Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
I see, could you help me go about this. I have not been able to figure out how
to do this with an annotation file. And I believe I already mapped my lgi to
fsaverage space before group level through recon-all -qcache. Is this what you
mean?
Thank you again for the help!
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: 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 space, or (and
probably better), map your lgi into fsaverage space.
doug
On 10/07/2013 02:18 PM, Tara Ann Miskovich wrote:
Thank you Doug, this did work. However, for every subject I get this line
repeated over and over before it outputs the stats. I still get a stats file
that seems to make sense but I am not sure if this is an issue.
MRISreadAnnotationIntoArray: vertex index out of range: 163841 i=,
in_array_size=136201
annot file:
./qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-trait-Cor/mc-z.abs.th13.sig.ocn.annot
Thank you for the help!
Tara
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, October 4, 2013 6:29:49 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 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_anatomical_stats -a
qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot
-t ${subject}/surf/lh.pial_lgi -f ${subject}/stats/lh.parietal_lgi.stats
${subject} lh
Thank you!
Tara
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
Did you generate the annotation from a qdec analysis of lgi? If so, then
there should be a file already there called something like
mc-z.abs.th13.sig.ocn.dat with a row for each subject and a column for
each cluster. The value will be the mean lgi for that subject and
cluster. Is this what you need?
doug
On 10/08/2013 09:04 AM, Tara Ann Miskovich wrote:
I see, could you help me go about this. I have not been able to figure out
how to do this with an annotation file. And I believe I already mapped my lgi
to fsaverage space before group level through recon-all -qcache. Is this what
you mean?
Thank you again for the help!
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: 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 space, or (and
probably better), map your lgi into fsaverage space.
doug
On 10/07/2013 02:18 PM, Tara Ann Miskovich wrote:
Thank you Doug, this did work. However, for every subject I get this line
repeated over and over before it outputs the stats. I still get a stats file
that seems to make sense but I am not sure if this is an issue.
MRISreadAnnotationIntoArray: vertex index out of range: 163841 i=,
in_array_size=136201
annot file:
./qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-trait-Cor/mc-z.abs.th13.sig.ocn.annot
Thank you for the help!
Tara
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, October 4, 2013 6:29:49 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 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_anatomical_stats -a
qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot
-t ${subject}/surf/lh.pial_lgi -f ${subject}/stats/lh.parietal_lgi.stats
${subject} lh
Thank you!
Tara
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
I did. This is what I get from my group analysis in the folder. I didn't find
the ocn.dat file. Is there something I need to do in Qdec to produce it?
C.dat maxvox.dat mc-z.abs.th13.sig.ocn.mgh
cnr.mgh mc-z.abs.th13.pdf.dat mc-z.abs.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 gr...@nmr.mgh.harvard.edu
To: Tara Ann Miskovich misko...@uwm.edu
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 8, 2013 10:48:10 AM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
Did you generate the annotation from a qdec analysis of lgi? If so, then
there should be a file already there called something like
mc-z.abs.th13.sig.ocn.dat with a row for each subject and a column for
each cluster. The value will be the mean lgi for that subject and
cluster. Is this what you need?
doug
On 10/08/2013 09:04 AM, Tara Ann Miskovich wrote:
I see, could you help me go about this. I have not been able to figure out
how to do this with an annotation file. And I believe I already mapped my lgi
to fsaverage space before group level through recon-all -qcache. Is this what
you mean?
Thank you again for the help!
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: 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 space, or (and
probably better), map your lgi into fsaverage space.
doug
On 10/07/2013 02:18 PM, Tara Ann Miskovich wrote:
Thank you Doug, this did work. However, for every subject I get this line
repeated over and over before it outputs the stats. I still get a stats file
that seems to make sense but I am not sure if this is an issue.
MRISreadAnnotationIntoArray: vertex index out of range: 163841 i=,
in_array_size=136201
annot file:
./qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-trait-Cor/mc-z.abs.th13.sig.ocn.annot
Thank you for the help!
Tara
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, October 4, 2013 6:29:49 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 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_anatomical_stats -a
qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot
-t ${subject}/surf/lh.pial_lgi -f ${subject}/stats/lh.parietal_lgi.stats
${subject} lh
Thank you!
Tara
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
what version of FS are you using?
On 10/08/2013 02:55 PM, Tara Ann Miskovich wrote:
I did. This is what I get from my group analysis in the folder. I didn't find
the ocn.dat file. Is there something I need to do in Qdec to produce it?
