Re: [Freesurfer] How to project SPM image

[Fischl, Bruce]

Can you summarize what you are trying to do? What kind of overlay are you 
trying to visualize and what exactly do you mean by a "3D image"?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Rachel Wagner
Sent: Thursday, June 30, 2022 2:48 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to project SPM image


External Email - Use Caution
Thank you so much for your response - I'm a master's student and am really 
struggling - I've been stuck trying to do this for about 2 weeks now, so the 
help is so appreciated!

My results look very grainy in mricron so my supervisor wants me to keep trying 
in FreeSurfer unfortunately for me.

I uploaded a the brain.mgz volume in freeview, but I'm not sure how to add an 
overlay and project as a 3D image. Would you happen to have any ideas?

Thank you so, so much again,
Rachel Wagner

From: niels.f...@gmx.de
Sent: June 30, 2022 2:35 PM
To: 'Freesurfer support list'
Subject: Re: [Freesurfer] How to project SPM image

You don't often get email from niels.f...@gmx.de. 
Learn why this is 
important
Sure is, through freeview, however if you already have spm format files, it is 
much easier to use mricron

Von: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 Im Auftrag von Rachel Wagner
Gesendet: Donnerstag, 30. Juni 2022 18:18
An: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Betreff: Re: [Freesurfer] How to project SPM image


External Email - Use Caution
Thanks very much, I will absolutely do so! Just so I know - is there not any 
way of generating such figures in Freesurfer?

From: niels.f...@gmx.de
Sent: June 30, 2022 4:47 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] How to project SPM image

You don't often get email from niels.f...@gmx.de. 
Learn why this is 
important

External Email - Use Caution
Rachel,  these figures were likely created with a software called mricron, not 
freesurfer.  Check it out :)

Holen Sie sich Outlook für 
Android


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Re: [Freesurfer] trac-all -prep -c ERROR

[Salar Dini, Elaheh]

External Email - Use Caution

Hi back,

Should be alright now. Please try this link: 
https://secure-web.cisco.com/1LYPTJn0s7YjdWTtPFS55k3z-IqjPfKIscsxsCg4qgjYm5i7hgZ47NYZ8BRHgQAtw4DZhP0bO52JhFFLI8LcEH2uXcDPnyyn6mXbi2PEZLkzub2KbFSDNMpQcj-DHyeMAdbjU8od-fcAnsd58VKB5nnYprNNUzbu4SeyZphucXtmwJOZO8ypI5PpTsAfrzXhwXhBNxFn7nI-I74hjqFmpZsF8mA4qlZouKMphk5t0qqcAKNcUjlISrWw3lxT_thARtkXppnJtpXaAU_6HUa3jcMs4Rjb4q7eJYv4jInujKXvt-OTVCGaGH7L5CAzEi3vhLtLwE1xKy4Hn046eARCCbdUuFPK4RiHKeapu1gceaxc/https%3A%2F%2Fdrive.google.com%2Fdrive%2Ffolders%2F1pkss2G7AYmlrCWYPVItnctl4W7H_OV7W%3Fusp%3Dsharing

Thank you,
Ela



Yendiki, 
Anastasia
 Thu, 30 Jun 2022 14:18:47 
-0700

Hi Ela - Can you make the google doc accessible by all?

Anastasia.


From: Salar Dini, Elaheh 
Sent: Thursday, June 30, 2022 5:08 PM
To: Freesurfer support list 
Subject: Re: trac-all -prep -c ERROR


Thank you for the reply. For some reason, when I change the DCM file to nii and 
look at them, in majority of our subjects, the cerebellum and lower brain stem 
has been cut off, but in this specific subject, I don't think the CST is 
truncated or out of field more than any other subjects that the TRACULA steps 
have been run for without any errors. I have taken a few screenshots of both 
this subject and another one whom -prep and -bedp have been run for without any 
errors and uploaded them to google drive. Please find the link here:

