[Freesurfer] Figures for publication

[Asuka Toyofuku]

External Email - Use Caution

Dear Freesurfer experts,

Thanks to all the help from this community, we're finally done with GLM 
analysis(mri_glimfit) and the cluster-wise correction (mri_glmfit_sim), and now 
I'm making figures for publication.

My question is

  1.
Which output mgh files are commonly used for making figures for publication? Do 
people use, for example, cache.th40.abs.sig.cluster.mgh (cluster-wise corrected 
map: overlay) or cache.th40.abs.sig.masked.mgh (uncorrected sig values masked 
by the clusters that survive correction) or even uncorrected ones, such as 
sig.mgh file in the contrast directory before running the correction? From my 
impression, not many people use e.g., cache.th40.abs.sig.cluster.mgh (which 
shows no colour gradation inside the clusters)...
  2.
How do you select the colour-bar cut-off and max values? Most publications I 
saw use min cut-off value: -log10(p) = 2.00 and max: -log10(p) = 5.00, but some 
uses min: p=0.05 and max: p=0.01. Obviously, if you set the max value (with the 
configure section) very low (e.g., 2.0), the size of the cluster gets bigger 
and looks more significant. Are there any suggestions for setting the 
configure/threshold for the figures?

Many thanks,
Asuka


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Re: [Freesurfer] Creating a custom registration template with FreeSurfer template

[Asuka Toyofuku]

External Email - Use Caution

Hi, thanks for your suggestion.

I added .mgh at the end of the input and output file, but I got a different 
type of error.

for d in Teen*
> do mris_preproc --surfreg sphere.reg.teenheart_average_template.mgh --s $d 
> --hemi lh --out lh.surfreg.teenheart_average_template.thickness.mgh --meas 
> thickness
> done
ERROR: cannot find fsaverage in /media/m-ssd5/FS7_Teen
ERROR: cannot find fsaverage in /media/m-ssd5/FS7_Teen
ERROR: cannot find fsaverage in /media/m-ssd5/FS7_Teen
...

Do we need the fsaverage folder when creating a custom template?
There is for example, lh.fsaverage.sphere.reg file in addition to 
sphere.reg.teenheart_average_template.

The previous error was ; ERORR: format for 
lh.surfreg.teenheart_average_template.thickness not recognized.
This time, the problem seems to lie in not having fsaverage folder, rather than 
the format for the thickness template?

Any input is appreciated.

Best,
Asuka

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: 26 February 2024 18:22
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Creating a custom registration template with 
FreeSurfer template

You need to specify a format for the output (eg, ...thickness.mgz)

On 2/26/2024 10:31 AM, Asuka Toyofuku wrote:

External Email - Use Caution

Hi, many thanks for your reply.
Here's the terminal output;

asuka@rigi:/media/.../FS7_Teen$<mailto:asuka@rigi:/media/.../FS7_Teen$> for d 
in Teen* EPK* epk*
> do mris_preproc --surfreg sphere.reg.teenheart_average_template --s $d --hemi 
> lh --out lh.surfreg.teenheart_average_template.thickness --meas thickness
> done
ERROR: format for lh.surfreg.teenheart_average_template.thickness not recognized
ERROR: format for lh.surfreg.teenheart_average_template.thickness not recognized
ERROR: format for lh.surfreg.teenheart_average_template.thickness not recognized
ERROR: format for lh.surfreg.teenheart_average_template.thickness not recognized
ERROR: format for lh.surfreg.teenheart_average_template.thickness not recognized

Error continued so I stopped running at a certain point.
What do you think?

Best regards,
Asuka

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
Sent: 23 February 2024 19:30
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Creating a custom registration template with 
FreeSurfer template

Can you include the full terminal output for one of the mris_preproc commands 
that is failing?

