Dear Doug,
Thank you very much for your reply.
There is one other thing that is not clear to me. When displaying group level
FSL zstats onto the FreeSurfer surface, which threshold (-log10(p) or z score)
should I use? Is it again -log10(p), and therefore p=.01 is 2?
If this is indeed the ca
quando avvio il trac-all (relase FS5.1) mi crea questo errore:
/opt/freesurfer/bin/trac-preproc
#-
#@# Image corrections Tue Mar 27 11:17:27 CEST 2012
mri_convert
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.294
Hi,
I got an error during the first step in recon-all (Mac OS 10.6.8,
FreeSurfer v5.1.0). The eror message in the log file is:
WARNING: file ./MR.1.3.12.2.1107.5.2.18.41016.201008031106017688438785.dcm
does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpa
Hi Jamaan,
Yes, I got the same error.
Ed
On 27 Mar 2012, at 13:36, Jamaan Alghamdi wrote:
> Hi Ed,
>
> Have you tried using mri_convert command directly without running recon-all.
>
> Best wishes,
> Jamaan
>
> Hi,
>
> I got an error during the first step in recon-all (Mac OS 10.6.8,
> FreeS
Hi,
I followed the instructions to visualize the hippocampal subfield segmentation
by entering the command (in the subject's mri directory)
freeview nu.mgz \
> -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \
> -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \
> -p-pr
Dear FreeSurfers,
I'm working on a structural dataset and after running recon-all -all,
I had to correct all cases (32 so far) from minimum pial/wm
corrections to massive pial corrections (only three cases needed
control points). Mostly, the corrections were needed due to remaining
dura/s
Hi Tanja,
I would recommend you try using some control points. Place one or two
just inside the wm surface near that wm finger which is not being
included, and then possibly one or two control points carefully placed
along the wm finger on voxels with the highest intensity (in the middle it
lo
Sorry, if you're loading a zstat, then you should interpret the values
(and thresholds) as z-stats.
doug
On 03/27/2012 04:54 AM, Zurcher Nicole wrote:
> Dear Doug,
>
> Thank you very much for your reply.
>
> There is one other thing that is not clear to me. When displaying group level
> FSL z
Is it a siemens dicom? If so, what happened to the ascii header? Did you
do something to the file? What are the contents of the image? Eg, a T1?
doug
On 03/27/2012 05:35 AM, Ed Gronenschild wrote:
> Hi,
>
> I got an error during the first step in recon-all (Mac OS 10.6.8,
> FreeSurfer v5.1.0). Th
Do you not have any eccen runs?
doug
On 03/27/2012 06:55 AM, Kiley Seymour wrote:
> Dear Doug,
>
> I am aware I am becoming a regular pain. But I now encounter the
> following problem when running selxavg3-sess -a rtopy.self.lh -s
> CMRU1711. I have also attached my analysis.info and Xtmp.mat fi
Hi Johnson, try something like this:
mri_label2vol --seg tracts.nii --temp orig.mgz --o tracts-in-fs.nii --regheader
tracts.nii
doug
On 03/26/2012 03:29 PM, Johnson wrote:
> OK
> T1 space is the space acquired from the machine, original anatomical space
> regards
> JG
>
> On 03/26/2012 2:25 PM
Ciao Sarina - The problem is here "fslorient: Command not found." You have
to make sure that FSL is properly installed and the FSL executables are in
your path, as trac-all calls a few of them.
Hope this helps,
a.y
On Tue, 27 Mar 2012, Sarina Sacco wrote:
quando avvio il trac-all (relase F
FSFAST assumes that you do. A silly way around this is to just replicate
your polar runs and call them eccen runs.
doug
On 03/27/2012 12:35 PM, Kiley Seymour wrote:
> no I don't.
>
> On Tue, Mar 27, 2012 at 6:17 PM, Douglas N Greve
> wrote:
>> Do you not have any eccen runs?
>> doug
>>
>> On 03
You will have to mri_convert all the .nii files so that they have the
proper TR.
On 03/27/2012 12:51 PM, Kiley Seymour wrote:
> Hi Doug. I just made a dummy folder with an eccen run. It got around
> the error XCond = cond(XtX) but took me back to the original error :
> TR mismatch error despite
I have an MRI volume dataset, which is deskulled beforehand .
Is it possible to run recon-all with an option stating to not deskull the data.
Regards
Darshan___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mai
Did you run fieldsign-sess? If you don't have an eccen run you can't
compute a fieldsign.
doug
ps. Please post emails to the list and not to me personally. Thanks!
On 03/27/2012 04:07 PM, Kiley Seymour wrote:
> Dear Doug,
>
> Thanks for all of your help today. I think I am almost there with this
And what coordinate system are the xyz in?
doug
ps. Please post questions to the list and not to me personally. Thanks!
On 03/27/2012 04:10 PM, Johnson wrote:
> Hi
> I have the tracts in (x,y,z) format not as an nii file
> regards
> JG
> On 03/27/2012 11:25 AM, Douglas N Greve wrote:
>> Hi John
Hi Jorge,
The global measurement enters in the model as a nuisance, not as an
effect of interest. Even if the estimator is inconsistent, it is still
useful as such. About which is noisier, it turns out that in general,
the bigger the structure, the less measurement noise is present. From
the
They are in the same coordinate system as the original T1 file supplied
to FS to generate the aparc+aseg file
JG
On 03/27/2012 4:41 PM, Douglas N Greve wrote:
> And what coordinate system are the xyz in?
> doug
> ps. Please post questions to the list and not to me personally. Thanks!
>
>
>
>
> On
Hi Johnson, can you be more specific? scanner coordinates? voxel
coordinates?
On 03/27/2012 06:20 PM, Johnson wrote:
> They are in the same coordinate system as the original T1 file
> supplied to FS to generate the aparc+aseg file
> JG
> On 03/27/2012 4:41 PM, Douglas N Greve wrote:
>> And what
Hi Darshan,
There are instructions on how to do this here:
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Ihavealreadyskull-strippeddata.CanIsubmitittorecon-all.3F
Allison
On Tue, 27 Mar 2012, Darshan P wrote:
I have an MRI volume dataset, which is deskulled beforehand .
Is
from my understanding, scanner coordinates (i.e. considering the
resolution of each voxel)
regards
JG
On 03/27/2012 6:14 PM, Douglas N Greve wrote:
> Hi Johnson, can you be more specific? scanner coordinates? voxel
> coordinates?
>
> On 03/27/2012 06:20 PM, Johnson wrote:
>> They are in the same
Hi everyone,
I realize I'm quickly becoming an annoyance, but I'm having trouble loading
my data file into qdec. I keep getting the error: QdecDataTable::Load
failed to tokenize string: on line 88 of HTN_FMRI_Qdec. HTN_FMRI_Qdec is
the name of my data file. I do not even have a line 88 as I have on
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