https://secure-web.cisco.com/1LCiPLQmcEsS4BCM0TJyZvxoi4nUKpJbfm_yczRtTlOqrMH5KpC7za-O8r7lqyFo-JyQKsclGI6CsTUjZrwJxa3LFt8Ra9TOXhcNICwqqPUCIpCtvGPg4fqvlheBZR2BgjDNUu8hlXxa4ooX5LTkyJbVhKipqSUoeaZPNuBfy-Tn3KOkwcImJ-NHThk6DVLD96Kfh3PNkMKqp0qWVYGY3P2kYyJuMFFaUTeEYSD0-suXOIWeDjnKSJoF62YOsqErHNxdilp773bgtuS8lcggEjYnlLrvL6n4AMteFS6Pk3cAfRKTD-Umy8DmTu6nUnKenIJ45sDXFiWIZ858fNzUiEgIgVme2ETnqMINE1Ee7WsA/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1twW57_d5f1G32GtcxYp-A2u2OsnQF3kF%2Fview%3Fusp%3Dsharing

Moreover, it is worth mentioning that this specific subject had profound global 
atrophy with diagnosis of Alzheimer's.


As always, I appreciate your time and help.

Kind regards,

Ela






Yendiki, 
Anastasia
 Wed, 29 Jun 2022 08:41:26 
-0700

Any chance that part of the left CST is truncated in this one subject? E.g., if
the top part of the brain was outside the field of view?

Anastasia.
___


From: Salar Dini, Elaheh 
Sent: Wednesday, June 29, 2022 11:38 AM
To: Freesurfer support list 
Subject: trac-all -prep -c ERROR

Dear experts,

I am running TRACULA for 90 subjects. Exceptionally, for one of the subjects, I 
get the following error in -prep step:

((INFO: Distances between consecutive points in test subject's space are 10 13 
12 13 13 12
WARN: Could not find satisfactory control point fit - try 17034
Writing output files to 
/home2/am2359/fs6_data/TRACULA/subjects_dir/47/dlabel/syn/lh.cst_avg16_syn_bbr_*
Writing spline volume to 

Re: [Freesurfer] Problem with sxconcat-sess

[Wighton, Paul]

Hi Noah,

These dof files were not created by recon-all.  I was hoping there would be 
other log files in the scripts directory describing the functional analysis.

I have no idea what these dof files are, but they look to be either inputs to 
or outputs from a first-level BOLD analysis.  Does the term 'PCC_Bold' mean 
anything to you?

Can you share one of these dof files so we can see what they look like?

-Paul



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shapiro, Noah Lorenz 

Sent: Wednesday, June 29, 2022 4:10 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Problem with sxconcat-sess

Hi Paul,

Thanks for your suggestion.

I examined all files within the /script directory from recon-all from two 
subjects where one subject created a dof, and another did not generate a dof. I 
used the vimdiff command to explore differences in the files. There were 
significant differences in three of the log files (from each subject); please 
be aware that I am new to FreeSurfer, and I am not sure what these differences 
indicate. For your convenience, I attached the files (.zip) and deidentified 
subject-specific information with "Subject_with_dof" or "Subject_with_no_dof".

What can I do to create the dof files to carry on with my analyses? Any 
suggestions are very much appreciated.

Thank you in advance for your help.

Best wishes,
Noah

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Wighton, Paul 

Sent: 28 June 2022 11:10
To: Freesurfer support list 
Subject: Re: [Freesurfer] Problem with sxconcat-sess

Hi Noah,

I'm not super familiar with the functional stream, but it looks like something 
has gone wrong during the first-level analysis for some of your subjects.

Can you compare the log files in the ./scripts directory for a subject that has 
the dof files vs a subject that doesn't and post any differences you find?

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shapiro, Noah Lorenz 

Sent: Tuesday, June 28, 2022 8:35 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Problem with sxconcat-sess

Hello,

I am trying to concatenate my functional data with the following command (Ps: I 
am relatively new to FreeSurfer):

sxconcat-sess -sf functional_ID_jun22_allSubjects -analysis PCC_Bold_R 
-contrast bilateral_isthmuscingulate_bold_config -o DMN_Right.

I get an error that says the dof file cannot be found for my 26 scans in 
$SUBJECTS_DIR. However, running:

find . -name "dof"

The dof file was created for 12 scans. I used the same analysis pipeline for 
all the scans. I searched the mailing list, and haven't found anything that 
could help my problem. Any idea why the dof was not created for all scans? How 
can I create the dof for the remaining scans? Please let me know if you need 
further details. I am using Freesurfer version 6.0.0.

