Hello, I am working through the PETsurfer surface based analysis and i have couple of question a) Since the procedure is the same as surface based analysis for cortical thickness except mri_vol2surf, Can I use the procedure for thickness? b) What is the difference between mris_preproc and mri_concat. If I use mris_preproc, do I also need to use mri_concat? Also, can I use mris_preproc instead of mri_concat? c) Can I use mri_surf2surf in place of mris_fwhm? If no, why? d) While researching PETsurfer surface based analysis in the forum, I came across multiple trends that used the "--projfrac" flag in both mri_vol2surf command and mris_preproc command. At what stage should I include this flag and why? e) If I want to perform a multimodal analysis using thickness&PET or Surface area&PET, Can anyone confirm if this is the correct steps.
- Perform surface base analysis for cortical thickness from step 1 (mris_preproc) to correction for multiple comparison - Perform PET surface based analysis from step 1 (gtmseg) to step 5. While conducting mri_glmfit, include the smoothed thickness map (?h.thickness.10B.mgh) as pvr (per vertex regressor) - e.g. mri_glmfit --y lh.pet.10.mgh --fsgd your.fsgd dods --pvr lh.thickness.10B.mgh --C contrast.mtx --surf fsaverage lh --cortex --glmdir pvr.lh.pet.thickness.glmdir - Lastly, build a new monte carlo correction for multiple comparison.
Thank you Best, Paul
On 3/22/17 11:02 AM, miracooloz@gmail.com wrote:
Sent from my BlackBerry 10 smartphone. *From: *miracle ozzoude miracooloz@gmail.com *Sent: *Tuesday, March 21, 2017 7:41 PM *To: *Douglas N Greve *Subject: *PETsurfer surface based analysis
Hello, I am working through the PETsurfer surface based analysis and i have couple of question a) Since the procedure is the same as surface based analysis for cortical thickness except mri_vol2surf, Can I use the procedure for thickness?
Yes
b) What is the difference between mris_preproc and mri_concat. If I use mris_preproc, do I also need to use mri_concat? Also, can I use mris_preproc instead of mri_concat?
mris_preproc is a fronend for mri_concat that makes running mri_concat easier. You can use one or the other but not both
c) Can I use mri_surf2surf in place of mris_fwhm? If no, why?
Yes, they use the same underlying code for surface smoothing.
d) While researching PETsurfer surface based analysis in the forum, I came across multiple trends that used the "--projfrac" flag in both mri_vol2surf command and mris_preproc command. At what stage should I include this flag and why?
At which the time you run the program. If you are using mri_vol2surf prior to mris_preproc, then you would not include it in mris_preproc.
e) If I want to perform a multimodal analysis using thickness&PET or Surface area&PET, Can anyone confirm if this is the correct steps.
- Perform surface base analysis for cortical thickness from step 1 (mris_preproc) to correction for multiple comparison
- Perform PET surface based analysis from step 1 (gtmseg) to step 5. While conducting mri_glmfit, include the smoothed thickness map (?h.thickness.10B.mgh) as pvr (per vertex regressor)
- e.g. mri_glmfit --y lh.pet.10.mgh --fsgd your.fsgd dods --pvr lh.thickness.10B.mgh --C contrast.mtx --surf fsaverage lh --cortex --glmdir pvr.lh.pet.thickness.glmdir
- Lastly, build a new monte carlo correction for multiple comparison.
That looks right. You should not need to build a new MC, at least based on that command line
Thank you Best, Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Doug, Thank you for the detailed reply. I do have other questions.
1) Can you confirm if this is the correct use of mris_preproc for Uncached PET data. mris_preproc --fsgd your.fsgd --target fsaverage --hemi lh --meas Pet --out lh.your.pet.00.mgh. This modification was made from the thickness thickness data. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
2) if both the thickness and pet maps have the same contrast matrices, can I use one of them as my matrix for multimodal analysis?
3)What if they don't share similar contrast matrices, Can i still perform multimodal analysis? This is because contrast matrices are based on regressors and class in fsgd files.
