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Hi Guodong,
On Di, 2019-10-22 at 16:05 +0800, Liu Guodong wrote:
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>
> Hello FreeSurfer Developers,
>
> I'm doing the LME tutorial, and I have some questions .
>
> 1. Why don’t we need to put the healthy
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Dear FreeSurfer experts:
I am trying to use my own data so I don’t have the same tutorial structure. I
do keep the folder structure as similar as possible in order for FreeSurfer to
run but I cannot have different sessions for example I just have rest
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In other words I cannot process TRACULA without the T1w images of my subjects?
Because this Parkinson database is from NITRC and I only have the diffusion
images not the T1. I can practice on other subjects that I have both the T1 and
diffusion image
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Dear FreeSurfer experts:
I am trying to run Spatial Normalization but I cannot get the morph file
because I get this error. I don’t know what to do with these libraries. Do I
need to copy them from where they are in freesurfer to somewhere else in the
You could register another subject's segmentation to your subjects, but having
the individual segmentations is ideal.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Renew Andrade
Sent: Thursday, October 24, 2019 9:53 AM
To: freesurfer@nmr.mgh.harvard
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Doug,
I copied over files and ran using the -conf2hires flag, however, the
orig.mgz/brainmask.mgz are resampled to 1mm isotropic not the native 0.8mm.
Using the -hires flag maintains the orig.mgz/brainmask.mgz at native 0.8mm
resolution.
Is this e
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Hello,
Yes sure, I checked my setup of Freesurfer enviroment - the same as the wiki
page I guess.
I loaded an image from the freesurfer distribution directly from the command
line - the same problem (the grey windows popping out).
The strange thing
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Hello Adam,
I’m doing some work with a VirtualBox VM running Ubuntu 18.04 -but hosted from
Mac OS instead of Windows. I will install the 6.0.0 freesurfer release in
the Ubuntu VM and run some of the freeview command tests we use, but so far I
have n
oh, sorry, yes it is. The surfaces are placed on the high res volumes,
but the aseg will be at 1mm. If you need the aseg at highres, then you
will need to use the -hires flag (but the surfaces will suffer)
On 10/24/19 2:55 PM, Alexopoulos, Dimitrios wrote:
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You have to have the directory structure set up properly. You can put
task and rest in the same session or in different sessions
On 10/24/19 9:43 AM, Renew Andrade wrote:
>
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>
> Dear FreeSurfer experts:
> I am trying to use my own data so I don’t have the sam
On 10/21/19 10:24 AM, miracle ozzoude wrote:
>
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> Hello Experts,
>
> I do have couple questions about using mri_glmfit and mri_glmfit-sim
> for this analysis based on the tutorial page.
> https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
> 1) Do i have
On 10/22/19 9:00 AM, Троицкий Антон Александрович wrote:
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> Dear free surfer developers,
>
>
> 1.
>
> I processed several items of data. And I have rh.w-g.pct file in my stats
> folders.
>
> How can I get process this file to get table reading file? I tri
I don't know what this refers to
On 10/18/19 4:45 PM, Renew Andrade wrote:
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>
> I have tried all the values it pinpoints to but none seem to work.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
>
If you are trying to determine whether the hemispheres are different,
then you need to do the subtraction between the hemis (ie, the
--paired-diff). If you want to look at the hemispheres separately, then
don't combine them in a single file
On 10/21/19 4:58 AM, Jose Graterol wrote:
>
>
try something like
mri_label2vol --reg $FREESURFER_HOME/average/mni152.register.dat --seg
your.mni152.roi.nii.gz --temp
$FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --o
your.mni152.roi-in-mni305.nii.gz
On 10/21/19 12:42 PM, Barbour, Tracy,M.D. wrote:
>
> Hello experts,
>
> I am trying to
For the aparc see Desikan, NI 2006, An automated labeling system for
subdividing the human cerebral cortex on MRI scans into gyral based
regions of interest
For the a2009s, see Destrieux, NI 2010, Automatic parcellation of human
cortical gyri and sulci using standard
anatomical nomenclature
O
In the qdec analysis it is hard because we don't really support qdec
anymore. You can run the command-line stream, and when you run
mri_glmfit-sim to do the clustering, set --cwp 1 to keep all the
clusters. At that point you can use mri_segstats with --i sig.mgh and
--seg ocn.mgh (where ocn is
Can you send the full terminal output?
On 10/14/19 12:01 AM, Sims, Sara A (Campus) wrote:
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> Freesurfers,
>
> I am trying to use mri_mask using surface overlays. I made a label
> into a volume and then into a surface with 1s inside the label and 0s
> out
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The cortical parcellations in the aseg and aparc+seg have some issues in the
orbital prefrontal regions and we're were hoping that the higher resolution
images would help. The surfaces look fine.
We should use the -hires flag instead in this scenario
You mean the surfaces using -hires look fine? If so, then continue to
use -hires
On 10/24/19 6:32 PM, Alexopoulos, Dimitrios wrote:
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> The cortical parcellations in the aseg and aparc+seg have some issues in the
> orbital prefrontal regions and we're were
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I apologize for the confusion. Whether I use the -hires or -conf2hires flag
the subcortical segmentations look good.
The cortical segmentations have some issues in the ventral medial area (see
snapshot below), which is likely caused by difficulty in
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