C.dat maxvox.dat mc-z.abs.th13.sig.ocn.mgh
cnr.mgh mc-z.abs.th13.pdf.dat mc-z.abs.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 gr...@nmr.mgh.harvard.edu
To: Tara Ann Miskovich misko...@uwm.edu
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 8, 2013 10:48:10 AM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
Did you generate the annotation from a qdec analysis of lgi? If so, then
there should be a file already there called something like
mc-z.abs.th13.sig.ocn.dat with a row for each subject and a column for
each cluster. The value will be the mean lgi for that subject and
cluster. Is this what you need?
doug
On 10/08/2013 09:04 AM, Tara Ann Miskovich wrote:
I see, could you help me go about this. I have not been able to figure out
how to do this with an annotation file. And I believe I already mapped my
lgi to fsaverage space before group level through recon-all -qcache. Is this
what you mean?
Thank you again for the help!
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: 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 space, or (and
probably better), map your lgi into fsaverage space.
doug
On 10/07/2013 02:18 PM, Tara Ann Miskovich wrote:
Thank you Doug, this did work. However, for every subject I get this line
repeated over and over before it outputs the stats. I still get a stats
file that seems to make sense but I am not sure if this is an issue.
MRISreadAnnotationIntoArray: vertex index out of range: 163841 i=,
in_array_size=136201
annot file:
./qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-trait-Cor/mc-z.abs.th13.sig.ocn.annot
Thank you for the help!
Tara
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, October 4, 2013 6:29:49 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 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_anatomical_stats -a
qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot
-t ${subject}/surf/lh.pial_lgi -f ${subject}/stats/lh.parietal_lgi.stats
${subject} lh
Thank you!
Tara
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
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 version of FS are you using?
On 10/08/2013 02:55 PM, Tara Ann Miskovich wrote:
I did. This is what I get from my group analysis in the folder. I didn't find
the ocn.dat file. Is there something I need to do in Qdec to produce it?
C.dat maxvox.dat mc-z.abs.th13.sig.ocn.mgh
cnr.mgh mc-z.abs.th13.pdf.dat mc-z.abs.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 gr...@nmr.mgh.harvard.edu
To: Tara Ann Miskovich misko...@uwm.edu
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 8, 2013 10:48:10 AM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
Did you generate the annotation from a qdec analysis of lgi? If so, then
there should be a file already there called something like
mc-z.abs.th13.sig.ocn.dat with a row for each subject and a column for
each cluster. The value will be the mean lgi for that subject and
cluster. Is this what you need?
doug
On 10/08/2013 09:04 AM, Tara Ann Miskovich wrote:
I see, could you help me go about this. I have not been able to figure out
how to do this with an annotation file. And I believe I already mapped my
lgi to fsaverage space before group level through recon-all -qcache. Is this
what you mean?
Thank you again for the help!
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: 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 space, or (and
probably better), map your lgi into fsaverage space.
doug
On 10/07/2013 02:18 PM, Tara Ann Miskovich wrote:
Thank you Doug, this did work. However, for every subject I get this line
repeated over and over before it outputs the stats. I still get a stats
file that seems to make sense but I am not sure if this is an issue.
MRISreadAnnotationIntoArray: vertex index out of range: 163841 i=,
in_array_size=136201
annot file:
./qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-trait-Cor/mc-z.abs.th13.sig.ocn.annot
Thank you for the help!
Tara
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, October 4, 2013 6:29:49 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 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_anatomical_stats -a
qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot
-t ${subject}/surf/lh.pial_lgi -f ${subject}/stats/lh.parietal_lgi.stats
${subject} lh
Thank you!
Tara
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
OK, the feature that computes that file was added after that. One thing
you can do is to download 5.3 and use 5.3 to do your stats. There should
not be any difference. Alternatively, you can run mri_segstats yourself,
something like
mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.ocn.mgh --avgwf
mc-z.abs.th13.sig.ocn.dat --excludeid 0
where y.mgh is the file created by qdec to be used in the glm analysis
doug
On 10/08/2013 03:01 PM, Tara Ann Miskovich wrote:
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 version of FS are you using?
On 10/08/2013 02:55 PM, Tara Ann Miskovich wrote:
I did. This is what I get from my group analysis in the folder. I didn't
find the ocn.dat file. Is there something I need to do in Qdec to produce it?
