In addition to that: I am always getting positive correlations (when I load
sig.mgh) every time i.e. even when I correlated thickness and gyrification.
None of the voxels/areas showing negative correlation between any of the
structural measures
On Thu, May 11, 2017 at 11:26 AM, Martin Juneja wrot
Hi Doug,
Why Qdec offer "volume, area, thickness ,...etc " in the drop down menu
"measures"?
In this menu there are many measures and I understand that I can run surface
based analysis depending on the choice of this drop down menu. Is this Correct?
Please see attached. Thank you for any clarif
The Program for Translational Research on Adversity and Neurodevelopment
(P-TRAN) at The Pennsylvania State University is seeking a qualified
postdoctoral researcher with expertise in human brain imaging, specifically
magnetic resonance imaging (MRI)) with children and adolescents. This
position
Thanks for your help, Doug. Here's what I get when I run mri_convert on its own:
mri_convert
151027_RMD057/RAW//151027_RMD057.MR.INVESTIGATORS_Dillon.5.1.20151027.152735.1oe820t.dcm
151027_RMD057/3danat/005/T1.nii --sdcmlist 151027_RMD057/3danat/005/flf -ot
nii --nspmzeropad 3 --in_type siemens
You should also look at the FSFAST tutorial on our wiki. What version
are you using? Version 6 should not need bet.fsl. Just in case you can
use this version
https://gate.nmr.mgh.harvard.edu/safelinks/greve/bet.fsl
On 05/11/2017 12:50 PM, Brad Matushewski wrote:
>
> Hello Freesurfer crowd. I
Hello Freesurfer crowd. I am working on try to get my first fMRI scan working.
I have come a long ways in terms of setting things up but have reached a road
block that I have unable to get past.
I have been following along the slides from the power point presentation
"FSFAST Part 2". I got a
what dat file? Can you give more specific details on the steps you are
taking? Can you send the dat file?
On 05/10/2017 06:37 PM, Benjamin Ubani wrote:
> Hello,
>
> I'm writing because I have had an issue with QDEC and it's ability to
> correctly read the number of subjects indicated on my data
Can you run that mri_convert command by itself and send me the terminal
output?
On 05/10/2017 02:26 PM, Dillon, Daniel G. wrote:
> Hi everyone. I’m unpacking dicoms collected on a 3T Tim Trio and I’m
> getting segmentation errors (see below) with two of ~80 subjects when
> using either unpacks
Is it just those few vertices that are appear to be on the sphere? Can
you send me the terminal output from the mri_label2label with the
--close operation?
On 05/10/2017 12:16 PM, Hengda He wrote:
> Hi Freesurfer Developers,
>
> I'm trying to map the vertices of caudal middle frontal in one sub
I'm not sure what you mean. Can you elaborate?
On 05/10/2017 11:19 AM, shi yao wang wrote:
> Dear FS experts:
> We generated a specific population of brain template.
> Just wondering if FS can use these templates to measure brain volume.
>
> thanks
> Lawrence
>
> Emory
>
>
>
Use mri_segstats with the --slabel option, eg,
mri_segstats --slabel subject $SUBJECTS_DIR/subject/label/lh.cortex --id
1 --i X.mgh --avgwf meanX.dat
On 05/10/2017 08:45 AM, Damien MARIE wrote:
> Hi,
>
> I’ve a .mgh that is a volume projected on the surface of the same subject at
> mid-thickn
Hi Dan
that's a pretty low-contrast, severely motion-corrupted scan. We did pretty
well given the input I think. To visualize the defects you can cd into the
subject's mri dir and run:
fv -v brain.mgz wm.mgz:colormap=heat -f \
../surf/lh.orig.nofix:overlay=../surf/lh.defect_labels:overlay_th
I'm not sure I follow. If I understand, you are finding sig diff in PCG
volume when you extract it the volume value for each subject (scaled by
etiv) and process in SPSS. The part I don't understand is what you are
doing with QDEC. I don't think QDEC can be used to test ROI volume.
On 05/09/20
mri_glmfit will not generate a pcc file with --pvr. I think I just did
not get around to adding support for this. What about the sig does not
look right? You can often get funny looking maps because each voxel is a
different design matrix.
On 05/09/2017 03:15 PM, Martin Juneja wrote:
> Dear Dr
Hi Guido,
I think you should wait until recon-all is done. Running 2 recon-all commands
on the same subject simultaneously: a) would need hacking recon-all; b) it’s a
bad idea. Moreover, the subfields make use of wmparc.mgz, which is produced
towards the very end of recon-all -all anyway.
Cheers
Hi Dan
I'll take a look, but make sure that you are loading the lh.defect_labels
as a surface overlay onto the lh.orig.nofix and lh.inflated.nofix surfaces.
It is *not* a surface, but a scalar field over the surface
cheers
Bruce
On Thu, 11 May 2017, Weisholtz, Daniel S.,M.D. wrote:
Dear
Dear Bruce,
Thank you so much for your suggestions. Unfortunately, I was not able to open
lh.defect_labels in freeview. When I try, Freeview crashes. There are no rh
surfaces in the surf folder, so I presume this means the problem occurred in
the left hemisphere. I was able to view the inflat
Hi Experts,
I am running Freesurfer v6.0 on a Cluster. I've traied this command:
*recon-all -i $IMAGEN -s $SUJETO -all -hippocampal-subfields-T1
-brainstem-structures*
Although all step in recon-all works fine, hippocampal-subfields process
allocate much more RAM than previous step (10 GB of RAM
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