On 2/22/2024 7:12 AM, Asuka Toyofuku wrote:
External Email - Use Caution

Dear Freesurfer experts,


I have issues with creating a custom registration template. (I'm following this 
instruction: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
be<https://secure-web.cisco.com/1_qfYxT5WNAR-lGRNh895Kl4pqE513hIRdGqZt0w-oDRR8NwLSUh8ataurmByizdN5-6NPpWldetuOVhBt0OSuQVw_fTGTUnlfnRy5cZOC8gQ6xkn-I0sETntn5X7pssvIBMvxipctrdnnR0sdsJ_SEe-szwdE6WbG2z6qSW6mRoR1O_TSBtVJN6id4aZVTo30KwQes1T6AeGXG7volizYQI0te7HhF9DiqFp19oym11wqmrG8OvtY5FBou3V7ihQabCPQZdP81Qr6NFvLvkDT-D9iLBlRl7VIvT9MFviOs55EDcMS1LivQnETY_fTpuV_tnuLQHAkyphGLkrH_xwYA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSurfaceRegAndTemplates>MailScanner
 has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
be  
https://secure-web.cisco.com/14_cfpLH54kbz6PNtpkLs-Zg-Ukn75DgTKnHN1F2RhmFAPqEO2oFAt9z7Rt8DN3qE8Vx8Z69ZCf1dbuR6b9KyjxmM7OAubbfbHwVGiFo1brthkj4C6-4cmr2gsJw8r6PNj4x7DhwbEp0rzUROv1nBUjyJgxhf3oNzp7DuAZjVEUGuzqGNvaTes_v0KmnGwEwvFZZUZ7REfx9bhCfQJU7q19kFpwu_ZatHCHy6ptOhNA-MXfr_8ccKaarmPWgNLlVbnY6-tHRJFK0DlREflGkvACa4zHfpwKpu7wNSUkdJn51l2pHRZRay5l3DkiqtjK2IBhoTK3BWlpCHvZPPyEX23A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSurfaceRegAndTemplates<https://secure-web.cisco.com/1_qfYxT5WNAR-lGRNh895Kl4pqE513hIRdGqZt0w-oDRR8NwLSUh8ataurmByizdN5-6NPpWldetuOVhBt0OSuQVw_fTGTUnlfnRy5cZOC8gQ6xkn-I0sETntn5X7pssvIBMvxipctrdnnR0sdsJ_SEe-szwdE6WbG2z6qSW6mRoR1O_TSBtVJN6id4aZVTo30KwQes1T6AeGXG7volizYQI0te7HhF9DiqFp19oym11wqmrG8OvtY5FBou3V7ihQabCPQZdP81Qr6NFvLvkDT-D9iLBlRl7VIvT9MFviOs55EDcMS1LivQnETY_fTpuV_tnuLQHAkyphGLkrH_xwYA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSurfaceRegAndTemplates>
 )


According to the instructions, we need to

1) Create an average subject (Creates $SUBJECTS_DIR/newtemplate)

2) Register each subject to the new template (do for both lh and rh), resulting 
in lh.sphere.reg.newtemplate and rh.sphere.reg.newtemplate
3) Get thickness values in the newtemplate space for GLM analysis
4) Create another average templat

Re: [Freesurfer] Creating a custom registration template with FreeSurfer template

[Asuka Toyofuku]

External Email - Use Caution

Hi, many thanks for your reply.
Here's the terminal output;

asuka@rigi:/media/.../FS7_Teen$ for d in Teen* EPK* epk*
> do mris_preproc --surfreg sphere.reg.teenheart_average_template --s $d --hemi 
> lh --out lh.surfreg.teenheart_average_template.thickness --meas thickness
> done
ERROR: format for lh.surfreg.teenheart_average_template.thickness not recognized
ERROR: format for lh.surfreg.teenheart_average_template.thickness not recognized
ERROR: format for lh.surfreg.teenheart_average_template.thickness not recognized
ERROR: format for lh.surfreg.teenheart_average_template.thickness not recognized
ERROR: format for lh.surfreg.teenheart_average_template.thickness not recognized

Error continued so I stopped running at a certain point.
What do you think?

Best regards,
Asuka

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: 23 February 2024 19:30
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Creating a custom registration template with 
FreeSurfer template

Can you include the full terminal output for one of the mris_preproc commands 
that is failing?

