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POST-DOCTORAL FELLOWSHIP IN NEUROIMAGINGTHOMAS JEFFERSON UNIVERSITY/
SIDNEY KIMMEL MEDICAL COLLEGE, PHILA., PA.
The Department of Neurology at Thomas Jefferson University/Jefferson
Medical College has an opening for a Two-Year Postdoctoral Research
Fel
Don't log in, select the "I am not a Martinos Center user"
When it asks for recipients, use gr...@nmr.mgh.harvard.edu
On 05/17/2018 03:19 AM, Naka Beguedou wrote:
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>
> HI Douglas,
> sorry for my late reply. I can't log in to
> https://gate.nmr.mgh.harvard.
This usually means that the registration failed. Have you looked at
the image to make sure that there are no obvious problems? Is the voxel
size about 1mm? Is it T1 weighted?
On 05/21/2018 05:31 PM, Fernanda Hansen P. de Moraes wrote:
>
> Dear FreeSurfer experts,
>
> I am having some trouble
You can run this:
recon-all -s -all -hires
but it might run more things than you need (no harm, just computer time).
Depending on what you have edited, you may be able to use one of the -autorecon
flags to speed things up.
On 05/21/2018 04:48 PM, Alexopoulos, Dimitrios wrote:
> Externa
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Dear FreeSurfer experts, I am having some trouble to understand this error
that showed up in some subjects that my group is processing. The recon-all
log shows that message: *ERROR: mpr2mni305 failed, see
transforms/talairach_avi.log * All talairach_avi
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We have not re-run anything yet. The data was originally generated using'
recon-all -s -all -hires -qcache'.
We have since made manual edits to the wm, brainmask and added control points,
and now want to rerun to incorporate these changes.
What would
If you have editeid all your subjects and re-run (with -all or
appropirate -auto-reconX flag), then you can run -qcache without those flags
On 05/21/2018 04:36 PM, Alexopoulos, Dimitrios wrote:
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>
> Ok. So no my '-all' flag?
> I just want to make sure as
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Ok. So no my '-all' flag?
I just want to make sure as we're re-running a 100+ edited subjects and I had
read elsewhere that the '-all' flag is required.
Jim
"The materials in this email are private and may contain Protected Health
Information. If
You don't even need to include -hires (though I don't think it hurts
anything)
On 05/21/2018 04:25 PM, Alexopoulos, Dimitrios wrote:
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>
> OK, so I only need to run a single command to incorporate the all edits:
> recon-all -s subj -hires -qcache
>
> Jim
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OK, so I only need to run a single command to incorporate the all edits:
recon-all -s subj -hires -qcache
Jim
"The materials in this email are private and may contain Protected Health
Information. If you are not the intended recipient, be advised t
Yes, run the same optional flag. When you run -qcache, do not include -all
On 05/21/2018 04:02 PM, Alexopoulos, Dimitrios wrote:
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>
> Just want to confirm which command to issue to rerun 6.0 incorporating manual
> edits to the wm.mgz, brainmask.mgz andaddin
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Just want to confirm which command to issue to rerun 6.0 incorporating manual
edits to the wm.mgz, brainmask.mgz andadding control points that were made in
no specific order.
The data was originally processed using the following:
recon-all -s subj -
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Hello,
We are finishing up manual inspection and editing of our dataset. As part
of this process, we used QATools to generate QA reports. While we were
running our reports the tmp/control.dat file was deleted from many of our
subject directories (the br
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Dear Experts,
I would like to run statistical analyses with the output of cortical
thickness. The problem is that I would like to do it with FSL as I have
more experience.
Any one of you could tell me which are the two outputs (right and left
hemispher
Hi Freesurfers,
I sent this help request some days ago but had some problems in receiving the
reply because of mailing list subscription issues...
Sorry for submitting this request again:
I used the command mris_preproc to have all the surfaces of my cohort
concatenated in fs average and I obtai
The problem appears to be that your data are not really T2* weighted in
that the intensity of cortex (about 830) is less than that of WM (about
862). Try running preproc-sess with -t1 to indicate to bbregister that
your data are t1 weighted.
On 05/17/2018 03:57 AM, Patrycja Naumczyk wrote:
>
>
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Yes the symbolic link did exist, but the fsaverage directory was empty. I
downloaded and reinstalled FreeSurfer again and everything seems to be working
fine. I’m not sure why my version of FreeSurfer was missing everything inside
the fsaverage direc
Does this file exist?
/panfs/pan.fsl.byu.edu/scr/usr/74/intj5/analyses/ACAP-BRAVOS/freesurfer/fsaverage/label/lh.BA1_exvivo.label
If not, can you send a listing of that folder?
On 5/19/18 9:06 PM, Naomi Hunsaker wrote:
Hello FreeSurfer Developers,
I'm attempting to run FreeSurfer but I get
What is the actual problem? That the surface is a little rough?
On 5/18/18 3:47 PM, Pam Garcia wrote:
Hello, experts
I have a problem with the results of mris_make_surfaces to pial and
white matter surfaces.
I am working with high resolution (0.75x0.75x0.75) monkey images,
mris_makes_surf
The mask has to be a 3-dimensional binary volume. I'm not sure there is
a way to do what (I think) you want to do (would not make sense).
On 5/17/18 11:02 AM, Eduard Vilaplana Martinez wrote:
Dear freesurfer experts,
I would like to ask you about the mris_fwhm script. What does the flag
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Hello, FreeSurfer Developers.
I run "recon-all -s test01_t1 -local GI" for my subject after the MATLAB
path (%PATH = “/Applications/MATLAB_R2014b.app/bin”:”$PATH”)
The original Setting of the FreeSurfer(Mac OS) is like this :
But it exited with error
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