggia, PhD
Cara Angela,
La maggioranza degli utenti di questa mailing list (incluso il team di
freesurfer, che mi ha chiesto di risponderti) non parla italiano. Per
comunicazioni future ti suggerirei di scrivere in inglese, in modo da
assicurarti assistenza diretta dal team.
Per preprocessare i tuoi
Building 120, suite 101E
Charlestown, Massachusetts 02129
Phone: (617) 643-7267
Fax: (617) 643-7340 ma...@nmr.mgh.harvard.edu
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, February 16, 2011 11:52 AM
To: Marco Loggia, PhD
Cc: freesurfer
Dear all,
I am trying to use the 3D view in freeview to prepare some figures, and
would like to be able to rotate the volume along one axis only (e.g., yaw).
Is there a way to constrain the rotation with the mouse, and/or to enter the
numerical value of parameters such as azimuth and
, November 17, 2010 10:06 AM
To: Marco Loggia
Cc: 'freesurfer'
Subject: Re: [Freesurfer] 3D view in freeview
Try using 'mris_decimate_gui' -- if you pass it a --decimationLevel of
1.00, you can view the surface (un-decimated) and add tweak the Up
Vector and Position to move the viewpoint.
Look
the 'max'?
Marco
-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Monday, October 18, 2010 11:30 AM
To: Marco Loggia, PhD; freesurfer
Subject: Re: [Freesurfer] bug in --projfrac-max?
The problem was in the way I documented the flag for mris_preproc
Dear all,
I have some questions about the outputs of mri_glmfit-sim (which I used to
perform permutation tests on my surface analyses).
When I compare *.sig.clusters.mgh and *.sig.masked.mgh surfaces, I notice
that the clusters reported as statistically significant also include some
Dear all,
Is it possible that the --projfrac-max has a bug (at least when used with
mris_preproc)?
I sampled the same volume using --projfrac 0.5 and --projfrac-max (see
below) and, when I overimposed the two surfaces, I noticed that in some
vertices the first surface (i.e., 0.5) appear to have
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