Dear Experts, I am trying to use Freeview to view volumes using the command
listed on the website:
http://freesurfer.net/fswiki/FsTutorial/OutputData_freeview but the only volume
that loads is the aseg. I am not able to load the T1, wm, or brainmask mgz’s .
either from the terminal or through
Hi Bruce,
Yes, they exist.but this seems strange...-rwx--+ 1 mxx MF\Domain Users
0 Aug 26 09:12 T1.mgz
-rwx--+ 1 mxx MF\Domain Users 0 Aug 26 09:12 wm.mgz
-rwx--+ 1 mxx MF\Domain Users 0 Aug 26 09:12 brainmask.mgz
On Wednesday, August 26, 2015 12:04
they are empty (zero size). Maybe your disk filled up?
On Wed, 26 Aug 2015, Cat Chong wrote:
Hi Bruce,
Yes, they exist.
but this seems strange...
-rwx--+ 1 mxx MF\Domain Users 0 Aug 26 09:12 T1.mgz
-rwx--+ 1 mxx MF\Domain Users 0 Aug 26 09:12 wm.mgz
-rwx--+ 1 mxx
did you run recon-all? If so, check the recon-all.log for errors
On Wed, 26 Aug 2015, Cat Chong wrote:
no, seems to be plenty left.. 240 TB
On Wednesday, August 26, 2015 12:23 PM, Bruce Fischl
fis...@nmr.mgh.harvard.edu wrote:
they are empty (zero size). Maybe your disk filled up?
On
Sounds like you had a clinical scan and got a copy of a sagittal scan series and an axial scan series. Those would be 2D acquisitions in which the slice thickness is probably considerably thicker than the in-plane resolution. That kind of data isn't
ideal for FS. Rather, data for FS is
Hi Philip,
It seems that for a strange reason your ROIs are not getting saved. I never saw
this one. I suppose that you are getting this error for all subjects? Do you
have a way to transfer me one of your subject so that I can have a closer look?
Thanks,
Marie
On Aug 26, 2015, at 11:37
Typically we use an mprage with 1mm isotropic resolution, but depending on
your coil/field strength you might want it to be a bit lower res to improve
CNR (say 1.1mm isotropic,which as 20% more SNR than 1mm)
On Wed, 26 Aug 2015,
Alexander van Dijk wrote:
Thanks Michael.
Yes, it was a
Hi all,
I am an interested neuroscience newbie and I am following this excellent online
guide on how to create a 3d print of my cortex using an MRI scan and
freesurfer: http://nmarinsek.com/3D-printed-brain/
http://nmarinsek.com/3D-printed-brain/
Sofar, i have been successful in generating
what version should I try?
On Aug 26, 2015, at 7:06 AM, Bruce Fischl wrote:
it would fix the hippocampal problems and maybe the cortical ones as well
cheers
Bruce
On
Tue, 25 Aug 2015, fmri wrote:
I have already processed 88 subjects in this version,
would it matter if I process or
no, seems to be plenty left.. 240 TB
On Wednesday, August 26, 2015 12:23 PM, Bruce Fischl
fis...@nmr.mgh.harvard.edu wrote:
they are empty (zero size). Maybe your disk filled up?
On Wed, 26 Aug 2015, Cat Chong wrote:
Hi Bruce,
Yes, they exist.
but this seems strange...
Hi Cat
do those file exist? What does ls -l tell you for them?
Bruce
On Wed, 26 Aug 2015, Cat Chong wrote:
Dear Experts,
I am trying to use Freeview to view volumes using the command listed on the
website: http://freesurfer.net/fswiki/FsTutorial/OutputData_freeview but the
only volume that
Thanks Michael.
Yes, it was a clinical scan. I basically went looking for a place to get an MRI
scan which I could pay for out-of-pocket. I told them it was for my personal
interest, in particular to create a 3d model, but I hadn’t found the freesurfer
guideline by then yet, so I couldnt
Thanks Bruce.
Yes, I was honestly also a bit surprised I only had 32 images in one scan. See
my reply to Michael, I basically went looking for a place where I could get a
general MRI scan which I could pay out-of-pocket. I guess I should keep looking
to get a better 3D MRI scan.
I will have
Hi Emma
not yet, sorry
Bruce
On Wed, 26 Aug 2015, Emma Thompson wrote:
Dear Freesurfers,
Is it possible to segment using freesurfer specific thalamic nuclei, for
example, the VPL?
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Hi Alexander
I doubt it actually has a whole. We have automated topology correction
that prevents this. You can use mris_euler_number to check.
I am a bit surprised that you only have 30-something images. That is
typically not nearly enough to cover the brain at high-enough resolution
for
Thanks for the quick response, Marie. Here's the full recon-all.log for this
subject:
FREESURFER_HOME /Volumes/apps/rhel6/freesurfer/freesurfer-latest
Actual FREESURFER_HOME /Volumes/apps/rhel6/freesurfer/freesurfer_5.10_x86_64
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Ok thanks, i’ll keep looking for a better scan. I was already very happily
surprised with how the 3d mesh for my left hemisphere came out with my 32-image
T1 scan.
