On 6/30/2022 2:31 PM, Mark Ebden wrote:
External Email - Use Caution
Hi Douglas,
Thank you. From your explanation, the software's numbers from 0 to 1
aren't corrected p-values -- specifically, they aren't corrections in
the well-accepted sense of Bonferroni corrections or other analagous
multiple-comparisons corrections. They seem to be *percentiles* (what
you refer to as ranks), where 1 corresponds to an extreme ranking in
the basket of 10k, and 0 indicates the other extreme, per voxel/vertex.
They are -log10(pvalue)*sign(effect) as with all FS.
Hope I have that right. I'm also not sure what you meant about
converting the noise into p-values. Below is my interpretation of what
the pseudocode would be. Is it right? I suspect it's not quite ready
yet for sharing, because the concept of a maximum needs to be inserted.
for each voxel:
p0 = the p-value from a t-test or similar between the two
groups, as they are
x0 = -log10(p0)
for i from 1 to 10k:
perform a random split between the two groups comprising the
contrast analysis
p = the p-value from a t-test or similar between the two groups
x[i] = -log10(p)
r = percentile indicating where x0 falls within the distribution
of x's 10k values
# N.B.: r represents the result for this voxel, from 0 to 1, to
go in cache.th40.pos.sig.voxel.mgh
Almost, it is more like this:
for i = 1 to 10k
construct a z map (white gaussian noise) on the surface
smooth by a given FWHM (look in glmfit/fwhm.dat)
renormalize the z map so that std=1
find the voxel with the largest z value; keep track of the z value
(convert the z to a p)
Now you have a list of 10k largest z values (or smallest p-values)
-- for mc-z simulations these are cached in
$FREESURFER_HOME/average/mult-comp-cor
For each voxel in your data
get uncorrected p-value
compute a corrected p-value by counting the number in the 10k list
that are smaller than the uncorrected p-value (divide by 10k)
compute the -log10(corrected pvalue)
Thanks for any help. Also, how would the pseudocode differ for
sig.cluster.mgh vs sig.voxel.mgh?
Thanks,
Mark
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Sent:* Sunday, June 19, 2022 10:37 AM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] How is cache.th40.pos.sig.voxel.mgh
computed, exactly?
from mri_glmfit-sim --help csdbase.sig.voxel.mgh - the sig volume
corrected for multiple comparisons on a voxel-wise basis. The
threshhold and sign are irrelevant. The value at each voxel is the
corrected -log10(p-value) for that voxel.
from mri_glmfit-sim --help
csdbase.sig.voxel.mgh - the sig volume corrected for multiple
comparisons on a voxel-wise basis. The threshhold and sign are
irrelevant. The value at each voxel is the corrected -log10(p-value)
for that voxel.
It is computed from a simulation in which gaussian noise is smoothed,
then converted to p-values (log10(p)), then the maximum log10(p) is
found. This is repeated 10,000 times to give 10k maximums. A corrected
p-value for each voxel is then computed based upon the rank of the raw
pvalue in this list of 10k.
On 6/10/2022 4:14 PM, Mark Ebden wrote:
External Email - Use Caution
Hi,
I was wondering if anyone knows how the numbers
incache.th40.pos.sig.voxel.mghare computed, or where I'd look to
learn this. There is a one-liner in the documentation
<https://secure-web.cisco.com/1mZPhKugTZV0zciGbO88IW1AMYXyEgFtcZoIj7XLR0Jz1HIEvbCJkL4A7fX-p9YT9PqXmYanl22wOWqtBVNKGfpIp3t451w5ALS2dsuCwQbPF_U6gywrjK2UlE8i2ikgbsNzuv6MQQwGeEQBDvYVfd8fnL5QhJ22E194tBsbTjN3WO0QR40tF0aRy6GD8nmmZdXIwbZxDyjaLlrxSFrpVMcsPl4x8d46hpqt3oVDIlfYnGv--EBw4LtKPGi1FW3KzEcL9gLeJb4TToo63FGDRQmjyhNx3aDOZKK1Aw7T774MTIB-3EOccH_SHcGNscWvwvEb6Ou2STAxKqt8rcvZX1Q/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1R2vQZUhHj-zAreoIH8kMlOuUPh5jYx8TyPmfmDzbM1Dl-B4qgLgEGd_WS_0Y5_08itpZ4Auiw4Ht4r-hZ9db1vTTyWFnxXY06DL9M-Ci_nUhFSEnnkt_VUhZ9nYtm6g3lKY9WxqmhllQYKLUlIVPuYUr9yQZM5iZ6Xch2DDFIJGKuCp0kg3Kjhj46CcO51Ub9WSI2iVIE6_gITNGjAVTztvV-E11_RxVX55KRwYo-EajEf4x60XUOm2hGcu4-35_LsmGynDaEemN9U59zZJ1IJbizmUoXnrJiPR51WNVRzaKtg2AbVbNm7aAc85WKKTpCNVU7IXaexwkzxZk0C3XmQ%2Fhttps%2A3A%2A2F%2A2Fsurfer.nmr.mgh.harvard.edu%2A2Ffswiki%2A2FFsTutorial%2A2FMultipleComparisonsV6.0__%3BJSUlJSUl%21%21D0zGoin7BXfl%21-uix2-pXnTtUAAjZD2VXdB_BxqAGHYynqpQihjlROtSs1aHk1Q-Z5k228EMsY8kR8VlVUutWd0OpqLrgcx8zEWq4ug%24>
but I'd like the mathematical details of the correction etc. so I can
determine what the final numbers (from 0 to 1) represent. I've
noticed from browsing the plot in FreeView that significant areas
have values close to 1, which is puzzling.
