Re: [Freesurfer] recon-all errors (cannot execute binary file +

[김민지]

External Email - Use Caution

 do not wish to continue communication over unencrypted e-mail, 

-Original Message-From:  "김민지" To: 
"Freesurfer support list" ; Cc:Sent:  
2024-01-17 (수) 13:01:17 (UTC+09:00)Subject: Re: [Freesurfer] recon-all errors 
(cannot execute binary file 
+External Email - Use 
Caution

 do not wish to continue communication over unencrypted e-mail



-Original Message-From:  "윤혜정" To: 
"Freesurfer support list" ; Cc:Sent:  
2024-01-17 (수) 10:49:56 (UTC+09:00)Subject: [Freesurfer] recon-all errors 
(cannot execute binary file 
+External Email - Use 
Caution

Good day.

When I run recon-all for my nii files I get either one of the following error 
messages:

1. ERROR: could not configure recon-all parameters Killed 

2. ERROR: could not configure recon-all parameters 
/Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: cannot execute binary file 
/Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: Undefined error: 0

Or 

3. a Pop Up message "_struct.cpython-38-darwin.so" cannot be opened because the 
developer cannot be verified. 
mac OS cannot verify that this app is free from malware. 

I googled the third error message and tried "Allow anyways" from the privacy 
setting. Then the next message pops up, then the next and the next. 

Could you please help me to understand the cause of the above 3 error 
messages? 
I tried to redownload freesurfer as well as python but none worked. 

Thank you in advance. 

Best,
Alice mailto:hyejung7...@amc.seoul.kr

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Re: [Freesurfer] recon-all errors (cannot execute binary file +

[김민지]

External Email - Use Caution

 do not wish to continue communication over unencrypted e-mail



-Original Message-From:  "윤혜정" To: 
"Freesurfer support list" ; Cc:Sent:  
2024-01-17 (수) 10:49:56 (UTC+09:00)Subject: [Freesurfer] recon-all errors 
(cannot execute binary file 
+External Email - Use 
Caution

Good day.

When I run recon-all for my nii files I get either one of the following error 
messages:

1. ERROR: could not configure recon-all parameters Killed 

2. ERROR: could not configure recon-all parameters 
/Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: cannot execute binary file 
/Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: Undefined error: 0

Or 

3. a Pop Up message "_struct.cpython-38-darwin.so" cannot be opened because the 
developer cannot be verified. 
mac OS cannot verify that this app is free from malware. 

I googled the third error message and tried "Allow anyways" from the privacy 
setting. Then the next message pops up, then the next and the next. 

Could you please help me to understand the cause of the above 3 error 
messages? 
I tried to redownload freesurfer as well as python but none worked. 

Thank you in advance. 

Best,
Alice mailto:hyejung7...@amc.seoul.kr

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Re: [Freesurfer] recon-all errors (cannot execute binary file +

[fsbuild]

