Re: [Freesurfer] ROI analyses using SPM AAL ROIs
not sure, a pointer to the page would make it easier. probably it is the T1 image of the mni152 that is distributed with FSL and SPM On 7/3/17 1:33 AM, M Janani wrote: Hi Team, Currently I’m working on ROI analyses. I saw one article related to VolumeROICorticalThickness in Free surfer wiki. Could anyone please tell me what is the anatomical file(*TT_avg152T1.nii*) they are referring to? I took AAL ROIs from SPM. In that case, which anatomical file should I use for my analyses? Any help would be really grateful. Thanks in advance. Regards, Janani ::DISCLAIMER:: The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ___ 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] ROI analyses using SPM AAL ROIs
Hi Team, Currently I'm working on ROI analyses. I saw one article related to VolumeROICorticalThickness in Free surfer wiki. Could anyone please tell me what is the anatomical file(TT_avg152T1.nii) they are referring to? I took AAL ROIs from SPM. In that case, which anatomical file should I use for my analyses? Any help would be really grateful. Thanks in advance. Regards, Janani ::DISCLAIMER:: The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ___ 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] ROI analyses using SPM AAL ROIs
Hi Team, Currently I'm working on ROI analyses. I saw one article related to VolumeROICorticalThickness in Free surfer wiki. Could anyone please tell me what is the anatomical file(TT_avg152T1.nii) they are referring to? I took AAL ROIs from SPM. In that case, which anatomical file should I use for my analyses? Any help would be really grateful. Thanks in advance. Regards, Janani ::DISCLAIMER:: The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ___ 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] ROI analyses
Use --id 1 or --excludeid 0 with mri_segstats. 3rd question answered below.
On 04/01/2014 10:42 AM, Emily Boeke wrote:
> Hi Doug,
>
> I am able to run mri_segstats with slabel below, but it is finding two
> segmentations in my label and producing a column for each. one is associated
> with an ID of 0 and one is associated with an ID of 1. I assume that I want
> the 2nd column (the ID of 1). What is the command doing? Is it creating one
> segmentation out of my label and one out of the rest of the cortical surface?
>
> Also, could you please address the 3rd question from the email below? Thanks
> so much!
>
> Best,
> Emily
> On Mar 28, 2014, at 12:37 PM, Douglas N Greve wrote:
>
>> On 03/28/2014 12:04 PM, Emily Boeke wrote:
>>> Hi Doug,
>>>
>>> Thanks for the response.
>>>
>>> Regarding #1, I am still confused. if the ROI boundaries computed in native
>>> space are mapped to fsaverage/mni305 space, doesn't that mean the actual
>>> computing of the averages is done in fsaverage/mni305 space? Why would
>>> mapping to fsaverage/mni305 space be necessary in the ROI analysis if the
>>> averages are computed in native space
>> What I mean is that the ROI used is that of the native subject, not
>> fsaverage. If you were to map the hippocampus to fsaverage and overlay it
>> with the hippo of fsaverage you would see that they are different. FSFAST
>> resamples the time series data into fsaverage/mni space and computes all the
>> stats there, so the ROI boundaries need to be transferred to that space.
>>> Regarding #2, I tried that already and got the error "must specify an
>>> output table file" (I used the exact same command, just swapping out
>>> -slabel for -seg.)
>> You can't swap them out. Read the docs for it.
>>> Also, this analysis is purely done in mni305/fsaverage space because it is
>>> using the concatenated file, correct? If I want to do it in native space,
>>> would I use label to label (as written below) and then funcroi? Do you
>>> think it would make a difference either way?
I think you can do it in native space if you specify native when you run
mkanalysis-sess
doug
>>>
>>> mri_label2label --srclabel ${SUBJECTS_DIR}/fsaverage/label/mylabel.label
>>> --src subject fsaverage --trglabel
>>> ${SUBJECTS_DIR}/subject/label/mylabel.label --trgsubject subject -regmethod
>>> surface --hemi lh
>>>
>>> Thanks,
>>> Emily
>>>
>>> On Mar 28, 2014, at 11:15 AM, Douglas N Greve wrote:
>>>
On 03/28/2014 08:51 AM, Emily Boeke wrote:
> Hi Freesurfers,
>
> I have some questions about ROI analyses.
>
> 1. I use the mni305 and fsaverage flags during preprocessing. Does this
> mean that when I run funcroi-config, funcroi-sess, etc, the analysis is
> being done for each subject in mni305 space, as opposed to native space?