On 2/22/2024 7:12 AM, Asuka Toyofuku wrote:
External Email - Use Caution

Dear Freesurfer experts,


I have issues with creating a custom registration template. (I'm following this 
instruction: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
be<https://secure-web.cisco.com/1_qfYxT5WNAR-lGRNh895Kl4pqE513hIRdGqZt0w-oDRR8NwLSUh8ataurmByizdN5-6NPpWldetuOVhBt0OSuQVw_fTGTUnlfnRy5cZOC8gQ6xkn-I0sETntn5X7pssvIBMvxipctrdnnR0sdsJ_SEe-szwdE6WbG2z6qSW6mRoR1O_TSBtVJN6id4aZVTo30KwQes1T6AeGXG7volizYQI0te7HhF9DiqFp19oym11wqmrG8OvtY5FBou3V7ihQabCPQZdP81Qr6NFvLvkDT-D9iLBlRl7VIvT9MFviOs55EDcMS1LivQnETY_fTpuV_tnuLQHAkyphGLkrH_xwYA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSurfaceRegAndTemplates>
 
https://secure-web.cisco.com/14OtCqttBqWbYfCMoChsBvplhJCm7DA2sZ2-eErVNHV_OGYKSMTYomS5-MKzc9smNvjmbLFDxPbiXqCpxna-AEp0j7CdalRRmlrmAtR1b6_kL17vl7ig9z-4jQNbOsxWkb1vtpkaf34KiKlbNFKXPZfB-ckg0Oy8VPigj7BG3M3ruIEOncIkWgsAHzcW3PzaQifRZrQMe7GErLPfCnvyrrxwRKRHspJjz8_ZANkmUeOMOZbvvCIemLI3RTSIxmt9MhdpB3lJqfrQ6AZas7103xqUPeogxsq3VBSD6ILXqk7TVU9cnDpGoE7YLio_5AinktX0JD8odbBBm7blLAhvZwg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSurfaceRegAndTemplates<https://secure-web.cisco.com/1_qfYxT5WNAR-lGRNh895Kl4pqE513hIRdGqZt0w-oDRR8NwLSUh8ataurmByizdN5-6NPpWldetuOVhBt0OSuQVw_fTGTUnlfnRy5cZOC8gQ6xkn-I0sETntn5X7pssvIBMvxipctrdnnR0sdsJ_SEe-szwdE6WbG2z6qSW6mRoR1O_TSBtVJN6id4aZVTo30KwQes1T6AeGXG7volizYQI0te7HhF9DiqFp19oym11wqmrG8OvtY5FBou3V7ihQabCPQZdP81Qr6NFvLvkDT-D9iLBlRl7VIvT9MFviOs55EDcMS1LivQnETY_fTpuV_tnuLQHAkyphGLkrH_xwYA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSurfaceRegAndTemplates>
 )


According to the instructions, we need to

1) Create an average subject (Creates $SUBJECTS_DIR/newtemplate)

2) Register each subject to the new template (do for both lh and rh), resulting 
in lh.sphere.reg.newtemplate and rh.sphere.reg.newtemplate
3) Get thickness values in the newtemplate space for GLM analysis
4) Create another average template based on the previous one: (Creates 
$SUBJECTS_DIR/newnewtemplate)

I'm stuck with the 3) command.
Instruction suggests:
mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s subj3 ...

and this is my code:
for d in Teen*
do mris_preproc --surfreg sphere.reg.teenheart_average_template --s $d --hemi 
lh --out lh.surfreg.teenheart_average_template.thickness --meas thickness
done


( I specified hemi and output because, without it, I got ERROR: no source hemi 
specified)

My command led to an error saying:

ERROR: format for lh.surfreg.teenheart_average_template.thickness not recognized

So my questions are:

a) what does it mean that "format for lh.surfreg.average_template.thickness not 
recognised"? Any ideas on how to fix this?

b) Does this mris_preproc --surfreg command produce different smoothing mgh 
files? (e.g., fwhm10, fwhm15, fwhm20...?)

