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
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
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
. 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 response Doug. On my help it only goes up to example 5. I
am
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 Miskovich
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 any one has any experience
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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Freesurfer@nmr.mgh.harvard.edu
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 created in QDEC into a format I could use
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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Freesurfer mailing list
, 2013 1:00:18 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 --sum
Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Tara Ann Miskovich misko...@uwm.edu
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
.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 gr...@nmr.mgh.harvard.edu
To: Tara Ann Miskovich misko
version 5.0.0
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Tara Ann Miskovich misko...@uwm.edu
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
Thank you so much!
Tara
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Tara Ann Miskovich misko...@uwm.edu
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
opps sorry one last question. Will segstats get me LGI estimates of the pial
surface?
Tara
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Tara Ann Miskovich misko...@uwm.edu
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 8, 2013 2:15:33 PM
Subject
I see. Thank you so much for everything!
Tara
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Tara Ann Miskovich misko...@uwm.edu
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 8, 2013 2:42:36 PM
Subject: Re: [Freesurfer] Cluster Annotation file
PM
Subject: 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 mris_anatomical_stats
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
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?
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
, Tara Ann Miskovich wrote:
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
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
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:
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