Hello Everyone,
Is there a way to extract the significant clusters as masks from significant group comparisons using qdec?
All I can seem to find is mri_glmfit-sim which doesn't quite replicate the QDEC FDR 0.05 output and doesn't seem to make anything that I could extract as a label, or hand drawing an ROI.
I am working with a longitudinal model of cortical thickness, and would like to extract the average thickness of each significant cluster to understand the change in thickness.
Thank you.
Kate Damme
Try mri_surfcluster. Run it with --help to get usage. You can set the threshold with --fdr. Make sure to use the --mask option passing it the mask.mgh from the qdec output
On 01/22/2017 07:56 PM, Katherine Damme wrote:
Hello Everyone,
Is there a way to extract the significant clusters as masks from significant group comparisons using qdec?
All I can seem to find is mri_glmfit-sim which doesn't quite replicate the QDEC FDR 0.05 output and doesn't seem to make anything that I could extract as a label, or hand drawing an ROI.
I am working with a longitudinal model of cortical thickness, and would like to extract the average thickness of each significant cluster to understand the change in thickness.
Thank you.
Kate Damme
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you so much!
This got me to the stage of having separate labels for each significant cluster, but I would like to extract the values from each subject to look at the raw data.
Do I have to use mri_label2label to move the label into each individual's space?
Can I use aparcstats2table to get a table of the individual values of the label? (It seems that this is set up for the segmentation data)
Thank you again!
On Mon, Jan 23, 2017 at 11:44 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Try mri_surfcluster. Run it with --help to get usage. You can set the threshold with --fdr. Make sure to use the --mask option passing it the mask.mgh from the qdec output
On 01/22/2017 07:56 PM, Katherine Damme wrote:
Hello Everyone,
Is there a way to extract the significant clusters as masks from significant group comparisons using qdec?
All I can seem to find is mri_glmfit-sim which doesn't quite replicate the QDEC FDR 0.05 output and doesn't seem to make anything that I could extract as a label, or hand drawing an ROI.
I am working with a longitudinal model of cortical thickness, and would like to extract the average thickness of each significant cluster to understand the change in thickness.
Thank you.
Kate Damme
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.
It is probably better to work with the y.mgh file that qdec produces. It is in fsaverage space. If you create an ocn file with mri_surfcluster, you can feed that as the --seg to mri_segstats (along with --i y.mgh), spec the output with --avgwf to get a matrix of nsubjects by nclusters (make sure to also include --exludeid 0)
On 01/23/2017 08:00 PM, Katherine Damme wrote:
Thank you so much!
This got me to the stage of having separate labels for each significant cluster, but I would like to extract the values from each subject to look at the raw data.
Do I have to use mri_label2label to move the label into each individual's space?
Can I use aparcstats2table to get a table of the individual values of the label? (It seems that this is set up for the segmentation data)
Thank you again!
On Mon, Jan 23, 2017 at 11:44 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Try mri_surfcluster. Run it with --help to get usage. You can set the threshold with --fdr. Make sure to use the --mask option passing it the mask.mgh from the qdec output On 01/22/2017 07:56 PM, Katherine Damme wrote: > Hello Everyone, > > Is there a way to extract the significant clusters as masks from > significant group comparisons using qdec? > > All I can seem to find is mri_glmfit-sim which doesn't quite > replicate the QDEC FDR 0.05 output and doesn't seem to make anything > that I could extract as a label, or hand drawing an ROI. > > I am working with a longitudinal model of cortical thickness, and > would like to extract the average thickness of each significant > cluster to understand the change in thickness. > > Thank you. > > Kate Damme > > > _______________________________________________ > 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.
Thanks Douglas. I am not sure that I understand. Will you please review the commands below?
I believe I need to complete something like:
mri_surfcluster --in ${qdecoutputfolder}/cache.th40.abs.sig.masked.mgh --fdr 0.05 --mask ${qdecoutputfolder}/mask.mgh --csd /usr/local/freesurfer/average/mult-comp-cor/rh/cortex/fwhm25/abs/th40/mc-z.csd --surf pial --ocn ${qdecoutputfolder}/
Which puts out a *.w file, a COR-00#, and COR.info, but I am not sure which file I should supply to -- seg
mri_segstats --seg ?? --i y.mgh --avgfw ${nameoftextoutput} --exludeid 0
Could I supply the ocn file from the mri_glmfit-sim?
On Mon, Jan 23, 2017 at 7:10 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
It is probably better to work with the y.mgh file that qdec produces. It is in fsaverage space. If you create an ocn file with mri_surfcluster, you can feed that as the --seg to mri_segstats (along with --i y.mgh), spec the output with --avgwf to get a matrix of nsubjects by nclusters (make sure to also include --exludeid 0)
On 01/23/2017 08:00 PM, Katherine Damme wrote:
Thank you so much!
This got me to the stage of having separate labels for each significant cluster, but I would like to extract the values from each subject to look at the raw data.
Do I have to use mri_label2label to move the label into each individual's space?
Can I use aparcstats2table to get a table of the individual values of the label? (It seems that this is set up for the segmentation data)
Thank you again!
On Mon, Jan 23, 2017 at 11:44 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Try mri_surfcluster. Run it with --help to get usage. You can set the threshold with --fdr. Make sure to use the --mask option passing it the mask.mgh from the qdec output On 01/22/2017 07:56 PM, Katherine Damme wrote: > Hello Everyone, > > Is there a way to extract the significant clusters as masks from > significant group comparisons using qdec? > > All I can seem to find is mri_glmfit-sim which doesn't quite > replicate the QDEC FDR 0.05 output and doesn't seem to make anything > that I could extract as a label, or hand drawing an ROI. > > I am working with a longitudinal model of cortical thickness, and > would like to extract the average thickness of each significant > cluster to understand the change in thickness. > > Thank you. > > Kate Damme > > > _______________________________________________ > 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.eduhttps://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.-- 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/
Hi, I am not sure that someone responded you yet. Once you get results on the qdec using the shift mouse you can draw an ROI out of your cluster. Once done there is a bottom in the guy called “add the selection to the ROI you will see the entire ROI highlighted. Under the “file” command you will find “Map Label to subjects”
Edu
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Katherine Damme <katherine.damme@gmail.commailto:katherine.damme@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Sunday, January 22, 2017 at 4:56 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Extracting significant clusters after qdec analyses
Hello Everyone,
Is there a way to extract the significant clusters as masks from significant group comparisons using qdec?
All I can seem to find is mri_glmfit-sim which doesn't quite replicate the QDEC FDR 0.05 output and doesn't seem to make anything that I could extract as a label, or hand drawing an ROI.
I am working with a longitudinal model of cortical thickness, and would like to extract the average thickness of each significant cluster to understand the change in thickness.
Thank you.
Kate Damme
freesurfer@nmr.mgh.harvard.edu
-
Caverzasi, Eduardo -
Douglas N Greve -
Katherine Damme