> Meaning, If I specify -seg aseg.mgz 18 in funcroi-config, the analysis
> will not be done using the left amygdala from that individual's aseg, but
> instead will be done in mni305 space with the fsaverage left amygdala ROI?
No, it is done in native space. The voxelwise analysis is done in
fsaverage/mni305 space, but the ROI boundaries used to compute the ROI
averages are computed in native space and mapped to fsaverage/mni305 space.
> 2. I sometimes want to use labels I've created on fsaverage from averaged
> group activation to do ROI analyses. If the ROI is in the volume, I
> convert the label to a mask and run:
>
> mri_segstats --i cespct.nii.gz --seg mymask.mgz --id 1 --avgwf
> ces.mymask.dat
>
> In the appropriate contrast folder. What should I do if I want to do the
> same thing, but with a surface label (in a lh or rh surface analysis, not
> an mni305 analysis)?
You can still use mri_segstats, just spec --slabel instead of seg
doug
> Thanks!
>
> Emily
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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/
>>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@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/
>>
>>
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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
Re: [Freesurfer] ROI analyses
Hi Doug,
I am able to run mri_segstats with slabel below, but it is finding two
segmentations in my label and producing a column for each. one is associated
with an ID of 0 and one is associated with an ID of 1. I assume that I want the
2nd column (the ID of 1). What is the command doing? Is it creating one
segmentation out of my label and one out of the rest of the cortical surface?
Also, could you please address the 3rd question from the email below? Thanks so
much!
Best,
Emily
On Mar 28, 2014, at 12:37 PM, Douglas N Greve wrote:
>
> On 03/28/2014 12:04 PM, Emily Boeke wrote:
>> Hi Doug,
>>
>> Thanks for the response.
>>
>> Regarding #1, I am still confused. if the ROI boundaries computed in native
>> space are mapped to fsaverage/mni305 space, doesn't that mean the actual
>> computing of the averages is done in fsaverage/mni305 space? Why would
>> mapping to fsaverage/mni305 space be necessary in the ROI analysis if the
>> averages are computed in native space
> What I mean is that the ROI used is that of the native subject, not
> fsaverage. If you were to map the hippocampus to fsaverage and overlay it
> with the hippo of fsaverage you would see that they are different. FSFAST
> resamples the time series data into fsaverage/mni space and computes all the
> stats there, so the ROI boundaries need to be transferred to that space.
>>
>> Regarding #2, I tried that already and got the error "must specify an output
>> table file" (I used the exact same command, just swapping out -slabel for
>> -seg.)
>
> You can't swap them out. Read the docs for it.
>> Also, this analysis is purely done in mni305/fsaverage space because it is
>> using the concatenated file, correct? If I want to do it in native space,
>> would I use label to label (as written below) and then funcroi? Do you think
>> it would make a difference either way?
>>
>> mri_label2label --srclabel ${SUBJECTS_DIR}/fsaverage/label/mylabel.label
>> --src subject fsaverage --trglabel
>> ${SUBJECTS_DIR}/subject/label/mylabel.label --trgsubject subject -regmethod
>> surface --hemi lh
>>
>> Thanks,
>> Emily
>>
>> On Mar 28, 2014, at 11:15 AM, Douglas N Greve wrote:
>>
>>> On 03/28/2014 08:51 AM, Emily Boeke wrote:
Hi Freesurfers,
I have some questions about ROI analyses.
1. I use the mni305 and fsaverage flags during preprocessing. Does this
mean that when I run funcroi-config, funcroi-sess, etc, the analysis is
being done for each subject in mni305 space, as opposed to native space?
Meaning, If I specify -seg aseg.mgz 18 in funcroi-config, the analysis
will not be done using the left amygdala from that individual's aseg, but
instead will be done in mni305 space with the fsaverage left amygdala ROI?
>>> No, it is done in native space. The voxelwise analysis is done in
>>> fsaverage/mni305 space, but the ROI boundaries used to compute the ROI
>>> averages are computed in native space and mapped to fsaverage/mni305 space.
2. I sometimes want to use labels I've created on fsaverage from averaged
group activation to do ROI analyses. If the ROI is in the volume, I
convert the label to a mask and run:
mri_segstats --i cespct.nii.gz --seg mymask.mgz --id 1 --avgwf
ces.mymask.dat
In the appropriate contrast folder. What should I do if I want to do the
same thing, but with a surface label (in a lh or rh surface analysis, not
an mni305 analysis)?
>>> You can still use mri_segstats, just spec --slabel instead of seg
>>> doug
Thanks!