Because standard mris_preproc before GLM analysis(MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to 
be<https://secure-web.cisco.com/1lH2n5girv1pSO3WmL3I9nDeL07oFU0ViiAmz_tUClrPQjFwGxFIj8Uw-HpRNXN4_ADUrXeK8GQcI91O76PQUoilqcBBTuz_cbBfg2BUYMoPChwgcqvL5jiL3mJuCIhROFLqmz6Ay1m-Mt3VqQfQiArWs7KPRzGvA7altNpSDzxPE8sB-_TlC3JKVV06-mzVggUwD3kS7BkRaXe1z174NmNbHyzHlcoUEX12pXebgZgGEv6bLiKxH2Wrka404J_vPCmOb8me-0QbLp1HJJdw_vbklt9SSNhdXnR2XCQ-vZeRZep_w5lp7gvo-TBU4Fdow4MtnGe-Oy6yM7OBUf0230w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis>
 
https://secure-web.cisco.com/1jQn6upf-Qs0NdxKH7O3JdL3Jjn4FvRFaY6TsuQty9xVFrwvKo8BUspg0x389Ldjw2iExC-LOFBlmmTK0G06VqctOvwX-Ck3Vno2_YSNuvJzCVxmNxdOEyFFrP11fMesdpLmGo_PUgySenoZrNrJgsicBx2OzZgMwYPlsiGcilISeEFnzTIx8X1KhJIlSY

[Freesurfer] Creating a custom registration template with FreeSurfer template

[Asuka Toyofuku]

External Email - Use Caution

Dear Freesurfer experts,


I have issues with creating a custom registration template. (I'm following this 
instruction: 
https://secure-web.cisco.com/1_qfYxT5WNAR-lGRNh895Kl4pqE513hIRdGqZt0w-oDRR8NwLSUh8ataurmByizdN5-6NPpWldetuOVhBt0OSuQVw_fTGTUnlfnRy5cZOC8gQ6xkn-I0sETntn5X7pssvIBMvxipctrdnnR0sdsJ_SEe-szwdE6WbG2z6qSW6mRoR1O_TSBtVJN6id4aZVTo30KwQes1T6AeGXG7volizYQI0te7HhF9DiqFp19oym11wqmrG8OvtY5FBou3V7ihQabCPQZdP81Qr6NFvLvkDT-D9iLBlRl7VIvT9MFviOs55EDcMS1LivQnETY_fTpuV_tnuLQHAkyphGLkrH_xwYA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSurfaceRegAndTemplates
 )


According to the instructions, we need to

1) Create an average subject (Creates $SUBJECTS_DIR/newtemplate)

2) Register each subject to the new template (do for both lh and rh), resulting 
in lh.sphere.reg.newtemplate and rh.sphere.reg.newtemplate
3) Get thickness values in the newtemplate space for GLM analysis
4) Create another average template based on the previous one: (Creates 
$SUBJECTS_DIR/newnewtemplate)

I'm stuck with the 3) command.
Instruction suggests:
mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s subj3 ...

and this is my code:
for d in Teen*
do mris_preproc --surfreg sphere.reg.teenheart_average_template --s $d --hemi 
lh --out lh.surfreg.teenheart_average_template.thickness --meas thickness
done


( I specified hemi and output because, without it, I got ERROR: no source hemi 
specified)

My command led to an error saying:

ERROR: format for lh.surfreg.teenheart_average_template.thickness not recognized

So my questions are:

a) what does it mean that "format for lh.surfreg.average_template.thickness not 
recognised"? Any ideas on how to fix this?

b) Does this mris_preproc --surfreg command produce different smoothing mgh 
files? (e.g., fwhm10, fwhm15, fwhm20...?)

Because standard mris_preproc before GLM 
analysis(https://secure-web.cisco.com/1lH2n5girv1pSO3WmL3I9nDeL07oFU0ViiAmz_tUClrPQjFwGxFIj8Uw-HpRNXN4_ADUrXeK8GQcI91O76PQUoilqcBBTuz_cbBfg2BUYMoPChwgcqvL5jiL3mJuCIhROFLqmz6Ay1m-Mt3VqQfQiArWs7KPRzGvA7altNpSDzxPE8sB-_TlC3JKVV06-mzVggUwD3kS7BkRaXe1z174NmNbHyzHlcoUEX12pXebgZgGEv6bLiKxH2Wrka404J_vPCmOb8me-0QbLp1HJJdw_vbklt9SSNhdXnR2XCQ-vZeRZep_w5lp7gvo-TBU4Fdow4MtnGe-Oy6yM7OBUf0230w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis)
 are done with previously qcashed data (e.g., need thickness.fwhm10.fsaverage 
to run mris_preproc), but at this point, I don't have any of these thickness 
files with different smoothing levels.

c ) If this mris_preproc --surfreg command does not generate a set of thickness 
maps in **newtemplate space** at different smoothing levels, what kind of 
command should I run?


