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=00000000, 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" greve@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

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" greve@nmr.mgh.harvard.edu To: "Tara Ann Miskovich" miskovi2@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=00000000, 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" greve@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

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" greve@nmr.mgh.harvard.edu To: "Tara Ann Miskovich" miskovi2@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" greve@nmr.mgh.harvard.edu To: "Tara Ann Miskovich" miskovi2@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=00000000, 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" greve@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

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" greve@nmr.mgh.harvard.edu To: "Tara Ann Miskovich" miskovi2@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" greve@nmr.mgh.harvard.edu To: "Tara Ann Miskovich" miskovi2@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" greve@nmr.mgh.harvard.edu To: "Tara Ann Miskovich" miskovi2@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=00000000, 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" greve@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

opps sorry one last question. Will segstats get me LGI estimates of the pial surface?

Tara

----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Tara Ann Miskovich" miskovi2@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" greve@nmr.mgh.harvard.edu To: "Tara Ann Miskovich" miskovi2@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" greve@nmr.mgh.harvard.edu To: "Tara Ann Miskovich" miskovi2@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" greve@nmr.mgh.harvard.edu To: "Tara Ann Miskovich" miskovi2@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=00000000, 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" greve@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

I see. Thank you so much for everything!

Tara

----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Tara Ann Miskovich" miskovi2@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" greve@nmr.mgh.harvard.edu To: "Tara Ann Miskovich" miskovi2@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" greve@nmr.mgh.harvard.edu To: "Tara Ann Miskovich" miskovi2@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" greve@nmr.mgh.harvard.edu To: "Tara Ann Miskovich" miskovi2@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" greve@nmr.mgh.harvard.edu To: "Tara Ann Miskovich" miskovi2@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=00000000, 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" greve@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