Re: [Freesurfer] Ubuntu VM Error - /dev/sda1 contains a file system with errors

2022-06-14 Thread fsbuild 
External Email - Use Caution

If you boot into recovery mode, there is an fsck option available there you can 
try.   I will send some screenshots of booting into recovery mode to your 
email directly.
- R.

On Jun 14, 2022, at 21:06, Joanna L Eckhardt  
wrote:External Email - Use 
CautionDear FS Help 
Team, I run FS on Ubuntu VM Virtualbox 6.1 on Windows. Out of nowhere, my 
Virtualbox is no longer opening and has errors. See screenshots below. First 
screen looks like this upon launching the Virtualbox and so I click Ubuntu and 
then it shows the error /dev/sda1 contains a file system with errors, check 
forced. I tried doing a website fix that I found online: fsck -f 
/dev/sda1 but it did not work. Do you have any insights on how to resolve 
this issue? Thank you very much for your time and assistance!All my 
best,Joanna Joanna EckhardtNeurosciences 
Graduate ProgramUniversity of California, San 
Diego___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
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Re: [Freesurfer] TRACULA -bedp parallel processing

2022-06-14 Thread Yendiki, Anastasia 
Unfortunately it's not something we've been able to replicate here ?

From: Salar Dini, Elaheh 
Sent: Tuesday, June 14, 2022 8:53 PM
To: Yendiki, Anastasia ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing


External Email - Use Caution

I tried to troubleshoot this, but I couldn't. I just want to follow-up and make 
sure no other solutions come to your mind. If not, we will run it out of 
cluster which seems to work just fine.

Thanks and all the best,
Ela

From: Salar Dini, Elaheh 
Sent: Wednesday, June 8, 2022 3:32 PM
To: Yendiki, Anastasia ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing


Thanks Paul.

bedpostx_preproc.sh is the first job that is I submit to my cluster. My input 
file is attached to this email.


Thanks,

Ela



From: Wighton, 
Paul
Sent: Wed, 08 Jun 2022 10:06:21 
-0700

Subject:Re: TRACULA -bedp parallel processing


Hi Ela,

It looks to me like line 79 of bedpostx_preproc.sh is:

if [ ${gflag} -eq 1 ]; then

Which is consistent with the error:

-eq: unary operator expected

What this error is saying is that the variable `gflag` has not been set, so the
script does not know how to perform the comparison.

`gflag` is set a few lines above to the second parameter passed when executing
`bedpostx_preproc.sh`.  I would investigate how `bedpostx_preproc.sh` is being
invoked to chase down the cause of this error.

-Paul


From: Salar Dini, Elaheh 
Sent: Wednesday, June 8, 2022 12:32 PM
To: Yendiki, Anastasia ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing

That actually helps but not solving all the problems. So, what happens is that 
if I create dmri.bedpostX folder, the first error goes away, a.k.a. (cp: target 
'/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX' is not a 
directory). However, the second error still exists: a.k.a. 
(home1/es2263/fsl//bin/bedpostx_preproc.sh: line 79: [: -eq: unary operator 
expected". line 79 is "${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask). And 
when I try to run Parallel lines, I still get the error 
(dmri.bedpostX/logs/log: No such file or directory). So, my guess is, it 
still doesn't copy the whole needed package for some reason. So, what we end up 
having in dmri.bedpostX folder is a)bvals, b)bvecs, c) nodif_brain_mask.nii.gz.

I can always manually copy all needed file from fsl folder to our subjects 
folder, but I am curious why we get the error and why everything is not copied 
automatically. I also don't know what files we need to manually copy.

Thanks again,
Ela

From: Yendiki, Anastasia 
Sent: Tuesday, June 7, 2022 2:46 PM
To: Salar Dini, Elaheh ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing

What if you create the directory (that shows up in the "not a directory" error)?

