Thanks Bruce,
Doing the bias correct and -odt float fixed the issue. Adding -odt short did
not.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Tuesday, 8 March 2016 11:46 AM
To: Freesurfer s
FYI
-- Forwarded message --
Date: Tue, 8 Mar 2016 02:00:35 +
From: THOMAS J. GRABOWSKI
To: Bruce Fischl
Subject: Position at UW
Hi Bruce,
I am looking for a research scientist with expertise in fMRI experimental
design and neuroscience to fill an unexpected vacancy at o
Hi Bruce,Thanks, I uploaded my subject in your ftp site.case name:
train_emc_010.tar.gz
Best,Maryam
On Monday, March 7, 2016 5:26 AM, Bruce Fischl
wrote:
Hi Maryam
I guess, although it's hard to say without looking at your data. I think
the upcoming V6 does much better on
On 7 March 2016 at 11:25, Francis Tyson Thomas
wrote:
> That information was a lot helpful. At this point I'm currently trying to
> reduce the recon-all processing time as much as possible and for this reason
> I was looking to get the -use-gpu flag working. I'm currently running a
> freesurfer v
it might, but you will need to make some fixes that are in 6.0 (soon) but
not in 5.3. The 5.3 recon-all changes the T2 datatype to uchar when it
resamples it to be in register with the T1. You should change that line to
have -odt short or -odt float so that it doesn't saturate at 255, which is
I see it now. I will try to perform a bias correction on the image prior to
importing and see if that helps. Thanks Bruce.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Tuesday, 8 March 2016
On 03/04/2016 06:01 AM, Silas wrote:
> Thanks Douglas!
>
> 1 - I have two functional files per subject (.mgh). Is it possible to insert
> two files per subject in mris_preproc? In my former functional analysis I
> haven't concatenated my data using a FSGD-file when running mris_preproc.
Are the
is this still a problem?
On 03/04/2016 01:24 PM, Sahil Bajaj wrote:
> Dear all,
>
> I am working on calculation of cortical thickness from a set of
> subjects. I am following the instructions from
> https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness and
> I am able to run up-t
what happens when you run the following?
cd /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
--i orig.mgz --o orig_nu.mgz
On 03/07/2016 04:09 PM, Flavia Niccolini new wrote:
> Hello,
>
> I was wondering whether yo
/*!
\fn MRISvolumeTH3(MRIS *w, MRIS *p, MRI *vol)
\brief Compute vertex-wise volume based on dividing each obliquely
truncated
trilateral pyramid into three tetrahedra. Based on Anderson M. Winkler's
srf2vol matlab script.
\params w is white surface, p is pial. Output is an MRI stru
what are your command lines?
On 03/04/2016 09:01 PM, Kaiming Yin wrote:
> Dear guys,
>
> I was doing group analysis (command-line) on two groups (patients and
> control, no age or other information). The data has been "qcached",
> and after following the three steps as "mris_preproc, mri_glmfit
The code that does this is hard-coded and hard for me to follow
(eventhough I wrote it:). It might be faster to to try to change
ROI5.mgh. How did you create
*/media/Storage/FTD_Data/fsaverage/surf/ROI5.mgh?*
On 03/04/2016 04:31 PM, Sahil Bajaj wrote:
>
> Hello again,
>
>
> To calculate cortica
the table file lh.aparc.thickness.table should be an ascii file. when you look
at it with cat/more/less, what do you see? Can you send that table file?
On 03/07/2016 04:33 AM, Caroline Beelen wrote:
> Hi Bruce,
>
> I'm a beginner in FS, so I just followed tutorial instructions for generating
>
It isn't recognized:
$ mris_convert --vol-geom mri/T1.mgz ../fsaverage5/surf/lh.pial.tvb.bad
surf/lh.pial.bad
unknown option --vol-geom
I can stick with the dev version if no command line utility is available for
this in the stable version.
De : freesurf
Are you sure the job was not killed in the middle? The recon-all.log
file just stops without a warning or error message. Or does this happen
repeatedly?
