Hi Marcos,
the hippocampal subfield volumes are single values for each subject and
hemisphere, so you cannot display them on the brain surface.
Cheers,
/Eugenio
On Thu, May 16, 2013 6:22 pm, Marcos Martins da Silva wrote:
Hi, Doug
Thank you for your answer.
Well I guess that after I read your
Dear Bruce,
Yes I have,
My input:
mris_convert ./neo024_2_lh.pial.asc ./neo024_2_lh.pial
Segmentation fault
Can you lead me as to why there is an error?
Thank you,
Tina
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Thursday, May 16, 2013 5:49
Dear Freesurfer list members,
Within QDEC I have found a number of clusters that show significantly different
cortical thickness and local gyrification between two groups.
The cluster summary exhibits the p value, coordinates and other information
regarding the cluster, however I wanted to
Dear Freesurfer list members,
Within QDEC I have found a number of clusters that show significantly different
cortical thickness and local gyrification between two groups.
The cluster summary exhibits the p value, coordinates and other information
regarding the cluster, however I wanted to
Hi Tina
can you send me the ascii file? Note that we assume in many places that
the surface files start with a hemisphere specifier, so your output
should probably be lh.neo024_2_pial or something like that. I doubt
that's why it's crashing though
Bruce
On Fri, 17 May 2013, Tina Jeon wrote:
Hi Tina
how did you create the ascii file? The problem is that some of the faces
contain vertex numbers that are you of range. Note that the vertex indices
in the face list must be 0-based, not 1-based. Your file specifies 12722
vertices, but then lists some faces as having vertex number
Hi Bruce,
I tried adding control points in the white matter in that region,
however, it does not seem to fix the issue. Also, the brainmask.mgz
does not seem to exclude this part of the brain, so that is not the
problem either.
I am attaching another screenshot (horizontal 119) to illustrate the
Hi Caspar
yes, that might help. There are expert opts for this. Sorry, I have
almost no experience analyzing monkey brains at .5mm, so I'm really not
sure what to advise you. Perhaps one of the other people on list who have
done a bunch can comment?
Bruce
On Fri, 17 May 2013, Caspar M.
I created the ascii file directly from amira, which from what I understand is 0
based.
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Friday, May 17, 2013 9:15 AM
To: Tina Jeon
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] conversion from
something is wrong as there should be no vertex indices 12721
On Fri, 17 May
2013, Tina Jeon wrote:
I created the ascii file directly from amira, which from what I
understand is 0 based.
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Friday, May
Hard to fix if that is the receive field and you don't have another image
like a T2w to remove it with. Perhaps mri_normalize can be tuned to
improve this with expert options as the white matter that is being
correctly segmented appears to be darker as well.
Peace,
Matt.
On 5/17/13 9:30 AM,
Great! I subtracted the vertices by one and now it works. Appreciate your help
and fast responses.
Tina
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Friday, May 17, 2013 9:37 AM
To: Tina Jeon
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: RE:
sure. Glad it worked out
Bruce
On Fri, 17 May 2013, Tina Jeon wrote:
Great! I subtracted the vertices by one and now it works. Appreciate your help
and fast responses.
Tina
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Friday, May 17, 2013 9:37 AM
v5.0.0
On May 16, 2013, at 2:18 PM, Bruce Fischl wrote:
Hi Sudhin
what FS version are you running?
Bruce
On Thu, 16 May 2013, Sudhin A. Shah wrote:
Hi,
I got the following error:
CORRECTING DEFECT 2 (vertices=30163, convex hull=6211)
error in the retessellation
normal vector
When I try to specify a different threshold using -p, mri_segment
reads in the threshold as the input volume.
I tried specifying the input with -i (as explained here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18826.html),
but now it does not recognize the -i flag.
Caspar
what is your command line? You are probably better off setting gray_hi,
gray_low, wm_hi, wm_low, etc...
Bruce
On Fri, 17 May 2013, Caspar M. Schwiedrzik
wrote:
When I try to specify a different threshold using -p, mri_segment
reads in the threshold as the input volume.
