Hi Doug,
mri_label2vol says it creates an mgz from a label, I need to do the reverse.
I'm starting with a mask_MNI.mgz (brought from FSL's MNI space via mri_convert)
and I need to be able to use that mask to extract thickness from the individual
subject.
Also, mni152reg fails because it expect
Hi, Bruce
Filedrop worked great and fast! Thank you for the tip.
It follows the bath I run for each subject:
mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippo lh.surfHippo
mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippoHead lh.surfHippoHead
mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippoBody lh
sorry, I don't think it completed as unzip can't find the end of directory
mark in the file. Try our filedrop instead:
https://gate.nmr.mgh.harvard.edu/filedrop2/
cheers
Bruce
On
Mon, 7 Oct 2013, Marcos Martins da
Silva wrote:
Hi, Bruce
I proceeded as explained at
http://surfer.nmr.mgh.h
Dear experts,
I updated FreeSurfer as a 5.3.0 version but have a problem about the
missing ribbon.mgz when running recon-all procedure.
I found the ftp address but couldn't find the mri_segstats.
(ftp:/surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats)
Could you let me know the
I am not sure about the lobule subdivisions, but there is a cerebellar
subdivisions based on functional connectivity since 5.2. See 5.2
release notes (https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes).
--Thomas
On Mon, Oct 7, 2013 at 11:23 PM, Alan Francis wrote:
> Hi Bruce et al,
>
> Is t
Hi, Bruce
I proceeded as explained at
http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange .
Using ftp method, it started at good rate but after I transferred about
3/4 of the file the transfer rate decreased to some bytes (not Kbytes)
per second. Tried using curl -T and it seemed to complete a
My freesurfer version document reads as follows:
freesurfer-i686-apple-darwin9.8.0-stable5-20110525
I am running freeview 5.3
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Monday, October 07, 2013 3:51 PM
To: Francesco Siciliano
Cc: freesurfer@nmr.
what version are you running?
On Mon, 7 Oct 2013, Francesco Siciliano wrote:
> Hello,
> After doing manual editing to the surface of a brain (brainmask.mgz, wm.mgz,
> and brain.finalsurfs.mgz) through freeview, I noticed that the volumes of
> some subcortical structures (specifically the hippocamp
Thank you for your help!
I will re-run this brain and see if it reads all 53 control points and then let
you know the outcome. However, the last time I ran this brain with this control
point set, it only read 22 control points.
From: Bruce Fischl [fis...@
Hello,
After doing manual editing to the surface of a brain (brainmask.mgz, wm.mgz,
and brain.finalsurfs.mgz) through freeview, I noticed that the volumes of some
subcortical structures (specifically the hippocampus, amygdala, and accumbens)
had changed, even though I did not edit aseg.mgz. Is
Oh, you'll need to map the annotation into the individual space, or (and
probably better), map your lgi into fsaverage space.
doug
On 10/07/2013 02:18 PM, Tara Ann Miskovich wrote:
> Thank you Doug, this did work. However, for every subject I get this line
> repeated over and over before it
Hi there,
I'm working on a project in which I manually "erased" voxels (changed to
'1') in the optic chiasm region in the wm.mgz and brainmask.mgz. This was
done to eliminate those voxels from the surface reconstructions. We've
since realized that this isn't necessary...our results are largely
unaf
Thank you Doug, this did work. However, for every subject I get this line
repeated over and over before it outputs the stats. I still get a stats file
that seems to make sense but I am not sure if this is an issue.
MRISreadAnnotationIntoArray: vertex index out of range: 163841 i=,
in_ar
and how many do you see in the control.dat file? Sounds like they aren't
getting saved to disk somehow
On Mon, 7 Oct 2013, Francesco Siciliano
wrote:
> I counted at least 28 control points on the brainmask when I loaded the set
> and my log indicates that freesurfer read 22 control points.
I counted at least 28 control points on the brainmask when I loaded the set and
my log indicates that freesurfer read 22 control points. I've attached part of
the log below.
#@# Intensity Normalization2 Mon Sep 16 19:44:17 EDT 2013
/Users/jonathanposner/Desktop/AdultControls/diffusion_recon/615
Not from the mri_cluster. If you run mri_binarize --i mask.nii --count
count.dat --min 0.5 the total volume of the mask will be in the count
file (along with some other numbers).
doug
ps. Please remember to post to the list instead of me directly. thanks!
On 10/07/2013 12:53 PM, pfot...@nm
how many control points are in it? Can you check the recon-all.log to see
if it says it reads as many as you think you should have (in the
mri_normalize step)?
On Mon, 7 Oct 2013, Francesco Siciliano wrote:
> Hi Bruce,
>
> Yes, I save it in the subject's tmp folder.
>
> -Francesco
>
if you can
On Mon, 7 Oct 2013, Caspar M. Schwiedrzik wrote:
Hi Bruce,
it sounds very possible that the bright spots (which are gadolinium-enhanced
blood vessels)
cause the problem.
I guess I will have to remove them. Does it make sense to manually delete them
from brain.mgz?
Caspar
2013/10/7
Hi Bruce,
Yes, I save it in the subject's tmp folder.
-Francesco
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Monday, October 07, 2013 12:47 PM
To: Francesco Siciliano
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] [FreeSurfer] contr
Hi Bruce,
it sounds very possible that the bright spots (which are
gadolinium-enhanced blood vessels) cause the problem.
