Hi,
i'm a novel freesurfer user and i'm afraid i need some help here, please!
-
FREESURFER_HOME: /usr/local/freesurfer-5.1
Build stamp:
Hi All,
I am still in need of finding the tool sequence to generate an ASCII file
containing (1) voxel RAS coordinates (2) for a specific label (3) using the
original MRI coordinates rather than freesurfer coordinates.
mri_convert -rl rawavg.mgz input vol output vol
does generate a
Good morning,
I’m just checking back in about a bbregister problem that I posted about
earlier this week (see email below). I was told to check back at the end of the
week about a patch.
Thanks so much for your time and assistance!
Marta Zamroziewicz
MD/PhD Candidate
Decision Neuroscience
Hi Alejandra
sorry, that's a bug we fixed in 5.3. You need a new version of
mris_topo_fixer and mris_fix_topology
cheers
Bruce
On Fri, 1 Aug 2014, Alejandra Machado wrote:
Hi,
i'm a novel freesurfer user and i'm afraid i need some help here, please!
Hi Don
try mri_label2label. Also, the if you are transforming label volumes you
need to use nearest neighbor interpolation, so include the -rt nearest
switch.
cheers
Bruce
On Fri, 1 Aug 2014, Krieger, Donald N. wrote:
Hi All,
I am still in need of finding the tool sequence to
Hi Freesurfer experts,
I ran the command trac-all -prep -c dmrirc.txt
on a bunch of subjects and all of them finished in ~90 minutes except one.
This subject keeps on going into a seemingly endless loop. It has been
running for almost 12 hours now. A section of the console output is
reproduced
Hi Don
the -rt nearest switch is for mri_convert. I'll leave the rest of the
questions for Doug :)
Bruce
On Fri, 1 Aug 2014, Krieger, Donald N. wrote:
Thanks for posting back so quickly, Bruce, and for the direction.
Just to clarify, here is the command which I am using so you can see
Hi Doug,
Just wanted to follow up on this. I'm getting the error that says that the
QDEC GLM design creates 0 factors, regardless of how many of the factors in the
data table I sent are included in the design. (There are a total of 2 discrete
and 9 continuous variables in the data table.)
I
Hi all,
I am trying to convert a group cluster to GIFTI (.gii) format. I just need
some help running mris_convert.
The example for a label to GIFTI is
mris_convert --label lh.V1.label V1 lh.white lh.V1.label.gii
I'm trying to figure out what is required here. I understand I put in the
label
Hi,
I am doing manual corrections of topological errors and am wondering if
there is a way to bypass recomputing the surfaces as suggested by the
topographical errors tutorial and instead doing some sort of manual editing
of the pial surface. Does such an editing option exist?
Thank you,
Hi Kate
I'll cc Andre and Dylan, but I would have thought some sat bands in the
neck would do it. I think vessels are usually bright in the mprage, but
don't usually case problems. Comments welcome
cheers
Bruce
On Fri, 1 Aug 2014,
McLaughlin, Katie wrote:
Hi Doug, Bruce, et al.
Hi Lindsay,
not really. It would be pretty hard to do, particularly if the topology
isn't right
sorry
Bruce
On Fri, 1 Aug 2014, Lindsay Gubernick wrote:
Hi,
I am doing manual corrections of topological errors and am wondering if
there is a way to bypass recomputing the surfaces as
Hi,
Thanks, yes, we have this problem on our scans from the Allegra and 7 T
scanners, where there's a local transmit coil (no body transmit coil)
and therefore blood with non-inverted spins enters the head after the
inversion pulse and appears bright in the images. With our Allegra scans
this
Hi Marta, I thought I was going to be ready to release it today, but my
checks failed on the new script, so now I have to dig into it to see
what is wrong. Check back next week.
doug
On 08/01/2014 09:19 AM, Zamroziewicz, Marta Karolina wrote:
Good morning,
I’m just checking back in about a
Hi Don, try looking at this page for more info on our coordinate systems
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 08/01/2014 10:47 AM, Bruce Fischl wrote:
Hi Don
the -rt nearest switch is for mri_convert. I'll leave the rest of the
questions for Doug :)
Bruce
On
So, did it generate the error when you loaded the table or when you hit
analyze? List the steps and buttons that produce this error.
doug
On 07/31/2014 05:20 PM, McLaughlin, Katie wrote:
Hi Doug,
I'm using 5.3.
