to:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of
> Julio Alberto González Torre [al099...@uji.es
> <mailto:al099...@uji.es>]
> Sent: Friday, April 15, 2016 11:42 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] fcseed-sess ERROR: could not dete
> From: freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Julio Alberto
> González Torre [al099...@uji.es]
> Sent: Friday, April 15, 2016 11:42 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfe
freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Julio Alberto González
Torre [al099...@uji.es]
Sent: Friday, April 15, 2016 11:42 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] fcseed-sess ERROR: could not determine file for
.../fmcpr
H
Hi Talia. Thanks for the quick answer.
But the preprocessing finished correctly without errors as I can check on
all the log files generated in the same project folder. "subjectname" and
$SUBJECTS_DIR are correctly placed.
The problem is a later step (STEP 5,
http://surfer.nmr.mgh.harvard.edu/fsw
Hi Julio,
In the past I received this error because the subject was not preprocessed
correctly. Make sure you have a link to the subject's structural recon folder
in the resting state folder. In order to do this, you have to create a txt
file(in this case it would 02_resting/subjectname) and wit
Thank you. issue resolved.
On Wed, 12 Aug 2015 11:20:53 -0400, Douglas N Greve wrote:
> The problem is that you are using the wrong segmentation number for
> left
> insula. You used 19, which is reasonable given that
> FreeSurferColorLUT.txt lists that as left insula, but the one you
> want
> is
The problem is that you are using the wrong segmentation number for left
insula. You used 19, which is reasonable given that
FreeSurferColorLUT.txt lists that as left insula, but the one you want
is actually 1035.
doug
On 08/12/2015 11:09 AM, Gay,Charles Wysaw wrote:
> Hi Doug -
> Here is so
Hi Doug -
Here is some of the information:
FREESURFER_HOME:
/Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer
Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Kernel info: Darwin 14.0.0 x86_64
-
Please inclu
Hi Chaz, we'll need more info. Please see
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On 08/11/2015 11:40 PM, Gay,Charles Wysaw wrote:
> I've completed steps 1 thru 4 successfully (i think). When I run the
> fcseed-sess with the segid for the left insula I'm getting an
> segmentation fault.
Hi Doug,
So I just tried making my ROI a little bit bigger in an earlier binarizing
step that created my segmentation, and when I ran fcseed-config and
fcseed-sess in this same subject it ran without error. I guess it was a
sizing issue! Let me know if you have any additional thoughts.
Thanks aga
I actually already tried rerunning fcseed-config and fcseed-sess lowering
the fillthresh (even brought it down to 0) and I still got the same error.
I just tried .05 to be thorough but no dice :(
> Try lowering the fillthreshold to .1 in fcseed-config (means you have to
> re-run fcseed-sess for al
Try lowering the fillthreshold to .1 in fcseed-config (means you have to
re-run fcseed-sess for all subjects, but see if it makes those two
work). For such a small seed, it may even be better to use .05.
On 05/21/2015 11:42 AM, Alexandra Tanner wrote:
> The voxel size for this functional sequenc
The voxel size for this functional sequence is 3x3x3mm
> What is the voxel size of your functional? 54 is small, but I would
> expect it to still work.
>
> On 05/21/2015 11:20 AM, Alexandra Tanner wrote:
>> Hi Doug,
>>
>> It is a pretty small segmentation. In subject NNC0931 (the example we're
>>
What is the voxel size of your functional? 54 is small, but I would
expect it to still work.
On 05/21/2015 11:20 AM, Alexandra Tanner wrote:
> Hi Doug,
>
> It is a pretty small segmentation. In subject NNC0931 (the example we're
> looking at) the segmentation has 54 voxels. fcseed-sess also didn'
Hi Doug,
It is a pretty small segmentation. In subject NNC0931 (the example we're
looking at) the segmentation has 54 voxels. fcseed-sess also didn't work
in subject NNC0901 -- in that subject the segmentation has 78 voxels. For
comparison, in one of the subjects where fcseed-sess completed withou
I'm not sure what is going wrong here, but it does not find any voxels
when the segmentation is mapped into the functional space. Can you look at
/cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz
And see how many voxels
Fabulous!!! It worked
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Monday, May 11, 2015 5:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fcseed-sess
oh, the 1126 is
Found 0 values in range
> Counting number of voxels
> Found 16777216 voxels in final mask
> mri_binarize done
>
>
> Thank you for any advice?
>
> Mohamad
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Grev
advice?
Mohamad
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, May 11, 2015 2:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer
Use aparc.a2009s+aseg.mgz
On 05/11/2015 02:01 PM, Alshikho, Mohamad J. wrote:
> Hi Doug,
>
> I want to use the command "fcseed-config" to configure the segment 1126 (in
> aparc+aseg) as a seed to pass it to connectivity analysis. I ran the command
> line:
>
> fcseed-config -segid 1126 -fcname L
Use 10 for thalamus and not 9. Not sure why there is a difference.
doug
On 01/08/2015 02:57 PM, std...@virgilio.it wrote:
>
> Hi list,
>
>
> I'm running FAST on resting state data.
>
>
> After
>
>
> fcseed-config -segid 9 -fcname L_Thalamus.dat -fsd rest -mean -cfg
> mean.L_Thalamus.config
>
>
>
Hi Doug,
This seems to have solved the problem with that subject.
Thank you so much.
Best,
Omar
>
> OK, the problem is that this subject has very small ventricles and no
> ventricle voxel exceeds 95% partial volume fraction. To get around this
> you can configure the seed to allow a smaller PVF
OK, the problem is that this subject has very small ventricles and no
ventricle voxel exceeds 95% partial volume fraction. To get around this
you can configure the seed to allow a smaller PVF, say 75%, with the
"-fillthresh .75". Specify -fillthresh AFTER -vcsf
You will have to re-run it for al
Hi Doug,
I ran 'mri_binarize --i aparc+aseg.nii.gz --match 4 --match 5 --match 43
--match 44 --match 31 --match 63 --count countfile.dat'
The following error message was produced:
ERROR: must specify output volume
So I added -o bin.nii.gz to the end of the command and reran it successfully.
The
That looks good. Run these commands
cd AC30_1319/Bold1/001
mri_label2vol --aparc+aseg --temp template.nii.gz --reg
register.dof6.dat --o aparc+aseg.nii.gz
mri_binarize --i aparc+aseg.nii.gz --match 4 --match 5 --match 43
--match 44 --match 31 --match 63 --count countfile.dat
then send me the c
Sorry about that. I must have clicked 'reply' by mistake rather than
'reply all'. I wouldn't want to deprive anyone of the opportunity to help
me resolve this issue.
--The issue--
I looked at the segmentation in tkmedit and the labels for the ventricles
showed up the same as in subjects that worke
Hi Omar, it is not finding any ventricle voxels. Check the FS
segmentation to make sure that the ventricles are labeled and also check
the registration to make sure it looks ok.
doug
On 8/14/13 12:04 PM, O S wrote:
> Dear Support,
>
> I am trying to use fcseed-sess to create a ventricle and C
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