Best, Paul
On Wed, Mar 22, 2017 at 1:11 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
On 3/22/17 11:02 AM, miracooloz@gmail.com wrote:
Sent from my BlackBerry 10 smartphone. *From: *miracle ozzoude miracooloz@gmail.com miracooloz@gmail.com *Sent: *Tuesday, March 21, 2017 7:41 PM *To: *Douglas N Greve *Subject: *PETsurfer surface based analysis
Hello, I am working through the PETsurfer surface based analysis and i have couple of question a) Since the procedure is the same as surface based analysis for cortical thickness except mri_vol2surf, Can I use the procedure for thickness?
Yes
b) What is the difference between mris_preproc and mri_concat. If I use mris_preproc, do I also need to use mri_concat? Also, can I use mris_preproc instead of mri_concat?
mris_preproc is a fronend for mri_concat that makes running mri_concat easier. You can use one or the other but not both
c) Can I use mri_surf2surf in place of mris_fwhm? If no, why?
Yes, they use the same underlying code for surface smoothing.
d) While researching PETsurfer surface based analysis in the forum, I came across multiple trends that used the "--projfrac" flag in both mri_vol2surf command and mris_preproc command. At what stage should I include this flag and why?
At which the time you run the program. If you are using mri_vol2surf prior to mris_preproc, then you would not include it in mris_preproc.
e) If I want to perform a multimodal analysis using thickness&PET or Surface area&PET, Can anyone confirm if this is the correct steps.
- Perform surface base analysis for cortical thickness from step 1
(mris_preproc) to correction for multiple comparison
- Perform PET surface based analysis from step 1 (gtmseg) to step 5.
While conducting mri_glmfit, include the smoothed thickness map (?h.thickness.10B.mgh) as pvr (per vertex regressor)
- e.g. mri_glmfit --y lh.pet.10.mgh --fsgd your.fsgd dods --pvr
lh.thickness.10B.mgh --C contrast.mtx --surf fsaverage lh --cortex --glmdir pvr.lh.pet.thickness.glmdir
- Lastly, build a new monte carlo correction for multiple comparison.
That looks right. You should not need to build a new MC, at least based on that command line
Thank you Best, Paul
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.
On 3/22/17 2:02 PM, miracle ozzoude wrote:
Hello Doug, Thank you for the detailed reply. I do have other questions.
- Can you confirm if this is the correct use of mris_preproc for
Uncached PET data. mris_preproc --fsgd your.fsgd --target fsaverage --hemi lh --meas Pet --out lh.your.pet.00.mgh. This modification was made from the thickness thickness data. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
You need to specify the pet input data. See for example the fMRI analysis tutorial here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_free...
- if both the thickness and pet maps have the same contrast matrices,
can I use one of them as my matrix for multimodal analysis?
No, you will need to as a regressor for the PVR. The way it works is that a design matrix is created from the FSGD. Then when glmfit goes to analyze a particular voxel, it gets the PVR data from that voxel and adds it as a column to the design matrix. So you need to include that column in your contrast matrix.
3)What if they don't share similar contrast matrices, Can i still perform multimodal analysis? This is because contrast matrices are based on regressors and class in fsgd files.
I don't know. It is your data and you are doing the analysis, so you will know what you are trying to test much better than me!
Best, Paul
On Wed, Mar 22, 2017 at 1:11 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
On 3/22/17 11:02 AM, miracooloz@gmail.com <mailto:miracooloz@gmail.com> wrote:Sent from my BlackBerry 10 smartphone. *From: *miracle ozzoude <miracooloz@gmail.com> <mailto:miracooloz@gmail.com> *Sent: *Tuesday, March 21, 2017 7:41 PM *To: *Douglas N Greve *Subject: *PETsurfer surface based analysis Hello, I am working through the PETsurfer surface based analysis and i have couple of question a) Since the procedure is the same as surface based analysis for cortical thickness except mri_vol2surf, Can I use the procedure for thickness?Yesb) What is the difference between mris_preproc and mri_concat. If I use mris_preproc, do I also need to use mri_concat? Also, can I use mris_preproc instead of mri_concat?mris_preproc is a fronend for mri_concat that makes running mri_concat easier. You can use one or the other but not bothc) Can I use mri_surf2surf in place of mris_fwhm? If no, why?Yes, they use the same underlying code for surface smoothing.d) While researching PETsurfer surface based analysis in the forum, I