Any help is very much appreciated.

Please find the terminal output below.

Best wishes,
Noah



actrumri[0]:RECONS$ echo $SUBJECTS_DIR
/autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS
actrumri[0]:RECONS$ isxconcat-sess -sf functional_ID_jun22_allSubjects 
-analysis PCC_Bold_R -contrast bilateral_isthmuscingulate_bold_config -o 
DMN_Right
DMN_Right/PCC_Bold_R/log/isxconcat.log
ERROR: cannot find 
/autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS/RIB_668_018_3_recon.long.RIB_668_018/bold/PCC_Bold_R/dof
actrumri[0]:RECONS$ find . -name "dof"
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_L/dof
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_V/dof
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_R/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_L/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_V/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_R/dof
./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_L/dof
./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_V/dof
./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_R/dof
./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_L/dof
./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_V/dof
./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_R/dof
actrumri[0]:RECONS$ isxconcat-sess -sf functional_ID_jun22_allSubjects 
-analysis PCC_Bold_L -contrast bilateral_isthmuscingulate_bold_config -o 
DMN_Left
DMN_Left/PCC_Bold_L/log/isxconcat.log
ERROR: cannot find 
/autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS/RIB_668_018_3_recon.long.RIB_668_018/bold/PCC_Bold_L/dof
actrumri[0]:RECONS$ find . -name "dof"
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_L/dof
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_V/dof
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_R/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_L/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_V/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_R/dof

Re: [Freesurfer] trac-all -prep -c ERROR

[Yendiki, Anastasia]

Hi Ela - Can you make the google doc accessible by all?

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Salar Dini, Elaheh 

Sent: Thursday, June 30, 2022 5:08 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] trac-all -prep -c ERROR


External Email - Use Caution

Thank you for the reply. For some reason, when I change the DCM file to nii and 
look at them, in majority of our subjects, the cerebellum and lower brain stem 
has been cut off, but in this specific subject, I don't think the CST is 
truncated or out of field more than any other subjects that the TRACULA steps 
have been run for without any errors. I have taken a few screenshots of both 
this subject and another one whom -prep and -bedp have been run for without any 
errors and uploaded them to google drive. Please find the link here:

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://drive.google.com/file/d/1twW57_d5f1G32GtcxYp-A2u2OsnQF3kF/view?usp=sharing

Moreover, it is worth mentioning that this specific subject had profound global 
atrophy with diagnosis of Alzheimer's.


As always, I appreciate your time and help.

Kind regards,

Ela






Yendiki, 
Anastasia
 Wed, 29 Jun 2022 08:41:26 
-0700

Any chance that part of the left CST is truncated in this one subject? E.g., if
the top part of the brain was outside the field of view?

Anastasia.
___


From: Salar Dini, Elaheh 
Sent: Wednesday, June 29, 2022 11:38 AM
To: Freesurfer support list 
Subject: trac-all -prep -c ERROR

Dear experts,

I am running TRACULA for 90 subjects. Exceptionally, for one of the subjects, I 
get the following error in -prep step:

((INFO: Distances between consecutive points in test subject's space are 10 13 
12 13 13 12
WARN: Could not find satisfactory control point fit - try 17034
Writing output files to 
/home2/am2359/fs6_data/TRACULA/subjects_dir/47/dlabel/syn/lh.cst_avg16_syn_bbr_*
Writing spline volume to 
/home2/am2359/fs6_data/TRACULA/subjects_dir/47/dlabel/syn/lh.cst_avg16_syn_bbr_cpts_7.nii.gz
Segmentation fault (core dumped)
Linux tauruspet.med.yale.edu 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 
UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Wed Jun 29 10:31:11 EDT 2022))

I am attaching the log file as well: MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be 
https://drive.google.com/file/d/1pgEmkMtk4UoELpGR2bU_Vac-2BDr-eNy/view?usp=sharing
 On a quick look, aparc+aseg seems to be properly done. Will you please help me 
to troubleshoot this if possible?

