Hi Richard,
Thanks again for the quick response. I am able to compile CUDA programs from
the SDK, so I will try to compile from the Fs source per the advice that you
provided and see what happens. Will let you know how it goes!
-Derek
From: freesurfer-bo
Hi Stephen
how did you create the patch? It looks like it is corrupted since that
vertex # is way too big. The total # of vertices in the patch is also
wrong.
cheers
Bruce
On Thu, 23 Jun 2016, S.V.Shepherd [work] wrote:
Hello all,
I'm trying to make a patch and have run into the 'bad vert
The UCSF Department of Radiology and Biomedical Imaging is looking for a
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Hello,
Usually this error only occurs when using the the mni tools with the
perl (version 5.22 or higher). But Yosemite should be pre 5.22 so Im not
sure why your encountering that issue.
Can you upload me you subject data so I can take a look?
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpF
I can see it so I don't know what the problem is. The script is short, so I've
just copied it below.
#!/usr/bin/python
# This script replaces carriage returns with line feeds
# Usage: rmcr inputfile > outputfile >
# $Id: rmcr,v 1.1 2015/03/24 21:56:02 greve Exp $
import sys;
import fileinput;
sy
After you run preproc-sess, there will be a file called
register.dof6.dat. Map fmri into the anatomical space, something like
mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o
fmcpr.anat.nii.gz
Then use mri_segstats with --seg aseg.mgz --i fmcpr.anat.nii.gz
However, I don't
You have no HDFemales so the 2nd column is 0.
On 6/21/16 7:40 PM, Arkadiy Maksimovskiy wrote:
Hello,
Hello,
I am getting the following error:
ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
Command line:
mri_glmfit --y lh.BD_SD.thickness.
Try
mri_vol2vol --targ fsaverage.DKT40+aseg.nii --mov
/usr/local/fsl/data/standard/MNI152_T1_2mm.nii.gz --o
fsaverage_MNI_DKT40+aseg.nii --interp nearest --reg
/Applications/freesurfer/average/mni152.register.dat --inv
On 6/22/16 12:45 AM, Skyler Gabriel Shollenbarger wrote:
Hi FS communi
$ tksurfer ${subj} lh inflated -sulc
1) closed cut line around corpus callossum etc.
2) four tension relief cuts
3) select connected region
4) save as patch
*stephen v. shepherd phd*
The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA
// 212.327.7699
On Thu, Jun 23
Does that file exist? What is in it? If it is empty, it may bneed to be
regenerated for that subject. Run
recon-all -s subject -segstats
On 6/22/16 7:17 PM, Elias Vergílio Da Cás wrote:
Hi,
*After the command: *
asegstats2table --subjects AntonioMagnani -- meas volume --tablefile
TESTE.tx
Hello,
Doing a recon-all -all yields some deprecation warnings.
defined(@array) is deprecated at
/freesurfer/mni/bin/nu_estimate_np_and_em line 165.
Use of ?PATTERN? without explicit operator is deprecated at
/freesurfer/mni/bin/sharpen_volume line 153.
I think my results should still be OK b
I should also note that I have had a couple problems, trying to fill the
uncut area, where I get the following error:
---
tksurfer.bin: ../../src/mesa/tnl/t_vertex.c:423: update_input_ptrs:
Assertion `a[j].inputstride == vptr->stride' failed.
Abort (core dumped)
---
*stephen v. shepherd phd*
Yes they are just warning and can be ignored. The upcoming release of
freesurfer v6 has addressed the deprecation issue.
-Zeke
On 06/23/2016 11:48 AM, Rockers, Elijah D. wrote:
> Hello,
>
> Doing a recon-all -all yields some deprecation warnings.
>
> defined(@array) is deprecated at
> /freesurfe
All,
Upon looking at online forums and the FreeSurfer wiki, I have come to the
understanding that "BrainSeg" volume in the aseg.stats file includes all
cortical and subcortical gray matter, cerebellar gray matter; cortical,
subcortical and cerebellar white matter and white matter hypointensiti
hmmm, are you sure that the partition isn't full or something?
On Thu, 23
Jun 2016, S.V.Shepherd [work] wrote:
$ tksurfer ${subj} lh inflated -sulc
1) closed cut line around corpus callossum etc.
2) four tension relief cuts
3) select connected region
4) save as patch
stephen v. shepher
Dear Freesurfer experts,
I wanted to run cortical thickness analysis between two groups to check the
diffetence in thickness between the groups. I used Qdec
My question is regarding correcting for multiple comparisons. There are two
options FDR and montecarlo.
Which option do you recommend? Are t
The error on flattening was caused by my saving the surface, instead of the
patch, to lh.full.patch.3d. I apologize -- it was a dumb mistake.