Emily
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@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/
>>>
>>>
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@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/
>
>
___
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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.
Re: [Freesurfer] ROI analyses
Hi Doug,
Thanks for the response.
Regarding #1, I am still confused. if the ROI boundaries computed in native
space are mapped to fsaverage/mni305 space, doesn't that mean the actual
computing of the averages is done in fsaverage/mni305 space? Why would mapping
to fsaverage/mni305 space be necessary in the ROI analysis if the averages are
computed in native space?
Regarding #2, I tried that already and got the error "must specify an output
table file" (I used the exact same command, just swapping out -slabel for
-seg.) Also, this analysis is purely done in mni305/fsaverage space because it
is using the concatenated file, correct? If I want to do it in native space,
would I use label to label (as written below) and then funcroi? Do you think it
would make a difference either way?
mri_label2label --srclabel ${SUBJECTS_DIR}/fsaverage/label/mylabel.label --src
subject fsaverage --trglabel ${SUBJECTS_DIR}/subject/label/mylabel.label
--trgsubject subject -regmethod surface --hemi lh
Thanks,
Emily
On Mar 28, 2014, at 11:15 AM, Douglas N Greve wrote:
>
> On 03/28/2014 08:51 AM, Emily Boeke wrote:
>> Hi Freesurfers,
>>
>> I have some questions about ROI analyses.
>>
>> 1. I use the mni305 and fsaverage flags during preprocessing. Does this mean
>> that when I run funcroi-config, funcroi-sess, etc, the analysis is being
>> done for each subject in mni305 space, as opposed to native space? Meaning,
>> If I specify -seg aseg.mgz 18 in funcroi-config, the analysis will not be
>> done using the left amygdala from that individual's aseg, but instead will
>> be done in mni305 space with the fsaverage left amygdala ROI?
> No, it is done in native space. The voxelwise analysis is done in
> fsaverage/mni305 space, but the ROI boundaries used to compute the ROI
> averages are computed in native space and mapped to fsaverage/mni305 space.
>>
>> 2. I sometimes want to use labels I've created on fsaverage from averaged
>> group activation to do ROI analyses. If the ROI is in the volume, I convert
>> the label to a mask and run:
>>
>> mri_segstats --i cespct.nii.gz --seg mymask.mgz --id 1 --avgwf ces.mymask.dat
>>
>> In the appropriate contrast folder. What should I do if I want to do the
>> same thing, but with a surface label (in a lh or rh surface analysis, not an
>> mni305 analysis)?
> You can still use mri_segstats, just spec --slabel instead of seg
> doug
>>
>> Thanks!
>>
>> Emily
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@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/
>
>
___
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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.
Re: [Freesurfer] ROI analyses
On 03/28/2014 12:04 PM, Emily Boeke wrote:
> Hi Doug,
>
> Thanks for the response.
>
> Regarding #1, I am still confused. if the ROI boundaries computed in native
> space are mapped to fsaverage/mni305 space, doesn't that mean the actual
> computing of the averages is done in fsaverage/mni305 space? Why would
> mapping to fsaverage/mni305 space be necessary in the ROI analysis if the
> averages are computed in native space
What I mean is that the ROI used is that of the native subject, not
fsaverage. If you were to map the hippocampus to fsaverage and overlay
it with the hippo of fsaverage you would see that they are different.
FSFAST resamples the time series data into fsaverage/mni space and
computes all the stats there, so the ROI boundaries need to be
transferred to that space.
>
> Regarding #2, I tried that already and got the error "must specify an output
> table file" (I used the exact same command, just swapping out -slabel for
> -seg.)
You can't swap them out. Read the docs for it.
> Also, this analysis is purely done in mni305/fsaverage space because it is
> using the concatenated file, correct? If I want to do it in native space,
> would I use label to label (as written below) and then funcroi? Do you think
> it would make a difference either way?
>
> mri_label2label --srclabel ${SUBJECTS_DIR}/fsaverage/label/mylabel.label
> --src subject fsaverage --trglabel
> ${SUBJECTS_DIR}/subject/label/mylabel.label --trgsubject subject -regmethod
> surface --hemi lh
>
> Thanks,
> Emily
>
> On Mar 28, 2014, at 11:15 AM, Douglas N Greve wrote:
>
>> On 03/28/2014 08:51 AM, Emily Boeke wrote:
>>> Hi Freesurfers,
>>>
>>> I have some questions about ROI analyses.
