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Hello experts,
I am following these instructions
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis to
analyze the association between IQ and whole brain cortical thickness of
brain areas (which by default uses Desikan atlas of 34 regio
I think they should give the same result, but try one or two to confirm
On 6/29/2020 6:12 PM, Yann Quidé wrote:
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Hi Andrew,
Thanks for this.
Just a quick follow up question: does that mean I will have to recon
all all the other scans that did not show this
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Hi Andrew,
Thanks for this.
Just a quick follow up question: does that mean I will have to recon all all
the other scans that did not show this error with v7.1.1 for consistency, or
will it be fine to keep them processed with v7.1.0?
Thanks,
Yann
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Hello all,
We are working on calculating the volume of thalamic nuclei in our
participants and noticed that there is often a discrepancy in measured
volume in the ThalamicNuclei.v12.T1.volumes.txt and the volume calculated
for the same thalamic nucleus
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Okay. I'll try.
The basic steps are, loading in a slightly adapted and I guess repaired version
of the T1.mgz file called hseg.mgz (this is created by the AtlasViewer toolbox
because I need to set the fiducials and some other reference points and thi
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Also I missed that you upsampled the volume fMRI file massively as well.
Indeed, this is not how I would recommend going about things, particularly in a
memory limited environment.
Matt.
From: on behalf of "Glasser, Matthew"
Reply-To: Freesurfer
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Yes you are probably low on memory (3.5GB is really low for brain imaging these
days). Like I said, probably best to use the ciftify outputs if you have them
and then resample the ICA maps back to the native mesh.
Matt.
From: on behalf of Mason We
what volume? how did you create it? please give some details
On 6/29/2020 1:19 PM, Franziska Klein wrote:
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Sorry. I am not using the mesh for this, but the volume.
*Von:* Franziska Kle
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Hi Matt,
I have 3.5GB free on my 64 bit linux machine, do you think the wb_command issue
is due to memory alone then? Perhaps I misunderstood your previous emails about
this, I thought that using the workbench commands was the best way. E.g.
running
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Sorry. I am not using the mesh for this, but the volume.
Von: Franziska Klein
Gesendet: Montag, 29. Juni 2020 19:15:01
An: freesurfer@nmr.mgh.harvard.edu
Betreff: AW: [Freesurfer] Question regarding MRIread
I've used
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I've used the MRIwrite function.
Von: freesurfer-boun...@nmr.mgh.harvard.edu
im Auftrag von Douglas N. Greve
Gesendet: Montag, 29. Juni 2020 18:55:01
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Ques
Not sure what is going on there. Can you take a look at lh.inflated and
lh.white.preaparc to make sure that they don't look crazy?
On 6/23/2020 11:17 AM, Malone, Ian wrote:
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Hello,
We've run into an issue with
freesurfer-linux-centos7_x86_64-7.1.0-2020051
How did you generate the nii file from the mesh?
On 6/29/2020 12:21 PM, Franziska Klein wrote:
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I know, a lot of steps.
1-based vs. 0-based, that is basically what I mean and what I think is
the problem, but I need to be sure. When I load in the *.nii fil
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Scratch that, I guess you did include a surface. How much RAM do you have
available and are you on a 64bit OS? As I mentioned last week, what you are
trying to do is not computationally efficient and not really the best approach
to go about things.
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Your command below is missing the argument:
wb_command -volume-to-surface-mapping
- the volume to map data from
- the surface to map the data onto
- output - the output metric file
[-ribbon-constrained] - use ribbon const
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The Alzheimer's Prevention Program of the Barcelonabeta Brain Research
center is seeking a Research Engineer in Neuroimaging. For further
information on the position, please visit the following link:
https://fpmaragall.org/wp-content/uploads/2020/06/R
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Dear experts,
I posted a message last week about converting NIFTI files into GIFTI format,
then GIFTI to CIFTI, whilst keeping these functional data in the same space as
the subjects FS surface. I got some information RE usign the HCP workbench, but
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I know, a lot of steps.