Any input is appreciated!


Best regards,

Asuka
___
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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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Re: [Freesurfer] make_average_subject command error

[Asuka Toyofuku]

External Email - Use Caution

Dear Yujing,

Thank you so much for your help.
It turned out the link was missing when we copied our subject data from the web 
server to the drive.
(I tried your command to create the link, but it did not work, making us 
realise something was wrong elsewhere.)

Many thanks!

Best,
Asuka




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: 07 February 2024 14:33
To: Freesurfer support list 
Subject: Re: [Freesurfer] make_average_subject command error


If you run recon-all, ?h.pial will appear as symbolic links to ?h.pial.T1.  
Here is the list of symbolic links you should find in your subject/surf 
directory:



rh.pial -> rh.pial.T1

lh.pial -> lh.pial.T1

rh.fsaverage.sphere.reg -> rh.sphere.reg

lh.fsaverage.sphere.reg -> lh.sphere.reg

rh.white.K -> rh.white.preaparc.K

rh.white.H -> rh.white.preaparc.H

lh.white.K -> lh.white.preaparc.K

lh.white.H -> lh.white.preaparc.H



I’m wondering why the symbolic links are not created.



To create the symbolic links,

1. cd to subject/surf directory

2. run ln command to create each link, for example, ‘ln -s lh.pial.T1 lh.pial’



Best,



Yujing





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Asuka Toyofuku
Sent: Wednesday, February 7, 2024 5:13 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] make_average_subject command error



External Email - Use Caution

Dear Freesurfer experts,



We're trying to make an average subject for group analysis using Freesurfer 
7.1, but the make_average_subject command exits with errors after calling 
make_average_surf:



MakeAverageSurf(): 129 lh pial sphere.reg talairach.xfm 1 1



It appears to be trying to find the lh.pial surface for the first participant, 
but this file is named "lh.pial.T1". (In FS 5.3 and 6.0, this file was labelled 
"lh.pial", but with FS7.1, it seems to be named lh.pial.T1).



Does anyone have a suggestion for how to fix this problem? (We want to avoid 
changing all the file names to "lh.pial" from "il.pial.T1")

Should we call make_average_subject again with -no-surf-to-surf ?



Best regards,

Asuka
___
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. 

Re: [Freesurfer] Freesurfer recon-all qcache partial failure

[Asuka Toyofuku]

External Email - Use Caution

Dear Yujing,

Thank you for your kind help (and sorry for my late reply).
It worked with the added flag; - measures thickness.
I appreciate your advice on adding directives at the end of the recon-all 
command.

Best,
Asuka

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: 16 January 2024 13:41
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer recon-all qcache partial failure


The command should look like this ‘recon-all -s subjid -qcache -all -i 
input-file’





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Asuka Toyofuku
Sent: Monday, January 15, 2024 9:45 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer recon-all qcache partial failure



External Email - Use Caution

Dear Yujing,



Thank you very much for your kind help.



So, you're saying I need more directive other than -qcashe?

My command was;

for d in Te* te* EPK* epk*

do recon-all -s $d -qcache

done



Do you think I should add another directive, such as -all or -autorecon-all?

So, the command line looks like this?

recon-all -s -subjid -qcashe - autorecon-all



I ran recon-all -qcashe not on the fsaverage folder, but in the SUBJECT_DIR.

In the previous post, I attached the wrong recon-all log (which was from 
fsaverage>scripts folder), but now I'm attaching the recon-all log file from a 
random subject folder.

Could you please look and check this recon-all as well?

Many thanks!



Best,

Asuka





From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: 12 January 2024 14:24
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer recon-all qcache partial failure



Your recon-all command doesn’t have the directive to tell it what to run. You 
also need to specify input files for your initial run.  See this wiki page for 
detail MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
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The recon-all.log attached contains runs between 2009 and 2010 on subject 
‘fsaverage’.