Thanks if you could point me in the right direction.
Kind regards,
Mark
Mar
******
*Mark Ebden**, D.Phil *
(Pronouns: He/Him)****
Research Analyst****
**
The Hospital for Sick Children****
555 University Ave, Toronto ON M5G 1X8****
P 416.888.0841****
*<https://secure-web.cisco.com/1u3Eqz6ChkU3GFI6wnbaKNNbADjIEtGg8BOlcsWcSByn6C9dLwfl2sukBYw7xhYOJtqNUT4e21Z737dZlIOw1H336Ythl-fbBFSlfA5abBBfVrs7KZ9srhvBoPDjSgNl4oufbmsog58dbcmUxq1VkbJ7_bz-xFa9zVfJ64IvPVhNbqOCq4ttZ5dnubGVGDi4NwjA_SD9817H73afLm6o4UVLhDmZs-JSJb4w9-ueYjEGfRT_vrNCmuWA0Jdmk5vKz4ImGFx_23rUgmD4UBCtG1VZCTTZc9OAsuC51NvIfJAGRL7EAsoW54afEMmnbumTaf5mvqdnLrwoD6-aN_nNf0g/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F17-WtJwO2uIWyZ7umzDRCiH0I5Q1NZ-tfYcx_zx9tznEDbF7wdGOPP86cK8jP9yFutBpKmq9LWYY1y8AuwZCWk6IdKEPIA_ZqP8Dc4C98j87Lk8ys1SjgVgzfrjoazrJXK1-elq3_KlOW4bq3ZHfgxipdcr_gUJh_cPtLG0NlOdBzxJTJsCkV6QEZr4IGT0O3TikkECFmDBAv1XuNHEgIwBgUXw_WqKw_shdKUaQCnYUv1W_51l_VsfpDdm5Poo9RCR3jMGbkmsxEt4j1UloOg316TI7_-R8Dw2hfZvmdbNCm5Vsf9hi82eN14AhwMOPt8eX4LmXbEDg7BYKxjbiEGg%2Fhttps%2A3A%2A2F%2A2Fwww.linkedin.com%2A2Fin%2A2Fmebden%2A2F__%3BJSUlJSUl%21%21D0zGoin7BXfl%21-uix2-pXnTtUAAjZD2VXdB_BxqAGHYynqpQihjlROtSs1aHk1Q-Z5k228EMsY8kR8VlVUutWd0OpqLrgcx_e50h1Fg%24>*
------------------------------------------------------------------------
This e-mail may contain confidential, personal and/or health
information(information which may be subject to legal restrictions on
use, retention and/or disclosure) for the sole use of the intended
recipient. Any review or distribution by anyone other than the person
for whom it was originally intended is strictly prohibited. If you
have received this e-mail in error, please contact the sender and
delete all copies.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1jZkuJD8rRcPUuxNordBiZkfOEY3lw_VGrcGWX92_UB2kky6BvRXNI0Owmb7DCX77JOftH7ebmWMmv7BVro1RE0GNojgls8x5pqs_SjLR7gxXXwrmpbVAlHgk6m558E2UKrECuyCpRDegIbaSo3uhMtdAc_sQwam7ALA4Fe8zzzBDALxdVlBU949qIvB_lNOGS3xkJ15R6N1Gx-F8mNaMlUHsUJXNjBf5aVejVPP7KtInQ701hVsYqdKcTDUER3W98DyLEkiHspAJVlJ2ClCGIBXQ0o3EWyvwF5qSUiGH3Kv1CYDEixB967kC6T3ZE3DeIQpRMVJwISluKyJh1ay_6w/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__%3B%21%21D0zGoin7BXfl%21-uix2-pXnTtUAAjZD2VXdB_BxqAGHYynqpQihjlROtSs1aHk1Q-Z5k228EMsY8kR8VlVUutWd0OpqLrgcx_mIhvLhg%24>
------------------------------------------------------------------------
This e-mail may contain confidential, personal and/or health
information(information which may be subject to legal restrictions on
use, retention and/or disclosure) for the sole use of the intended
recipient. Any review or distribution by anyone other than the person
for whom it was originally intended is strictly prohibited. If you
have received this e-mail in error, please contact the sender and
delete all copies.
_______________________________________________
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 Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