External Email - Use Caution

It looks like you did not use the .pkg file installer to install Freesurfer on 
the Mac, otherwise you would have a path like /Applications/freesurfer/7.4.1 to 
use as FREESURFER_HOME.  The installer should ensure the privileges should 
be correct to run commands.   There are several 7.X freesurfer releases, 
but the latest release is 7.4.1 and you can download it via the link, e.g.,
https://secure-web.cisco.com/1bTTDiznaFEJgJPDoi2yskrFqRdt_lNsr8LZ0PFjdBlc19JuHE6WaWHssFDdzwRLVMRUHA3qj7h4ea64BhZk97t2IniNpnSEBUfevruwnZRT-WXrHBzlmbnxwfB-eUVqRKZYuKEwgZupdFOKnrwiz0xxPKw5DTxfL31t8mtljoZBWCtHjo8uXtSylGlGyZRzw2b6Kjz5JBf1zzrJTR_GSBoP7UPjKW3-cqENylh36UvAaYHpdFnPoZ4CrWPzQwkw7vmD7cmQcG6jBsy_w7nUkvkrhCZTYVfLg5BUluX8L0H85LGn_CikykHFVbAsE-L8Zih6Q9g6D25IvisceU2Rl_g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-macOS-darwin_x86_64-7.4.1.pkg
I would first remove what you have on your system from the terminal window with,
$ sudo rm -rf /Applications/freesurfer
Then in a Finder Window navigate to the Downloads folder (or to wherever you 
downloaded freesurfer-macOS-darwin_x86_64-7.4.1..pkg).  You should be able 
to RIGHT CLICK on that file, select open with the default pkg installer, and 
then enter your password etc. to install it.  Right clicking should bypass 
having to do some of the security exemptions in system preferences.
Once the install is complete, setup the Freesurfer environment in the terminal 
window,
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh 
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.4.1
FSFAST_HOME       /Applications/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /Applications/freesurfer/7.4.1/subjects
MNI_DIR         
  /Applications/freesurfer/7.4.1/mni
You also need a license file, license.txt.  Once you complete the license 
request form 
at https://secure-web.cisco.com/1Svw39fuKLV2rL8mAOfpPDMZrLLodE_ScR0sKC5od9QRlt9jwKuDUSQ6WtLlT9V17W1wUaBdznmlv7nMRbyPA6LYSYXyCAnP8F-Tuz_VE6STeVAxkh40QhJ8_Hz3w6xgC49SELup9uGscJnea_a5_YfPe4v_s5sGckdUErRUBLgOMN41ow4CikTKbC-IfUIre0ikhv0rLYF0iFjK9EZGFCuzHN7-z5cvA1mPBIjRTyGJsmV-behjR7Zpaho6a5uOuq1I4CB61WxtecgERQIEuY6PCEpMSMO1vfX-v7GEXY61w_SZ_5yg0kRQoolU2kwNaTPReDO7q7kH9B3AAFtRMPQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html%26nbsp;you
 will receive a file “licesne..txt” via the email address used in the form. 
  Download/copy the license.txt file to your machine from the email.
If your home directory is for example /Users/hyejung then you will see the 
following in the terminal window,
$ cd$ pwd/Users/hyejung$ echo $HOME/Users/hyejung
… if you downloaded license.txt into your Download folder ...
$ cd Downloads$ ls license.txtlicense.txt$ cp -p -f  license.txt 
 $HOME/.$ cd $HOME$ ls license.txtlicense.txt
You could also use the Finder to navigate and drag/drop the license.txt into 
your home directory.   Once it it there, set the environment variable 
FS_LICENSE so freesurfer commands will find the license when they run,
$ export FS_LICENSE=$HOME/license.txt
Then it should work to run freesurfer commands from the terminal window 
including freeview.
- R.

On Jan 16, 2024, at 20:47, 윤혜정  
wrote:External Email - Use 
CautionGood day.When I run 
recon-all for my nii files I get either one of the following error 
messages:1. ERROR: could not configure recon-all parameters 
Killed 2. ERROR: could not configure recon-all 
parameters /Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: cannot execute binary 
file /Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: Undefined error: 0Or 3. a Pop 
Up message "_struct.cpython-38-darwin.so" cannot be opened because the 
developer cannot be verified. mac OS cannot verify that this app is free 
from malware. I googled the third error message and tried "Allow 
anyways" from the privacy setting. Then the next message pops up, 
then the next and the next. Could you please help me to understand the 
cause of the above 3 error messages? I tried to redownload freesurfer as 
well as python but none worked. Thank you in 
advance. Best,Alice___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] recon-all errors (cannot execute binary file +

[윤혜정]

External Email - Use Caution

Good day.

When I run recon-all for my nii files I get either one of the following error 
messages:

1. ERROR: could not configure recon-all parameters Killed 

2. ERROR: could not configure recon-all parameters 
/Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: cannot execute binary file 
/Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: Undefined error: 0

Or 

3. a Pop Up message "_struct.cpython-38-darwin.so" cannot be opened because the 
developer cannot be verified. 
mac OS cannot verify that this app is free from malware. 

I googled the third error message and tried "Allow anyways" from the privacy 
setting. Then the next message pops up, then the next and the next. 

Could you please help me to understand the cause of the above 3 error messages? 
I tried to redownload freesurfer as well as python but none worked. 

Thank you in advance. 

