Dear FS experts,
I am trying to analyse the cortical thickness for a group of MS patients and healthy controls. I have followed the instructions on how to perform group analysis but I am still unable to achieve what I am looking for.
I am trying to produce a significance map to show the cortical areas that are statistically different between MS and healthy controls (in terms of cortical thickness).
Would it be possible please to show you the matrix (fsgd) and contrasts files that I have used in my analysis?
Best regards and many thanks in advance,
Ali
what is your mri_glmfit command?
On 6/4/17 8:10 PM, Ali Radaideh wrote:
Dear FS experts,
I am trying to analyse the cortical thickness for a group of MS patients and healthy controls. I have followed the instructions on how to perform group analysis but I am still unable to achieve what I am looking for.
I am trying to produce a significance map to show the cortical areas that are statistically different between MS and healthy controls (in terms of cortical thickness).
Would it be possible please to show you the matrix (fsgd) and contrasts files that I have used in my analysis?
Best regards and many thanks in advance,
Ali
-- /Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
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Thanks alot.
Below are the commands I used in order:
mris_preproc --fsgd disease_Healthy_Age.fsgd --target fsaverage --hemi lh --meas thickness --out lh.disease_Healthy_Age.thickness.00.mgh
mri_surf2surf --hemi lh --s fsaverage --sval lh.disease_Healthy_Age.thickness.00.mgh --fwhm 10 --cortex --tval lh.disease_Healthy_Age.thickness.10.mgh
mri_glmfit --y lh.disease_Healthy_Age.thickness.10.mgh --fsgd disease_Healthy_Age.fsgd dods --C lh-MS_vs_Healthy.mtx --C lh-male_MS_vs_Healthy_Age.mtx --C lh-male_MS_vs_Healthy.mtx --C lh-female_MS_vs_Healthy_Age.mtx --C lh-female_MS_vs_Healthy.mtx --surf fsaverage lh --cortex --glmdir lh.disease_Healthy_Age.glmdir
mri_glmfit-sim --glmdir lh.disease_Healthy_Age.glmdir --cache 4 neg --cwp 0.05 --2spaces
On Mon, Jun 5, 2017 at 4:03 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
what is your mri_glmfit command?
On 6/4/17 8:10 PM, Ali Radaideh wrote:
Dear FS experts,
I am trying to analyse the cortical thickness for a group of MS patients and healthy controls. I have followed the instructions on how to perform group analysis but I am still unable to achieve what I am looking for.
I am trying to produce a significance map to show the cortical areas that are statistically different between MS and healthy controls (in terms of cortical thickness).
Would it be possible please to show you the matrix (fsgd) and contrasts files that I have used in my analysis?
Best regards and many thanks in advance,
Ali
--
*Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo ali.radaideh@hu.edu.jo * *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*
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Dear Douglas,
Can I check with you if you have received my reply below to your question??
Thanks, Ali
On Mon, Jun 5, 2017 at 10:16 PM Ali Radaideh ali.radaideh@hu.edu.jo wrote:
Thanks alot.
Below are the commands I used in order:
mris_preproc --fsgd disease_Healthy_Age.fsgd --target fsaverage --hemi lh --meas thickness --out lh.disease_Healthy_Age.thickness.00.mgh
mri_surf2surf --hemi lh --s fsaverage --sval lh.disease_Healthy_Age.thickness.00.mgh --fwhm 10 --cortex --tval lh.disease_Healthy_Age.thickness.10.mgh
mri_glmfit --y lh.disease_Healthy_Age.thickness.10.mgh --fsgd disease_Healthy_Age.fsgd dods --C lh-MS_vs_Healthy.mtx --C lh-male_MS_vs_Healthy_Age.mtx --C lh-male_MS_vs_Healthy.mtx --C lh-female_MS_vs_Healthy_Age.mtx --C lh-female_MS_vs_Healthy.mtx --surf fsaverage lh --cortex --glmdir lh.disease_Healthy_Age.glmdir
mri_glmfit-sim --glmdir lh.disease_Healthy_Age.glmdir --cache 4 neg --cwp 0.05 --2spaces
On Mon, Jun 5, 2017 at 4:03 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
what is your mri_glmfit command?
On 6/4/17 8:10 PM, Ali Radaideh wrote:
Dear FS experts,
I am trying to analyse the cortical thickness for a group of MS patients and healthy controls. I have followed the instructions on how to perform group analysis but I am still unable to achieve what I am looking for.
