External Email - Use Caution
Dear developers,
For a case-control study we are comparing the cortical thickness and cortical surface area on a vertex-base level, for which we found significant differences throughout the brain.
Is it possible that, in addition to the significance values (p < .05 after FDR correction) on a vertex-base level, we can include the exact thickness or surface area value (or difference) of the significant clusters on a vertex base-level between the groups. In order words, to provide some measures to highlight the size of the significant cluster or the differences in cortical thickness / cortical surface area to provide clinically useful context. For instance, a command comparable to 'voxel size' in TBSS.
As this is my first time using Freesurfer any help that you could offer on this matter would be highly appreciated.
Best wishes, Brigitte Dijkshoorn
I'm not sure what you mean. Do you want the mean thickness of a cluster and/or its surface area?
On 10/30/19 6:02 PM, Aicha Dijkshoorn wrote:
External Email - Use Caution
Dear developers,
For a case-control study we are comparing the cortical thickness and cortical surface area on a vertex-base level, for which we found significant differences throughout the brain.
Is it possible that, in addition to the significance values (p < .05 after FDR correction) on a vertex-base level, we can include the exact thickness or surface area value (or difference) of the significant clusters on a vertex base-level between the groups. In order words, to provide some measures to highlight the size of the significant cluster or the differences in cortical thickness / cortical surface area to provide clinically useful context. For instance, a command comparable to 'voxel size' in TBSS.
As this is my first time using Freesurfer any help that you could offer on this matter would be highly appreciated.
Best wishes, Brigitte Dijkshoorn
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Dear Greve,
Thank you for your quick respons.
Yes, I believe that is what I mean. Let me illustrate with some (fictive) data; We were able to prove these data for the entire hemisphere as can be seen below.
Group 1
Group 2
Difference
Sig.
Thickness
(in mm)
Left
1.48
1.46
.004
.19
Right
1.46
1.46
.003
.03
However, we would like to provide similar data in our vertex-base analyses:
Significantly different clusters between group 1 and group 2
Cortical thickness group 1
Cortical thickness group 2
Difference in mm2
Sig.
Left Cuneus
?
?
?
0.013
Left Fusiform gyrus
?
?
?
0.021
Right Paracentral lobule
?
?
?
0.001
Right parahippocampal gyrus
?
?
?
0.002
Does this clarify my question?
Best wishes, Aicha
________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu namens Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Verzonden: donderdag 31 oktober 2019 16:25 Aan: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] Cortical thickness values on a vertex base level
I'm not sure what you mean. Do you want the mean thickness of a cluster and/or its surface area?
On 10/30/19 6:02 PM, Aicha Dijkshoorn wrote:
External Email - Use CautionDear developers,
For a case-control study we are comparing the cortical thickness and cortical surface area on a vertex-base level, for which we found significant differences throughout the brain.
Is it possible that, in addition to the significance values (p < .05 after FDR correction) on a vertex-base level, we can include the exact thickness or surface area value (or difference) of the significant clusters on a vertex base-level between the groups. In order words, to provide some measures to highlight the size of the significant cluster or the differences in cortical thickness / cortical surface area to provide clinically useful context. For instance, a command comparable to 'voxel size' in TBSS.
As this is my first time using Freesurfer any help that you could offer on this matter would be highly appreciated.
Best wishes, Brigitte Dijkshoorn
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You can run mri_surfcluster with your fdr threshold as the --thmin value. This will output cluster number (ocn) map. This will assign the cluster number to a vertex. You can then use mri_segstats with --seg ocn.mgz --excludeid 0 and input being the mean thickness or area maps. When you use area as thhe input, make sure to --accumulate to get the total area. You can get an area map in the same way that you got the thickness map, ie, mris_preproc, etc
On 10/31/19 1:28 PM, Aicha Dijkshoorn wrote:
External Email - Use Caution
Dear Greve,
Thank you for your quick respons.
Yes, I believe that is what I mean. Let me illustrate with some (fictive) data; We were able to prove these data for the entire hemisphere as can be seen below.
*Group 1*
*Group 2*
*Difference*
*/Sig./*
Thickness
(in mm)
Left
1.48
1.46
.004
.19
Right
1.46
1.46
.003
.03
However, we would like to provide similar data in our vertex-base analyses:
*Significantly different clusters between group 1 and group 2*
*Cortical thickness group 1*
*Cortical thickness group 2*
*Difference in mm2*
*/Sig./*
Left Cuneus
?
?
?
0.013
Left Fusiform gyrus
?
?
?
0.021
Right Paracentral lobule
?
?
?
0.001
Right parahippocampal gyrus
?
?
?
0.002
Does this clarify my question?
Best wishes, Aicha
*Van:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu namens Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Verzonden:* donderdag 31 oktober 2019 16:25 *Aan:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Onderwerp:* Re: [Freesurfer] Cortical thickness values on a vertex base level I'm not sure what you mean. Do you want the mean thickness of a cluster and/or its surface area?
On 10/30/19 6:02 PM, Aicha Dijkshoorn wrote:
External Email - Use Caution
Dear developers,
For a case-control study we are comparing the cortical thickness and cortical surface area on a vertex-base level, for which we found significant differences throughout the brain.
Is it possible that, in addition to the significance values (p < .05 after FDR correction) on a vertex-base level, we can include the exact thickness or surface area value (or difference) of the significant clusters on a vertex base-level between the groups. In order words, to provide some measures to highlight the size of the significant cluster or the differences in cortical thickness / cortical surface area to provide clinically useful context. For instance, a command comparable to 'voxel size' in TBSS.