Best,
Alice​

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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Issue with mri_brainvol_stats for only some participants

[Huang, Yujing]

Can you attach recon-all.log of a failing subject?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Carly McIntyre-Wood
Sent: Tuesday, January 16, 2024 4:37 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Issue with mri_brainvol_stats for only some participants


External Email - Use Caution
Hi there,

I've come across a strange issue while running some new participants through 
Freesurfer 7.3.

A portion of participants (30%) are missing their stats files, although I have 
visually inspected the segmentation using Freeview and they look great. I have 
rerun autorecon3 and it only fixes the problem for select subjects. The exact 
error is below:


mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 
../surf/rh.thickness

   Update not needed

\n mri_brainvol_stats 1096 \n

Segmentation fault

I found one instance of this in the archives where someone recommended running:

recon-all -s subject -segstats -parcstats -parcstats2 -parcstats3 -wmparc 
-balabels

However, this command exits at the same point with the same error.

Thanks so much,
Carly
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[Freesurfer] Issue with mri_brainvol_stats for only some participants

[Carly McIntyre-Wood]

External Email - Use Caution

Hi there, 
 
I’ve come across a strange issue while running some new participants through Freesurfer 7.3.
 
A portion of participants (30%) are missing their stats files, although I have visually inspected the segmentation using Freeview and they look great. I have rerun autorecon3 and it only fixes the problem for select subjects.
 The exact error is below:
 
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness
   Update not needed
\n mri_brainvol_stats 1096 \n
Segmentation fault
 
I found one instance of this in the archives where someone recommended running:
 

recon-all -s subject -segstats -parcstats -parcstats2 -parcstats3 -wmparc -balabels

 
However, this command exits at the same point with the same error.
 
Thanks so much,
Carly




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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Freeview crashes when trying to load volumes

[Wang, Ruopeng]

I would also check if the license file is installed properly.

On Jan 15, 2024, at 7:06 PM, fsbuild 
mailto:fsbu...@contbay.com>> wrote:


External Email - Use Caution


It would help for us to know what your machine is running, e.g., linux or MacOS 
(Intel or Silicon Mac) - and what the version is for the operating system, e.g. 
Linux Ubuntu 22, MacOS 12, etc.  If you are running Linux on Windows thru 
either WSL or a VM then please mention that and if the Windows host is running 
Win 10 or 11.

- R.

On Jan 12, 2024, at 11:52, Ford, Jamie K 
mailto:j.f...@imperial.ac.uk>> wrote:

External Email - Use Caution

Hello,

Please could I get some advice on my installation? I've downloaded version 
7.4.0 using the same steps described in the installation video MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
behttps://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall?action=AttachFile&do=get&target=installFS_demo.mp4

Everything seems fine until I try to load any sort of volume, e.g., a Bert MRI 
file (like on the video). Freeview then crashes. This is the same for any 
volume.

Could someone please advice? Any guidance would be greatly appreciated.


Many Thanks,

Jamie


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Re: [Freesurfer] Sample registration question

[Douglas N. Greve]

Yes, that would be an ROI analysis

On 1/13/2024 1:00 PM, Mirsol Choi wrote:


External Email - Use Caution

Hello,

My goal is to compare the FA and MD values of hippocampal subfields 
(only inside the hippocampus) between cognitively normal, MCI, and AD 
subjects. I am unsure if this would require a voxel wise analysis or 
an ROI analysis… to my understanding this is more of a ROI analysis 
between subjects - is this assumption incorrect?


Thank you,
Peter

On Sat, Jan 13, 2024 at 10:44 AM Douglas N. Greve 
 wrote:


So this is where I get confused on your intentions because you say
that you want to do a voxel-wise analysis of an ROI. Do you mean
you want to do a voxelwise analysis but only inside, eg, whole
hippocampus?

On 1/12/2024 6:07 PM, Mirsol Choi wrote:


External Email - Use Caution

Hello,

Sorry I should have clarified. Yes, I would like to perform
voxelwise analysis of FA and MD values of hippocampal subfield
between subjects. Is this possible with free surfer?

Thank you again for your time.

M

On Fri, Jan 12, 2024 at 4:05 PM Douglas N. Greve
 wrote:

oh, I thought you wanted to do an ROI analysis. You mean for
a voxelwise analysis?

