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Thank you for your help.
I cannot load the label on surface, this is the error:
[toyama-no-iMac:/applications/freesurfer/subjects] toyama% qdec
Reading /applications/freesurfer/tktools/tkUtils.tcl
Using /applications/freesurfer/lib/tcl/fsgdfPlot.
Is the label valid? Can you load it on a surface? How many points are in it?
On 1/16/2020 9:51 PM, Tien Pham wrote:
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Thank you for your e-mail.
It seems I got another error. This is what it showed in terminal:
[toyama-no-iMac:/applications/freesurfer/subjects
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Thank you for your e-mail.
It seems I got another error. This is what it showed in terminal:
[toyama-no-iMac:/applications/freesurfer/subjects] toyama% mri_segstats --i
lh.pial_lgi --slabel VC001_1 lh lh.frontoinsula.label --id 1 --sum sum.dat
$Id:
Sorry, it should have been --sum instead of --o
the subject name is subject_id
--id 1 just means to take the vertices in the label (--id 0 would mean to take
the background)
On 1/16/2020 7:07 PM, Tien Pham wrote:
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Thank you very much for your e-mail.
I tried,
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Thank you very much for your e-mail.
I tried, but this '' --o '' is unknown showing in terminal and the '' --id
'' flag is subject name?
Could you please help me?
For example, I found the change in frontoinsula region between 2 groups in
my dataset and
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Hello Pascale,
Yes, that kind of symbol error has been posted before, and it can from the
version of the standard C++ (or C) libraries being too different on the machine
the binaries are running on - compared to the machine they were built on.
Gener
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It is the file computed longitudinal processing that represents the rate with
respect to the thickness at the first time point computed by long_mris_slopes.
Swati
Swati Rane Levendovszky, PhD
Interim Di
No, sorry, I don't have a simple fix.
On 1/11/2020 5:05 PM, Davide Momi wrote:
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Thanks Doug,
I followed your tips and try to run mris_remove_intersection. However the
result looks like the same than before. Maybe I am doing something wrong. Could
you pleas
It is seg faulting at the defect correction stage which is before the FLAIR
would be used. At this point it should be identical to the T1-only analysis.
Check your commands to make sure they are the same except for the FLAIR part
On 1/16/2020 9:55 AM, Swanson,Clayton wrote:
External Ema
On 1/15/2020 3:08 PM, Graduate Imaging wrote:
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Hello,
I recently ran a vertex wise analysis on two different projects the first had
three groups with three co-variates that looked at if group membership was
associated with brain volume. The second project
I don't think so, but you can run mris_ca_label by hand. Look in the
recon-all.log file for the command, then use the 2005 tif instead of the 2009
tif. I think it should work.
On 1/16/2020 3:31 PM, Grodin, Erica wrote:
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Hello,
I am running recon-all on my d
Sorry, qdec and tksurfer are becoming (have become?) obsolete. I think you can
load an fsgd file in freeview
On 1/15/2020 11:02 AM, Marcos Martins da Silva wrote:
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Hi! I use FreeSurfer 6.0 over CentOS 7. I have just notice a problem with
input/entry/edit box
Nothing wrong per se, it is just that the inflation was done assuming a certain
number of vertices. You can try changing the number of iterations in the
inflation with,eg,
cd $SUBJECTS/fsaverage/surf
mris_inflate -dist .01 -f .001 -no-save-sulc 5 lh.smoothwm lh.inflated
In this case I set it to
It might be easier to use mri_segstats, eg,
mri_segstats --i lh.pial_lgi --slabel subject_id lh lh.untitled.label --id 1
--o sum.dat
The mean value will be in the "Mean" column of the sum.dat
On 1/14/2020 7:08 PM, Tien Pham wrote:
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Dear FreeSurfer Experts,
Sorry, what is "pc1"?
On 1/14/2020 9:44 AM, Swati Rane wrote:
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Hello,
I was wondering if someone could answer my question below
Can I use mri_glmfit-sim after mri_glmfit on the longitudinal pc1 files.
Are there any set of parameters that should be set differ
Hi Tim, can you send a list of files that have the identifier. For
volumes and surfaces, it might be as easy as running
mri_convert/mris_convert using the same file as input and output.
On 1/13/2020 5:54 AM, Tim Schäfer wrote:
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>
> Dear FreeSurfer experts,
I'm guessing that the fragments might cause problems later either in gtmseg as
a hard failure or in gtmpvc as an ill-conditioned matrix. But you can try it
out:)
On 1/11/2020 6:04 PM, Boris Rauchmann wrote:
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Thanks, that solution seems to work finally. I jus
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Hello,
I am running recon-all on my data using freesurfer 6.0 which is working
correctly. However, I need to create some VOIs which labels are only outputted
from the aparc2005 set and do not appear in the aparc2009 set; specifically:
9001, 9501
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Hello FreeSurfer Developers,
I'm attempting to produce an automated segmentation of the hippocampal
substructures and the nuclei of the amygdala (see hippocampal module
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
Hi Christian, if you send me that surface, I can take a look at what's going
wrong.
best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Christian O'Reilly, Dr
Sent: Thursday, January 16, 2020 9:57 AM
To: freesurfer@nmr.mgh.harvard.ed
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Hi,
I got the following error running mris_topo_fixer:
~$ mris_topo_fixer -mgz -warnings ANTS6-0Months3T lh
INFO: assuming .mgz format
verbose mode on (medium mode): printing warnings
reading input surface
/usr/local/freesurfer/subjects/ANTS6-0Months
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It works! Thank you very much Bruce!
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