From: Salar Dini, Elaheh 
Sent: Tuesday, June 7, 2022 11:46 AM
To: Yendiki, Anastasia ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing


External Email - Use Caution

Hi Anastasia,


FSL version is 6.0.5.1


Thanks,

Ela





From: Yendiki, 
Anastasia

[Freesurfer] Ubuntu VM Error - /dev/sda1 contains a file system with errors

2022-06-14 Thread Joanna L Eckhardt 
External Email - Use Caution

Dear FS Help Team,

I run FS on Ubuntu VM Virtualbox 6.1 on Windows. Out of nowhere, my Virtualbox 
is no longer opening and has errors. See screenshots below. First screen looks 
like this upon launching the Virtualbox and so I click Ubuntu and then it shows 
the error /dev/sda1 contains a file system with errors, check forced. I tried 
doing a website fix that I found online: fsck -f /dev/sda1 but it did not work. 
Do you have any insights on how to resolve this issue?

Thank you very much for your time and assistance!

All my best,
Joanna
[cid:471109e4-6e90-411d-b653-14572ec8662b]
[cid:06b19041-fce6-416f-97cc-faeb5576040e]





Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego
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Re: [Freesurfer] TRACULA -bedp parallel processing

2022-06-14 Thread Salar Dini, Elaheh 
External Email - Use Caution

I tried to troubleshoot this, but I couldn't. I just want to follow-up and make 
sure no other solutions come to your mind. If not, we will run it out of 
cluster which seems to work just fine.

Thanks and all the best,
Ela

From: Salar Dini, Elaheh 
Sent: Wednesday, June 8, 2022 3:32 PM
To: Yendiki, Anastasia ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing


Thanks Paul.

bedpostx_preproc.sh is the first job that is I submit to my cluster. My input 
file is attached to this email.


Thanks,

Ela



From: Wighton, 
Paul
Sent: Wed, 08 Jun 2022 10:06:21 
-0700

Subject:Re: TRACULA -bedp parallel processing


Hi Ela,

It looks to me like line 79 of bedpostx_preproc.sh is:

if [ ${gflag} -eq 1 ]; then

Which is consistent with the error:

-eq: unary operator expected

What this error is saying is that the variable `gflag` has not been set, so the
script does not know how to perform the comparison.

`gflag` is set a few lines above to the second parameter passed when executing
`bedpostx_preproc.sh`.  I would investigate how `bedpostx_preproc.sh` is being
invoked to chase down the cause of this error.

-Paul


From: Salar Dini, Elaheh 
Sent: Wednesday, June 8, 2022 12:32 PM
To: Yendiki, Anastasia ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing

That actually helps but not solving all the problems. So, what happens is that 
if I create dmri.bedpostX folder, the first error goes away, a.k.a. (cp: target 
'/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX' is not a 
directory). However, the second error still exists: a.k.a. 
(home1/es2263/fsl//bin/bedpostx_preproc.sh: line 79: [: -eq: unary operator 
expected". line 79 is "${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask). And 
when I try to run Parallel lines, I still get the error 
(dmri.bedpostX/logs/log: No such file or directory). So, my guess is, it 
still doesn't copy the whole needed package for some reason. So, what we end up 
having in dmri.bedpostX folder is a)bvals, b)bvecs, c) nodif_brain_mask.nii.gz.

I can always manually copy all needed file from fsl folder to our subjects 
folder, but I am curious why we get the error and why everything is not copied 
automatically. I also don't know what files we need to manually copy.

Thanks again,
Ela

From: Yendiki, Anastasia 
Sent: Tuesday, June 7, 2022 2:46 PM
To: Salar Dini, Elaheh ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing

What if you create the directory (that shows up in the "not a directory" error)?

From: Salar Dini, Elaheh 
Sent: Tuesday, June 7, 2022 11:46 AM
To: Yendiki, Anastasia ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing


External Email - Use Caution

Hi Anastasia,


FSL version is 6.0.5.1


Thanks,

Ela





From: Yendiki, 
Anastasia

Re: [Freesurfer] using brain mask from older FreeSurfer version on a newer

2022-06-14 Thread Aaron Tanenbaum 
External Email - Use Caution

Great. glad I was of some help. I still need my questions answered.