On 1/12/2024 5:46 PM, Mirsol Choi wrote:


External Email - Use Caution

Hi there,


Following the first registration step, should I also run
another registration command to put all fa-in-subfields.mgz
for each subject onto the same space for inter subject
analysis of FA values?

Thanks again,
M

On Fri, Jan 12, 2024 at 3:00 PM Douglas N. Greve
 wrote:

Map the diffusion data to the subfield space, eg,
mri_vol2vol --mov fa.nii.gz --reg register.lta --targ
subfields.mgz --o fa-in-subfields.mgz
Then run mri_segstats
mri_segstats  --ctab-default --i fa-in-subfields.mgz
--seg subfields.mgz --sum fa-in-subfields.dat



On 1/12/2024 4:53 PM, Mirsol Choi wrote:


External Email - Use Caution

Hi there,

Is there a way to successfully obtain FA/MD values from
the hippocampus subfields?

Thank you,
M

On Fri, Jan 12, 2024 at 2:23 PM Douglas N. Greve
 wrote:

I'm not sure what you mean. The subfields are an
ROI-based analysis. Are you saying you want to do a
voxel-based analysis (without reference to ROIs)?

On 1/9/2024 12:05 PM, Mirsol Choi wrote:


External Email - Use Caution

Hi there Freesurfer,

I am currently using freesurfer to take DTI
metrics (FA, MD) from hippocampal subfields.
At this point of my exploration with freesurfer, I
am able to correctly register the hippocampal
subfields and diffusion data, and obtain my FA
values from the subfields. However, this is at the
individual subject level.

I will eventually need to register all of my
samples in the same space for me to do a group
analysis. However I am unsure what the order of
registration should be for this process to be
feasible.

Does this order seem feasible for accurate analysis?

1) recon-all all of my subjects
2) dt_recon all of my subjects (one of the outputs
is a registration file, which has registered the
DTI data to outputs of recon-all)
3) run the hippocampus segmentation command on all
subjects (segmentHA_T1.sh) to obtain hippocampal
subfield segmentation
4) register the segmentation file to the FA maps
(output of dt_recon) using vol2subfield command
5) After creating a subfield-FA map for each
subject, spatial normalize the samples onto the
same space using *mri_vol2vol*
*
*
Thank you so much for taking the time reading my
question. If there is a different method to
spatially normalizing my datasets, or if there is
a more optimal order of registration, I'd be happy
to hear from you.

Thank you,
M

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Re: [Freesurfer] Midline white/pial surface

[Douglas N. Greve]

I would also be helpful to have some pics of what you are seeing. The 
surface is not valid in the "medial well" -- ie all the non-cortical 
structures on the central sagittial plane such as thalamus an VDC.


On 1/16/2024 7:50 AM, Huang, Yujing wrote:


Can you try the troubleshooting methods from this page:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData

Best,

Yujing

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Sunniva Fenn-Moltu

*Sent:* Monday, January 15, 2024 6:35 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] Midline white/pial surface

*External Email - Use Caution *

Hi,

i'm running recon-all and have encountered an issue with the surface 
boundaries on several subjects. What I'm experiencing is that the 
midline surface is included in the white surface in one hemisphere, 
and in the pial surface on the other hemisphere. This results in the 
midline boundary of the thalamus and ventral DC being white surface in 
one hemisphere, and pial surface in the other. Do you have any idea 
why this is happening?


I am running freesurfer on NoMachine (freesurfer/7.4.1).

Best,

Sunniva


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Re: [Freesurfer] [External] Re: extracting measurements for mean gray matter thickness/LGI

[Douglas N. Greve]

why not just average them together? Or are you hoping that FS provides 
this last small step? I don't think that we do ...


On 1/16/2024 10:04 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:


External Email - Use Caution

Sorry, to be clear, there is a measurement for bilateral mean 
thickness offered by default? I'm able to gather the left mean 
thickness and the right mean thickness easily.


Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--

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


*Sent:* Friday, January 12, 2024 4:26 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* [External] Re: [Freesurfer] extracting measurements for 
mean gray matter thickness/LGI
I don't understand. Why not use the mean thickness from FS? We have an 
lGI module; we have not supported it in years, but maybe it still 
works. *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/LGI 



On 1/10/2024 9:52 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:


External Email - Use Caution

Hi,

We were wondering what the preferred command is for extracting mean 
gray matter thickness/LGI


I am aware that FS outputs left/right mean thickness but wanted to be 
conscious of the fact that left/right hemisphere might have different 
sizes.


Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--

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for a full directory of Beth Israel Lahey Health sites, staff, 
services and career opportunities.


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Re: [Freesurfer] [External] Re: extracting measurements for mean gray matter thickness/LGI

[Zeng, Victor (BIDMC - Keshavan - Psychiatry)]

External Email - Use Caution

Sorry, to be clear, there is a measurement for bilateral mean thickness offered 
by default? I'm able to gather the left mean thickness and the right mean 
thickness easily.

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--

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

Sent: Friday, January 12, 2024 4:26 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [External] Re: [Freesurfer] extracting measurements for mean gray 
matter thickness/LGI

I don't understand. Why not use the mean thickness from FS? We have an lGI 
module; we have not supported it in years, but maybe it still works. 
https://secure-web.cisco.com/1VsAamFIiyrHgC1fHpczhX9TaRNFmufCHxQtn-XOhmuyE9a3JzAxGIz-At0uYnBuvfcG72Job7Isg-NoUDQiTUK7HnlLZJG9ZN-je9SvWQQQH41Jei17EHcJkpWzSGVtb0ymhAORUoTEn11d_HOgK1t07nmoMF0wVvboiTMq_QdmkJ4luGL_KBtojoesZjIkUyD7v2ST_hor0q_L0LVkhIh3fytnvq_1GRHPM4c-xng5AwkBQLGH3u9EE0OiXUkoACoQrztbj3oC56Xk3qWb7CBfLBQaOt0sKwCwI7RJ_OGTwKNyDF89OKqGd-GBZUIE7sU0GAS5SadbgiIEQPkU0cg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLGI

On 1/10/2024 9:52 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:

External Email - Use Caution

Hi,

We were wondering what the preferred command is for extracting mean gray matter 
thickness/LGI

I am aware that FS outputs left/right mean thickness but wanted to be conscious 
of the fact that left/right hemisphere might have different sizes.

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--

PLEASE NOTE: This message is intended for the use of the person to whom it is 
addressed. It may contain information that is privileged, confidential and 
exempt from disclosure under applicable law. If you are not the intended 
recipient, your use of this message for any purpose is strictly prohibited. If 
you have received this communication in error, please delete the message and 
notify the sender so that we may correct our records. See our web page at 
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 for a full directory of Beth Israel Lahey Health sites, staff, services and 
career opportunities.



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Re: [Freesurfer] Midline white/pial surface

[Huang, Yujing]

Can you try the troubleshooting methods from this page:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Sunniva Fenn-Moltu
Sent: Monday, January 15, 2024 6:35 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Midline white/pial surface


External Email - Use Caution
Hi,

i'm running recon-all and have encountered an issue with the surface boundaries 
on several subjects. What I'm experiencing is that the midline surface is 
included in the white surface in one hemisphere, and in the pial surface on the 
other hemisphere. This results in the midline boundary of the thalamus and 
ventral DC being white surface in one hemisphere, and pial surface in the 
other. Do you have any idea why this is happening?
I am running freesurfer on NoMachine (freesurfer/7.4.1).

Best,
Sunniva

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Re: [Freesurfer] fsLR label to fsnative annotation

[Huang, Yujing]

Freesurfer .annot saves the annotation value at each vertex . The annotation is 
calculated from RGB in label file. Any labels with same RGB assigned will have 
the same annotations. They will appear to be the same label in .annot file.

Fix the label table in .gii, re-run mris_convert.

If you are running dev version, you can also fix RGB in separate LUT. Pass it 
to mris_convert -ctab  to replace the label table in .gii

Best,

Yujing




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Bram Diamond
Sent: Monday, January 15, 2024 5:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] fsLR label to fsnative annotation


External Email - Use Caution
Dear FreeSurfer experts,

Happy new year! I hope you all are doing well!