I am trying to produce a significance map to show the cortical areas that are statistically different between MS and healthy controls (in terms of cortical thickness).
Would it be possible please to show you the matrix (fsgd) and contrasts files that I have used in my analysis?
Best regards and many thanks in advance,
Ali
--
*Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo ali.radaideh@hu.edu.jo * *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 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.
--
*Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite University, Zarqa, JordanW.phone +962 5 3903333 ext.5422, 5355, 5364Email: ali.radaideh@hu.edu.jo ali.radaideh@hu.edu.jo* *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*
--
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Hi Ali, the FSGD and contrast matrices look right as do your command lines. What is the problem?
On 6/8/17 1:40 PM, Ali Radaideh wrote:
Dear Douglas,
Can I check with you if you have received my reply below to your question??
Thanks, Ali
On Mon, Jun 5, 2017 at 10:16 PM Ali Radaideh <ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo> wrote:
Thanks alot. Below are the commands I used in order: mris_preproc --fsgd disease_Healthy_Age.fsgd --target fsaverage --hemi lh --meas thickness --out lh.disease_Healthy_Age.thickness.00.mgh mri_surf2surf --hemi lh --s fsaverage --sval lh.disease_Healthy_Age.thickness.00.mgh --fwhm 10 --cortex --tval lh.disease_Healthy_Age.thickness.10.mgh mri_glmfit --y lh.disease_Healthy_Age.thickness.10.mgh --fsgd disease_Healthy_Age.fsgd dods --C lh-MS_vs_Healthy.mtx --C lh-male_MS_vs_Healthy_Age.mtx --C lh-male_MS_vs_Healthy.mtx --C lh-female_MS_vs_Healthy_Age.mtx --C lh-female_MS_vs_Healthy.mtx --surf fsaverage lh --cortex --glmdir lh.disease_Healthy_Age.glmdir mri_glmfit-sim --glmdir lh.disease_Healthy_Age.glmdir --cache 4 neg --cwp 0.05 --2spaces On Mon, Jun 5, 2017 at 4:03 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: what is your mri_glmfit command? On 6/4/17 8:10 PM, Ali Radaideh wrote:Dear FS experts, I am trying to analyse the cortical thickness for a group of MS patients and healthy controls. I have followed the instructions on how to perform group analysis but I am still unable to achieve what I am looking for. I am trying to produce a significance map to show the cortical areas that are statistically different between MS and healthy controls (in terms of cortical thickness). Would it be possible please to show you the matrix (fsgd) and contrasts files that I have used in my analysis? Best regards and many thanks in advance, Ali -- /Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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. -- /Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/-- Sent from iPhone
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Hi Douglas,
Thanks alot for your email. the issue is that when I try ti view the sig.mgh using the following command:
freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/sig.mgh:overlay_threshold=2,5 -viewport 3d
I get the attached images (please, see attached).
What are the blue and red clusters in this case? Are these the cortical regions that are statistically different between healthy and patients? or they represent the significant correlation with other variables?
What is the difference between F and sig maps?
My aim is to find/show cortical areas that are statistically different between health and patients (in terms of cortical thickness).
Many thanks in advance, Ali
On Fri, Jun 9, 2017 at 4:45 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Hi Ali, the FSGD and contrast matrices look right as do your command lines. What is the problem?
On 6/8/17 1:40 PM, Ali Radaideh wrote:
Dear Douglas,
Can I check with you if you have received my reply below to your question??
Thanks, Ali
On Mon, Jun 5, 2017 at 10:16 PM Ali Radaideh ali.radaideh@hu.edu.jo wrote:
Thanks alot.
Below are the commands I used in order:
mris_preproc --fsgd disease_Healthy_Age.fsgd --target fsaverage --hemi lh --meas thickness --out lh.disease_Healthy_Age.thickness.00.mgh
mri_surf2surf --hemi lh --s fsaverage --sval lh.disease_Healthy_Age.thickness.00.mgh --fwhm 10 --cortex --tval lh.disease_Healthy_Age.thickness.10.mgh
mri_glmfit --y lh.disease_Healthy_Age.thickness.10.mgh --fsgd disease_Healthy_Age.fsgd dods --C lh-MS_vs_Healthy.mtx --C lh-male_MS_vs_Healthy_Age.mtx --C lh-male_MS_vs_Healthy.mtx --C lh-female_MS_vs_Healthy_Age.mtx --C lh-female_MS_vs_Healthy.mtx --surf fsaverage lh --cortex --glmdir lh.disease_Healthy_Age.glmdir
mri_glmfit-sim --glmdir lh.disease_Healthy_Age.glmdir --cache 4 neg --cwp 0.05 --2spaces
On Mon, Jun 5, 2017 at 4:03 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
what is your mri_glmfit command?