>>>
>>> 1. I use the mni305 and fsaverage flags during preprocessing. Does this
>>> mean that when I run funcroi-config, funcroi-sess, etc, the analysis is
>>> being done for each subject in mni305 space, as opposed to native space?
>>> Meaning, If I specify -seg aseg.mgz 18 in funcroi-config, the analysis will
>>> not be done using the left amygdala from that individual's aseg, but
>>> instead will be done in mni305 space with the fsaverage left amygdala ROI?
>> No, it is done in native space. The voxelwise analysis is done in
>> fsaverage/mni305 space, but the ROI boundaries used to compute the ROI
>> averages are computed in native space and mapped to fsaverage/mni305 space.
>>> 2. I sometimes want to use labels I've created on fsaverage from averaged
>>> group activation to do ROI analyses. If the ROI is in the volume, I convert
>>> the label to a mask and run:
>>>
>>> mri_segstats --i cespct.nii.gz --seg mymask.mgz --id 1 --avgwf
>>> ces.mymask.dat
>>>
>>> In the appropriate contrast folder. What should I do if I want to do the
>>> same thing, but with a surface label (in a lh or rh surface analysis, not
>>> an mni305 analysis)?
>> You can still use mri_segstats, just spec --slabel instead of seg
>> doug
>>>
>>> Thanks!
>>>
>>> Emily
>>>
>>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@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/
>>
>>
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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/
___
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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] ROI analyses
On 03/28/2014 08:51 AM, Emily Boeke wrote: > Hi Freesurfers, > > I have some questions about ROI analyses. > > 1. I use the mni305 and fsaverage flags during preprocessing. Does this mean > that when I run funcroi-config, funcroi-sess, etc, the analysis is being > done for each subject in mni305 space, as opposed to native space? Meaning, > If I specify -seg aseg.mgz 18 in funcroi-config, the analysis will not be > done using the left amygdala from that individual's aseg, but instead will be > done in mni305 space with the fsaverage left amygdala ROI? No, it is done in native space. The voxelwise analysis is done in fsaverage/mni305 space, but the ROI boundaries used to compute the ROI averages are computed in native space and mapped to fsaverage/mni305 space. > > 2. I sometimes want to use labels I've created on fsaverage from averaged > group activation to do ROI analyses. If the ROI is in the volume, I convert > the label to a mask and run: > > mri_segstats --i cespct.nii.gz --seg mymask.mgz --id 1 --avgwf ces.mymask.dat > > In the appropriate contrast folder. What should I do if I want to do the same > thing, but with a surface label (in a lh or rh surface analysis, not an > mni305 analysis)? You can still use mri_segstats, just spec --slabel instead of seg doug > > > Thanks! > > Emily > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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.
[Freesurfer] ROI analyses
Hi Freesurfers, I have some questions about ROI analyses. 1. I use the mni305 and fsaverage flags during preprocessing. Does this mean that when I run funcroi-config, funcroi-sess, etc, the analysis is being done for each subject in mni305 space, as opposed to native space? Meaning, If I specify -seg aseg.mgz 18 in funcroi-config, the analysis will not be done using the left amygdala from that individual's aseg, but instead will be done in mni305 space with the fsaverage left amygdala ROI? 2. I sometimes want to use labels I've created on fsaverage from averaged group activation to do ROI analyses. If the ROI is in the volume, I convert the label to a mask and run: mri_segstats --i cespct.nii.gz --seg mymask.mgz --id 1 --avgwf ces.mymask.dat In the appropriate contrast folder. What should I do if I want to do the same thing, but with a surface label (in a lh or rh surface analysis, not an mni305 analysis)? Thanks! Emily ___ 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] ROI analyses
On 05/07/2013 05:21 AM, Tudor Popescu wrote: > Hi Doug, > I was just wondering whether you received my last email, with > follow-ups on your answers. Sorry for the multitude of questions - as > ever, I really appreciate the help! > Best wishes, > Tudor > > On 4 May 2013 20:31, Tudor Popescu <mailto:tud...@gmail.com>> wrote: > > Sorry Doug, wasn't sure whether you'd seen my reply > Tudor > > > -- Forwarded message -- > From: *Tudor Popescu* mailto:tud...