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Hi,
Where is the nifti output stored from running trac-all preprocess? Is
it dmri/dwi.nii.gz? Is there an additional step segment this nifti file
into the grey matter and white matter for later tensor-fitting?
Best,
Qi
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Does the hires flag still generate segs at the native hi resolution and place
surfaces on the 1mm volumes, whereas conf2hires generates volumes at 1mm but
places surfaces on the hires images?
Which option is recommended and why?
Jim
Get Outlook fo
Correct
On 9/8/2020 7:26 PM, Rizvi, Batool wrote:
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Thanks for the info, Dr. Greve!
So for the files I used for the --y argument were stacked files of
this file: lh.long.thickness-spc.fwhm10.fsaverage.mgh or
rh.long.thickness-spc.fwhm10.fsaverage.mgh.
So
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Hello,
I just wanted to follow up on this and see if anyone had any suggestions,
as I still have not resolved the issue.
Best,
Noriana Jakopin
On Tue, Aug 18, 2020 at 12:54 PM Noriana Jakopin
wrote:
> Hello FreeSurfer Developers,
> I am attempting t
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Thanks for the info, Dr. Greve!
So for the files I used for the --y argument were stacked files of this file:
lh.long.thickness-spc.fwhm10.fsaverage.mgh or
rh.long.thickness-spc.fwhm10.fsaverage.mgh.
So would my interpretation of the ocn.dat file be
OK, I see what you mean now, I'm just not sure how to fix it. What
version of FS are you using?
On 9/3/2020 12:07 PM, Marina Fernández wrote:
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Hi Doug,
I sent you the images attached to the email and also through FTP File
Exchange.
Thank you for your at
That scan looks low res and T2 weighted, so you would not run recon-all
on it. But even if it were the right contrast/resolution, I think it is
too extensive. I don't know if there is going to be something that we
have that is going to do that for you.
On 9/8/2020 1:44 PM, Harkey, Thomas Jarro
ue, 08 Sep 2020 08:14:19 -0700
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20200908>
Try something like this
mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.lobe.stats -b -a ../label/lh.lobe.annot fsm010 lh white
On 9/8/
The interpretation depends on what you pass mri_glmfit in the --y
argument. If you passed it differences in thicknesses, then the .dat
file will be differences
On 9/8/2020 12:29 PM, Rizvi, Batool wrote:
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Hi FreeSurfer team,
After running longitudinal FS,
Try using this version of recon-all
https://gate.nmr.mgh.harvard.edu/safelinks/greve/recon-all.711.parallel
On 9/8/2020 12:09 PM, Park, James wrote:
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Hello,
Thank you for such a prompt response.
This has happened consistently and across multiple mac lapt
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Hi all,
My group is working on a software platform with the hopes of some level of
commercialization. Our platform uses some freesurfer code. Is there a specific
person or group I can contact and work with to figure out the specifics of what
this si
N. Greve
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N.+Greve%22>
Tue, 08 Sep 2020 08:14:19 -0700
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20200908>
Try something like this
mris_anatomical_sta
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Hi FreeSurfer team,
After running longitudinal FS, and running mri_glmfit using files that measured
spc, we found clusters associated with our continuous variable (WMH volume)
after controlling for other covariates. I was wondering though, do the val
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Hello,
Thank you for such a prompt response.
This has happened consistently and across multiple mac laptops that we utilize
in our laboratory.
Below is the freesurfer version that we are utilizing as noted in the
build-stamp.txt file:
freesurfer-da
The issue with the ribbon is something we recently became aware of. does
it happen consistently for you? I can send you a recon-all that will fix
this for you, just tell me which version you are running.
On 9/8/2020 11:49 AM, Park, James wrote:
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Sincerely
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Sincerely,
James Park
From: "Park, James"
Date: Tuesday, September 8, 2020 at 11:48 AM
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: Troubleshooting -parallel flag for Freesurfer, error in the cortical
ribbon mask stage during recon-all
Dear Free
Are you running freeview locally or remotely?