On Tue, Jun 14, 2022 at 4:33 PM Bouchra Guelib <
bouchra.gue...@univ-constantine2.dz> wrote:

> External Email - Use Caution
>
> The problem is solved, I just changed the freesurfer version , thnx for
> your help
>
> Le mar. 14 juin 2022 à 22:27, Aaron Tanenbaum 
> a écrit :
>
>> External Email - Use Caution
>>
>> Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans
>> to do.  I see that you can give freesurfer a brainmask. I was thinking of
>> giving freesurfer a brainmask from the previous from 5.3 to 7.1. Is this a
>> wise idea? Do you have any objections?
>> ___
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Re: [Freesurfer] using brain mask from older FreeSurfer version on a newer

2022-06-14 Thread Bouchra Guelib 
External Email - Use Caution

The problem is solved, I just changed the freesurfer version , thnx for
your help

Le mar. 14 juin 2022 à 22:27, Aaron Tanenbaum 
a écrit :

> External Email - Use Caution
>
> Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans
> to do.  I see that you can give freesurfer a brainmask. I was thinking of
> giving freesurfer a brainmask from the previous from 5.3 to 7.1. Is this a
> wise idea? Do you have any objections?
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] using brain mask from older FreeSurfer version on a newer

2022-06-14 Thread Aaron Tanenbaum 
External Email - Use Caution

Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans to
do.  I see that you can give freesurfer a brainmask. I was thinking of
giving freesurfer a brainmask from the previous from 5.3 to 7.1. Is this a
wise idea? Do you have any objections?
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The information in this e-mail is intended only for the person to whom it is 
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[Freesurfer] recon-all -s exited with ERRORS

2022-06-14 Thread Wang, Yu 
External Email - Use Caution

Hi, FreeSurfer Developers,


 I am attempting to use the recon-all to reconstruction, I successfully run 
this command in some subjects, but it also failed in around 1/3 of subjects. 
And after running the recon-all of this 1/3 subjects. It will show 
“mri_watershed error:GLOBAL region of the brain empty” and I already solve this 
with the command “recon-all -skullstrip -no-wsgcaatlas -s smwrc1NT816”. And 
after working with this, I tried to use the command “recon-all -autorecon2 
-autorecon3 -s smwrc1NT816” and it shows the output as without given some 
detailed reasons:



recon-all -s smwrc1NT816 exited with ERRORS at Mon Jun 13 13:54:10 CDT 2022



For more details, see the log file 
/Applications/freesurfer/7.2.0/subjects/smwrc1NT816/scripts/recon-all.log

To report a problem, see 
http://secure-web.cisco.com/15s_oFH-kAftN57mqGI2bcqN1hKf4R5zXE_fPPasU_i9bJaX1BsgAq3K1S_fSTLY76gcIq3maFcAL1Wp2gSj07hGSEscorAynozW2EFSpI67Xebtf8tFFQSLh90SJGCMuqD6heT8WwwyAdjw8MJsfWzyAlePqW7TR2jsYkzdC4GaMhFnxeSamLAx_f3G8DiGpUvmhB7fssKSDdmycwTWW3UwENh74wNf9MQN0DIto_oZqyl-BKP5esesgP3O04RSY36xdr9z0HbBw5_UvX_QPATv58Ic-2BxIBoZJwecOdsfJ6whSNj8wr1XjKu63fWmHyWtfpfdervjU1DtsP2xPzA/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting


I’ve searched over the internet and did not find the reasons and solutions of 
my problems. And I will attached the recon-all.log in case it's of any use.

I try to work out on two machine, and they show the same problems :

  1.  FreeSurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b and 
freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
  2.  Platform: MacOs 11.4 and ubantu 20.04.4
  3.  uname -a:Darwin WANGs-MBP.attlocal.net 20.5.0 Darwin Kernel Version 
20.5.0: Sat May  8 05:10:31 PDT 2021; root:xnu-7195.121.3~9/RELEASE_ARM64_T8101 
arm64

or: Linux sulu 5.4.0-113-lowlatency #127-Ubuntu SMP PREEMPT Wed May 18 15:12:18 
UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

  1.  recon-all.log: see attached (this one is run by macOS)

I will be appreciated if you can give me a hand with these problems. And 
looking forward to your reply.

