Hi FreeSurfer experts,
I recently ran a simple fMRI analysis in FSL and now generating images of the activation in freesurfer using reg-feat2anat to register the functional activation to the freesurfer recon-all files, and generating the images using tksurfer:
tksurfer pilot_3 lh inflated -annot aparc.annot -ov run4578_COMB.gfeat/cope1.feat/stats/zstat1.nii.gz -ovreg run4_fwhm8.feat/reg/freesurfer/anat2std.register.dat -fthresh 4 -fslope 1
However I have come across a strange occurrence when I change the threshold. Specifically, when I set the -fthresh flag (bolded) as 4 (i.e. p=0.0001) or less, the activation colors comes off as they should (see 4_blue attached) in terms of how I set up the contrasts. But when I set my threshold to 5 or higher (changing nothing else), the colors of the activation invert (see 5_red attached).
What does this mean? How can I fix this?
Any ideas would be greatly appreciated!
Thank you! Gabriella
Mass. Eye and Ear Confidentiality Notice: This e-mail and any files transmitted with it are confidential and are intended solely for the use of the individual(s) addressed in the message above. This communication may contain sensitive or confidential information. If you are not an intended recipient, dissemination, forwarding, printing, or copying of this e-mail is strictly prohibited. If you believe you have received this e-mail in error and the email contains patient information, please contact the Mass. Eye and Ear Compliance Line at 617-263-1600. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and delete the e-mail.
There is another parameter called -fmid. The final mapping is a complicated combination of all three (fthresh, fmin, fslope). I usally use the -fminmax option which is easier to explain. -fminmax 2 5 means that the threshold is set to 2 and that at 5 the color will saturate. doug
On 01/11/2016 12:18 PM, Hirsch, Gabriella wrote:
Hi FreeSurfer experts,
I recently ran a simple fMRI analysis in FSL and now generating images of the activation in freesurfer using reg-feat2anat to register the functional activation to the freesurfer recon-all files, and generating the images using tksurfer:
/tksurfer pilot_3 lh inflated -annot aparc.annot -ov run4578_COMB.gfeat/cope1.feat/stats/zstat1.nii.gz -ovreg run4_fwhm8.feat/reg/freesurfer/anat2std.register.dat *-fthresh 4 *-fslope 1/
However I have come across a strange occurrence when I change the threshold. Specifically, when I set the -fthresh flag (bolded) as 4 (i.e. p=0.0001) or less, the activation colors comes off as they should (see 4_blue attached) in terms of how I set up the contrasts. But when I set my threshold to 5 or higher (changing nothing else), the colors of the activation invert (see 5_red attached).
What does this mean? How can I fix this?
Any ideas would be greatly appreciated!
Thank you! Gabriella
Mass. Eye and Ear Confidentiality Notice: This e-mail and any files transmitted with it are confidential and are intended solely for the use of the individual(s) addressed in the message above. This communication may contain sensitive or confidential information. If you are not an intended recipient, dissemination, forwarding, printing, or copying of this e-mail is strictly prohibited. If you believe you have received this e-mail in error and the email contains patient information, please contact the Mass. Eye and Ear Compliance Line at 617-263-1600. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and delete the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug! This is very good to know. Is there a ratio or relationship between the fmin and fmax that is optimal, as in, should we keep a 2 to 5 ratio?
Gabriella
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, January 11, 2016 12:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fMRI activation color inversion
There is another parameter called -fmid. The final mapping is a complicated combination of all three (fthresh, fmin, fslope). I usally use the -fminmax option which is easier to explain. -fminmax 2 5 means that the threshold is set to 2 and that at 5 the color will saturate. doug
On 01/11/2016 12:18 PM, Hirsch, Gabriella wrote:
Hi FreeSurfer experts,
I recently ran a simple fMRI analysis in FSL and now generating images of the activation in freesurfer using reg-feat2anat to register the functional activation to the freesurfer recon-all files, and generating the images using tksurfer:
/tksurfer pilot_3 lh inflated -annot aparc.annot -ov run4578_COMB.gfeat/cope1.feat/stats/zstat1.nii.gz -ovreg run4_fwhm8.feat/reg/freesurfer/anat2std.register.dat *-fthresh 4 *-fslope 1/
However I have come across a strange occurrence when I change the threshold. Specifically, when I set the -fthresh flag (bolded) as 4 (i.e. p=0.0001) or less, the activation colors comes off as they should (see 4_blue attached) in terms of how I set up the contrasts. But when I set my threshold to 5 or higher (changing nothing else), the colors of the activation invert (see 5_red attached).
What does this mean? How can I fix this?
Any ideas would be greatly appreciated!
