Dear experts,
I am going to run a group analysis on thickness but limit the results to certain regions, say prefrontal cortex. l did find this thread but failed to make it work on my data ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48693.html). I know I could extract the signal of the ROI but also interested in this way.
Here are my questions: 1. mri_binarize should be working on the average data or the single data in each participant. If it should be on individual data, what the loop should be (if I have a text file SUBJECTS listing the participants). 2. How the --match is used. I --helped the mri_binarize but did not get it. Is it for specifying the ROI by number, say the number of PFC? 3. If I could finish the mask creation and merge to label; do I have to undergo the data concatenating stage (i.e. preproc, surf2surf) or directly move to glm. I saw another thread skipping these stages but it's on volume data ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32190.html).
Thank you so much!
*-------------* Mr Xianwei Che PhD Candidate Monash Alfred Psychiatry Research Centre (MAPrc) Central Clinical School & the Alfred Monash University Level 4, 607 St Kilda Road, Melbourne 3004, Australia
On 09/10/2017 04:02 AM, Xianwei Che wrote:
Dear experts,
I am going to run a group analysis on thickness but limit the results to certain regions, say prefrontal cortex. l did find this thread but failed to make it work on my data (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48693.html). I know I could extract the signal of the ROI but also interested in this way.
Here are my questions:
- mri_binarize should be working on the average data or the single
data in each participant. If it should be on individual data, what the loop should be (if I have a text file SUBJECTS listing the participants).
Actually, I don't know what [subjects] is supposed to mean. You should include the index for the ROIs you want in the analysis
- How the --match is used. I --helped the mri_binarize but did not
get it. Is it for specifying the ROI by number, say the number of PFC?
There is no PFC ROI. You will have to piece it together from other ROIs. You can get the full list from $FREESURFER_HOME/FreeSurferColorLUT.txt. Look in the section for aparc+aseg.mgz
- If I could finish the mask creation and merge to label; do I have
to undergo the data concatenating stage (i.e. preproc, surf2surf) or directly move to glm. I saw another thread skipping these stages but it's on volume data (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32190.html).
Yu can move directly to the GLM
Thank you so much!
/-------------/ Mr Xianwei Che PhD Candidate Monash Alfred Psychiatry Research Centre (MAPrc) Central Clinical School & the Alfred Monash University Level 4, 607 St Kilda Road, Melbourne 3004, Australia
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doug,
Thank you for the answer. I will try it out.
Regards
*-------------* Mr Xianwei Che PhD Candidate Monash Alfred Psychiatry Research Centre (MAPrc) Central Clinical School & the Alfred Monash University Level 4, 607 St Kilda Road, Melbourne 3004, Australia
On 12 September 2017 at 01:44, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
On 09/10/2017 04:02 AM, Xianwei Che wrote:
Dear experts,
I am going to run a group analysis on thickness but limit the results to certain regions, say prefrontal cortex. l did find this thread but failed to make it work on my data (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.
edu/msg48693.html).
I know I could extract the signal of the ROI but also interested in this way.
Here are my questions:
- mri_binarize should be working on the average data or the single
data in each participant. If it should be on individual data, what the loop should be (if I have a text file SUBJECTS listing the participants).
Actually, I don't know what [subjects] is supposed to mean. You should include the index for the ROIs you want in the analysis
- How the --match is used. I --helped the mri_binarize but did not
get it. Is it for specifying the ROI by number, say the number of PFC?
There is no PFC ROI. You will have to piece it together from other ROIs. You can get the full list from $FREESURFER_HOME/FreeSurferColorLUT.txt. Look in the section for aparc+aseg.mgz
- If I could finish the mask creation and merge to label; do I have
to undergo the data concatenating stage (i.e. preproc, surf2surf) or directly move to glm. I saw another thread skipping these stages but it's on volume data (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.
edu/msg32190.html). Yu can move directly to the GLM
Thank you so much!
/-------------/ Mr Xianwei Che PhD Candidate Monash Alfred Psychiatry Research Centre (MAPrc) Central Clinical School & the Alfred Monash University Level 4, 607 St Kilda Road, Melbourne 3004, Australia
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 greve@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.
Dear Doug,
After some trial and error I am still not able to run group analysis in ROI manner.
Here is my understanding: I need to define a label (mri_binarize ?) in which my ROIs should be labeled as 1 with other regions being 0. Then I can take this label to glm with --lable and then run correction. If this is a right way can you tell me a little bit more of how to do this. I am working on cortical thickness data.