On 6/4/17 8:10 PM, Ali Radaideh wrote:
Dear FS experts,
I am trying to analyse the cortical thickness for a group of MS patients and healthy controls. I have followed the instructions on how to perform group analysis but I am still unable to achieve what I am looking for.
I am trying to produce a significance map to show the cortical areas that are statistically different between MS and healthy controls (in terms of cortical thickness).
Would it be possible please to show you the matrix (fsgd) and contrasts files that I have used in my analysis?
Best regards and many thanks in advance,
Ali
--
*Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo ali.radaideh@hu.edu.jo * *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 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.
--
*Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo ali.radaideh@hu.edu.jo * *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*
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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 but does not contain patient information, please contact the sender and properly dispose of the e-mail.
I can't open that image (what is .odp?). The red/yellow is a positive contrast, blue/cyan is negative contrast. The contrast depends on your contrast matrix. Assuming that you have MS-Heal, the red/yellow is MS>Healthy. It is thresholded at an UNCORRECTED level of p<.01 (-log10(.01) = 2). F is the F ratio. sig is -log10(p)*sign of the contrast (two-tailed).
On 06/09/2017 11:54 AM, Ali Radaideh wrote:
Hi Douglas,
Thanks alot for your email. the issue is that when I try ti view the sig.mgh using the following command:
freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/sig.mgh:overlay_threshold=2,5 -viewport 3d
I get the attached images (please, see attached).
What are the blue and red clusters in this case? Are these the cortical regions that are statistically different between healthy and patients? or they represent the significant correlation with other variables?
What is the difference between F and sig maps?
My aim is to find/show cortical areas that are statistically different between health and patients (in terms of cortical thickness).
Many thanks in advance, Ali
On Fri, Jun 9, 2017 at 4:45 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Ali, the FSGD and contrast matrices look right as do your command lines. What is the problem? On 6/8/17 1:40 PM, Ali Radaideh wrote:Dear Douglas, Can I check with you if you have received my reply below to your question?? Thanks, Ali On Mon, Jun 5, 2017 at 10:16 PM Ali Radaideh <ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>> wrote: Thanks alot. Below are the commands I used in order: mris_preproc --fsgd disease_Healthy_Age.fsgd --target fsaverage --hemi lh --meas thickness --out lh.disease_Healthy_Age.thickness.00.mgh mri_surf2surf --hemi lh --s fsaverage --sval lh.disease_Healthy_Age.thickness.00.mgh --fwhm 10 --cortex --tval lh.disease_Healthy_Age.thickness.10.mgh mri_glmfit --y lh.disease_Healthy_Age.thickness.10.mgh --fsgd disease_Healthy_Age.fsgd dods --C lh-MS_vs_Healthy.mtx --C lh-male_MS_vs_Healthy_Age.mtx --C lh-male_MS_vs_Healthy.mtx --C lh-female_MS_vs_Healthy_Age.mtx --C lh-female_MS_vs_Healthy.mtx --surf fsaverage lh --cortex --glmdir lh.disease_Healthy_Age.glmdir mri_glmfit-sim --glmdir lh.disease_Healthy_Age.glmdir --cache 4 neg --cwp 0.05 --2spaces On Mon, Jun 5, 2017 at 4:03 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: what is your mri_glmfit command? On 6/4/17 8:10 PM, Ali Radaideh wrote:Dear FS experts, I am trying to analyse the cortical thickness for a group of MS patients and healthy controls. I have followed the instructions on how to perform group analysis but I am still unable to achieve what I am looking for. I am trying to produce a significance map to show the cortical areas that are statistically different between MS and healthy controls (in terms of cortical thickness). Would it be possible please to show you the matrix (fsgd) and contrasts files that I have used in my analysis? Best regards and many thanks in advance, Ali -- /Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. -- /Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>/ -- Sent from iPhone _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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.-- /Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
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