Thank you! Gabriella
Mass. Eye and Ear Confidentiality Notice: This e-mail and any files transmitted with it are confidential and are intended solely for the use of the individual(s) addressed in the message above. This communication may contain sensitive or confidential information. If you are not an intended recipient, dissemination, forwarding, printing, or copying of this e-mail is strictly prohibited. If you believe you have received this e-mail in error and the email contains patient information, please contact the Mass. Eye and Ear Compliance Line at 617-263-1600. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and delete the e-mail.
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.
no, it is a matter of taste. Note that 2 is the threshold. If you are looking at sig maps, then the threshold may be important. The p-value threshold is 10^-fthresh
On 01/11/2016 02:19 PM, Hirsch, Gabriella wrote:
Thanks Doug! This is very good to know. Is there a ratio or relationship between the fmin and fmax that is optimal, as in, should we keep a 2 to 5 ratio?
Gabriella
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, January 11, 2016 12:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fMRI activation color inversion
There is another parameter called -fmid. The final mapping is a complicated combination of all three (fthresh, fmin, fslope). I usally use the -fminmax option which is easier to explain. -fminmax 2 5 means that the threshold is set to 2 and that at 5 the color will saturate. doug
On 01/11/2016 12:18 PM, Hirsch, Gabriella wrote:
Hi FreeSurfer experts,
I recently ran a simple fMRI analysis in FSL and now generating images of the activation in freesurfer using reg-feat2anat to register the functional activation to the freesurfer recon-all files, and generating the images using tksurfer:
/tksurfer pilot_3 lh inflated -annot aparc.annot -ov run4578_COMB.gfeat/cope1.feat/stats/zstat1.nii.gz -ovreg run4_fwhm8.feat/reg/freesurfer/anat2std.register.dat *-fthresh 4 *-fslope 1/
However I have come across a strange occurrence when I change the threshold. Specifically, when I set the -fthresh flag (bolded) as 4 (i.e. p=0.0001) or less, the activation colors comes off as they should (see 4_blue attached) in terms of how I set up the contrasts. But when I set my threshold to 5 or higher (changing nothing else), the colors of the activation invert (see 5_red attached).
What does this mean? How can I fix this?
Any ideas would be greatly appreciated!
Thank you! Gabriella
Mass. Eye and Ear Confidentiality Notice: This e-mail and any files transmitted with it are confidential and are intended solely for the use of the individual(s) addressed in the message above. This communication may contain sensitive or confidential information. If you are not an intended recipient, dissemination, forwarding, printing, or copying of this e-mail is strictly prohibited. If you believe you have received this e-mail in error and the email contains patient information, please contact the Mass. Eye and Ear Compliance Line at 617-263-1600. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and delete the e-mail.
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
OK, thanks!
Gabriella
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, January 11, 2016 2:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fMRI activation color inversion
no, it is a matter of taste. Note that 2 is the threshold. If you are looking at sig maps, then the threshold may be important. The p-value threshold is 10^-fthresh
On 01/11/2016 02:19 PM, Hirsch, Gabriella wrote:
Thanks Doug! This is very good to know. Is there a ratio or relationship between the fmin and fmax that is optimal, as in, should we keep a 2 to 5 ratio?
Gabriella
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, January 11, 2016 12:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fMRI activation color inversion
There is another parameter called -fmid. The final mapping is a complicated combination of all three (fthresh, fmin, fslope). I usally use the -fminmax option which is easier to explain. -fminmax 2 5 means that the threshold is set to 2 and that at 5 the color will saturate. doug
On 01/11/2016 12:18 PM, Hirsch, Gabriella wrote:
Hi FreeSurfer experts,
I recently ran a simple fMRI analysis in FSL and now generating images of the activation in freesurfer using reg-feat2anat to register the functional activation to the freesurfer recon-all files, and generating the images using tksurfer:
/tksurfer pilot_3 lh inflated -annot aparc.annot -ov run4578_COMB.gfeat/cope1.feat/stats/zstat1.nii.gz -ovreg run4_fwhm8.feat/reg/freesurfer/anat2std.register.dat *-fthresh 4 *-fslope 1/
However I have come across a strange occurrence when I change the threshold. Specifically, when I set the -fthresh flag (bolded) as 4 (i.e. p=0.0001) or less, the activation colors comes off as they should (see 4_blue attached) in terms of how I set up the contrasts. But when I set my threshold to 5 or higher (changing nothing else), the colors of the activation invert (see 5_red attached).
What does this mean? How can I fix this?
Any ideas would be greatly appreciated!
Thank you! Gabriella
Mass. Eye and Ear Confidentiality Notice: This e-mail and any files transmitted with it are confidential and are intended solely for the use of the individual(s) addressed in the message above. This communication may contain sensitive or confidential information. If you are not an intended recipient, dissemination, forwarding, printing, or copying of this e-mail is strictly prohibited. If you believe you have received this e-mail in error and the email contains patient information, please contact the Mass. Eye and Ear Compliance Line at 617-263-1600. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and delete the e-mail.
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.
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
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Hirsch, Gabriella