As this is my first time using Freesurfer any help that you could offer on this matter would be highly appreciated.
Best wishes, Brigitte Dijkshoorn
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thank you so much for your repsonse. Could you maybe please tell us which input file we should use?
Best wishes, AIcha ________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu namens Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Verzonden: donderdag 31 oktober 2019 19:16 Aan: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] Cortical thickness values on a vertex base level
You can run mri_surfcluster with your fdr threshold as the --thmin value. This will output cluster number (ocn) map. This will assign the cluster number to a vertex. You can then use mri_segstats with --seg ocn.mgz --excludeid 0 and input being the mean thickness or area maps. When you use area as thhe input, make sure to --accumulate to get the total area. You can get an area map in the same way that you got the thickness map, ie, mris_preproc, etc
On 10/31/19 1:28 PM, Aicha Dijkshoorn wrote:
External Email - Use CautionDear Greve,
Thank you for your quick respons.
Yes, I believe that is what I mean. Let me illustrate with some (fictive) data; We were able to prove these data for the entire hemisphere as can be seen below.
*Group 1*
*Group 2*
*Difference*
*/Sig./*
Thickness
(in mm)
Left
1.48
1.46
.004
.19
Right
1.46
1.46
.003
.03
However, we would like to provide similar data in our vertex-base analyses:
*Significantly different clusters between group 1 and group 2*
*Cortical thickness group 1*
*Cortical thickness group 2*
*Difference in mm2*
*/Sig./*
Left Cuneus
?
?
?
0.013
Left Fusiform gyrus
?
?
?
0.021
Right Paracentral lobule
?
?
?
0.001
Right parahippocampal gyrus
?
?
?
0.002
Does this clarify my question?
Best wishes, Aicha
*Van:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu namens Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Verzonden:* donderdag 31 oktober 2019 16:25 *Aan:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Onderwerp:* Re: [Freesurfer] Cortical thickness values on a vertex base level I'm not sure what you mean. Do you want the mean thickness of a cluster and/or its surface area?
On 10/30/19 6:02 PM, Aicha Dijkshoorn wrote:
External Email - Use CautionDear developers,
For a case-control study we are comparing the cortical thickness and cortical surface area on a vertex-base level, for which we found significant differences throughout the brain.
Is it possible that, in addition to the significance values (p < .05 after FDR correction) on a vertex-base level, we can include the exact thickness or surface area value (or difference) of the significant clusters on a vertex base-level between the groups. In order words, to provide some measures to highlight the size of the significant cluster or the differences in cortical thickness / cortical surface area to provide clinically useful context. For instance, a command comparable to 'voxel size' in TBSS.
As this is my first time using Freesurfer any help that you could offer on this matter would be highly appreciated.
Best wishes, Brigitte Dijkshoorn
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The sig file
On 11/15/19 9:16 AM, Aicha Dijkshoorn wrote:
External Email - Use Caution
Thank you so much for your repsonse. Could you maybe please tell us which input file we should use?
Best wishes, AIcha
*Van:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu namens Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Verzonden:* donderdag 31 oktober 2019 19:16 *Aan:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Onderwerp:* Re: [Freesurfer] Cortical thickness values on a vertex base level You can run mri_surfcluster with your fdr threshold as the --thmin value. This will output cluster number (ocn) map. This will assign the cluster number to a vertex. You can then use mri_segstats with --seg ocn.mgz --excludeid 0 and input being the mean thickness or area maps. When you use area as thhe input, make sure to --accumulate to get the total area. You can get an area map in the same way that you got the thickness map, ie, mris_preproc, etc
On 10/31/19 1:28 PM, Aicha Dijkshoorn wrote:
External Email - Use Caution
Dear Greve,
Thank you for your quick respons.
Yes, I believe that is what I mean. Let me illustrate with some (fictive) data; We were able to prove these data for the entire hemisphere as can be seen below.
*Group 1*
*Group 2*
*Difference*
*/Sig./*
Thickness
(in mm)
Left
1.48
1.46
.004
.19
Right
1.46
1.46
.003
.03
However, we would like to provide similar data in our vertex-base analyses:
*Significantly different clusters between group 1 and group 2*
*Cortical thickness group 1*
*Cortical thickness group 2*
*Difference in mm2*
*/Sig./*
Left Cuneus
?
?
?
0.013
Left Fusiform gyrus
?
?
?
0.021
Right Paracentral lobule
?
?
?
0.001
Right parahippocampal gyrus
?
?
?
0.002
Does this clarify my question?
Best wishes, Aicha
*Van:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu namens Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Verzonden:* donderdag 31 oktober 2019 16:25 *Aan:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Onderwerp:* Re: [Freesurfer] Cortical thickness values on a vertex base level I'm not sure what you mean. Do you want the mean thickness of a cluster and/or its surface area?
On 10/30/19 6:02 PM, Aicha Dijkshoorn wrote:
External Email - Use Caution
Dear developers,
For a case-control study we are comparing the cortical thickness and cortical surface area on a vertex-base level, for which we found significant differences throughout the brain.
Is it possible that, in addition to the significance values (p < .05 after FDR correction) on a vertex-base level, we can include the exact thickness or surface area value (or difference) of the significant clusters on a vertex base-level between the groups. In order words, to provide some measures to highlight the size of the significant cluster or the differences in cortical thickness / cortical surface area to provide clinically useful context. For instance, a command comparable to 'voxel size' in TBSS.
As this is my first time using Freesurfer any help that you could offer on this matter would be highly appreciated.
Best wishes, Brigitte Dijkshoorn
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Aicha Dijkshoorn -
Greve, Douglas N.,Ph.D.