Thank you,
Ela
___
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you 

Re: [Freesurfer] trac-all -prep -c ERROR

[Salar Dini, Elaheh]

External Email - Use Caution

Thank you for the reply. For some reason, when I change the DCM file to nii and 
look at them, in majority of our subjects, the cerebellum and lower brain stem 
has been cut off, but in this specific subject, I don't think the CST is 
truncated or out of field more than any other subjects that the TRACULA steps 
have been run for without any errors. I have taken a few screenshots of both 
this subject and another one whom -prep and -bedp have been run for without any 
errors and uploaded them to google drive. Please find the link here:

https://secure-web.cisco.com/1k1b1WDzayyyD0xHY4p5-vf5EdJF_BVSuSDFQcDRugrS488ehdTeSW-0-0Jlapa98Ol5ZJ9N2omu6Bxq8qt5cYlJODgmoi845cOZDQP0D_ARPiMUYRTRLJ2W6BPuXHqlcL0D07An8slriOSp7kS8YvvJC5kWY_JBoNRUzjYIaZtBjjjZvDf-DYuRvm5bPE8MSI4Dvqbyp3mWwH-Y-C1j5xSqd_3vNPutIz6CaRAGywYjZKNiky50Oo9yBEQT1B16qkKZeLiIqvjgwT9lg0I3oIzipmUTDQHoYZYW-c8ak8ykSmTHCsrCiwIMdlf571zqWHFDIS-7M-Mj_mJaMj6JYQ7hdpFbg4d7LfTX_hlTq9HE/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1twW57_d5f1G32GtcxYp-A2u2OsnQF3kF%2Fview%3Fusp%3Dsharing

Moreover, it is worth mentioning that this specific subject had profound global 
atrophy with diagnosis of Alzheimer's.


As always, I appreciate your time and help.

Kind regards,

Ela






Yendiki, 
Anastasia
 Wed, 29 Jun 2022 08:41:26 
-0700

Any chance that part of the left CST is truncated in this one subject? E.g., if
the top part of the brain was outside the field of view?

Anastasia.
___


From: Salar Dini, Elaheh 
Sent: Wednesday, June 29, 2022 11:38 AM
To: Freesurfer support list 
Subject: trac-all -prep -c ERROR

Dear experts,

I am running TRACULA for 90 subjects. Exceptionally, for one of the subjects, I 
get the following error in -prep step:

((INFO: Distances between consecutive points in test subject's space are 10 13 
12 13 13 12
WARN: Could not find satisfactory control point fit - try 17034
Writing output files to 
/home2/am2359/fs6_data/TRACULA/subjects_dir/47/dlabel/syn/lh.cst_avg16_syn_bbr_*
Writing spline volume to 
/home2/am2359/fs6_data/TRACULA/subjects_dir/47/dlabel/syn/lh.cst_avg16_syn_bbr_cpts_7.nii.gz
Segmentation fault (core dumped)
Linux tauruspet.med.yale.edu 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 
UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Wed Jun 29 10:31:11 EDT 2022))

I am attaching the log file as well: 
https://secure-web.cisco.com/15-8S7r3lU0XDOIlrdxpOnDhx0fy3ryeu6Aqb_HnL7Ku7kLYxrk2vMN2WFQm9Rat8MkZr_jIc4MFw6tLPOiBy9FozcSwChVsqvwnJ8BL4ElBOGP1t9VfdjZkOV00dsW7ZQIoF2Pxv2NehIrYR0fuiUoFyVeJyzCPp2LJ0ncaN4Ib4cN3TU-2Yv0Lq1Hkx25lJ5L2PdMPBhijgJxRlU1u53IF0dgaFSzUJAvADnGtnfSWCRAOdKQHyn9yJwqCaVvnlaDEatp4X_xpHOAqor42tyAu-JBiAnnDpGH2w9tyfV_jiGf-RrQ-0rprnqICVFR_VDgWJ631OpA4KwmOnAhx6oNSONd5fzFphN1DKXdNln24/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1pgEmkMtk4UoELpGR2bU_Vac-2BDr-eNy%2Fview%3Fusp%3Dsharing
 On a quick look, aparc+aseg seems to be properly done. Will you please help me 
to troubleshoot this if possible?