C.dat maxvox.dat mc-z.abs.th13.sig.ocn.mgh
cnr.mgh mc-z.abs.th13.pdf.dat mc-z.abs.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 gr...@nmr.mgh.harvard.edu
To: Tara Ann Miskovich misko...@uwm.edu
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 8, 2013 10:48:10 AM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
Did you generate the annotation from a qdec analysis of lgi? If so, then
there should be a file already there called something like
mc-z.abs.th13.sig.ocn.dat with a row for each subject and a column for
each cluster. The value will be the mean lgi for that subject and
cluster. Is this what you need?
doug
On 10/08/2013 09:04 AM, Tara Ann Miskovich wrote:
I see, could you help me go about this. I have not been able to figure out
how to do this with an annotation file. And I believe I already mapped my
lgi to fsaverage space before group level through recon-all -qcache. Is
this what you mean?
Thank you again for the help!
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: 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 space, or (and
probably better), map your lgi into fsaverage space.
doug
On 10/07/2013 02:18 PM, Tara Ann Miskovich wrote:
Thank you Doug, this did work. However, for every subject I get this line
repeated over and over before it outputs the stats. I still get a stats
file that seems to make sense but I am not sure if this is an issue.
MRISreadAnnotationIntoArray: vertex index out of range: 163841 i=,
in_array_size=136201
annot file:
./qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-trait-Cor/mc-z.abs.th13.sig.ocn.annot
Thank you for the help!
Tara
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, October 4, 2013 6:29:49 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 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_anatomical_stats -a
qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot
-t ${subject}/surf/lh.pial_lgi -f ${subject}/stats/lh.parietal_lgi.stats
${subject} lh
Thank you!
Tara
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact
Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
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
OK, the feature that computes that file was added after that. One thing
you can do is to download 5.3 and use 5.3 to do your stats. There should
not be any difference. Alternatively, you can run mri_segstats yourself,
something like
mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.ocn.mgh --avgwf
mc-z.abs.th13.sig.ocn.dat --excludeid 0
where y.mgh is the file created by qdec to be used in the glm analysis
doug
On 10/08/2013 03:01 PM, Tara Ann Miskovich wrote:
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 version of FS are you using?
On 10/08/2013 02:55 PM, Tara Ann Miskovich wrote:
I did. This is what I get from my group analysis in the folder. I didn't
find the ocn.dat file. Is there something I need to do in Qdec to produce it?
C.dat maxvox.dat mc-z.abs.th13.sig.ocn.mgh
cnr.mgh mc-z.abs.th13.pdf.dat mc-z.abs.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 gr...@nmr.mgh.harvard.edu
To: Tara Ann Miskovich misko...@uwm.edu
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 8, 2013 10:48:10 AM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
Did you generate the annotation from a qdec analysis of lgi? If so, then
there should be a file already there called something like
mc-z.abs.th13.sig.ocn.dat with a row for each subject and a column for
each cluster. The value will be the mean lgi for that subject and
cluster. Is this what you need?
doug
On 10/08/2013 09:04 AM, Tara Ann Miskovich wrote:
I see, could you help me go about this. I have not been able to figure out
how to do this with an annotation file. And I believe I already mapped my
lgi to fsaverage space before group level through recon-all -qcache. Is
this what you mean?
Thank you again for the help!
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: 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 space, or (and
probably better), map your lgi into fsaverage space.
doug
On 10/07/2013 02:18 PM, Tara Ann Miskovich wrote:
Thank you Doug, this did work. However, for every subject I get this line
repeated over and over before it outputs the stats. I still get a stats
file that seems to make sense but I am not sure if this is an issue.
MRISreadAnnotationIntoArray: vertex index out of range: 163841 i=,
in_array_size=136201
annot file:
./qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-trait-Cor/mc-z.abs.th13.sig.ocn.annot
Thank you for the help!
Tara
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, October 4, 2013 6:29:49 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 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_anatomical_stats -a
qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot
-t ${subject}/surf/lh.pial_lgi -f ${subject}/stats/lh.parietal_lgi.stats
${subject} lh
Thank you!
Tara
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
The information in this e-mail is intended only for the person to whom
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: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
OK, the feature that computes that file was added after that. One thing
you can do is to download 5.3 and use 5.3 to do your stats. There should
not be any difference. Alternatively, you can run mri_segstats yourself,
something like
mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.ocn.mgh --avgwf
mc-z.abs.th13.sig.ocn.dat --excludeid 0
where y.mgh is the file created by qdec to be used in the glm analysis
doug
On 10/08/2013 03:01 PM, Tara Ann Miskovich wrote:
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 version of FS are you using?
