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Hi Douglas, Because the Jove article recommends using a study-specific template
(cited the article in the original post) and our analyses is being run on an
adolescent sample. Therefore, "average" corresponds to the average template for
our current
Sure, just updated it!
Andrew
On 9/1/20, 4:44 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Andrew J. Worth" wrote:
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Hello,
I’m very happy that there is an official Freesurfer Docker image! But it
doesn’t match the
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Hello,
I’m very happy that there is an official Freesurfer Docker image! But it
doesn’t match the Dockerfile in the Github repo. I’d really like to take a
look at that Dockerfile. Would it be appropriate to add it to the Github repo?
Thanks,
Ah, I see. Um. Well, at the time of that publication, mris_preproc had
a bug in that it was actually sampling onto fsaverage and not truly the
target subject (though it was smoothing on the target subject). So, in
version 6, I changed it to sample to the target subject by requiring
that the
I'm not sure about this. The FS segmentation atlas was not created to be
symmetrical, so interpreting the asymmetry of aseg results can be
tricky. I know that Eugenio often creates his atlases to be symmetric;
unfortunately, he's away until next week. Thalamus is also quite tricky
because the
What is TLRC? Otherwise, it sounds reasonable. I'd definitely look at
the image to make sure:)
On 9/1/2020 12:11 PM, 刘梦醒 wrote:
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Thanks!
I have a work-around solution but want to hear your comment on it.
I use the TLRC transform matrix in mri/transform to
You do not need to re-run recon-all. You can use v6 recon-all output
with v7 mris_preproc, mri_glmfit, mri_glmfit-sim, and fspalm
On 9/1/2020 11:56 AM, 정현우 wrote:
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Hi Douglas,
Thank you for your advice. I just wanted to make sure what I should
expect
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Thanks!
I have a work-around solution but want to hear your comment on it.
I use the TLRC transform matrix in mri/transform to translate the
coordinates in native to TLRC, so that the origin set to anterior
commisure. Then I cut the brain stem to left
Hi Ken,
Hmm, not sure. Does it give a reason why it cannot be loaded? Could be read
permissions, could be corrupted.
Generally the commands look good. You could also try to check the subject SPC
on the base-template surface. Those files should also be there in the base dir.
Best, Martin
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Hi Douglas,
Thank you for your advice. I just wanted to make sure what I should expect
before installing v7.1.1 - will v7.1.1 allow me to run commands for
analyses (e.g. mri_glmfit, mri_glmfit-sim, fspalm) with the recon-all
outputs from v6.0.0? Or
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The Cognition and Brain Circuitry Laboratory at the Ohio State University is
recruiting a research assistant. Primary duties include: conducting
neuroscience research on the functional and structural architecture of the
human brain, and its role in
Sorry, that's been a problem for a while now. I just added something
that replaces the commas with decimal points, will be in the next version
On 8/31/2020 9:39 AM, Rovai Antonin wrote:
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>
> Hi,
>
> this is not really a question but rather a comment that,
I don't think so. You might be better off fixing the error manually. See
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
On 8/28/2020 4:57 AM, k3...@free.fr wrote:
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>
> Hi Douglas,
>
> thanks for your answer.
> I agree that
Not that I know of, sorry
On 9/1/20 10:20 AM, 刘梦醒 wrote:
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Hi Freesurfer group,
For some reason, I have to use the left and right brain stem separately.
I wonder if there is one way to have a midline, to cut the brain stem
into Left and Right?
Many
Try running it with --no-surfs
On 8/29/20 12:34 PM, Jie Zhao wrote:
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Hi, Douglas
I first heared the tkregisterfv, tryed the tkregisterfv --fstal --s
mprage
the output error was this:
ERROR: cannot find
You can use the Transform volume tool in FreeView, though it will be a
pain if you have to do a bunch. Getting the original dicoms is a much
better place to start.
On 9/1/20 9:13 AM, Ellen Ji wrote:
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Dear Bruce (and Jie),
I believe I am encountering the same
In 7.1.1, you can use tkregisterfv instead of tkregister2 (same command
line otherwise). If you don't want to download 7.1.1, you can get just
tkregisterfv from
https://gate.nmr.mgh.harvard.edu/safelinks/greve/tkregisterfv
On 8/31/20 3:42 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry)
Why are you specifying the target as average instead of fsaverage?
On 8/31/20 12:13 PM, chelseach...@yahoo.com wrote:
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Hello,
I am running into an error while running the LGI analyses using
FreeSurfer 6.0 following Jove article recommendations (
Yes, that is the effect of including the cortex.label
On 8/31/20 8:28 AM, Palin, Tara wrote:
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When using the following command line:
mris_anatomical_stats -th3 -mgz- cortex ../label/?h.cortex.label -f
../stats/?h.aparc.pial.stats -b -a
No, not published. Probably won't be. It has a small effect on the
output anyway
On 8/31/20 1:47 AM, Hye Min Shin wrote:
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Hello,
I understand that from a previous FreeSurfer question the Schwartz
atlas used in the 3T flag during recon-all is not
There is a bug in recon-all when trying to only run with one hemi
(actually there are several bugs). Currently, it is failing at
mris_volmask, which needs to have --lh appended to the command line. You
can do this with an expert options file. This is simple text file that
should have the
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Hi Freesurfer group,
For some reason, I have to use the left and right brain stem separately.
I wonder if there is one way to have a midline, to cut the brain stem into
Left and Right?
Many thanks,
Mengxing
Try looking at our wiki
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
On 8/30/20 7:16 AM, Vinny K wrote:
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Hi,
I've tried to process a scan but it gets hung up on a particular large
defect and then exits with error. I've
Yes, this is not unusual. The GTM (which RBV is based on) is just a GLM
where it uses a linear model to estimate the ROI intensities. There are
no constraints on positivity. When the model is not exactly correct
(which it never will be) it is possible to get negative values. Usually
this only
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Hello,
I have processed (recon-all) my data both with the latest Freesurfer 7.1.1
version, and with the older Freesurfer 6.0 on Mac. I am interested in the
hippocampal subfields and processed those using the segmentHA_T1.sh command on
the 7.1.1
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