I guess I will have to remove them. Does it make sense to manually delete
them from brain.mgz?
Caspar
2013/10/7 Bruce Fischl
> Hi Caspar
>
> I'm not sure what to tell you. Th
Hi Francesco
where do you save the file control.dat? It must be in the directory
$SUBJECTS_DIR/$subject/tmp/control.dat
otherwise recon-all won't find it
cheers
Bruce
On Mon, 7 Oct 2013, Francesco
Siciliano wrote:
> Hello,
> I am still having issues getting all of my control points to be ef
Hello,
I am still having issues getting all of my control points to be effective. When
I load my original point set (control.dat) and add control points to the set
(using the control points edit tool), the new control points are visible but
are not taken into account when I re-run recon-all (re
Hello!
I'm having problems running the trac-all -tensor step. dtifit appears to
run correctly; the problem seems to be in mapping the output files to the
template space. The command I run is:
trac-all -tensor -c
/cluster/manoach/dod/BU_pipeline/data/DOD_DODCON004/tracula.cfg
--
Thanks for pointing that out Kayle!
On 10/07/2013 10:40 AM, Kayle Sawyer wrote:
> If you want the global thickness for all your subjects in a single table, use
> asegstats2table, e.g.
>
> aparcstats2table --subjects bert ernie fred margaret --hemi rh --meas
> thickness --tablefile rh.aparc_stats
If you save a segmentation from mri_volcluster (--ocn), then you can
feed that into mri_segstats as the segmentation and it will create
another summary file with the volumes of each cluster
doug
On 10/07/2013 10:12 AM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi FS Community,
>
> I have a binary m
Hi Maya, do the ces.nii.gz files have multiple frames? If so, then that
is definitely the problem as the currently distributed version of
mri_binarize does not handle multiple frames. I've put a more
up-to-date one here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binari
Hi Bruce et al,
Is the parcellation of the cerebellar subdivisions in the works for the
next version of FS? Is there an ETA for this?
thanks so much,
Alan
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what version was the table generated with? 5.3 does not use ICV in the
table anymore. It uses eTIV. Can you send an example of one of your tables?
On 10/07/2013 03:12 AM, Daniel Ferreira wrote:
> Dear Douglas and Martin,
>
> Thanks for your replies.
>
> So far I have always been able to get eTIV
Hi Ruth, run mni152reg for each subject to create a registration from
the subject to the 152. Then use mri_label2vol to map the mask into each
subject's space.
doug
On 10/05/2013 04:08 PM, Ruth Carper wrote:
> Doug,
> I'd like to get them into the individual's space, but I assume I have
> t
If you want the global thickness for all your subjects in a single table, use
asegstats2table, e.g.
aparcstats2table --subjects bert ernie fred margaret --hemi rh --meas thickness
--tablefile rh.aparc_stats.txt
The first column will be the rh thickness, which you can average with the lh in
a s
Dear Gregory,
we are indeed working on a new version, but we don't know when it will
be available yet.
Cheers,
Eugenio
On 10/04/2013 03:05 AM, Gregory Kirk wrote:
> I heard from Koen a while back that a new improved version was in the works.
> I have
> several projects I would be interested in u
Hi FS Community,
I have a binary mask and have used the mri_volcluster command to come up
with different clusters and their volumes based on that binary mask.
However, I was wondering if it would be possible to come up with the sum
of the sizes (in mm3) of all the different clusters that come out
Hi Bruce,
Thanks for getting back to me! I am using my own ROIs, created based on an ALE
(Activation Likelihood Estimation) conducted in the gingerALE software, and
dividing the ALE map into smaller clusters in Marsbar (SPM).
I then applied the ROIs to the surface based registration(fsaverage
hmmm, I guess you should upload the subject so that we can track it down
On
Mon, 7 Oct 2013, Marcos Martins da Silva wrote:
Hi, Bruce.
Thank you for your fast answer.
I used a script and It took less than 15 min to process all files from all
subjects, except
the 3 files (surfaces) mris_smooth
Hi, Bruce.
Thank you for your fast answer.
I used a script and It took less than 15 min to process all files from all
subjects, except the 3 files (surfaces) mris_smooth seems to enter a loop.
When I tried to smooth surfLeftHippobody I waited for more than 4 hours.
Comparing to the total time I nee
Hi Sarah
what ROIs do you mean? And did you correct for the reduced surface area
in fsaverage w.r.t. the individual surfaces? If not, it's not surprising
that fsaverage ROIs have less surface area. It is an average surface and
less folded than any individual.
cheers
Bruce
On Mon, 7 Oct 201
Hi Caspar
I'm not sure what to tell you. There are bright spots and rings out near
the pial surface that are probably part of your problem, and the images
even in the zoom look really inhomogenous. I don't think we ever have to
add thousands of control points, but I have no experiences with NH
Hi Freesurfer users,
I am analysing some volumetric data and have noticed that the volumes I extract
from my participants are very different from the volumes of my templates in
fsaverage space. I for instance have two ROIs that stand out as big (about 6-8
times larger that the other ROIS) in f
Thank you Doug!
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail wa
Dear Douglas and Martin,
Thanks for your replies.
So far I have always been able to get eTIV when running asegstats2table
(last column on the spreadsheet). But my current FreeSurfer version (5.3.0)
is not grabbing it.
I can found eTIV in the header and extract it for all the subjects with
mri_se
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