Can you send the terminal output of mris_preproc?
On 3/6/2020 4:28 PM, Marina Fernández wrote:
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Dear freesurfer experts,
I run the following commands to perform analysis with projected
surfaces on my
urfer
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These are the previous emails:
1 » » » » » » » » » » » »
Dear freesurfer experts,
I run the following commands to perform analysis with projected
surfaces on my average subject:
make_average_subject --out my_avg_subject --fsgd fsgd.txt
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can you include the previous emails?
On 3/6/2020 1:50 PM, Marina Fernández wrote:
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We are using Freesurfer v6.0
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Hi,
Thanks for your help.
I am now seeing this error:
Admins-iMac:XXXneurology$ trac-all -prep -c XXX.24.14Configfile.rtf
Missing }.
Missing }.
}: Command not found.
Missing }.
red255green255blue255: Command not found.
}: Command not found.
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We are using Freesurfer v6.0
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the space in which the image was aqcuired.
Am Fr., 6. März 2020 um 18:31 Uhr schrieb Douglas N. Greve <
dgr...@mgh.harvard.edu>:
> what is "native space"?
>
> On 3/6/2020 12:09 PM, Benjamin Ineichen wrote:
>
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what is "native space"?
On 3/6/2020 12:09 PM, Benjamin Ineichen wrote:
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example.mgz is just some example mask created on a template in native
space. And I would need to transform it to MNI space. Thus, I ran:
mri_vol2vol --talres 1 --interp nearest --mov
what is your command line and terminal output?
On 2/24/2020 10:50 AM, Russo, Andrew William wrote:
Hello Freesurfer Developers,
I am trying to use the "samseg" function in /usr/local/freesurfer/dev
but do not have permission to access the directory
*Od:* freesurfer-boun...@nmr.mgh.harvard.edu
za uživatele Adam Rytina
*Odesláno:* sobota 15. února 2020 19:52
*Komu:* Freesurfer support list
*Předmět:* Re: [Freesurfer] Apply transformation
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What is example.mgz?
If you want to transfer the orig.mgz, you can do it with
mri_vol2vol --tal --talres 1 --interp nearest --mov orig.mgz --s subject
--o example.mni305.mgz
On 2/20/2020 3:53 PM, Benjamin Ineichen wrote:
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Dear Freesurfer experts,
In
On 3/6/2020 11:15 AM, Milde, Christopher wrote:
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Dear Freesurfer Experts,
I have a very basic questions about creating subject-wise contrasts
between runs
*
*
*Background*
Study with two runs per subject where each run corresponds two a
different
Try
mris_convert -n lh.white lh.white.norm.asc
On 3/6/2020 11:07 AM, Jedy wrote:
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Dear FreeSurfer friends,
Does anybody know how to extract vertex information of lh.white and
lh.pial? I would like to extract normal vector and other information
of
I cannot replicate this in either v6 or v7beta. Can you send the
terminal output?
On 3/5/2020 1:32 PM, Dincer, Aylin wrote:
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Hello PetSurfer experts,
We are using the cerebellum cortex as our reference region, but
noticed that the SUVR values for lh/rh
what version of freesurfer are you running?
On 3/6/2020 10:03 AM, Marina Fernández wrote:
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Dear freesurfer experts,
I run the following commands to perform analysis with projected surfaces on my
average subject:
make_average_subject --out my_avg_subject
I think Andrew H might have a way to do this, but he's on vacation until
next week. Try back then.
On 3/5/2020 12:29 PM, Ardesch, D.J. wrote:
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Dear FreeSurfer experts,
I am working on some monkey data and trying to get an accurate
nonlinear transform to
what is your command line?
On 3/5/2020 1:50 AM, Tien Pham wrote:
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Thank you for your suggestion.
I tried to use freeview to load surface on the label I created. But
terminal showed this error '' freadFloat: fread failed '' many times.
I tried to load label
Sorry, not sure what you are trying to do. From your equation it looks
like you are not doing a voxel-wise analysis but instead using maps to
try to predict cognition? If so, this is a multivariate analysis whereas
mri_glmfit does voxel-wise analysis. We don't really have any tools to
do
yes, your command looks correct
On 3/3/2020 2:05 PM, Xiaojiang Yang wrote:
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Hi all,
I want to register DIR (Double Inversion Recovery) series to T1 series
using Freesurfer. I used the command line similar to that used for
FLAIR registration:
bbregister
I cannot replicate this, eg
In matlab
a = fast_vol2mat(MRIread('gtm.nii.gz'));
a(1:10)
Columns 1 through 7
0.7957 1.0565 1.5711 1.7842 1.8625 1.9539 1.2499
Columns 8 through 10
1.3188 1.4063 1.2536
From gtm,.stats.dat
1 2 Left-Cerebral-White-Matter wm
Try this instead
set gcam =
$SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z
set dstreg =
$FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta
mri_vol2vol --gcam ${meanb0_bet} ${b0toT1mat_bet} $gcam $dstreg 0 1
${b0_to040_2_t1w}
This (admittedly cryptic)
why not just use the aseg? it has been cleaned up with the surfaces, so
it should represent everything inside the pial surface pretty well.
On 3/2/2020 4:52 PM, Octavian Lie wrote:
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>
> Dear Bruce & All,
>
> Sure, I wanted some advice from the greats before
What quantity do you want to compare across subjects/goggle condition?
Sorry for the delay, I have not worked much with the retinotopy code in
a while and don't have it at my fingertips
On 3/2/2020 9:08 AM, Marco Ninghetto wrote:
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Since that each subject
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Dear Freesurfer Experts,
I have a very basic questions about creating subject-wise contrasts between runs
Background
Study with two runs per subject where each run corresponds two a different
condition (i.e. Stimulation A (on - off) and
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Dear FreeSurfer friends,
Does anybody know how to extract vertex information of lh.white and
lh.pial? I would like to extract normal vector and other information of
each vetex.
I would be very appreciated if someone can give me some suggestions.
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Sorry for spamming. The contact email in the previous mail contains a typo
The Perception & Brain Dynamics Laboratory (http://www.med.nyu.edu/helab/) at
New York University School of Medicine is looking for a lab manager to start in
spring/summer
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The Perception & Brain Dynamics Laboratory (http://www.med.nyu.edu/helab/) at
New York University School of Medicine is looking for a lab manager to start in
spring/summer 2020. The Laboratory is within the Neuroscience Institute at NYU
Langone
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Dear freesurfer experts,
I run the following commands to perform analysis with projected
surfaces on my average subject:
make_average_subject --out my_avg_subject --fsgd fsgd.txt
surfreg --s s_001 --t my_avg_subject --o
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Dear Tim,
The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will
affect the process Recon-all? If yes, how would it impact my output results?
Regards
Frank
From:
Hi Lara,
if you are sure you will stick with 15fwhm, you can do either one.
If you plan to also run analysis at different fwhm, you can first map
and then smooth at different levels.
Either way, it should not make a big difference.
Best, Martin
On Fri, 2020-02-21 at 15:41 +, Lara
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