On 03/07/2016 03:10 PM, Julian Jäckle wrote:
> Thank you so much for the response. Unfortunately I am not so familiar
> with freesurfer but th
Try mris_convert with --vol-geom option
On 03/07/2016 02:34 PM, dgw wrote:
> Marmaduke,
>
> Could you describe what it is you want to do? What do you mean by
> volume geometry? What type of information do you want to put on the
> surface?
>
> d
>
> On Mon, Mar 7, 2016 at 2:31 PM, marmaduke woodman
I mean that the mri_surface structure and the file format it uses both
allow a vox2ras transform to be stored. I guess the matlab code doesn't
support it, but it could be modified to do so if anyone was interested
Bruce
On
Mon, 7 Mar 2016, WOODMAN Michael wrote:
> sorry to bother, but can you e
sorry to bother, but can you elaborate? mris_convert --help doesn't show
anything.
De : freesurfer-boun...@nmr.mgh.harvard.edu
de la part de Bruce Fischl
the surface files do support embedding a ras2vox transform in them
_
Hello,
I was wondering whether you could help with this error:
#
#@# MotionCor Thu Mar 3 11:35:51 GMT 2016
Found 1 runs
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one
Dear Anastasia,
Thank you! Wouldn't you mind for example sending me these tables? As far as I
am concerned I need only one table for all my subjects, so that would help me a
lot. The issue with flipped coordinates in the gradient table is, as I
mentioned before, due to the fact that I obtained
Thank you so much for the response. Unfortunately I am not so familiar with
freesurfer but these files do not exist: transforms/talairach_with_skull.lta,
brainmask.auto.mgz, brainmask.mgz. I don’t know if it is helpful but below
I listed all files which can be found in the subjects directory
*Touc
On 03/07/2016 08:34 PM, dgw wrote:
> Marmaduke,
>
> Could you describe what it is you want to do? What do you mean by
> volume geometry? What type of information do you want to put on the
> surface?
I wish to approximate the effect of the --tval-xyz vol argument to
mris_surf2surf in the dev ver
the surface files do support embedding a ras2vox transform in them
On Mon, 7 Mar 2016, dgw
wrote:
> Marmaduke,
>
> Could you describe what it is you want to do? What do you mean by
> volume geometry? What type of information do you want to put on the
> surface?
>
> d
>
> On Mon, Mar 7, 2016 at 2
Marmaduke,
Could you describe what it is you want to do? What do you mean by
volume geometry? What type of information do you want to put on the
surface?
d
On Mon, Mar 7, 2016 at 2:31 PM, marmaduke woodman
wrote:
> hi
>
> Is it possible to embed a volume geometry in a surface file explicitly?
>
hi
Is it possible to embed a volume geometry in a surface file explicitly?
I'm unable to find a mri_ or mris_ command which seems to do this. Is
there any workaround via the GUI tools?
Thanks,
Marmaduke
___
Freesurfer mailing list
Freesurfer@nmr.mgh.
Hi Julian
can you give us more details about what exactly is missing?
cheers
Bruce
On Mon, 7 Mar
2016, Julian Jäckle wrote:
Dear FS-team
For purposes of measuring cortical thickness I’ve been running recon-all as
described on your RecommendedReconstruction site.
However I am missing some
Dear FS-team
For purposes of measuring cortical thickness I’ve been running recon-all as
described on your RecommendedReconstruction site. However I am missing some
files including e.g the skullstripped file. Could you check my log file for
the root cause?
Greetings
Julian
recon-all.log
Des
Hi Prad - I'm guessing the tutorial was generated with an earlier version
of bedpostx, tracula, or a combination of both. So I wouldn't expect to
find the exact same values. As long as things run and the files are
generated, it looks like you're fine.
Best,
a.y
On Mon, 7 Mar 2016, Bharadwaj,
Hi Anastasia,
Thank you for clarifying that. I have a follow up question.
To avoid this error while running the ball and stick model fit( Syntax error:
"(" unexpected), I ran it locally using "bedpostx $path_to_dmri".
The results of the overall path statistics differ from those in the tutorial
Anatorig will take you to freesurfer space. I's suggest smoothing these to
make them more presentable, and potentially also thresholding them based
on the probability map (which is the sum of these streamlines).