On Aug 26, 2015, at 12:36 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Typically we use an mprage with 1mm isotropic
it is the registration between input volume and the surfaces/conformed
volumes. If you are just using the volumes used for recon then it can be
identity.nofile
cheers
Bruce
On Wed, 26 Aug 2015, Yun Wang wrote:
Usage: mri_compute_layer_fractions [options] reg file input volume
output stem
Dear FS experts,Reposting my message below.Thanks
I have run two group comparison on qdec and I get differences in a number of
clusters, which also survive cluster wise correction. I would like to extract
the values for each of my subjects (to run further stats) on each of these
clusters. Is
Usage: mri_compute_layer_fractions [options] reg file input volume output
stem
What is reg file ? input volume?
On Aug 26, 2015, at 10:37, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
we have toold for doing this but they aren't documented (mris_expand,
mri_compute_layer_fractions,
Thanks a lot a Doug!
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Wednesday, August 26, 2015 11:31 AM
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Create matrix
So do you
Dear Anastasia,
Thank you very much for the quick help.
Best wishes,
Barbara Anne
On 25/08/2015 22:10, Anastasia Yendiki wrote:
Hi Barbara - Yes, just correct with the method of your choice, apply the
rotation to the gradient vectors, pass the corrected images and gradient
vectors to
Hi Anastasia,
Thank you very much for your help and recommendations. I will try to fix
These Problems. I would like to ask you one more question. Is there any
command which could help me to invert the gradient vectors for my DWI
scan in the z direction?
Best
Bahram
2015-08-24 17:57 GMT+02:00
Hi Doug,
I am using the following command line to create single voxel has the same
dimensions and position ( from single voxel (svs) MRS data):
mri_volsynth --vol BS.nii --pdf const --dim 40 40 40 1 --res 0.5 0.5 0.5 1
--cdircos 0.025458 -0.999671 0.003154 --rdircos -0.670601 -0.014738 0.741673
No pic attached. That command will create a volume with 40 voxels on a
side and FoV of 20mm. What more do you want?
On 8/26/15 10:26 AM, Alshikho, Mohamad J. wrote:
Hi Doug,
I am using the following command line to create single voxel has the same
dimensions and position ( from single voxel
Hi list,
I'm performing slice time correction on preproc-sess -s Sess201 -fwhm 5
-surface fsaverage lhrh -mni305-1mm -fsd rest -per-run.I have acquired data
using a Philipps scanner (interleaved). Thefore, shuold I use -sliceorder
siemens?The command line:preproc-sess -s Sess201 -fwhm 5
Hi Doug,
I am using the command mri_volsynth to create voxel has specific dimensions
and position in the brain.
Kindly, I would like to inquire if there is any tool in Freesurfer that can
help to create volumetric matrix has a number of columns and rows ( and as a
results number of voxels)
Hi Bahram - The gradient table is a text file with 3 columns. You need to
multiply the 3rd column by -1. You can do this in matlab, awk, perl, or
any scripting language that handles text files.
Best,
a.y
On Wed, 26 Aug 2015, B M wrote:
Hi Anastasia,
Thank you very much for your help and
Dear all experts,
I am currently dividing the gray matter into 6 different layers using
bbregister, however, does anyone know how to make the space between layers into
ROIs? Thanks! Appreciating your idea.
Yun
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Hi Freesurfer Support,
I posted this question about a month ago, and I still haven't found a solution.
Any help would be greatly appreciated.
When running the recon-all -localGI command, I get the following errors, which
result in the message: make_roi_paths did not complete successfully!
Hi Philip,
Can you send me the full recon-all.log for this subject so that I can see also
matlab version and whether other vertices ran or if it crashed on the first one.
Thanks,
Marie
On Aug 26, 2015, at 8:00 AM, Philip Deming
pdem...@wisc.edumailto:pdem...@wisc.edu wrote:
Hi Freesurfer
it would fix the hippocampal problems and maybe the cortical ones as well
cheers
Bruce
On
Tue, 25 Aug 2015, fmri wrote:
I have already processed 88 subjects in this version,
would it matter if I process or re-process subjects with another version?
On Aug 25, 2015, at 3:44 PM, Bruce Fischl
does mri_volsynth not work for this?
On 8/26/15 9:25 AM, Alshikho, Mohamad J. wrote:
Hi Doug,
I am using the command “mri_volsynth” to create voxel has specific
dimensions and position in the brain.
Kindly, I would like to inquire if there is any tool in Freesurfer
that can help to create
Hello All,
I am hoping to make some edits to subcortical segmentations, and while I have
found instructions for manual edits, there are also stern warnings to avoid
these if possible and pursue automated avenues. I cannot, however, seem to find
clear instructions on how to automatically edit
So do you need anything else?
On 8/26/15 10:51 AM, Alshikho, Mohamad J. wrote:
I attached the photo.
Actually I didn't realize that this FOV 20 will be consisted of 40 voxels
because when I view the output of the previous command line this will look like
one big volume!
I'm not sure what you mean. bbregister does not divide gm into layers.
Can you elaborate on what you have done and trying to do?
On 8/26/15 11:02 AM, Yun Wang wrote:
Dear all experts,
I am currently dividing the gray matter into 6 different layers using
bbregister, however, does anyone
we have toold for doing this but they aren't documented (mris_expand,
mri_compute_layer_fractions, mris_compute_layer_intensities). This is what
Rebecca Shafee used in her recent two-compartment paper
http://www.ncbi.nlm.nih.gov/pubmed/25449739
cheers
Bruce
On Wed, 26 Aug 2015, Douglas Greve
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