@gmail.com>> > Date: 2 May 2013 21:54 > Subject: Re: [Freesurfer] ROI analyses > To: freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > Thanks Doug! If I may follow up: > > > 3) (I can't see whether there's a tutorial for this, as the > main FS > > site seems to be down at the moment) How can a group > comparison of CT > > be done inside a given ROI, and in what ways can the ROI be > specified? > > I guess the command line version of QDEC would produce, in > this case, > > the same contrasts as QDEC, but within the ROI as opposed to > the whole > > brain > You mean you want to do an exploratory analysis within a mask > of an ROI > or that you want to average the CT scan within the ROI and do > a group > analysis of the ROI values? If the former, you can use > mri_glmfit with > the -label or -mask option. If the latter, you can create a > table with > asegstats2table then run mri_glmfit with --table > > 3') Is it the case that mri_glmfit with mask=brainmask.mgz is > equivalent to doing a whole-brain analysis in QDEC? > QDEC is only doing surface-based analysis. brainmask.mgz is a volume. But in principle the idea is similar. > > > 3'') I didn't find, on the mri_glmfit help page, how masks can be > formed out of one of the atlas structures, e.g. > "lh_S_intrapariet_and_P_trans "... The --table argument is also > not present anywhere on that page.. > You can run mri_annotation2label to convert an annotation to label, then pass the label to glmfit. > > > 3''') Would it not be a/parc/stats2table rather than > a/seg/stats2table, if the ROI in question was cortical and not > subcortical? Is the difference between what FS calls > "segmentation" and "parcellation" just terminology, i.e. the > former delineates subcortical structures and the latter delineates > cortical structures? Or does it imply anything else? > Whether you use one or the other depends on whether you generate the individual table with mris_anatomical_stats (aparcstats2table) or mri_segstats (asegstats2table) > > > 4) How do the results of these two different types of ROI group > > analyses differ, and is one of them more "correct" than the > other: > > A) running the command prompt version of QDEC within the > confines > > of a certain atlas-defined ROI, and looking at the resulting > > statistical map (clusters), as per question 3; > > B) extracting the CT values for that ROI for all > subjects using > > aparcstats2table, and doing t-tests to look for a group > difference. > Oops, looks like these are the two I mentioned from #3 above. > The first > is an exploratory analysis in which the groups are compared on a > vertex-by-vertex basis. If there is a subset of vertices that are > different between the groups, it may show up in the exploratory > analysis. However, the effect may be small at each vertex and > averaging > over the vertices may improve your power (unless the effect is > only at a > few vertices). One is not more correct than the other, just > testing > different hypotheses. > > 4') Can the second option (averaging the CT values within the ROI) > not also be done by taking the values from the table into SPSS and > simply doing an independent samples t-test? Is that not equivalent > to what mri_glmfit would do in this case? > Yes, it should be the same. > > > And one more question: > 5) Can the statistical map in QDEC be built using a lower, > uncorrected p value (e.g. 0.0001) instead of an FDR-corrected test > value? > Yes, just set the threshold (FDR is off by default). doug > > > Thanks!! > Tudor &g
Re: [Freesurfer] ROI analyses
Thanks Doug! If I may follow up: > 3) (I can't see whether there's a tutorial for this, as the main FS > > site seems to be down at the moment) How can a group comparison of CT > > be done inside a given ROI, and in what ways can the ROI be specified? > > I guess the command line version of QDEC would produce, in this case, > > the same contrasts as QDEC, but within the ROI as opposed to the whole > > brain > You mean you want to do an exploratory analysis within a mask of an ROI > or that you want to average the CT scan within the ROI and do a group > analysis of the ROI values? If the former, you can use mri_glmfit with > the -label or -mask option. If the latter, you can create a table with > asegstats2table then run mri_glmfit with --table > 3') Is it the case that mri_glmfit with mask=brainmask.mgz is equivalent to doing a whole-brain analysis in QDEC? 3'') I didn't find, on the mri_glmfit help page, how masks can be formed out of one of the atlas structures, e.g. "lh_S_intrapariet_and_P_trans "... The --table argument is also not present anywhere on that page.. 3''') Would it not be a*parc*stats2table rather than a*seg*stats2table, if the ROI in question was cortical and not subcortical? Is the difference between what FS calls "segmentation" and "parcellation" just terminology, i.e. the former delineates subcortical structures and the latter delineates cortical structures? Or does it imply anything else? > > 4) How do the results of these two different types of ROI group > > analyses differ, and is one of them more "correct" than the other: > > A) running the command prompt version of QDEC within the confines > > of a certain atlas-defined ROI, and looking at the resulting > > statistical map (clusters), as per question 3; > > B) extracting the CT values for that ROI for all subjects using > > aparcstats2table, and doing t-tests to look for a group difference. > Oops, looks like these are the two I mentioned from #3 above. The first > is an exploratory analysis in which the groups are compared on a > vertex-by-vertex basis. If there is a subset of vertices that are > different between the groups, it may show up in the exploratory > analysis. However, the effect may be small at each vertex and averaging > over the vertices may improve your power (unless the effect is only at a > few vertices). One is not more correct than the other, just testing > different hypotheses. > 4') Can the second option (averaging the CT values within the ROI) not also be done by taking the values from the table into SPSS and simply doing an independent samples t-test? Is that not equivalent to what mri_glmfit would do in this case? And one more question: 5) Can the statistical map in QDEC be built using a lower, uncorrected p value (e.g. 0.0001) instead of an FDR-corrected test value? Thanks!! Tudor > doug > > > > > ___ > > 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 > gr...@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. > > ___ 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] ROI analyses