Ruopeng
On Sep 5, 2020, at 1:11 AM, Wei Shao
mailto:ws...@research.baycrest.org>> wrote:
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Hi, Freesurfer Team
My name is Wei Shao, as you can see, whenever I tried to Freeview Inflated
image , it gives me the
Try something like this
mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.lobe.stats -b -a ../label/lh.lobe.annot fsm010 lh white
On 9/8/2020 7:58 AM, Marina Fernández wrote:
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Dear experts,
I would like to get a .stats file
you just want to compute the log of the voxel values in a volume? You
can use fscalc
On 9/8/2020 6:30 AM, Jose Graterol wrote:
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Hey Tim,
thanks for the quick response and for the script. I will try that.
Best,
José
On Tue, Sep 8, 2020 at 11:07 AM Tim S
On 9/7/2020 10:52 PM, Paul wrote:
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Dear Freesurfer Experts,
I have few questions regarding CWP values from mri_glmfit-sim using
--cwp 0.05, --cwp 0.1, --cwp 0.999.
Using the 3 three commands below (A, B and C):
A. mri_glmfit-sim --glmdir lh_status.glmdir
The noise properties depends on the sequence, but the MP2RAGE sequence I
use is a little noisier than the MEMPRAGE. The B0 distortion is
different. Since it is a different sequence, there will be systematic
differences between the acqs. Generally, this is nothing to be done
about it. The bias w
Run mri_glmfit-sim --help to get details on the output
On 9/7/2020 12:35 PM, Steve Petersen wrote:
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Dear Freesurfer experts,
I performed group analysis in QDEC in order to compare cortical
thickness between two groups using the Monte Carlo Z simulation
co
This is not something we do. I have seen it done before, so do a search
online and/or talk to the authros
On 9/6/2020 11:43 PM, Jie Zhao wrote:
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Hi, Bruce and all
The paper attached quoted "A semiautomated process was implemented to convert
FreeSurfer ge
Yes, you just need a registration file. You can use mri_label2vol
passing the aal atlas with the --seg option
On 9/6/2020 1:30 PM, Diógenes Bispo wrote:
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Dear,
Can I use Freesurfer to convert aal atlas 3 from the MNI space to the
native space of the T1 se
Very interesting, Chris! The atlas is indeed designed to be symmetric, such
that left-right differences arise from the data rather than the prior.
Did you try on a larger sample? Are these differences in asymmetry significant?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MG
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Dear experts,
I would like to get a .stats file this the volume and thickness of lobe
annotation, so I am following the steps indicated in this link
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation.
Specifically, I used these commands:
m
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Hi Alex,
I see via a search for,
ubuntu 16 Failed to initialize XRandr
- that what you report happens when trying to connect remotely, e.g., via VNC,
to something running X windows/graphics (for other flavors of linux as well).
This
thread,https://s
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Hey Tim,
thanks for the quick response and for the script. I will try that.
Best,
José
On Tue, Sep 8, 2020 at 11:07 AM Tim Schäfer wrote:
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>
> Hi José,
>
> most likely there is an easier way to do this with s
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Hi José,
most likely there is an easier way to do this with some FreeSurfer command that
others can suggest (and I am not aware of), but I would do it in R with this
script: https://gist.github.com/dfsp-spirit/ccdc8c5efb0cff2ba5b139190bbfb397
Best,
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Hello FreeSurfer Developers,
I have a technical question for which I have not yet found the answer.
First, I am running FreeSurfer stable-pub-v6.0.0-2beb96c on CentOS 7.
Now to the question: is there a way to apply, say, a logarithmic
transformation v
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Dear Eugenio,
Douglas referred me to you for this question. Do you have an
explanation for the difference in asymmetry between the native (aseg) and
ThalamicNuclei.v12 segmentation?
kind regards, Chris
*I'm not sure about this. The FS segmentation a
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