[Freesurfer] Segmentation of hippocampal subfields / version 6.0 release date
Hello, I wanted to inquire about when you think that this new package for freesurfer 6.0 will be complete? I am interested in pursuing hippocampal segmentation, but it seems that I should not use the segmentation from your older program and I should wait, would you agree? Thank you, Josh -- Josh Gray Graduate Student Psychology Dept. - Clinical Program Experimental & Clinical Psychopharmacology Laboratory University of Georgia ___ 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] 2 unrelated questions regarding structural data
Hello, 1) I am working with the recent release of human connectome data and am trying to run group analysis ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis). I want to correlate brain volume with an behavioral variable. It is difficult to tell which files I need in order for the pipeline to run properly. Since I did not run recon-all locally, their file arrangement is unique, many files are zipped, etc. Therefore the scripts (e.g., mris_preproc) do not know where to look, as they do with the typical file structure. Can you tell me what specific files this pipeline needs to generate the GLM? Alternatively, if you have performed this process with the human connectome data you can tell me which directories/files need to be unzipped and placed in SUBJECTS_DIR. Just need to know what specific files the scripts in the group analysis pipeline are searching for when I run them. 2) I am interested in applying the Yeo 2015 cognitive atlas to structural data. Basically, I want to quantify networks C1-12 in my structural data by exporting the voxel size of each network for each subject into an text file (so I would have left and right hemisphere voxel totals for networks C1-12 for each subject). It is analogous to what is routinely done with the desikan and destrieux atlas. I know you can change the threshold of the networks, but I suspect 1e-5 is fine (i.e., what is depicted on the website). Is there a quick way to do this? Thank you for your help! Josh -- Graduate Student Psychology Dept. - Clinical Program Experimental & Clinical Psychopharmacology Laboratory University of Georgia ___ 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] Question on Yeo 2015 cognitive atlas
Hello, I am interested in applying the Yeo 2015 cognitive atlas to structural data. Basically, I want to quantify networks C1-12 in my structural data by exporting the voxel size of each network for each subject into an text file (so I would have left and right hemisphere voxel totals for networks C1-12 for each subject). It is analogous to what is routinely done with the desikan and destrieux atlas. I know you can change the threshold of the networks, but I suspect 1e-5 is fine (i.e., what is depicted on the website). Is there a quick way to do this? Thank you, Josh Gray -- Graduate Student Psychology Dept. - Clinical Program Experimental & Clinical Psychopharmacology Laboratory University of Georgia ___ 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] Question about group analysis
Hello, I've got a very basic question related to group analysis. If I want run a correlation of voxels in the cortex with a variable *controlling *for another continous variable, how do I do this. I know how to run them both in a GLM simultaneously by coding the matrix 0 1 1, however, how do I look at the first variable after controlling for the other? Here is an example of my current fsgd input (I want to control for income): GroupDescriptorFile 1 Title MyTitle Class Class1 plus blue CLASS Class2 circle green SomeTag Variables impulsivity income Input subjid1 Main 10100 Input subjid2 Main 20200 etc. -- Graduate Student Psychology Dept. - Clinical Program Experimental & Clinical Psychopharmacology Laboratory University of Georgia ___ 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] error in dev version for quantifyHAsubregions.sh
Hello,
I found a small bug in recent dev version bin quantifyHAsubregions.sh:
leftVolFile="$resultsDirectory/$subjectName/mri/lh.${suffix}Volumes-${suffix}.v20.txt"
rightVolFile="$resultsDirectory/$subjectName/mri/rh.${suffix}Volumes-${suffix}.v20.txt"
Should say
leftVolFile="$resultsDirectory/$subjectName/mri/lh.${suffix}Volumes-${
*prefix*}.v20.txt"
rightVolFile="$resultsDirectory/$subjectName/mri/rh.${suffix}Volumes-${
*prefix*}.v20.txt"
because as specified "T1" is the ${prefix} which is how the subfields file
names end. Obviously, can flip suffix and prefix throughout so it is more
intuitive. Seems to work fine after this adjustment.
Josh
--
Joshua C. Gray, PhD
Psychology Instructor
Center for Deployment Psychology
Work: (301) 816-4768
www.deploymentpsych.org
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Re: [Freesurfer] error in dev version for quantifyHAsubregions.sh
Realized in my tooling around I had flipped T1 and hippoSf in my command.
Here is how the adjustment needs to be made for:
quantifyHAsubregions.sh hippoSf -
leftVolFile="$resultsDirectory/$subjectName/mri/lh.${*prefix*}Volumes-${*suffix*}.v20.txt"
rightVolFile="$resultsDirectory/$subjectName/mri/rh.${*prefix*}Volumes-${*suffix*}.v20.txt"
On Tue, Sep 19, 2017 at 9:23 AM, Josh Gray wrote:
> Hello,
>
> I found a small bug in recent dev version bin quantifyHAsubregions.sh:
> leftVolFile="$resultsDirectory/$subjectName/mri/lh.${suffix}Volumes-${
> suffix}.v20.txt"
> rightVolFile="$resultsDirectory/$subjectName/mri/rh.${suffix}Volumes-${
> suffix}.v20.txt"
>
>
> Should say
> leftVolFile="$resultsDirectory/$subjectName/mri/lh.${suffix}Volumes-${
> *prefix*}.v20.txt"
> rightVolFile="$resultsDirectory/$subjectName/mri/rh.${suffix}Volumes-${
> *prefix*}.v20.txt"
>
>
> because as specified "T1" is the ${prefix} which is how the subfields file
> names end. Obviously, can flip suffix and prefix throughout so it is more
> intuitive. Seems to work fine after this adjustment.
>
> Josh
> --
> Joshua C. Gray, PhD
> Psychology Instructor
> Center for Deployment Psychology
> Work: (301) 816-4768
> www.deploymentpsych.org
>
--
Joshua C. Gray, PhD
Psychology Instructor
Center for Deployment Psychology
Work: (301) 816-4768
www.deploymentpsych.org
___
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addressed. If you believe this e-mail was sent to you in error and the e-mail
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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
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[Freesurfer] Question about annotation of surface volume in freeview
Hello, I am looking to highlight specific regions from desikan atlas (i.e., ?h.apart.annot; https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation) rather than all of the regions in freeview. For example, I would like to highlight middle frontal gyrus and superior frontal gyrus on the surface lh_inflated only. Is there a way to easily do this? Thank you, Josh ___ 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.