I tried specifying the
Hi Ali - The last row of your gradient table is 0 0 0. And yet, based on
the b-value table, it is supposed to correspond to a diffusion-weighted
volume with b=800. So there must have been a diffusion-encoding gradient
vector that was applied to acquire that volume, and you need to find out
Hi Benjamin - This means that the initial guess for the path based on the
atlas average is way off, due to poor alignment between your subject and
the atlas subejcts. Ways to get around this is to look into the options
for registration, whether diffusion-to-anatomical or anatomical-to-atlas,
Hi Celine - Since 5.2, there are 2 types of measures in the
pathstats.byvoxel.txt file: The value at every point along the trajectory
sampled at roughly the center of the bundle, or the value at every point
along the trajectory averaged over the width of the bundle. Sorry, there
are no other
Hi Philip, the p-value for the cluster is not computed from a t or z. It
is computed from a simulation in which random noise is generated on the
surface, smoothed, clustered. The maximum cluster size is found. This is
repeated 1 times to give a list of 1 cluster sizes. The p-value
for
Hi Skyler - How does the brain mask look like? Any major chunks of brain
missing in the area of the left uncinate? That's the tract where the error
occurs, and based on this info in the log file, I'm guessing it's a
masking issue:
[...]
INFO: Rejected 4221 streamlines for straying off mask
Hi Matt - Can you source try this on the command line:
source dmrirc_53beta
echo $b0mlist
echo $b0plist
Are these filenames correct, do these files exist? This is how you define
them in your configuration file:
set b0mlist = (`ls ${subjlist}/fmag/MR.* | sort -n | head
Hi Benjamin - The tractography algorithm running under the hood hasn't
changed from 5.1 to 5.2, but the way the initial guess for the path is
chosen that's fed into the algorithm has changed. Also several defaults
for the registration method, number of samples, number of control points
have
mri_segment \
-v \
-fillv \
-fillbg \
-wlo 104 \
-ghi 118 \
-whi 140 \
-n 4 \
-keep \
brain.mgz wm.mgz
The pial surface in the rest of the brain is ok, it is only the
orbitofrontal/piriform cortex that is problematic. I now wanted to add
-p 0.7.
Caspar
2013/5/17 Bruce Fischl
Hi Matt - Have you ever ran any parallelized FSL program (like bedpostx)
on your SGE cluster? Our scripts have built on the FSL scripts, adding
support for our PBS cluster, but in theory the SGE functionality is still
there, so it should be possible to make it work. Of course practice is
Hi
I am having trouble with the license file.
I created in Freesurfer a file named .license but I cannot open this and
copy the license.
where and how should I put the 3 lines license?
I tried to test my freesurfer installation with Bert but I got as answer
command non found.
Please help
BW
Hi Anastasia,
I apologize for jumping in here, but I have run bedpostx parallelized on
a cluster. Are there files that we can modify to run the script in
parallel? I noticed the '-prior' step is particularly long and cumbersome.
Thank you!
Susie Kuo
NIH
On Fri, May 17, 2013 at 12:47 PM,
Dear Anastasia,
When running the longitudinal tracula version on our 39 subjects I found
for some of them nan-values for the center_avg variables of some tracts.
When I have a look at the tract distribution and the highest probability
path, everything seems to be ok. However, when checking the
Hi Susie - The underlying script doing the job submission is called
fsl_sub_mgh (a modification of fsl_sub).
BTW, the -prior step should be about 70% less long and cumbersome in
5.2/5.3 than it was in 5.1. Which version are you running?
a.y
On Fri, 17 May 2013, Susan Kuo wrote:
Hi
Hello Flavia,
The .license file should be placed in the /Applications/freesurfer
directory.
To load freesurfer, you must open the terminal type the following :
setenv FREESURFER_HOME /Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
-Zeke
On 05/17/2013 12:49 PM, Flavia
and what happens? Can you send the full screen output?