1-based vs. 0-based, that is basically what I mean and what I think is the
problem, but I need to be sure. When I load in the *.nii file generated from
the mesh and display it in SPM, then the origin shown in the SPM Gui is t
BTW, I just created a new version of tkregisterfv
https://gate.nmr.mgh.harvard.edu/safelinks/greve/tkregisterfv
Copy it to $FREESURFER_HOME/bin
Then run
tkregisterfv --s subject --fstal
If you have to edit the reg, save the lta in the pre-selected location
(talairach.lta)
When done, exit out ot
Hi Yann (and anyone else with mri_cc failures on mac),
We have a fix that we'll include in an upcoming 7.1.1 patch release. If you'd
like a quick local fix, you can update your distribution with the new version
of mri_cc by running the following commands (this might require sudo):
cd $FREESURFER_
Hi Jocelyn - It's strange to get this in the tutorial data, it's the kind of
thing you might get if the FS recon was missing part of the brain or if the
alignment between datasets was not good. So I'm surprised you're getting this
in the tutorial data. Can you please send your entire trac-all.lo
We don't have a replacement yet for tkregsiter2, but here is a work-around
cd $SUBJECTS_DIR/subject/mri/transforms
First, convert the xfm to an lta file
lta_convert --src ../orig.mgz --trg
$FREESURFER_HOME/average/mni305.cor.mgz --inxfm talairach.xfm --outlta
talairach.xfm2.lta --subject fs
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Hi all,
After running the trac-all command in the pre-processing step in the
official TRACULA tutorial, I ran into the following error:
WARN: Could not find satisfactory control point fit - try 4718
Writing output files to
/home1/jr2359/diffusion_tuto
How did you generate 102.mgz? It looks like it was created by a pretty
old version of FS.
On 6/28/2020 5:41 PM, Fischl, Bruce wrote:
And how did you generate the volumes? I wouldn’t name them 001.mgz,
that will end up being confusing. Maybe something like sub.001.mgz
might be better, since o
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I have attached the log - is there any chance you could tell me what the
problem is?
Thanks,
Ian
--
Mon Jun 29 10:53:22 UTC 2020
/execute/freesurfer2016
/usr/local/freesurfer/bin/recon-all
-all -subjid ./freesurfer2016
subjid freesurfer2016
setenv
Not sure. Can you run this
cd /execute/freesurfer2016/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
--i orig.mgz --o orig_nu.mgz
and send the terminal output?
On 6/29/2020 7:01 AM, Ian wrote:
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I have attached the log - is th
Hard to say. We are not supporting QDEC anymore for these types of
reasons. Can you cut and paste that mri_glmfit command into the terminal
and see what happens?
On 6/29/2020 7:05 AM, Mateus Aranha wrote:
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Hello,
Iḿ trying to perform a group analysis usin
I guess you could use something like
mri_segstats --i lh.lgi.mgz --slabel subject lh
$SUBJECTS_DIR/subject/label/lh.cortex.label --excludeid 0 --o lh.lgi.sum
On 6/28/2020 11:08 AM, Alexopoulos, Dimitrios wrote:
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Is generating a Global hemispheric Gyrific
There's a lot of stuff going on there, so it's hard to say withhout more
detail. But it sounds like you might not be taking into account that the
voxel coords in matlab are 1-based.
On 6/26/2020 12:04 PM, Franziska Klein wrote:
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Hello,
I am using the iso
We don't use MNI152 much. We have an affine matrix to convert from 305
to 152, and that 152 is the one in FSL
On 6/25/2020 4:27 PM, Inês Pereira wrote:
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Dear FreeSurfer developers,
Which MNI152 space is used within FreeSurfer? Is it the MNI152
nonlinear 6
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Hello,
Iḿ trying to perform a group analysis using qdec, but the analysis stops at
70% and the following error message is shown:
[image: Screenshot from 2020-06-29 13-03-27.png]
How should I proceed?
Thanks,
Mateus
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