This error was generated when I had more variables in the model, so I used
We don't compute density. You can run mri_compute_volume_fractions to
produce such images
doug
On 07/31/2014 09:54 PM, Qiongmin wrote:
Dear All,
I wonder if there are any functions that can calculate the grey matter
density of the vertices or in the ROI manner? I figured out that
Hello users or support team,
after using FS successfully for some time, now, after
a trivial command such as
mri_convert -it analyze T1.img -ot mgz 001.mgz
an error appears as follows:
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from T1.img...
On 07/31/2014 03:16 PM, Mohammed Goryawala wrote:
Hello All,
I have some questions related to the qdec analysis I have run.
1. On running the qdec I see that FWHM is an input which changes
cluster definition significantly. How would I choose the right FWHM
for the analysis and can it be
what was your command line?
On 07/21/2014 03:43 PM, April Clausen wrote:
Hi Dr. Greve, I tried to upload the images with the Martinos Centre
Dropbox but I could not activate the dropbox … so the images are
attached. The 6 labels and annot file were created on fsaverage and
the image shows
not sure what is going wrong. How did you create the file? Make sure it
is a simple ascii text file not created under Windows
On 08/01/2014 04:10 PM, Saemann Philipp wrote:
Hello users or support team,
after using FS successfully for some time, now, after
a trivial command such as
Hello Douglas,
the file created on Linux, no Windows involved, and was 100% identical
to the old license file that was successfully used for some time.
Do I need a new download?
Thanks,
Philipp
At 16:14 01.08.2014 -0400, you wrote:
not sure what is going wrong. How did you create the file?
Hi Doug,
The issue seems to be that qdec can't find the subjects in the SUBJECTS_DIR
(see output below) when loading the data table.
The subjects are all in the directory, however, with permissions set to 777 on
all. I've found a number of previous posts with the same error, but no
solution.
How did you create your qdec table? It looks like it might have been
created on a windows machine. If so, try creating it in linux.
doug
On 08/01/2014 04:53 PM, McLaughlin, Katie wrote:
Hi Doug,
The issue seems to be that qdec can't find the subjects in the SUBJECTS_DIR
(see output below)
Hi Doug,
Same error when data table created in Linux
There are a number of messages about this same issue in the Archive (e.g.):
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033471.html
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-October/008618.html
Thanks Doug.
On Aug 1, 2014 4:16 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
On 07/31/2014 03:16 PM, Mohammed Goryawala wrote:
Hello All,
I have some questions related to the qdec analysis I have run.
1. On running the qdec I see that FWHM is an input which changes
cluster
you could get a T2 or FLAIR and use it to fix the pial surface
On Fri, 1 Aug
2014, McLaughlin, Katie wrote:
Hi Andre and Bruce,
Thanks for your input here. The sat band has helped, although it hasn't
entirely corrected the problem (the image attached was from a subject with
the sat bands
what version of Linux are you using?
On Fri, 1 Aug 2014, Saemann Philipp
wrote:
Hello Douglas,
the file created on Linux, no Windows involved, and was 100% identical
to the old license file that was successfully used for some time.
Do I need a new download?
Thanks,
Philipp
At 16:14
Hello Bruce,
I am trying to check the output of the mri data that I processed I start using
MNE. I placed the file in a folder called Practice in my documents, and I am
using the following command:
tcsh
source your_freesurfer_dir/SetUpFreeSurfer.csh
setenv SUBJECTS_DIR
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