Hi,
I have done recon-all -all processing for 2 groups in separate subjects
directories. I want to put all subjects in one dkirectory. Should I copy
paste all subject’s folders in one directory or is there any others steps
to merge?
Thanks in advance
RB
Hi all,
I have Freesurfer version
freesurfer-i386-apple-darwin11.4.2-stable6-20170119 installed on my MacOS
Sierra 10.12.5 environment, and am experiencing similar library issues to
what others have reported. I have tried previously offered suggestions to
update and test MacPorts, as well as $
Andrew,
Thanks, this helped me get past the error I was receiving. I am now
trying to determine exactly which QT libraries are required to
successfully complete compilation. I've tried both qt5-qtbase-devel as
well as qt-devel. Here are the resulting errors from each:
qt5-qtbase-devel:
Well, it looks the *_cuda files for mri_glmfit and mri_robust_register and some
others were dropped from the repository. Downloaded fresh copy today but the
files are not there. So no errors.
-Henk
From: Meij, Henk
Sent: Monday, November 27, 2017 11:02:44 AM
Hi Doug,
Thank you for your response.
I ran the funcroi-config command the same way the tutorial suggested:
*"funcroi-config -annot aparc fusiform -analysis eba-fba.native.rh
-contrast faces-vs-objects -thresh 2 -sign pos -roi rh.fus.test.roicfg
-force"*
However, I got this error:
Dear experts,
I recently finished processing a subject for whom I had performed a skull-strip
on the brainmask.mgz volume. I decreased the watershed parameter and re-examined
the brainmask and the portion of the skull was gone, although some dura was
left over. I did a recon-all using the
An easy solution is just to use a symbolic link (the ln command under
linux). That way you don't have to move anything at all. If you want to
move things, I would copy them, make sure the copy is ok, then delete
the old version. rsync is good for this kind of thing too
On 11/27/2017 12:14 PM,
This is a bug in make_average_subject. I have created patch which you
can get from here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/
Follow the instructions in the README file for this bug. Please let me
know if this works.
doug
On 11/21/2017 10:03 AM, Duran, Tugce
Hi,
I have done recon-all -all processing for 2 groups in separate subjects
directories. I want to put all subjects in one dkirectory. Should I copy
paste all subject’s folders in one directory or is there any others steps
to merge?
Thanks in advance
RB
Hi Sahil, in the paper we looked at the clusterwise false positive rates
(FPRs) of thickness, surface area, and volume as a function of smoothing
level and cluster forming threshold (CFT). I've attached plots for each
measure. Thickness is much better than volume and surface area in all
cases.
Thanks a lot Dr. Fischl.
I am looking forward to hearing back from Dr. Greve soon.
That's really exciting news that a paper addressing this issue (authored by
Dr. Greve and his team) will be out very soon.
Thanks for the updates !
Best,
Sahil
On Thu, Nov 23, 2017 at 8:15 AM, Bruce Fischl
Dear Lilla,
Thank you for your quick response. Since I am new to freesurfer I have still a
few questions... Thank you in advance for your time!
Where can I read more about building my own template? And if I cannot plug this
into the adult processing pipeline, what could I do with it? My
What do you mean you only get one vertex for the medial wall? Can you
send the make_average_{subject,surface,volume}.log files (located in the
scripts folder of the average subject)
On 11/22/2017 05:01 AM, M del Mar Velasco wrote:
>
> Dear Freesurfer experts,
>
>
> I have a question related to
Hi Aicha,
We do have a pipeline and I am trying to get it released by the end of the
year.
You should be able to build your own template independent from the adults,
but you will not be able to just plug this new one in to the adult
processing pipeline.
Lilla
On Mon, 27 Nov 2017,
what do you mean? We generally don't move data from fsaverage to the
individual space. All the anatomical analysis (recon-all) is done in the
native space
On 11/21/2017 11:43 PM, Avideh Gharehgazlou wrote:
> Hi experts,
>
> Will you please briefly explain to me the rationale behind why
>
Dear all,
I want to build my own neonatal control reference template (n=35)to investigate
cortical thickness measures and compare these to neonates with a rare type of
bleeding. I read that freesurfer uses an adult reference atlas, but that a
neonatal-infant (0-2y) is being made/has been made.
Just wanted to report back a success. I had to do some fixes so hope this helps
anybody.
My gpus are GTX1080Ti and the CPU involved is E5-2620 dual 10 core on this
server.
The vanilla cpu recon-all finished in 7 hours, the gpu run finished in 4.3
hours.
Q: I seem to not have any errors or
Hi Sofia
most of us are just getting back from Thanksgiving holiday. We will take
a look at your problem this week
cheers
Bruce
On Mon, 27 Nov 2017, Sofia Rodriguez Penuela wrote:
Hello,
when using "make_average_subject" in Freesurfer 6, we have noted that the
medial wall label only
Hello,
when using "make_average_subject" in Freesurfer 6, we have noted that
the medial wall label only contains 1 vertex leading, after applying
"mri_glmfit, to significant results in regions of the medial wall. This
problem didn't appear in Fresurfer 5.3
Is there something different with the
Dear Donatas,
I believe that mri_segstats is just counting voxels using the hard
segmentation, whereas the volume in lh.hippoSfVolumes-T1.long.v20.txt is
obtained using a soft segmentation. If you’re interested in this, look up the
WRITE_POSTERIORS option in the wiki.
Cheers,
/Eugenio
--
Juan
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