Thanks huge
*-------------* Mr Xianwei Che PhD Candidate Monash Alfred Psychiatry Research Centre (MAPrc) Central Clinical School & the Alfred Monash University Level 4, 607 St Kilda Road, Melbourne 3004, Australia
On 12 September 2017 at 08:42, Xianwei Che xianwei.che@monash.edu wrote:
Dear Doug,
Thank you for the answer. I will try it out.
Regards
*-------------* Mr Xianwei Che PhD Candidate Monash Alfred Psychiatry Research Centre (MAPrc) Central Clinical School & the Alfred Monash University Level 4, 607 St Kilda Road, Melbourne 3004, Australia
On 12 September 2017 at 01:44, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
On 09/10/2017 04:02 AM, Xianwei Che wrote:
Dear experts,
I am going to run a group analysis on thickness but limit the results to certain regions, say prefrontal cortex. l did find this thread but failed to make it work on my data (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu
/msg48693.html).
I know I could extract the signal of the ROI but also interested in this way.
Here are my questions:
- mri_binarize should be working on the average data or the single
data in each participant. If it should be on individual data, what the loop should be (if I have a text file SUBJECTS listing the
participants). Actually, I don't know what [subjects] is supposed to mean. You should include the index for the ROIs you want in the analysis
- How the --match is used. I --helped the mri_binarize but did not
get it. Is it for specifying the ROI by number, say the number of PFC?
There is no PFC ROI. You will have to piece it together from other ROIs. You can get the full list from $FREESURFER_HOME/FreeSurferColorLUT.txt. Look in the section for aparc+aseg.mgz
- If I could finish the mask creation and merge to label; do I have
to undergo the data concatenating stage (i.e. preproc, surf2surf) or directly move to glm. I saw another thread skipping these stages but it's on volume data (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu
/msg32190.html). Yu can move directly to the GLM
Thank you so much!
/-------------/ Mr Xianwei Che PhD Candidate Monash Alfred Psychiatry Research Centre (MAPrc) Central Clinical School & the Alfred Monash University Level 4, 607 St Kilda Road, Melbourne 3004, Australia
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 greve@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.
Pass it with --mask, not --label
On 09/11/2017 09:42 PM, Xianwei Che wrote:
Dear Doug,
After some trial and error I am still not able to run group analysis in ROI manner.
Here is my understanding: I need to define a label (mri_binarize ?) in which my ROIs should be labeled as 1 with other regions being 0. Then I can take this label to glm with --lable and then run correction. If this is a right way can you tell me a little bit more of how to do this. I am working on cortical thickness data.
Thanks huge
/-------------/ Mr Xianwei Che PhD Candidate Monash Alfred Psychiatry Research Centre (MAPrc) Central Clinical School & the Alfred Monash University Level 4, 607 St Kilda Road, Melbourne 3004, Australia
On 12 September 2017 at 08:42, Xianwei Che <xianwei.che@monash.edu mailto:xianwei.che@monash.edu> wrote:
Dear Doug, Thank you for the answer. I will try it out. Regards /-------------/ Mr Xianwei Che PhD Candidate Monash Alfred Psychiatry Research Centre (MAPrc) Central Clinical School & the Alfred Monash University Level 4, 607 St Kilda Road, Melbourne 3004, Australia On 12 September 2017 at 01:44, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: On 09/10/2017 04:02 AM, Xianwei Che wrote: > Dear experts, > > I am going to run a group analysis on thickness but limit the results > to certain regions, say prefrontal cortex. l did find this thread but > failed to make it work on my data > (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48693.html <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48693.html>). > I know I could extract the signal of the ROI but also interested in > this way. > > Here are my questions: > 1. mri_binarize should be working on the average data or the single > data in each participant. If it should be on individual data, what the > loop should be (if I have a text file SUBJECTS listing the participants). Actually, I don't know what [subjects] is supposed to mean. You should include the index for the ROIs you want in the analysis > 2. How the --match is used. I --helped the mri_binarize but did not > get it. Is it for specifying the ROI by number, say the number of PFC? There is no PFC ROI. You will have to piece it together from other ROIs. You can get the full list from $FREESURFER_HOME/FreeSurferColorLUT.txt. Look in the section for aparc+aseg.mgz > 3. If I could finish the mask creation and merge to label; do I have > to undergo the data concatenating stage (i.e. preproc, surf2surf) or > directly move to glm. I saw another thread skipping these stages but > it's on volume data > (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32190.html <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32190.html>). Yu can move directly to the GLM > > Thank you so much! > > > /-------------/ > Mr Xianwei Che > PhD Candidate > Monash Alfred Psychiatry Research Centre (MAPrc) > Central Clinical School & the Alfred > Monash University > Level 4, 607 St Kilda Road, Melbourne 3004, Australia > > > _______________________________________________ > 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> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ 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.
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