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I used the SPM default coregistration settings -- which it calls "4th degree
B-spline".
From: "Douglas N. Greve"
Subject: Re: [Freesurfer] Different results on same MRI in different
space ?
To:
Message-ID:
Content-Type: text/plain; char
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Hi Douglas,
I am sorry I have to bug you once more. While the inflation step completed
with the suggested flag, as did the flattening step (for creating a flat map),
when I went to register a functional scan to the inflated and flat map the
comman
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Freesurfer experts,
I have two MRIs for a patient separated by 5 years. I would like to look at
progression of atrophy. These MRIs are different, however, firstly in terms of
resolution (new one is 1x1x1, old one is 1.05x1.05x1.2), and secondly just
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It looks like your first answer, i.e. use of mri_annotation2label to extract
pial labels almost gets me there. I see that the pial and white labels have
exactly the same number and values for their indices. Does this mean I can use
the distance betwe
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Thanks for getting back so quickly, Doug.
Creating pial label files will enable me to write something which does what I
want.
What I want to do is generate a list of cortical thickness values, one for each
vertex in a ctx label file. The main questio
Not sure what you mean as the pial files are surfaces not labels or
annotations. If you want to extract labels from the annotations you can
use mri_annotation2label
On 2/11/2021 12:55 PM, Krieger, Donald N. wrote:
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Dear freesurfer group,
I wish to measure
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Dear freesurfer group,
I wish to measure a cortical thickness value for each entry in a label file,
e.g. SubNo/wmparc/ctx-lh-lateraloccipital_1011.label .
Is there a function in the freesurfer distribution which includes this
capability?
Also, is the
If you send the mri_nu_correct.mni.log we can figure it out for sure.
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Michele Valotti
Date: Thursday, February 11, 2021 at 12:07 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mincRead error
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Dear all,
We are excited to announce an upcoming Research Topic, jointly within
Frontiers in Neuroinformatics and Frontiers in Computational Neuroscience,
on “Neuroinformatics of Large-Scale Brain Modelling”.
This Research Topic will document the vari
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Hi Andrew,
I do think the problem is in the MINC but the minc paths point to the
freesurfer installation, so I think it should be running using that
thank you,
Michele
On Thu, 11 Feb 2021 at 16:29, Hoopes, Andrew
wrote:
> Hi Michele,
>
> I think tha
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Hi Andrew,
on my machine those variables are all empty but in the container they return
in the container
echo $MNI_DIR returns:
echo $MINC_BIN_DIR returns:
/usr/local/freesurfer/mni/bin
echo $MINC_LIB_DIR returns:
/usr/local/freesurfer/mni/lib
I'll
When you mapped to the new space, what kind of interpolation did you use?
On 2/11/2021 11:30 AM, Funk, Quentin wrote:
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Freesurfer experts,
I have two MRIs for a patient separated by 5 years. I would like to
look at progression of atrophy. These MRIs are di
Hi Michele,
I think that’s the problem then. The freesurfer code is written to work with
the specific version of minc that we distribute with the release. If possible,
you should run freesurfer without setting any MINC paths to your local install
to see if that fixes things.
Andrew
From: freesu
Can you provide a bit more information about how you installed the license(s)
and what errors you’re encountering?
best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Fernanda Hansen P. de
Moraes
Date: Thursday, February 11, 2021 at 9:45 AM
To: Freesurfer support list
Sub
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Hi Trisanna,
thank you for your reply, I am using minc2 (version 1.9.16) but this is the
same version I use on my local machine and it does not give any errors
there, and SetUpFreesurfer is sourced before exporting MINC paths and
variables.
Michele
On
No, that flag is for something else. Probably the easiest thing to do is
in matlab, eg,
a = MRIread('dwi.nii.gz');
a.vol = prod(a.vol,4).^(1/a.nframes);
MRIwrite(a,'geomean.nii.gz');
btw, I've never heard that you can compute the ADC this way, but maybe
it's right
On 2/11/2021 6:53 AM, Mateus
For the "spaces" it depends on whether you are going to eventually test
cortex. If your hypotheses are only for subcortical regions, then you do
not need to include --3spaces. I would also use the permutation as the
GRF has eleveated false positives.
On 2/10/2021 9:43 PM, Kim, Gwang-Won wrote
Can you send the log file?
On 2/10/2021 10:26 AM, Bohorquez Montoya, Luisa wrote:
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Hello Freesurfer
I have been trying to run this subject 3 times (with different
walltime) and I am having the same error. Would you mind please to
explain me what I am doi
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Here goes de recon-all_error log after copying the license file again:
--
SUBJECT sub-0002
DATE qui fev 11 12:16:23 -03 2021
USER root
HOST computador
PROCESSOR x86_64
OS Linux
Linux computador 4.15.0-115-generic #116-Ubuntu
Hi Sair,
Just to make sure, could you run?
fspython -m pip install nibabel
Otherwise you can re-install the distribution as we have update the latest one
with the missing nibabel package.
Best, Lilla
From: Carlos Sair Flores Bautista
Sent: Wednesday, February 10,
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Dear Freesurfer experts,
I installed another Freesurfer version on my computer and used the same
license of the version installed before. But, it is not working. How should
I proceed?
Best regards,
Fernanda Hansen P. de Moraes
fernandahmor...@gmail.co
External Email - Use CautionDear Freesurfers I’m running freesurfer through the VirtualBox and when trying to run “recon-all -s mybrain -all -i /home/developer/Desktop/brainscan.nii.gz” I got three error messages telling me I couldn’t create the directories in “/usr/local/freesurfer
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Dear all,
I have 32 directions DTI images and I need to compute DWI and ADC maps from
these images. As far as I know the DWI is obtained by calculating the
geometric mean of the 32 b1000 images. Can it be done with mri_concat
--gmean Ng?
Many thanks,
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