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After some feedback and some more testing, I can reproduce that freeview..app
in the 7.2.0 release will segfault on MacOS 11.4 if the license file cannot be
found or it cannot be read. One user reported that he had to get a new
license file in order
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Hi Simon,
This could be an issue with the affine registration or the subsequent head
masking step in samseg, both of which have been upgraded/improved in the
development version.
Would you be able to try the dev version and see if this resolves the is
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Hi,
I want to investigate lGI differences between 4 groups (n=449) while
controlling for sex, age and surface area using DODS design matrix on the
command line stream of FreeSurfer. Will you please tell me which of the
below two contrasts are correct f
It should be pretty close but not exact. The surface area is computed
inside the ?h.cortex.label mask which does not align perfectly with the
aparc labels
On 7/20/2021 4:16 PM, Alexopoulos, Dimitrios wrote:
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Hi,
Are t
I'm not sure what you mean. Do you want to remove certain brainmask
edits and not others?
On 7/21/2021 1:43 PM, Kishore Vakamudi wrote:
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Dear Freesurfer Experts,
Is there any way to remove pial edits selectively after you go through
the first round of edit
You might be able to run both through longitudinal samseg as samseg will
create a "base" image from both and try to bias correct both with
respect to this image.
On 7/21/2021 1:31 PM, Fischl, Bruce wrote:
There isn’t really anything available for the latter approach. I would
suggest the form
Can you send your retinotopy.par file (or just the contents of it)?
On 7/21/2021 11:40 PM, Yaoda Xu wrote:
Dear all,
Using FreeSurfer 7.1.1, I made my analysis file with the following (I assume
-nksip should be in the number of TRs and not in seconds):
mkanalysis-sess -analysis retino_surf_pr_
I'm not sure what you mean by a QC rating. For white matter, the volume
will depend upon the boundaries with both subcortical and cortical GM,
so, in theory, you must check both. For eTIV, the value is computed from
the talairach registration, not from a segmentation, so you'd have to
check the
You should be able to use asegstats2table specifying the samseg inputs
with --inputs samseg1/seg.stats samseg2/seg.stats samseg3/seg.stats ...
On 7/26/2021 11:12 PM, AJ wrote:
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Hi,
I was wondering if there is a simple command for generating a table
from al
Hi Avi, if you want to compute an interaction between two continuous
variables, you have to create a new regressor where you multiply them
together. The contrast you have created would test whether the age slope
is different than the IQ slope. This contrast does not make sense since
the to vari
Use rh.hippoAmygLabels-T1.v21.CA.mgz
On 7/30/2021 11:00 AM, Shane Schofield wrote:
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Hi Freesurfer Tema,
I am trying to use vol2subfield to extract DTI measurements like FA
and MD.
For this purpose, should I be using the
rh.hippoAmygLabels-T1.v21.CA.FSv
If you want to test TD vs the mean of the other groups, you'd need
0.5 0.5 -x -x -x -x -x -x 0 0 ...
where x = 1/6
Contrast 2 is the correct test for a multivariate (F) test.
On 8/2/2021 9:56 AM, Avi Gharehgazlou wrote:
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Hi,
I want to investigate lGI diffe
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Many thanks.
My best
On Mon, Aug 2, 2021, 10:13 Douglas N. Greve wrote:
> You should be able to use asegstats2table specifying the samseg inputs
> with --inputs samseg1/seg.stats samseg2/seg.stats samseg3/seg.stats ...
>
> On 7/26/2021 11:12 PM, AJ
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Bruce, thank you for this response. In fact I had the T1 path wrong despite
having read it over and over 20 times.. listing directory contents indeed
revealed my error…
-andrew
> On Jul 30, 2021, at 13:38, Fischl, Bruce wrote:
>
> Can you load
> /
I’m glad to hear it worked out. We have all done this….
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Andrew
Sent: Monday, August 2, 2021 12:07 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] niiRead: error opening file, through mri_convert
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Confirm, just requesting a new license file fixed my FreeView MacOS 11.4
segfault errors.
Requesting a new license file with my same credentials produced an
identical text file (same email, same license #, same two strings of random
letter/digit/symbol
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I should add: I've used this license file for several years wtih FS v.5.1,
v5.3, v6, v7+ and developer versions. It runs FreeSurfer perfectly on two
MacOS computers and on a RedHat Linux cluster where it has run thousands of
recons + additional processi
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Dear Freesurfer experts,
I tried to run Recon-all on a T1 series .nii file. A error occurred: "ERROR:
input(s) cannot have multiple frames!". I tried to google the method of
converting multi frame dicom to single frame dicom. I found software of
Hi Frank
Do you know why there are multiple frames? What kind of MRI acquisition are you
trying to use as input? Most standard T1-weighted series only have a single
frame
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Frank Chau
Sent: Monday, August 2, 2021 3:49 PM
To: freesu
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Dear Bruce,
I have briefly read a article about multiple frames DICOM. As my understanding,
it can reduce the amount of data repetition and decreases the time required to
read and parse DICOM studies.
Yes, I want to use T1-weighted series as input
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I started getting segfaults again but I was able to diagnose what was
different.
It turns out it was *not the license file for me*. I registered a new
license file this morning --> it worked on my Mac and I assumed it was the
new license; I went into t
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Thanks Adam for pointing out different behavior at different screen
resolutions. I would be interested to know if those resolutions are not
the native resolution of the external monitor. The manual/info for any
monitor should state what it’s nativ
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Thank you so much for your reply. Will you please confirm that I am
doing the below correctly now based on your reply?
I created a new variable called “product” that is the age and IQ multiplied
together for each participant in my dataset. I then added
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