Thank you,
Ela
___
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The information in this e-mail is intended only for the person to whom it is 
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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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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 
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Re: [Freesurfer] How to project SPM image

[Rachel Wagner]

External Email - Use Caution

Thank you so much for your response – I’m a master’s student and am really 
struggling - I’ve been stuck trying to do this for about 2 weeks now, so the 
help is so appreciated!

My results look very grainy in mricron so my supervisor wants me to keep trying 
in FreeSurfer unfortunately for me.

I uploaded a the brain.mgz volume in freeview, but I’m not sure how to add an 
overlay and project as a 3D image. Would you happen to have any ideas?

Thank you so, so much again,
Rachel Wagner

From: niels.f...@gmx.de
Sent: June 30, 2022 2:35 PM
To: 'Freesurfer support list'
Subject: Re: [Freesurfer] How to project SPM image

You don't often get email from niels.f...@gmx.de. Learn why this is 
important
Sure is, through freeview, however if you already have spm format files, it is 
much easier to use mricron

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Rachel Wagner
Gesendet: Donnerstag, 30. Juni 2022 18:18
An: Freesurfer support list 
Betreff: Re: [Freesurfer] How to project SPM image


External Email - Use Caution
Thanks very much, I will absolutely do so! Just so I know – is there not any 
way of generating such figures in Freesurfer?

From: niels.f...@gmx.de
Sent: June 30, 2022 4:47 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] How to project SPM image

You don't often get email from niels.f...@gmx.de. 
Learn why this is 
important

External Email - Use Caution
Rachel,  these figures were likely created with a software called mricron, not 
freesurfer.  Check it out :)

Holen Sie sich Outlook für 
Android


___
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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 Mass General Brigham 
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 .
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 
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Re: [Freesurfer] How to project SPM image

[niels.foit]

Sure is, through freeview, however if you already have spm format files, it
is much easier to use mricron

 

Von: freesurfer-boun...@nmr.mgh.harvard.edu
 Im Auftrag von Rachel Wagner
Gesendet: Donnerstag, 30. Juni 2022 18:18
An: Freesurfer support list 
Betreff: Re: [Freesurfer] How to project SPM image

 

External Email - Use Caution

Thanks very much, I will absolutely do so! Just so I know – is there not any
way of generating such figures in Freesurfer?

 

From: niels.f...@gmx.de  
Sent: June 30, 2022 4:47 AM
To: Freesurfer support list  
Subject: Re: [Freesurfer] How to project SPM image

 


You don't often get email from niels.f...@gmx.de 
. Learn why this is important
 



External Email - Use Caution

Rachel,  these figures were likely created with a software called mricron,
not freesurfer.  Check it out :) 

 

Holen Sie sich Outlook für Android
 

 



smime.p7s
Description: S/MIME cryptographic signature
External Email - Use Caution___
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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 Mass General Brigham 
Compliance HelpLine at 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 
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Re: [Freesurfer] How is cache.th40.pos.sig.voxel.mgh computed, exactly?

[Mark Ebden]

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.

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

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 
 on behalf of Douglas N. Greve 

Sent: Sunday, June 19, 2022 10:37 AM
To: 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 in cache.th40.pos.sig.voxel.mgh 
are computed, or where I'd look to learn this. There is a one-liner in the 
documentation
 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




[cid:part1.6uP0sXFm.v04hdL0E@mgh.harvard.edu]

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

Re: [Freesurfer] How to project SPM image

[Rachel Wagner]

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Thanks very much, I will absolutely do so! Just so I know – is there not any 
way of generating such figures in Freesurfer?

From: niels.f...@gmx.de
Sent: June 30, 2022 4:47 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] How to project SPM image

You don't often get email from niels.f...@gmx.de. Learn why this is 
important

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Rachel,  these figures were likely created with a software called mricron, not 
freesurfer.  Check it out :)

Holen Sie sich Outlook für 
Android

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Re: [Freesurfer] How to project SPM image

[niels.foit]

External Email - Use CautionRachel,  these figures were likely created with a software called mricron, not freesurfer.  Check it out :)Holen Sie sich Outlook für Android
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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 Mass General Brigham 
Compliance HelpLine at 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 
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