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Your output shows you should you should be ready to work with freesurfer
version 6.0 which is an older release from ~2017. So people there may
have used version 6 for quite some time. If there was something missing
on the system that freesurfer 6
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Hi,
I was using version 6.0.0 but I have just tried 7.1.1 and it works fine. Thank
you!
Amanda
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Wang, Ruopeng
Sent: 23 September 2021 16:56
To: Freesurfer
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additionally, running freeview gives me the following error:
banikr2@banikr:~$ freeview
freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open
shared object file: No such file or directory
Then I tried to install
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banikr2@banikr:~$ bash
banikr2@banikr:~$ export FREESURFER_HOME=/usr/local/freesurfer
banikr2@banikr:~$ source SFREESURFER_HOME/SetUpFreeSurfer.sh
bash: SFREESURFER_HOME/SetUpFreeSurfer.sh: No such file or directory
Instead, I changed the command as:
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OK, then try setting FREESURFER_HOME and setting the environment in a terminal
window with the commands,
$ bash
$ export FREESURFER_HOME=/usr/local/freesurfer$ source
$FREESURFER_HOME/SetUpFreeSurfer.sh
Then you should see what the output reports for
Here is what I get for the mask:
__
Volume information for
/autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/rois/recall/lIFG_surf_rad10.nii.gz
type: nii
dimensions: 163842 x 1 x 1
voxel sizes: 1.00, 1.00,
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Hello,
There is no directory called /7.2.0 rather the directory i am finding the files
is:
banikr2@banikr:/usr/local/freesurfer$ pwd
/usr/local/freesurfer
Trying the same in the /freesurfer folder
Rana Banik
From:
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Hello,
I have a question regarding the conversion of functional fsaverage lh and
rh files (created from the Yeo lab MNI to fsaverage projection software:
It looks like the mask is the wrong size. What is the dimension of
/autofs/cluster/neuromod/NIFTI/OCD_N
M/derivatives/fsfast/rois/recall/lIFG_surf_rad10.nii.gz
you can check with mri_info
On 9/17/2021 8:32 PM, Pedersen, Walker Scott wrote:
Hi,
I am running glmfit on some functional data
On 9/23/2021 11:05 AM, Corinna Bauer wrote:
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Hi Doug,
I'm about to start edits on subjects that have been re-processed in
7.2 using the -fill flag. Before doing so, can you clarify/verify that
we edit the new filled.mgz just the same as we would the
Sorry, we don't support that atlas. Have you tried contacting FSL?
On 9/23/2021 7:08 AM, DRON Noramon wrote:
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Dear Freesurfer Team
I have a very naive question. I am in urgent need to get a cortical
region volume base on the Harvard-Oxford Cortical
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Dear FreeSurfer Developers,
I am attempting to create some figures which display regional (Destrieux atlas)
values which are typically in the range of 0-10. I would like to have an
inflated brain with those regional values overlaid, for both
You don't need the -legacy flag. Just make a copy of your v6 data and
then run recon-all -all -s subject
It will see and apply your previous edits.
On 9/22/2021 2:14 AM, Amanda Boyes wrote:
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Hi FreeSurfer experts,
Just checking whether anyone has any
They are only changed as part of the resampling process (ie, a form of
interpolation). Volume and surface area are jacobian corrected.
On 9/22/2021 1:24 AM, 周冬跃 wrote:
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Dear FreeSurfer experts:
I use the command recon-all qcache to get file
We are no longer supporting qdec
On 9/21/2021 2:15 PM, Fabiola Macruz wrote:
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Dear freesurfer experts,
I have installed the freesurfer version 7.1.1 in my computer (Mac).
After running the longitudinal pipeline in all
Did the size of the defect change?
On 9/19/2021 8:36 PM, Paul, Rahul wrote:
Hi freesurfer experts,
I was using FreeSurfer v6 for my research. Recently, I started move to
FreeSurfer v7.2.
I encountered the following issue:
Some patients, that had extra large error (xL error), were running
Do you see the note: "make sure at least one voxel has a non-zero value
for each input"? To do this, you can try loading the input into
freeview, eg,
tksurferfv fsaverage lh inflated -ov h.N0s2_e4pos.10.mgh -fminmax .0001 1
It will come up with a map of the first subject. Scroll through the
What version of freesurfer are you using? I tried the latest freeview build and
had no problem inserting colors at arbitrary value for customized color option.
Best,
Ruopeng
On Sep 23, 2021, at 9:00 AM, Worker, Amanda
mailto:amanda.wor...@kcl.ac.uk>> wrote:
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It is quite likely that in the next year or two we will be releasing versions
that have GPU support, so getting a card with a reasonable amount of RAM would
be a good idea
Cheers
Bruce
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Tim Schäfer
Sent:
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Dear FreeSurfer experts: I use the command recon-all qcache to get file
sub_01/surf/lh.thickness.fwhm10.fsaverage.mgh file. And I am confused that the
cortical thickness in this file is measured in common space after sub is
aligned with the common
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Dear Freesurfer Team
I have a very naive question. I am in urgent need to get a cortical region
volume base on the Harvard-Oxford Cortical Atlas(from FSL). I have T1 images in
nifti files, brain extracted. How can I get the cortical volume using
Glad to hear!
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
On Sep 22, 2021, at 16:37, Szulia Agata
mailto:agata.szu...@stud.umed.lodz.pl>> wrote:
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Dear
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Dear Eugenio,
Thanks so much for your reply. I will certainly follow your instructions on
"small volume" registration. That will certainly allow us to benefit from the
more specialized volume showing neuromelanin within the LC area in conjunction
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Freesurfer dropped support for CUDA builds because it’s too much work to keep
up with the compatible combinations of machines, graphics hardware and
supported CUDA drivers.
Freeview depends upon graphics packages such as Qt and VTK. My
understanding
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FreeSurfer does not require any special graphics card, you can chose whatever
card you like (as long as it works under Linux, but I haven't come across one
that did not in the last 10 years or so).
*If* you want to run stuff on the GPU (the current
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Hello Freesurfer Developers,
the old Linux-Computer Freesurfer was running on broke down and now we
need to buy a new one.
The recommondations in the systems requirements were very helpful, but
they seem a bit outdated.
For Graphics Card it says:
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