On Fri, 17 May 2013,
Caspar M. Schwiedrzik wrote:
mri_segment \
-v \
-fillv \
-fillbg \
-wlo 104 \
-ghi 118 \
-whi 140 \
-n 4 \
-keep \
brain.mgz wm.mgz
The pial surface in the rest of the brain is ok, it is only the
filling ventricles
filling basal ganglia
using white lolim = 104.0
using gray hilim = 118.0
using white hilim = 140.0
running border classification 4 times
preserving editing changes in output volume...
using 70% threshold
mri_read(): couldn't determine type of file /.../.700
Hi Caspar
can you include the command line and all the output?
Bruce
On Fri, 17 May 2013,
Caspar M. Schwiedrzik wrote:
filling ventricles
filling basal ganglia
using white lolim = 104.0
using gray hilim = 118.0
using white hilim = 140.0
running border classification 4 times
preserving
set threshold = `echo 7/10 | bc -l`
set segment_options = -v -fillv -fillbg -wlo 104 -ghi 118 -whi 140
-n 4 -p $threshold -keep
mri_segment ${segment_options} \
-i brain.mgz -seg wm.mgz
filling ventricles
filling basal ganglia
using white lolim = 104.0
using gray hilim = 118.0
using white hilim
Your line continuation isn't working for some reason? Type the command
line all on one line and see if that fixes the problem.
Matt.
On 5/17/13 1:37 PM, Caspar M. Schwiedrzik
cschwie...@mail.rockefeller.edu wrote:
set threshold = `echo 7/10 | bc -l`
set segment_options = -v -fillv -fillbg -wlo
Hi Matt and Bruce,
still the same problem. What about the fix that was mentioned in the
earlier discussion? Was that not for version 4.5?
Caspar
2013/5/17 Matt Glasser m...@ma-tea.com:
Your line continuation isn't working for some reason? Type the command
line all on one line and see if that
Try leaving out the -i and -seg
Those are mandatory parameters and don't need hyphens
On May 17, 2013, at 3:11 PM, Caspar M. Schwiedrzik
cschwie...@mail.rockefeller.edu wrote:
Hi Matt and Bruce,
still the same problem. What about the fix that was mentioned in the
earlier discussion? Was that
Hi Bruce,
I only put them in because it was not working without them and that
was the solution in the previous discussion.
To summarize: Once I put in -p 0.7, mri_segment misinterprets 0.7 as
the input file name, no matter whether I use -i or not.
Caspar
2013/5/17 Bruce Fischl
Hi Anastasia,
I am operating on 5.1... I'm glad to know that there is such a huge
difference in versions; and that there's so much gain in upgrading. I will
look at the fsl_sub_mgh script, and I'll post back what I figure out (if
anything), if other people are interested. Otherwise, it's vox
Hi Freesurfer team
I would have a question about the Tracula output. If I understand it
correctly, the output of the file: pathstats.byvoxel.txt can give us a
mean average of DTI metrics at each section of the tract.
Is there a way to get the weighted_FA, AD RD and MD at each section?
Thanks for
Hi Anastasia
I am very sorry I didn't see this email so it may be a doubloon with my
question I just post.
Indeed I am interested in a profile of the DTI metrics along the tract. So
if I take the average value of each section it can give me a kind of
profile, and so I was just wondering if taking
Hi Anastasia,
To follow up, yes, those files exist.
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Friday, May 17, 2013 12:31 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula problem
Hi Matt - Can you
Hi Anastasia,
I'm just forwarding a modified version of the email I'd sent you earlier to the
list so everyone can see it.
I solved this particular problem in a new dmrirc, but it seemed that I had to
modify trac-preproc to remove the ${dcmroot} in front of:
infile, b0mfile and b0pfile:
diff
Hi, Eugenio
Thank you for your answer.
Em Sex, 2013-05-17 às 07:49 -0400, Juan Eugenio Iglesias escreveu:
Hi Marcos,
the hippocampal subfield volumes are single values for each subject and
hemisphere, so you cannot display them on the brain surface.
Cheers,
/Eugenio
On Thu, May 16, 2013
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