Hi everyone ,
After "recon-all",how to determine quickly the quality of whiter matter
segmentation ,surfaces(e.g. whiter matter surface and pial surface) and
topological fix ? what anatomy should be paid more attention?
Best regards?
Xin-Fa Shi .
___
Fr
I can't remember what the issue was. Can you run
funcroi-table-sess -debug -roi l_ant_cingulate_allVfix.roicfg -analysis
NMASA_induction.lh -contrast allVfix -sf induction_all2.lst -o
l_ant_cingulate_induction_FIR_f0.dat -frame 0 |& tee dng.log
and send me dng.log
doug
On 12/12/2014 03:03 PM
No, she is saying that you should open a terminal, and type only
"trac-all". This should display the help for that program, including the
program's flags. If you don't see "-qa" listed, then the trac-all you're
using is an older version.
You need to verify that you have downloaded the latest ver
Hi Deniz
if you rerun them all with 5.3 that should be ok
Bruce
On Fri, 12 Dec 2014, Deniz
Ozgen wrote:
Hi everyone,
We have a number of Freesurfer segmentations performed with version 5.0.
Some of these will need to be corrected, most likely with adding control
points.
The question is we c
Hi everyone,
We have a number of Freesurfer segmentations performed with version 5.0.
Some of these will need to be corrected, most likely with adding control
points.
The question is we currently have version 5.3 running on our server. Is it
okay to add the control points and run the segmentation
If the -qa flag is not recognized, then you're still running the old
version of trac-all, not the updated version.
On Fri, 12 Dec 2014, Anri WATANABE wrote:
I tried to run trac-all -qa -c the_name_of_my_configuration_file after trac-all
-corr -c
the_name_of_my_configuration_file, but it fai
Does a file called "dmri/dwi_motion.txt" get created? That's the output of
the QA step. This is explained in the tutorial, under "Outputs from
quality assessment":
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaOutputs
On Fri, 12 Dec 2014, Anri WATANABE wrote:
Thanks, Anastasia.
Hi there,
I'm having the same problem referenced in this thread from last year. When I
send the command:
funcroi-table-sess -roi l_ant_cingulate_allVfix.roicfg -analysis
NMASA_induction.lh -contrast allVfix -sf induction_all2.lst -o
l_ant_cingulate_induction_FIR_f0.dat -frame 0
I get t
Thank you Doug! I replaced all my spaces with new spaces and it worked!
Much appreciated!
Lindsay
On Fri, Dec 12, 2014 at 12:09 PM, lindsay hanford wrote:
>
> Hi Doug!
>
> Thank you very much for your reply. I made the fsgd file in a plain-text
> file using the textedit program on a Mac and when
Sorry, I never got around to downloading them and now they are gone. Can
you re-upload them?
doug
On 12/08/2014 06:07 PM, Gurney, Jenny wrote:
>
> Hi all,
>
> Doug, just wondering if anyone has had time to look into the issue of
> using mri_convert with multiframe/enhanced DICOM. My colleague,
You can also use mri_binarize which has more documentation :-)
On 12/11/2014 01:31 AM, pradeep mahato wrote:
> There is no documentation or example for mri_extract_label.
> What should be the syntax for it. What kernel and xform file should be
> used.
>
> On Wed, Dec 10, 2014 at 6:50 PM, Bruce F
I'm pretty sure this is due to the language locale settings. Can you do
an experiment? Run
echo $LANG
if the result is not en_US.utf8 try
setenv LANG en_US.utf8
And see if that fixes it. If it does, I can change the script
doug
On 12/11/2014 03:11 AM, Milde, Christopher wrote:
> Dear Doug,
Are you sure your path isn't look for the older "trac-all" first? If you didn't
remove/overwrite it, that is.
Type "which trac-all" (without the quotes) and see if the correct one is shown.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@
The file I looked at had a bunch of carriage returns (try looking at it
with more or less or cat). As long as those are in there, it will create
an error.
Try running this and using the new one
cat g4v1.73.fsgd | sed 's/\r/\n/g' > new.g4v1.73.fsgd
On 12/12/2014 12:09 PM, lindsay hanford wrote:
Hi Doug!
Thank you very much for your reply. I made the fsgd file in a plain-text
file using the textedit program on a Mac and when that didn't work I tried
modifying in the terminal window using: nano -w g4v1.73.fsgd.
This also didn't solve the problem. I am not sure what to try next.
Lindsay
O
Ack. Can't believe I missed that. Thank you. I'll run it again and see how
that turns out.
On Thu, Dec 11, 2014 at 2:07 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> Hi Thomas - No bother at all! If you search for the word "error" in your
> trac-all.log, you'll see that it coul
Dear experts,
I have created a label from Qdec and used mri_label2label to apply it to
all subjects. Now I need to extract the pc1 measure from longitudinal
analysis in my label. Would you please advise how to do this since
kris_anatomical_stats doesn't work here?
Best regards,
Amirhossein Manzou
Its my understanding is that CUDA is specific only to NVIDIA graphics
devices.
http://www.nvidia.com/object/cuda_home_new.html
-Zeke
On 12/12/2014 08:54 AM, Salil Soman wrote:
> Dear List Members,
>
> Does anyone know if it is possible to use freesurfer gpu based
> acceleration using amd video
Hi Peng
yes, for sure. This is what Matti Hamalainen's excellent MNE package is
designed for. I'll cc Matti so he can chime in
cheers
Bruce
On Fri, 12 Dec 2014, peng
wrote:
> Dear freesurfer users,
>
> I have installed freesurfer and freeview. The visualization of
> brain surfaces looks gre
Dear freesurfer users,
I have installed freesurfer and freeview. The visualization of
brain surfaces looks great. Is it possible to visualize functional
MEG/EEG source data with freeview?
What I have:
1. Source locations (Nx3)
2. Activation strength (Nx1) at these locations
3. The anatomy data
Dear List Members,
Does anyone know if it is possible to use freesurfer gpu based acceleration
using amd video cards?
Thanks,
Salil Soman, MD, MS
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Hi Xin-Fa
scroll through your data with the surfaces overlaid on the volume and
make sure that they follow where you think the gray/white and pial
boundaries are and do the same for the aseg.mgz
cheers
Bruce
On Fri, 12 Dec 2014, Xinfa
Shi wrote:
Hi everyone,
After pre-process "recon-all"
Hi Xin-Fa
the easiest way to check the quality of the cortical registration is to
look at one of the parcellations (e.g. lh.aparc.annot) and see if it
labeled the major sulci correctly
cheers
Bruce
On Fri, 12 Dec 2014, Xinfa Shi wrote:
After 'recon-all' ,how to check its accuracy of registr
After 'recon-all' ,how to check its accuracy of registration ? what anatomy
should be paid more attention ?
Best regards .
Xin-Fa Shi .
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Hi everyone,
After pre-process "recon-all",what parts of its process need to check
visually ?how to determine its necessity for check ? and how to check them
? Could you provide me for a guide or pipeline?
Best regards.
Xin-Fa Shi.
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Hello Freesurfer Gurus,
I have been conducting cortical thickness and LGI analyses at my lab using
Qdec. We have gotten some really promising results thanks to your help!
However I have a few withstanding questions which need answered to make
sure our results are methodologically valid:
1) After w
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