subject:"\[Freesurfer\] Cortical thickness

Re: [Freesurfer] Cortical thickness_Group analysis

2017-06-09 Thread Douglas N Greve

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 
> > 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
>> > 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
>> > > 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 5 390 ext.5422, 5355, 5364
>>> Email: ali.radai...@hu.edu.jo
>>> 
>>> /
>>> /webpage:
>>> http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
>>> /
>>>
>>>
>>>
>>> ___
>>> 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
>>

Re: [Freesurfer] Cortical thickness_Group analysis

2017-06-09 Thread Douglas Greve

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 > 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
> 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 5 390 ext.5422, 5355, 5364
Email: ali.radai...@hu.edu.jo 
/
/webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/



___
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 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 5 390 ext.5422, 5355, 5364
Email: ali.radai...@hu.edu.jo 
/
/webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/

--
Sent from iPhone


___
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 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] Cortical thickness_Group analysis

2017-06-08 Thread Ali Radaideh

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  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 
> 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 5 390 ext.5422, 5355, 5364 Email:
>> ali.radai...@hu.edu.jo  *
>> *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
>> *
>>
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@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 5 390 ext.5422, 5355, 5364Email:
> ali.radai...@hu.edu.jo *
> *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
> *
>
> --
Sent from iPhone
___
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] Cortical thickness_Group analysis

2017-06-05 Thread Ali Radaideh

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 
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 5 390 ext.5422, 5355, 5364 Email:
> ali.radai...@hu.edu.jo  *
> *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
> *
>
>
>
> ___
> Freesurfer mailing 
> listfreesur...@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 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo *
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
*
___
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] Cortical thickness_Group analysis

2017-06-05 Thread Douglas Greve


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 5 390 ext.5422, 5355, 5364
Email: ali.radai...@hu.edu.jo 
/
/webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/



___
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 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] Cortical thickness_Group analysis

2017-06-04 Thread Ali Radaideh

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. PhDHead of Department of Medical ImagingVice Dean of
the Faculty of Allied Health SciencesThe Hashemite University, Zarqa,
JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo *
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
*


disease_Healthy_Age.fsgd
Description: Binary data


lh-MS_vs_Healthy.mtx
Description: Binary data


lh-female_MS_vs_Healthy.mtx
Description: Binary data


lh-female_MS_vs_Healthy_Age.mtx
Description: Binary data


lh-male_MS_vs_Healthy.mtx
Description: Binary data


lh-male_MS_vs_Healthy_Age.mtx
Description: Binary data
___
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] Cortical thickness_Group analysis

Re: [Freesurfer] Cortical thickness_Group analysis

Re: [Freesurfer] Cortical thickness_Group analysis

Re: [Freesurfer] Cortical thickness_Group analysis

Re: [Freesurfer] Cortical thickness_Group analysis

[Freesurfer] Cortical thickness_Group analysis

6 matches

Site Navigation

Mail list logo

Footer information