came across multiple trends that used the "--projfrac" flag in both mri_vol2surf command and mris_preproc command. At what stage should I include this flag and why?At which the time you run the program. If you are using mri_vol2surf prior to mris_preproc, then you would not include it in mris_preproc.e) If I want to perform a multimodal analysis using thickness&PET or Surface area&PET, Can anyone confirm if this is the correct steps. * Perform surface base analysis for cortical thickness from step 1 (mris_preproc) to correction for multiple comparison * Perform PET surface based analysis from step 1 (gtmseg) to step 5. While conducting mri_glmfit, include the smoothed thickness map (?h.thickness.10B.mgh) as pvr (per vertex regressor) * e.g. mri_glmfit --y lh.pet.10.mgh --fsgd your.fsgd dods --pvr lh.thickness.10B.mgh --C contrast.mtx --surf fsaverage lh --cortex --glmdir pvr.lh.pet.thickness.glmdir * Lastly, build a new monte carlo correction for multiple comparison.That looks right. You should not need to build a new MC, at least based on that command lineThank you Best, Paul _______________________________________________ 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you Doug. I am trying to perform pvc for my pet data based on the tutorial however, I keep getting this error:
" mri_gtmpvc --i C6_01_001_140813_PET_AV45_coreg_avg.nii.gz --reg C6_01_001_140813_PET_AV45_coreg_avg.reg.lta --psf 6mm --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx 0.01 --o C6_01_001_140813.gtmpvc.output Loading input C6_01_001_140813_PET_AV45_coreg_avg.nii.gz done loading input 1 frames
$Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ setenv SUBJECTS_DIR /net/synapse/nt/paul/Analysis cd /net/synapse/nt/paul/Analysis mri_gtmpvc --i C6_01_001_140813_PET_AV45_coreg_avg.nii.gz --reg C6_01_001_140813_PET_AV45_coreg_avg.reg.lta --psf 6mm --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx 0.01 --o C6_01_001_140813.gtmpvc.output sysname Linux hostname neuron2.sri.utoronto.ca machine x86_64 user paul vgthresh 0.001000 nReplace 18 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 24 avail.processors, using 1 Creating output directory C6_01_001_140813.gtmpvc.output Loading seg for gtm /net/synapse/nt/paul/Analysis/C6_01_001_140813/mri/gtmseg.mgz Loading seg ctab /net/synapse/nt/paul/Analysis/C6_01_001_140813/mri/gtmseg.ctab Reading /net/synapse/nt/paul/Analysis/C6_01_001_140813/mri/gtmseg.lta Replacing 18 Pruning ctab ERROR: CTABpruneCTab(): ctab does not have segid 192 Checking tissue type Segmentation fault"
Step 1 and 2 were successful. Please can you tell me what is wrong. Thanks Best, Paul
On Wed, Mar 22, 2017 at 3:07 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
On 3/22/17 2:02 PM, miracle ozzoude wrote:
Hello Doug, Thank you for the detailed reply. I do have other questions.
- Can you confirm if this is the correct use of mris_preproc for Uncached
PET data. mris_preproc --fsgd your.fsgd --target fsaverage --hemi lh --meas Pet --out lh.your.pet.00.mgh. This modification was made from the thickness thickness data. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ GroupAnalysis
You need to specify the pet input data. See for example the fMRI analysis tutorial here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ MultiModalFmriGroup_freeview
- if both the thickness and pet maps have the same contrast matrices, can
I use one of them as my matrix for multimodal analysis?
No, you will need to as a regressor for the PVR. The way it works is that a design matrix is created from the FSGD. Then when glmfit goes to analyze a particular voxel, it gets the PVR data from that voxel and adds it as a column to the design matrix. So you need to include that column in your contrast matrix.
3)What if they don't share similar contrast matrices, Can i still perform multimodal analysis? This is because contrast matrices are based on regressors and class in fsgd files.
I don't know. It is your data and you are doing the analysis, so you will know what you are trying to test much better than me!
Best, Paul
On Wed, Mar 22, 2017 at 1:11 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
On 3/22/17 11:02 AM, miracooloz@gmail.com wrote:
Sent from my BlackBerry 10 smartphone. *From: *miracle ozzoude miracooloz@gmail.com miracooloz@gmail.com *Sent: *Tuesday, March 21, 2017 7:41 PM *To: *Douglas N Greve *Subject: *PETsurfer surface based analysis
Hello, I am working through the PETsurfer surface based analysis and i have couple of question a) Since the procedure is the same as surface based analysis for cortical thickness except mri_vol2surf, Can I use the procedure for thickness?
