>
> Hi Tara, The problem is that the lGI is already very smooth and then it
> gets smoothed again. This causes the total smoothness level to go beyond
> what has been done for the simulation. Try using fwhm=0.
>
> doug
>
>
> On 09/04/2013 09:48 AM, Tara Ann Miskovi
Hello Freesurfer experts,
I am having difficulty when trying to extract LGI values from a specific label
I made. mris_anatomical seems to work when I run it with an annotation, so I am
not sure why I am having this error.
mris_anatomical_stats -l sub200/label/lh.precuneus.label -t
sub200/surf/
Hi Jack,
You can specify the .stats file created. Here is an example from the script I
use.
Anyone, correct me if this is wrong!
Tara
mris_anatomical_stats -l ${subject}/label/lh.frontalmerge.label -f
${subject}/stats/lh_frontal_surface.stats ${subject} lh pial
aparcstats2table --hemi lh \
-
Hello Freesurfer experts,
I am having difficulty when trying to extract LGI values from a specific label
I made. mris_anatomical seems to work when I run it with an annotation, so I am
not sure why I am having this error.
mris_anatomical_stats -l sub200/label/lh.precuneus.label -t
sub200/surf/
Hi Everyone,
I am having trouble running mris_anatomical_stats on an annotation file
produced from my group analysis in qdec.
This is my code, but it seems to want to pull the annotation file from the
subject/label directory. Should I just make a copy into everyone's label file?
mris_anatomic
ubject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
This may sound incredibly trivial, but try putting a "./" infront of
qdec, ie, "-a ./qdec/..."
doug
On 10/04/2013 03:42 PM, Tara Ann Miskovich wrote:
> Hi Everyone,
>
> I am having trouble running
Message -
From: "Douglas N Greve"
To: "Tara Ann Miskovich"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Monday, October 7, 2013 1:59:37 PM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
Oh, you'll need to map the annotation into the individual
.th13.sig.vertex.mgh
F.mgh mc-z.abs.th13.sig.cluster.mgh sig.mgh
gamma.mgh mc-z.abs.th13.sig.cluster.summary
gammavar.mgh mc-z.abs.th13.sig.ocn.annot
Thank you again for the help!
Tara
- Original Message -
From: "Douglas N Greve"
To: "Tara Ann Miskov
version 5.0.0
- Original Message -
From: "Douglas N Greve"
To: "Tara Ann Miskovich"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 8, 2013 1:57:35 PM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
what version of FS are you u
Thank you so much!
Tara
- Original Message -
From: "Douglas N Greve"
To: "Tara Ann Miskovich"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 8, 2013 2:15:33 PM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
OK, the featur
opps sorry one last question. Will segstats get me LGI estimates of the pial
surface?
Tara
- Original Message -
From: "Douglas N Greve"
To: "Tara Ann Miskovich"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 8, 2013 2:15:33 PM
Subject: Re: [Freesurfer
I see. Thank you so much for everything!
Tara
- Original Message -
From: "Douglas N Greve"
To: "Tara Ann Miskovich"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 8, 2013 2:42:36 PM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_
Hello,
I am extracting sulci depth using the following
mri_segstats --annot ${subject} lh aparc --sum lh.sulc.sum --i surf/lh.sulc
Do you know how I could put this into aparcstats2table?
Thank you,
Tara
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PM
Subject: Re: [Freesurfer] sulci depth in table
If you are using mri_segstats then you should use asegstats2table
doug
On 11/08/2013 11:35 AM, Tara Ann Miskovich wrote:
> Hello,
>
> I am extracting sulci depth using the following
>
> mri_segstats --annot ${subject} lh aparc -
Hello,
I am conducting group analyses with LGI data in qdec, and I am having an issue
with the monte carlo simulation I am hoping to get help with.
Under design I leave the Smoothing (FWHM) at 10, and when I try to run the
monte carlo simulation after running the analysis I get this error: Err
Hello everyone,
I am trying to gather the curvature (of a frontal ROI created through
mri_mergelabels) through mris_anatomical_stats using the following
mris_anatomical_stats -l 1220/label/lh.frontalmerge.label -f frontal_table 1220
lh pial
The table produced doesn't upload well into a spread
Hi all,
I am wondering if any one has any experience with converting a freesurfer
surface based ROI created in QDEC into a format I could use on functional data
in afni.
Thank you,
Tara
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htt
Hopefully that's all clear. Let me know if I can help in another way.
Cheers,
Paul
On Thu, Jun 5, 2014 at 12:13 PM, Tara Ann Miskovich < misko...@uwm.edu > wrote:
Hi all,
I am wondering if any one has any experience with converting a freesurfer
surface based ROI create
x
ROI_name.nii.gz
You can then do your AFNI-based analyses with your ROIs.
Hopefully that's all clear. Let me know if I can help in another way.
Cheers,
Paul
On Thu, Jun 5, 2014 at 12:13 PM, Tara Ann Miskovich < misko...@uwm.edu > wrote:
Hi all,
I am wondering if a
nly a couple of minutes.
Run @SUMA_Make_Spec_FS -help to see the command line syntax. Look for
the relevant files in the SUMA folder. You can also edit the @SUMA
program to add any file you have newly created that is not a standard
freesurfer file.
Anthony
On 6/9/14, 11:15 AM, Tara Ann
Hello,
I was hoping someone could help me map with mapping my annotation from my
significant qdec clusters into each individual space.
Thanks!
Tara
Tara A. Miskovich, B.A.
Affective Neuroscience Laboratory
Department of Psychology
University of Wisconsin-Milwaukee
334 Garland Hall
misko...@uw
: Thursday, June 26, 2014 11:05:49 AM
Subject: Re: [Freesurfer] Qdec Annotation to Individual
You can use mri_surf2surf with the --sval-annot option. Run it with
--help and look at example 6
doug
On 06/26/2014 11:04 AM, Tara Ann Miskovich wrote:
> Hello,
>
> I was hoping someone could help
: this is not a substitute
for running the cortical parcellation! The parcellations that it
maps to the new subject may not be appropriate for that subject.
On 06/26/2014 12:34 PM, Tara Ann Miskovich wrote:
> Thank you for your response Doug. On my help it only goes up to example 5. I
> am
to nnf so that
the annot indices are not averaged. Note: this is not a substitute
for running the cortical parcellation! The parcellations that it
maps to the new subject may not be appropriate for that subject.
On 06/26/2014 12:34 PM, Tara Ann Miskovich wrote:
> Thank you for your re
Hello,
I am trying to convert my significant cluster from qdec into a .gii file, and I
have a couple of questions.
My mri_convert is not working, but it is my first time using it so I may be
missing something, but it just keeps opening up the usage and gives no errors.
mris_convert --annot mc-
Hello,
I am trying to convert my significant cluster from qdec into a .gii file, and I
have a couple of questions.
My mri_convert is not working, but it is my first time using it so I may be
missing something, but it just keeps opening up the usage and gives no errors.
mris_convert --annot mc-
Hello,
I am trying to convert my significant cluster from qdec into a .gii file, and I
have a couple of questions.
My mri_convert is not working, but it is my first time using it so I may be
missing something, but it just keeps opening up the usage and gives no errors.
mris_convert --annot mc-
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