On 10/08/2013 02:55 PM, Tara Ann Miskovich wrote:
I did. This is what I get from my group analysis in the folder. I didn't
find the ocn.dat file. Is there something I need to do in Qdec to produce it?
C.dat maxvox.dat mc-z.abs.th13.sig.ocn.mgh
cnr.mgh mc-z.abs.th13.pdf.dat mc-z.abs.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 gr...@nmr.mgh.harvard.edu
To: Tara Ann Miskovich misko...@uwm.edu
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 8, 2013 10:48:10 AM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
Did you generate the annotation from a qdec analysis of lgi? If so, then
there should be a file already there called something like
mc-z.abs.th13.sig.ocn.dat with a row for each subject and a column for
each cluster. The value will be the mean lgi for that subject and
cluster. Is this what you need?
doug
On 10/08/2013 09:04 AM, Tara Ann Miskovich wrote:
I see, could you help me go about this. I have not been able to figure out
how to do this with an annotation file. And I believe I already mapped my
lgi to fsaverage space before group level through recon-all -qcache. Is
this what you mean?
Thank you again for the help!
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: 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 space, or (and
probably better), map your lgi into fsaverage space.
doug
On 10/07/2013 02:18 PM, Tara Ann Miskovich wrote:
Thank you Doug, this did work. However, for every subject I get this line
repeated over and over before it outputs the stats. I still get a stats
file that seems to make sense but I am not sure if this is an issue.
MRISreadAnnotationIntoArray: vertex index out of range: 163841 i=,
in_array_size=136201
annot file:
./qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-trait-Cor/mc-z.abs.th13.sig.ocn.annot
Thank you for the help!
Tara
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, October 4, 2013 6:29:49 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 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_anatomical_stats -a
qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot
-t ${subject}/surf/lh.pial_lgi -f ${subject}/stats/lh.parietal_lgi.stats
${subject} lh
Thank you!
Tara
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve
Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
it gives you estimates of whatever you give it. If the y.mgh file are
pial estimates, then that is what you will get
doug
On 10/08/2013 03:40 PM, Tara Ann Miskovich wrote:
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: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
OK, the feature that computes that file was added after that. One thing
you can do is to download 5.3 and use 5.3 to do your stats. There should
not be any difference. Alternatively, you can run mri_segstats yourself,
something like
mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.ocn.mgh --avgwf
mc-z.abs.th13.sig.ocn.dat --excludeid 0
where y.mgh is the file created by qdec to be used in the glm analysis
doug
On 10/08/2013 03:01 PM, Tara Ann Miskovich wrote:
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 version of FS are you using?
On 10/08/2013 02:55 PM, Tara Ann Miskovich wrote:
I did. This is what I get from my group analysis in the folder. I didn't
find the ocn.dat file. Is there something I need to do in Qdec to produce
it?
C.dat maxvox.dat mc-z.abs.th13.sig.ocn.mgh
cnr.mgh mc-z.abs.th13.pdf.dat
mc-z.abs.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 gr...@nmr.mgh.harvard.edu
To: Tara Ann Miskovich misko...@uwm.edu
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 8, 2013 10:48:10 AM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
Did you generate the annotation from a qdec analysis of lgi? If so, then
there should be a file already there called something like
mc-z.abs.th13.sig.ocn.dat with a row for each subject and a column for
each cluster. The value will be the mean lgi for that subject and
cluster. Is this what you need?
doug
On 10/08/2013 09:04 AM, Tara Ann Miskovich wrote:
I see, could you help me go about this. I have not been able to figure out
how to do this with an annotation file. And I believe I already mapped my
lgi to fsaverage space before group level through recon-all -qcache. Is
this what you mean?
Thank you again for the help!
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: 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 space, or (and
probably better), map your lgi into fsaverage space.
doug
On 10/07/2013 02:18 PM, Tara Ann Miskovich wrote:
Thank you Doug, this did work. However, for every subject I get this line
repeated over and over before it outputs the stats. I still get a stats
file that seems to make sense but I am not sure if this is an issue.
MRISreadAnnotationIntoArray: vertex index out of range: 163841
i=, in_array_size=136201
annot file:
./qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-trait-Cor/mc-z.abs.th13.sig.ocn.annot
Thank you for the help!
Tara
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, October 4, 2013 6:29:49 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 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_anatomical_stats -a
qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot
-t ${subject}/surf/lh.pial_lgi -f
${subject}/stats/lh.parietal_lgi.stats ${subject} lh
Thank you!