Yes
b) What is the difference between mris_preproc and mri_concat. If I use mris_preproc, do I also need to use mri_concat? Also, can I use mris_preproc instead of mri_concat?
mris_preproc is a fronend for mri_concat that makes running mri_concat easier. You can use one or the other but not both
c) Can I use mri_surf2surf in place of mris_fwhm? If no, why?
Yes, they use the same underlying code for surface smoothing.
d) While researching PETsurfer surface based analysis in the forum, I came across multiple trends that used the "--projfrac" flag in both mri_vol2surf command and mris_preproc command. At what stage should I include this flag and why?
At which the time you run the program. If you are using mri_vol2surf prior to mris_preproc, then you would not include it in mris_preproc.
e) If I want to perform a multimodal analysis using thickness&PET or Surface area&PET, Can anyone confirm if this is the correct steps.
- Perform surface base analysis for cortical thickness from step 1
(mris_preproc) to correction for multiple comparison
- Perform PET surface based analysis from step 1 (gtmseg) to step 5.
While conducting mri_glmfit, include the smoothed thickness map (?h.thickness.10B.mgh) as pvr (per vertex regressor)
- e.g. mri_glmfit --y lh.pet.10.mgh --fsgd your.fsgd dods --pvr
lh.thickness.10B.mgh --C contrast.mtx --surf fsaverage lh --cortex --glmdir pvr.lh.pet.thickness.glmdir
- Lastly, build a new monte carlo correction for multiple comparison.
That looks right. You should not need to build a new MC, at least based on that command line
Thank you Best, Paul
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.e du/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 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.
Never mind Doug. I was able to solve the problem. Best, Paul
On Wed, Mar 22, 2017 at 3:34 PM, miracle ozzoude miracooloz@gmail.com wrote:
Thank you Doug. I am trying to perform pvc for my pet data based on the tutorial however, I keep getting this error:
" mri_gtmpvc --i C6_01_001_140813_PET_AV45_coreg_avg.nii.gz --reg C6_01_001_140813_PET_AV45_coreg_avg.reg.lta --psf 6mm --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx 0.01 --o C6_01_001_140813.gtmpvc.output Loading input C6_01_001_140813_PET_AV45_coreg_avg.nii.gz done loading input 1 frames
$Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ setenv SUBJECTS_DIR /net/synapse/nt/paul/Analysis cd /net/synapse/nt/paul/Analysis mri_gtmpvc --i C6_01_001_140813_PET_AV45_coreg_avg.nii.gz --reg C6_01_001_140813_PET_AV45_coreg_avg.reg.lta --psf 6mm --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx 0.01 --o C6_01_001_140813.gtmpvc.output sysname Linux hostname neuron2.sri.utoronto.ca machine x86_64 user paul vgthresh 0.001000 nReplace 18 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 24 avail.processors, using 1 Creating output directory C6_01_001_140813.gtmpvc.output Loading seg for gtm /net/synapse/nt/paul/Analysis/ C6_01_001_140813/mri/gtmseg.mgz Loading seg ctab /net/synapse/nt/paul/Analysis/ C6_01_001_140813/mri/gtmseg.ctab Reading /net/synapse/nt/paul/Analysis/C6_01_001_140813/mri/gtmseg.lta Replacing 18 Pruning ctab ERROR: CTABpruneCTab(): ctab does not have segid 192 Checking tissue type Segmentation fault"
Step 1 and 2 were successful. Please can you tell me what is wrong. Thanks Best, Paul
On Wed, Mar 22, 2017 at 3:07 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
On 3/22/17 2:02 PM, miracle ozzoude wrote:
Hello Doug, Thank you for the detailed reply. I do have other questions.
- Can you confirm if this is the correct use of mris_preproc for
Uncached PET data. mris_preproc --fsgd your.fsgd --target fsaverage --hemi lh --meas Pet --out lh.your.pet.00.mgh. This modification was made from the thickness thickness data. https://surfer.nmr.mgh.h arvard.edu/fswiki/FsTutorial/GroupAnalysis
You need to specify the pet input data. See for example the fMRI analysis tutorial here http://surfer.nmr.mgh.harvard. edu/fswiki/FsTutorial/MultiModalFmriGroup_freeview
- if both the thickness and pet maps have the same contrast matrices,
can I use one of them as my matrix for multimodal analysis?