On 04/29/2013 04:13 PM, Tudor Popescu wrote: > Dear Freesurfers, > > I am doing an ROI analysis (group comparison) of cortical thickness, > and I have some questions that I could use some help with. Many thanks > in advance! > > Tudor > > 1) I used aparcstats2table to extract CT values for structures from > the Destrieux atlas, but I cannot identify some important cortical > structures among the names in that list. For example, I don't see > anything corresponding to the Superior Parietal Lobule, or the > Intraparietal Sulcus (the latter actually does appear but is coupled > with another structure, under the name > "lh_S_intrapariet_and_P_trans_thickness") Have you looked in Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature Christophe Destrieux, NI, 2010? > > 2) Can the same table (of the average CT of each cortical > parcellation) be extracted using parcellations based on an atlas other > than the Destrieux (e.g. the Harvard-Oxford, or the Julich)? There is nothing automatic do to it, but if you have those atlases mapped to the individual, you can create a color table (like FreeSurferColorLUT.txt) and run mri_segstats then asegstats2table > > 3) (I can't see whether there's a tutorial for this, as the main FS > site seems to be down at the moment) How can a group comparison of CT > be done inside a given ROI, and in what ways can the ROI be specified? > I guess the command line version of QDEC would produce, in this case, > the same contrasts as QDEC, but within the ROI as opposed to the whole > brain You mean you want to do an exploratory analysis within a mask of an ROI or that you want to average the CT scan within the ROI and do a group analysis of the ROI values? If the former, you can use mri_glmfit with the -label or -mask option. If the latter, you can create a table with asegstats2table then run mri_glmfit with --table > > 4) How do the results of these two different types of ROI group > analyses differ, and is one of them more "correct" than the other: > A) running the command prompt version of QDEC within the confines > of a certain atlas-defined ROI, and looking at the resulting > statistical map (clusters), as per question 3; > B) extracting the CT values for that ROI for all subjects using > aparcstats2table, and doing t-tests to look for a group difference. Oops, looks like these are the two I mentioned from #3 above. The first is an exploratory analysis in which the groups are compared on a vertex-by-vertex basis. If there is a subset of vertices that are different between the groups, it may show up in the exploratory analysis. However, the effect may be small at each vertex and averaging over the vertices may improve your power (unless the effect is only at a few vertices). One is not more correct than the other, just testing different hypotheses. doug > > ___ > 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 gr...@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.
[Freesurfer] ROI analyses
Dear Freesurfers, I am doing an ROI analysis (group comparison) of cortical thickness, and I have some questions that I could use some help with. Many thanks in advance! Tudor 1) I used aparcstats2table to extract CT values for structures from the Destrieux atlas, but I cannot identify some important cortical structures among the names in that list. For example, I don't see anything corresponding to the Superior Parietal Lobule, or the Intraparietal Sulcus (the latter actually does appear but is coupled with another structure, under the name "lh_S_intrapariet_and_P_trans_thickness") 2) Can the same table (of the average CT of each cortical parcellation) be extracted using parcellations based on an atlas other than the Destrieux (e.g. the Harvard-Oxford, or the Julich)? 3) (I can't see whether there's a tutorial for this, as the main FS site seems to be down at the moment) How can a group comparison of CT be done inside a given ROI, and in what ways can the ROI be specified? I guess the command line version of QDEC would produce, in this case, the same contrasts as QDEC, but within the ROI as opposed to the whole brain 4) How do the results of these two different types of ROI group analyses differ, and is one of them more "correct" than the other: A) running the command prompt version of QDEC within the confines of a certain atlas-defined ROI, and looking at the resulting statistical map (clusters), as per question 3; B) extracting the CT values for that ROI for all subjects using aparcstats2table, and doing t-tests to look for a group difference. ___ 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.