‘fsaverage’ is an average subject comes with Freesurfer distribution in 
$FREESURFER_HOME/subjects/. fsaverage is a template brain based on a 
combination of 40 MRI scans of real brains. It can be used as a common space 
for group comparison. You don’t want to run recon-all on it.



Your SUBJECTS_DIR should not set to your Freesurfer download/install directory. 
Set it to some other directory where you have the write permission.



You should see ‘fsaverage’ as a symbolic link in your SUBJECTS_DIR.



Best,



Yujing







From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Asuka Toyofuku
Sent: Friday, January 12, 2024 4:31 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Freesurfer recon-all qcache partial failure



External Email - Use Caution

Dear Freesurfer researchers,



I have an issue with recon-all-qcashe results. (please find the recon-all.log 
attached.)

The command created fsaverage mgh files (e.g., lh.thickness.fsaverage.mgh), but 
it did not create fsaverage files with different smoothing levels (e.g.,  
lh.thickness.fwhm10.fsaverage.mgh, lh.thickness.fwhm15.fsaverage.mgh, 
lh.thickness.fwhm20.fsaverage.mgh...etc) in the individual subject "surf" 
folder.



I used the command below:

for d in Te* te* EPK* epk*

do recon-all -s $d -qcache

done



(Subjects names start from either Te, te, EPK or epk)

For several subjects with failed recon-all commands, I re-ran the command 
individually:

 recon-all -s subjectname -qcashe



(output from the terminal window)

It could also be that recon-all was running at one point but died in an 
unexpected way.

If i

[Freesurfer] make_average_subject command error

[Asuka Toyofuku]

External Email - Use Caution

Dear Freesurfer experts,


We're trying to make an average subject for group analysis using Freesurfer 
7.1, but the make_average_subject command exits with errors after calling 
make_average_surf:


MakeAverageSurf(): 129 lh pial sphere.reg talairach.xfm 1 1


It appears to be trying to find the lh.pial surface for the first participant, 
but this file is named "lh.pial.T1". (In FS 5.3 and 6.0, this file was labelled 
"lh.pial", but with FS7.1, it seems to be named lh.pial.T1).


Does anyone have a suggestion for how to fix this problem? (We want to avoid 
changing all the file names to "lh.pial" from "il.pial.T1")
Should we call make_average_subject again with -no-surf-to-surf ?

Best regards,
Asuka
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[Freesurfer] Freesurfer recon-all qcache partial failure

[Asuka Toyofuku]

External Email - Use Caution

Dear Freesurfer researchers,


I have an issue with recon-all-qcashe results. (please find the recon-all.log 
attached.)

The command created fsaverage mgh files (e.g., lh.thickness.fsaverage.mgh), but 
it did not create fsaverage files with different smoothing levels (e.g.,  
lh.thickness.fwhm10.fsaverage.mgh, lh.thickness.fwhm15.fsaverage.mgh, 
lh.thickness.fwhm20.fsaverage.mgh...etc) in the individual subject "surf" 
folder.


I used the command below:

for d in Te* te* EPK* epk*
do recon-all -s $d -qcache
done

(Subjects names start from either Te, te, EPK or epk)

For several subjects with failed recon-all commands, I re-ran the command 
individually:

 recon-all -s subjectname -qcashe


(output from the terminal window)

It could also be that recon-all was running at one point but died in an 
unexpected way.
If it is the case that there is a process running, you can kill it and start 
over or just let it run.
If the process has died, you should type:
 rm 
/media/m-proc/Vol03/FREESURFER7_SUBJECTS/teen_subject_name/scripts/IsRunning.lh+rh
**Try to copy the line and then rerun again with the quche code.


I'm currently using

freesurfer-x86_64-redhat-linux-gnu-dev4-20090216.

Do you have any ideas why the command did not produce different fwhm files?
I'm thinking about re-running the recon-all again, so I would appreciate it if 
you could help me modify the commands.
Thank you very much in advance.



Best regards,

Asuka




recon-all.log
Description: recon-all.log
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