No, you will need to as a regressor for the PVR. The way it works is that a design matrix is created from the FSGD. Then when glmfit goes to analyze a particular voxel, it gets the PVR data from that voxel and adds it as a column to the design matrix. So you need to include that column in your contrast matrix.
3)What if they don't share similar contrast matrices, Can i still perform multimodal analysis? This is because contrast matrices are based on regressors and class in fsgd files.
I don't know. It is your data and you are doing the analysis, so you will know what you are trying to test much better than me!
Best, Paul
On Wed, Mar 22, 2017 at 1:11 PM, Douglas Greve <greve@nmr.mgh.harvard.edu
wrote:
On 3/22/17 11:02 AM, miracooloz@gmail.com wrote:
Sent from my BlackBerry 10 smartphone. *From: *miracle ozzoude miracooloz@gmail.com miracooloz@gmail.com *Sent: *Tuesday, March 21, 2017 7:41 PM *To: *Douglas N Greve *Subject: *PETsurfer surface based analysis
Hello, I am working through the PETsurfer surface based analysis and i have couple of question a) Since the procedure is the same as surface based analysis for cortical thickness except mri_vol2surf, Can I use the procedure for thickness?
Yes
b) What is the difference between mris_preproc and mri_concat. If I use mris_preproc, do I also need to use mri_concat? Also, can I use mris_preproc instead of mri_concat?
mris_preproc is a fronend for mri_concat that makes running mri_concat easier. You can use one or the other but not both
c) Can I use mri_surf2surf in place of mris_fwhm? If no, why?
Yes, they use the same underlying code for surface smoothing.
d) While researching PETsurfer surface based analysis in the forum, I came across multiple trends that used the "--projfrac" flag in both mri_vol2surf command and mris_preproc command. At what stage should I include this flag and why?
At which the time you run the program. If you are using mri_vol2surf prior to mris_preproc, then you would not include it in mris_preproc.
e) If I want to perform a multimodal analysis using thickness&PET or Surface area&PET, Can anyone confirm if this is the correct steps.
- Perform surface base analysis for cortical thickness from step 1
(mris_preproc) to correction for multiple comparison
- Perform PET surface based analysis from step 1 (gtmseg) to step 5.
While conducting mri_glmfit, include the smoothed thickness map (?h.thickness.10B.mgh) as pvr (per vertex regressor)
- e.g. mri_glmfit --y lh.pet.10.mgh --fsgd your.fsgd dods --pvr
lh.thickness.10B.mgh --C contrast.mtx --surf fsaverage lh --cortex --glmdir pvr.lh.pet.thickness.glmdir
- Lastly, build a new monte carlo correction for multiple
comparison.
That looks right. You should not need to build a new MC, at least based on that command line
Thank you Best, Paul
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.e du/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 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.
Can you tar up the output folder and send it to me at our file drop?