I recently wrote the following question to the HCP-User Google Group and was 
directed to cross-post in the FreeSurfer list server by Dr. Matt Glasser.

I have created individualized rs-fMRI maps as dlabel fsLR 32k space using Kong 
et al. 
(2021)
 and I would like to resample them to a FreeSurfer annotation in anatomical 
space without losing individual parcel assignments. The method below resamples 
the maps but loses parcel assignments.

echo "running -cifti-seperate"
wb_command \
-cifti-separate \
$dlabel_in \
COLUMN \
-label CORTEX_LEFT 
$dlabel_dir/${dlabel_in_base_name}.L.fsLR_32k.label.gii \
-label CORTEX_RIGHT 
$dlabel_dir/${dlabel_in_base_name}.R.fsLR_32k.label.gii

for hemi in L R; do

gii_in=$dlabel_dir/${dlabel_in_base_name}.${hemi}.fsLR_32k.label.gii

sphere_in=$standard_dir/resample_fsaverage/fs_LR-deformed_to-fsaverage.${hemi}.sphere.32k_fs_LR.surf.gii

sphere_out=$standard_dir/resample_fsaverage/fsaverage_std_sphere.${hemi}.164k_fsavg_${hemi}.surf.gii

gii_out=$dlabel_dir/${dlabel_in_base_name}.${hemi}.fsaverage_164k.label.gii

area_in=$standard_dir/resample_fsaverage/fs_LR.${hemi}.midthickness_va_avg.32k_fs_LR.shape.gii

area_out=$standard_dir/resample_fsaverage/fsaverage.${hemi}.midthickness_va_avg.164k_fsavg_${hemi}.shape.gii

echo "running -label-resample for "$hemi""
wb_command \
-label-resample \
$gii_in \
$sphere_in $sphere_out \
ADAP_BARY_AREA \
$gii_out \
-area-metrics \
$area_in $area_out

hemilower=$(echo $hemi | tr '[:upper:]' '[:lower:]')
fshemi=${hemilower}h

annot_out=${out_dir}/${fshemi}.${dlabel_in_base_name}.fsaverage.annot

echo "running mri_convert for "$fshemi""
mris_convert \
--annot $gii_out \
$FREESURFER_HOME/subjects/fsaverage/surf/${fshemi}.pial 
\
$annot_out

echo "running mri_surf2surf"
mri_surf2surf \
--srcsubject fsaverage \
--trgsubject $sub_id \
--hemi $fshemi \
--sval-annot $annot_out \
--tval 
$SUBJECTS_DIR/$sub_id/label/${fshemi}.${dlabel_in_base_name}.${sub_id}.annot \
--sd ${SUBJECTS_DIR}

mri_segstats \
--annot $sub_id $fshemi 
Ind_parcellation_MSHBM_${sub_num}_w20_MRF5.${sub_id} \
--i $SUBJECTS_DIR/$sub_id/surf/${fshemi}.thickness \
--sum 
${out_dir}/${fshemi}.Ind_parcellation_MSHBM_${sub_num}_w20_MRF5.${sub_id}.thickness

done

The original dlabel has a parcel label table with the following column names, 
"KEY" (int, 0-400), "NAME" (string, detailed below), and "RED,
"GREEN," "BLUE," "ALPHA" for RGB/1 (image_1).

NAME is , where atlas is always "17networks," 
hemi is "LH" or "RH," network is one of 17 networks (e.g., "DefaultA"), region 
is ≥1 unique anatomical region for each network (e.g., "FPole" and "IPL" for 
"DafaultA"), and int is an integer ID for repeat parcels in the same network 
and region (e.g., "DefaultA_IPL_1" and "DefaultA_IPL_2").

However, when converted to a FreeSurfer annotation file using the method above, 
parcels are collapsed across  and the name is taken from the first 
instance (image_2).

For example, I have parcels "17networks_LH_DefaultA_IPL_1" and 
"17networks_LH_DefaultA_IPL_2" in the dlabel, but only a single label called 
"17networks_LH_DefaultA_IPL_1" includi

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

[Huang, Yujing]

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>>
 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 
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all



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>>
 On Behalf Of Asuka Toyofuku
Sent: Friday, January 12, 2024 4:31 AM
To: 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 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


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