Tara
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki
Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
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 and mris_anatomical_stats
it gives you estimates of whatever you give it. If the y.mgh file are
pial estimates, then that is what you will get
doug
On 10/08/2013 03:40 PM, Tara Ann Miskovich wrote:
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: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
OK, the feature that computes that file was added after that. One thing
you can do is to download 5.3 and use 5.3 to do your stats. There should
not be any difference. Alternatively, you can run mri_segstats yourself,
something like
mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.ocn.mgh --avgwf
mc-z.abs.th13.sig.ocn.dat --excludeid 0
where y.mgh is the file created by qdec to be used in the glm analysis
doug
On 10/08/2013 03:01 PM, Tara Ann Miskovich wrote:
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 version of FS are you using?
On 10/08/2013 02:55 PM, Tara Ann Miskovich wrote:
I did. This is what I get from my group analysis in the folder. I didn't
find the ocn.dat file. Is there something I need to do in Qdec to produce
it?
C.dat maxvox.dat mc-z.abs.th13.sig.ocn.mgh
cnr.mgh mc-z.abs.th13.pdf.dat
mc-z.abs.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 gr...@nmr.mgh.harvard.edu
To: Tara Ann Miskovich misko...@uwm.edu
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 8, 2013 10:48:10 AM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
Did you generate the annotation from a qdec analysis of lgi? If so, then
there should be a file already there called something like
mc-z.abs.th13.sig.ocn.dat with a row for each subject and a column for
each cluster. The value will be the mean lgi for that subject and
cluster. Is this what you need?
doug
On 10/08/2013 09:04 AM, Tara Ann Miskovich wrote:
I see, could you help me go about this. I have not been able to figure out
how to do this with an annotation file. And I believe I already mapped my
lgi to fsaverage space before group level through recon-all -qcache. Is
this what you mean?
Thank you again for the help!
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: 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 space, or (and
probably better), map your lgi into fsaverage space.
doug
On 10/07/2013 02:18 PM, Tara Ann Miskovich wrote:
Thank you Doug, this did work. However, for every subject I get this line
repeated over and over before it outputs the stats. I still get a stats
file that seems to make sense but I am not sure if this is an issue.
MRISreadAnnotationIntoArray: vertex index out of range: 163841
i=, in_array_size=136201
annot file:
./qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-trait-Cor/mc-z.abs.th13.sig.ocn.annot
Thank you for the help!
Tara
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, October 4, 2013 6:29:49 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 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_anatomical_stats -a
qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot
-t ${subject}/surf/lh.pial_lgi -f
${subject}/stats/lh.parietal_lgi.stats ${subject} lh
Thank you!
Tara
Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
Thank you Doug, this did work. However, for every subject I get this line
repeated over and over before it outputs the stats. I still get a stats file
that seems to make sense but I am not sure if this is an issue.
MRISreadAnnotationIntoArray: vertex index out of range: 163841 i=,
in_array_size=136201
annot file:
./qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-trait-Cor/mc-z.abs.th13.sig.ocn.annot
Thank you for the help!
Tara
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, October 4, 2013 6:29:49 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 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_anatomical_stats -a
qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot
-t ${subject}/surf/lh.pial_lgi -f ${subject}/stats/lh.parietal_lgi.stats
${subject} lh
Thank you!
Tara
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
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Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
Oh, you'll need to map the annotation into the individual space, or (and
probably better), map your lgi into fsaverage space.
doug
On 10/07/2013 02:18 PM, Tara Ann Miskovich wrote:
Thank you Doug, this did work. However, for every subject I get this line
repeated over and over before it outputs the stats. I still get a stats file
that seems to make sense but I am not sure if this is an issue.
MRISreadAnnotationIntoArray: vertex index out of range: 163841 i=,
in_array_size=136201
annot file:
./qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-trait-Cor/mc-z.abs.th13.sig.ocn.annot
Thank you for the help!
Tara
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, October 4, 2013 6:29:49 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 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_anatomical_stats -a
qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot
-t ${subject}/surf/lh.pial_lgi -f ${subject}/stats/lh.parietal_lgi.stats
${subject} lh
Thank you!
Tara
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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 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_anatomical_stats -a
qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot
-t ${subject}/surf/lh.pial_lgi -f ${subject}/stats/lh.parietal_lgi.stats
${subject} lh
Thank you!
Tara
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