https://gate.nmr.mgh.harvard.edu/filedrop2
Also, please send the following 3 files /net/synapse/nt/paul/Analysis/C6_01_001_140813/mri/gtmseg.mgz /net/synapse/nt/paul/Analysis/C6_01_001_140813/mri/gtmseg.ctab /net/synapse/nt/paul/Analysis/C6_01_001_140813/mri/gtmseg.lta
On 3/22/17 3:34 PM, miracle ozzoude wrote:
Thank you Doug. I am trying to perform pvc for my pet data based on the tutorial however, I keep getting this error:
" mri_gtmpvc --i C6_01_001_140813_PET_AV45_coreg_avg.nii.gz --reg C6_01_001_140813_PET_AV45_coreg_avg.reg.lta --psf 6mm --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx 0.01 --o C6_01_001_140813.gtmpvc.output Loading input C6_01_001_140813_PET_AV45_coreg_avg.nii.gz done loading input 1 frames
$Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ setenv SUBJECTS_DIR /net/synapse/nt/paul/Analysis cd /net/synapse/nt/paul/Analysis mri_gtmpvc --i C6_01_001_140813_PET_AV45_coreg_avg.nii.gz --reg C6_01_001_140813_PET_AV45_coreg_avg.reg.lta --psf 6mm --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx 0.01 --o C6_01_001_140813.gtmpvc.output sysname Linux hostname neuron2.sri.utoronto.ca http://neuron2.sri.utoronto.ca machine x86_64 user paul vgthresh 0.001000 nReplace 18 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 24 avail.processors, using 1 Creating output directory C6_01_001_140813.gtmpvc.output Loading seg for gtm /net/synapse/nt/paul/Analysis/C6_01_001_140813/mri/gtmseg.mgz Loading seg ctab /net/synapse/nt/paul/Analysis/C6_01_001_140813/mri/gtmseg.ctab Reading /net/synapse/nt/paul/Analysis/C6_01_001_140813/mri/gtmseg.lta Replacing 18 Pruning ctab ERROR: CTABpruneCTab(): ctab does not have segid 192 Checking tissue type Segmentation fault"
Step 1 and 2 were successful. Please can you tell me what is wrong. Thanks Best, Paul
On Wed, Mar 22, 2017 at 3:07 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
On 3/22/17 2:02 PM, miracle ozzoude wrote:Hello Doug, Thank you for the detailed reply. I do have other questions. 1) Can you confirm if this is the correct use of mris_preproc for Uncached PET data. mris_preproc --fsgd your.fsgd --target fsaverage --hemi lh --meas Pet --out lh.your.pet.00.mgh. This modification was made from the thickness thickness data. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>You need to specify the pet input data. See for example the fMRI analysis tutorial here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_freeview <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_freeview>2) if both the thickness and pet maps have the same contrast matrices, can I use one of them as my matrix for multimodal analysis?No, you will need to as a regressor for the PVR. The way it works is that a design matrix is created from the FSGD. Then when glmfit goes to analyze a particular voxel, it gets the PVR data from that voxel and adds it as a column to the design matrix. So you need to include that column in your contrast matrix.3)What if they don't share similar contrast matrices, Can i still perform multimodal analysis? This is because contrast matrices are based on regressors and class in fsgd files.I don't know. It is your data and you are doing the analysis, so you will know what you are trying to test much better than me!Best, Paul On Wed, Mar 22, 2017 at 1:11 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: On 3/22/17 11:02 AM, miracooloz@gmail.com <mailto:miracooloz@gmail.com> wrote:Sent from my BlackBerry 10 smartphone. *From: *miracle ozzoude <miracooloz@gmail.com> <mailto:miracooloz@gmail.com> *Sent: *Tuesday, March 21, 2017 7:41 PM *To: *Douglas N Greve *Subject: *PETsurfer surface based analysis Hello, I am working through the PETsurfer surface based analysis and i have couple of question a) Since the procedure is the same as surface based analysis for cortical thickness except mri_vol2surf, Can I use the procedure for thickness?Yesb) What is the difference between mris_preproc and mri_concat. If I use mris_preproc, do I also need to use mri_concat? Also, can I use mris_preproc instead of mri_concat?mris_preproc is a fronend for mri_concat that makes running mri_concat easier. You can use one or the other but not bothc) Can I use mri_surf2surf in place of mris_fwhm? If no, why?Yes, they use the same underlying code for surface smoothing.d) While researching PETsurfer surface based analysis in the forum, I came across multiple trends that used the "--projfrac" flag in both mri_vol2surf command and mris_preproc command. At what stage should I include this flag and why?At which the time you run the program. If you are using mri_vol2surf prior to mris_preproc, then you would not include it in mris_preproc.e) If I want to perform a multimodal analysis using thickness&PET or Surface area&PET, Can anyone confirm if this is the correct steps. * Perform surface base analysis for cortical thickness from step 1 (mris_preproc) to correction for multiple comparison * Perform PET surface based analysis from step 1 (gtmseg) to step 5. While conducting mri_glmfit, include the smoothed thickness map (?h.thickness.10B.mgh) as pvr (per vertex regressor) * e.g. mri_glmfit --y lh.pet.10.mgh --fsgd your.fsgd dods --pvr lh.thickness.10B.mgh --C contrast.mtx --surf fsaverage lh --cortex --glmdir pvr.lh.pet.thickness.glmdir * Lastly, build a new monte carlo correction for multiple comparison.That looks right. You should not need to build a new MC, at least based on that command lineThank you Best, Paul _______________________________________________ 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> . 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