On Mon, 7 Mar 2016, Peled, Noam wrote:
> I want to display it in my new 3d visuali
I want to display it in my new 3d visualization tool, along the hemispheres and
the subcortical regions.
The hemispheres and the subcortical regions I import from freesurfer.
Thanks,
Noam
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nm
Hi Chris
I took a look, and the problem is that there are big changes in contrast
between occipital and frontal lobes. If we normalize both posterior and
frontal wm to 110, occipital gray matter gets mapped to 180 but frontal
gray gets >255. This kind of thing can be caused by a transmit "bia
What to you want to display it on? If you want to display in on the FA
map, or anything that's in diffusion space, you don't need any transform.
On Mon, 7 Mar 2016, Peled, Noam wrote:
> So for plotting the fibers, like in freeview, should I just use the
> /dmri/xfms/diff2anatorig..mat or
> /d
Hi Prad - What will affect the speed is whether you run it locally on your
computer (in which case it'll process one slice after the other) or on a
cluster (in which case all the slices will be processed in parallel on
different nodes of the cluster). This is the case regardless of the
versio
So for plotting the fibers, like in freeview, should I just use the
/dmri/xfms/diff2anatorig..mat or
/dmri/xfms/diff2anat..mat transformation matrices?
Thanks again,
Noam
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.ed
Yes, native diffusion space.
On Mon, 7 Mar 2016, Peled, Noam wrote:
> Thanks!
> Do you in which space are the voxel coordinates coordinates? Are they in the
> diffusion space?
>
> Thanks again,
> Noam
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [
Hi Jacek - I looked at the data that you uploaded. The problem is that
both the b-value table and the gradient table that you were using were
assuming that the b=0 images were interspersed throughout your scan, when
in fact based on your dicoms they are all in the begining of the scan. So
the
I got it, thanks
Bruce
On Mon, 7 Mar 2016, Champe Barton wrote:
Hey Bruce,
I got a notification saying the email my recon-all.log file attachment was too
large and had to await moderator approval to be posted to the support list. I
was just wondering if you received it or if I should resend
Hi Richard,
That information was a lot helpful. At this point I'm currently trying to
reduce the recon-all processing time as much as possible and for this
reason I was looking to get the -use-gpu flag working. I'm currently
running a freesurfer v6 beta version on Ubuntu 14.04.4. With regard to th
Hey Bruce,
I got a notification saying the email my recon-all.log file attachment was too
large and had to await moderator approval to be posted to the support list. I
was just wondering if you received it or if I should resend it.
Best,
Champe
Sent from my iPhone
> On Mar 6, 2016, at 9:53
Hello,
The Nantz National Alzheimer Center, in Houston, TX is looking to fill two
positions pertaining to neuroimaging and analysis.
Be aware that we cannot accept remote employment, the candidate would have to
work day-to-day in the city of Houston.
Any interested person is encouraged to revi
Thanks!
Do you in which space are the voxel coordinates coordinates? Are they in the
diffusion space?
Thanks again,
Noam
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki
[ayend...@nmr.m
Dear all,
I have just installed FreeSurfer 5.3.0. on Ubuntu 14.04 LTS (64-bit).
The mri_convert doesn't work with no error message. which mri_convert gives
/usr/local/freesurfer/bin/mri_convert. Of course neither does recon-all (which
exits with errors with no error message in the log).
I mad
Hi Maryam
I guess, although it's hard to say without looking at your data. I think
the upcoming V6 does much better on the midline. If you upload your
data I can take a look. For the command line you can check out the
recon-all help and just rerun the pial surface generation
cheers
Bruce
On
Hi developers,
My environment:
MacPro OSX10.7 installed on a partition of 20 GByte;
FreeSurfer v6 beta
During processing recon-all on 4 subjects in parallel
using 4 terminal windows, the 20 GByte partition got
full. This happened twice and I managed to trace down
the offending stage in the pipeli
Hi Bruce,I am editing aseg to correct the boundaries that excluded the lateral
ventricle. The problem with lateral ventricle has been solved after running the
process with -noaseg flag. But the boundaries in the middle, is crossing to the
other hemesphere in some cases.
I even tried -autorecon2
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