I am unsure what caused the """ Assertion `a[j].inputstride ==
vptr->stride' failed. """ error, but it only occurred on a few attempts, so
I was able to wo
Thanks for the update. This information could be of potential help if
this error is ever come across again by other users.
-Zeke
On 06/23/2016 01:53 PM, S.V.Shepherd [work] wrote:
> The error on flattening was caused by my saving the surface, instead of
> the patch, to lh.full.patch.3d. I apolo
no problem. The stride error is something buried in the depths of openGL.
It seems to be OS/version specific and there isn't much we can do about it
Glad you figure out your error though
Bruce
On Thu, 23 Jun 2016, S.V.Shepherd
[work] wrote:
The error on flattening was caused by my saving t
Is there any other layer loaded? It looks like there is at least another
overlay on top of the volume layer?
Best,
Ruopeng
> On Jun 23, 2016, at 2:37 PM, Ramtilak Gattu wrote:
>
> Hello ,
>
> I am having strange freeview display problem. The images doesnt appear in
> gray scale anymore. Plea
That is just one layer the yellow contrast is from when we tune the contrast up
or down.
From: Ramtilak Gattu
Sent: Thursday, June 23, 2016 2:37:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: freeview display problem
Hello ,
I am having strange freeview dis
That’s indeed strange. I wonder if it is a graphics card issue. Does the blue
tone appear all the time? on any volume?
> On Jun 23, 2016, at 3:31 PM, Ramtilak Gattu wrote:
>
> That is just one layer the yellow contrast is from when we tune the contrast
> up or down.
> From: Ramtilak Gattu
> S
This issue is only with freesurfer , images on fslview doesnt have this problem.
From: Ramtilak Gattu
Sent: Thursday, June 23, 2016 3:31:41 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: freeview display problem
That is just one layer the yellow contrast is
So it happens with freeview all the time? Freeview uses openGL as backend for
rendering, which I believe is not the case for fslview. Would it be possible
for you to update your graphics card driver?
> On Jun 23, 2016, at 4:10 PM, Ramtilak Gattu wrote:
>
> This issue is only with freesurfer ,
When loading qdec I get
can't find package BLT
FsgdfPlot::InitFsgdf: Couldn't find fsgdfPlot.tcl
on Ubuntu with FreeSurfer5.3
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Freesurfer mailing list
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The
contents of
$FREESURFER_HOME/lib/tcl/
allisons_surfaces.tcl offsetmovie.tcl TclChartWindow.tcl
curv-flat.tcl phasemovie.tcl test_layers.tcl
curv-views.tcl polar-flat.tcl test_ScubaFrame.tcl
dara_data.tcl polar-views.tcl test_ScubaLayers.tcl
dipmovi
Hi Richard,
Hope this finds you well. I followed your instructions and compiled from source
(you were right-- compiling Fs from source isn't too bad at all!) I also made
your tweak to configure.in and then ran ./configure like so:
./configure --disable-Werror --enable-fermi-gpu --with-cuda="/us
May be thats the problem. I'll try to give it a shot to see if it fixes the
problem.
Thanks.
From: Ramtilak Gattu
Sent: Thursday, June 23, 2016 4:10:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: freeview display problem
This issue is only with freesurf
Research Specialist-86782
The Center for Healthy Minds (CHM), a component of the Waisman Center, was
founded and is led by neuroscientist Richard J. Davidson. CIHM's mission is to
cultivate well-being and relieve suffering through a scientific understanding
of the mind. CHM is a leader in rig
Dear FS experts,
I ran cortical thickness analysis between two groups using Qdec and I want to correct the results for multiple comparison.
In Qdec there are two choices to correct the data for multiple comparison (FDR and montecarlo) . Which method do you recommend montecarlo or FDR. Are there a
Hi Richard,
I resolved the make error. Just needed to point my libcudart.so in
/usr/local/cuda/lib to the 64-bit equivalent in /usr/local/cuda/lib64. Running
into other cuda-related issues with gcc now, but that should be much easier to
resolve.
-Derek
On 23 June 2016 at 16:26, Derek Pisner wrote:
> Hi Richard,
>
> Hope this finds you well. I followed your instructions and compiled from
> source (you were right-- compiling Fs from source isn't too bad at all!) I
> also made your tweak to configure.in and then ran ./configure like so:
>
> ./con
Hi Richard,
Fixed the gcc problems as well (this required a tweak to host_config.h in
/usr/local/cuda/include). Now, I've hit another roadblock:
Makefile:4542: recipe for target 'libutils_cuda_a-mrisurf.o' failed
make[3]: *** [libutils_cuda_a-mrisurf.o] Error 1
make[3]: *** Waiting for unfinishe
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