Sincerely,
Yu
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Re: [Freesurfer] mris_preproc read error

2022-06-14 Thread Joanna L Eckhardt 
External Email - Use Caution

Dear FS team,

There was indeed a problem with recon-all and I reran the subject and did what 
you said, and now there is no mris_preproc read error. Thank you very much for 
your assistance!

All my best,
Joanna


--

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego


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

Sent: Thursday, June 9, 2022 1:27 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mris_preproc read error

It looks like something might have gone wrong during recon-all for that 
subject. Does recon-all.log say it completed successfully? Try deleting the 
lh.sphere.reg (and any other file with 0 size) and running recon-all 
-autorecon2-surfonly -autorecon3, then do -qcache

On 6/7/2022 12:41 PM, Joanna L Eckhardt wrote:

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Dear FS team,

I am emailing to check in on the status of this issue. Any insights on how to 
move forward with this error? I can try rerunning this subject in the meantime 
to see if that fixes the problem.

Thank you very much your assistance!

Best wishes,
Joanna


--

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Joanna L Eckhardt 

Sent: Friday, June 3, 2022 10:37 AM
To: Freesurfer support list 

Subject: Re: [Freesurfer] mris_preproc read error


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Dear FreeSurfer team,

I reran -qcache for sub-101 (also, I had specified -qcache processing for all 
subjects during initial recon-all so it should have already occurred), and it 
exited with errors. Below is the output from the -qcache rerun, with the error 
being:

ERROR: reading 
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.sphere.reg
Read 0 bytes, expected 1
error: No such file or directory
error: mri_surf2surf: could not read surface 
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.sphere.reg
Command exited with non-zero status 1

Let me know if you have any insights, or if I need to rerun the recon-all for 
this subject.

Thank you for your assistance!
Joanna


developer@developer-VirtualBox:~/FreeSurfer/osg-outputs/cannabis-BL$ recon-all 
-s sub-101 -qcache
INFO: FreeSurfer build stamps do not match
Subject Stamp:
Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
INFO: SUBJECTS_DIR is /home/developer/FreeSurfer/osg-outputs/cannabis-BL
Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0
-rw-rw-r-- 1 developer developer 35431 Jun  3 13:28 
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/scripts/recon-all.log
Linux developer-VirtualBox 5.4.0-113-generic #127~18.04.1-Ubuntu SMP Wed May 18 
15:40:23 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
~/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri/transforms 
~/FreeSurfer/osg-outputs/cannabis-BL/sub-101
~/FreeSurfer/osg-outputs/cannabis-BL/sub-101
#@# white curv lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
   Update not needed
#@# white area lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
   Update not needed
#@# pial curv lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
   Update not needed
#@# pial area lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
   Update not needed
#@# thickness lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 
../surf/lh.thickness
   Update not needed
#@# area and vertex vol lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 
../surf/lh.thickness
   Update not needed
#@# white curv rh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
   Update not needed
#@# white area rh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
   Update not needed
#@# pial curv rh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri

Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

2022-06-14 Thread Huang, Yujing 
Hi Ben,

I was able to reproduce the core dump.  In my case, it was because a mismatch 
of color scheme between input annotation file and the color table loaded with 
the surface.

I suspect it might be the same issue for you too. But I’m not sure what the 
right action is to work around this.

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Benjamin Deck
Sent: Friday, June 10, 2022 11:47 AM
To: Freesurfer support list 
Subject: [Freesurfer] mri_label2vol fill-ribbon segmentation fault


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Hi there,

Having issues with the following command:

mri_label2vol --annot lh.yeo_2011.annot --temp 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz  --hemi lh 
--fill-ribbon --identity --subject sub-DAEK --o lh.sub-DAEK_annot_nat.nii.gz


produces the following error:

Number of labels: 0
Annot File:  lh.yeo_2011.annot
Template Volume: /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz
Outut Volume: lh.sub-DAEK_annot_nat.nii.gz
Registration File: (null)
Fill Threshold: 0
Label Vox Vol:  1
ProjType:   (null)
ProjTypeId: 0
ProjStart:  0
ProjStop:   0
ProjDelta:  0.1
Subject:  sub-DAEK
Hemi: lh
UseNewASeg2Vol:  0
DoLabelStatVol  0
LabelCodeOffset  0
setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects
7.2.0
Template RAS-to-Vox: 
-1.25000  -0.0  -0.0   160.0;
-0.0  -0.0  -1.25000   160.0;
-0.0   1.25000  -0.0   160.0;
-0.0  -0.0  -0.0   1.0;
Template Voxel Volume: 0.512
nHits Thresh: 0
Using Identity Matrix
RegMat: 
 1.0   0.0   0.0   0.0;
 0.0   1.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0   0.0   0.0   1.0;
Label RAS-to-Vox: 
-1.25000   0.0   0.0   160.0;
 0.0   0.0  -1.25000   160.0;
 0.0   1.25000   0.0   160.0;
 0.0   0.0   0.0   1.0;
  INFO: loading surface  
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white
nvertices = 253237
Reading thickness 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness
Loading annotations from lh.yeo_2011.annot
annotidmax = 48
nlabels = 48
Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz
Mapping
Segmentation fault


But when I run the same command without fill-ribbon the process runs to 
completion.

Not sure if this is a memory issue or something else.

Ben

--
Benjamin L. Deck
Doctoral Student
Applied Cognitive and Brain Sciences
Department of Psychological and Brain Sciences
Drexel University

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[Freesurfer] Incorporating samseg segmentation into the recon-all pipeline

2022-06-14 Thread Cerri, Stefano 
Hi Julian,

You can use the command "samseg" with the --recon flag. See the helper function 
for more details (--help)

Stefano

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/Hello everyone,/



/We have been utilizing freesurfer for our brain morphometry and processing 
pipelines, and have recently tested the samseg segmentation algorithm on a 
clinical cohort./

/With respect to some regions, we currently prefer its results to the ones 
generated by the standard freesurfer segmentation algorithm.

/



/As SAMSEG only provides volume calculation (please correct me if I am wrong) 
and does not feature cortical thickness measurements,/

/I was wondering if the recon-all pipeline can be modified to utilize the 
samseg segmentation instead, and if so, which script(s) or chain of commands 
would be a good starting point to implement this./

/Looking forward to your feedback,/

/Julian
/

Julian McGinnis

PhD Candidate
TUM-Neuroimaging Center, School of Medicine, Technical University of Munich,
Munich, Germany
Department of Computer Science, Technical University of Munich, Munich, Germany

Email:julian.mcgin...@tum.de


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[Freesurfer] about the error on running TRACULA using tutorial data

2022-06-14 Thread Xin Qi 
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Hi

I downloaded the FreeSurfer tutorial data  (
https://secure-web.cisco.com/1tDso4rjIlURcoFeNGyGUBBs1I7uczKauIIt12c78g81fRPOWsCdQGwqpysQpOHQv0zCfd4ugm0Hc5rEJwBAoS2uuC6V3tPvJ7pPBrzpiXz-2lMVqq14rv-USdZ-PY38Ec-9wLMQE4FbcZWz7V0k95amZWvMPhp0vrbfxmtXJcHkn5Mjb-k3Sz1Jxf0s30X9NTusTTZaWclbgEtt7s5bH2zg-EpAMnfoDGUaQmWvY4mAyVMHs24tMEasM9sRXWe5ba-3skUJHWqiO5MG45rjZztMV_x2snAgMxXwsKqdQUBBzZL1O_eFYN8s_Xx019DQUWK-LSqkGq0H8isbJ7hHqZA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FData)
 and tried to
test TRACULAR.

In the preprocessing step by running $trac-all -prep -c
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial, I got the following
error messages.

ERROR: length of pathway list (lh.cst_AS rh.cst_AS lh.ilf_AS rh.ilf_AS
lh.unc_AS rh.unc_AS fmajor_PP fminor_PP lh.atr_PP rh.atr_PP lh.cab_PP
rh.cab_PP lh.ccg_PP rh.ccg_PP lh.slfp_PP rh.slfp_PP lh.slft_PP rh.slft_PP)
and endpoint label ID list
ERROR: () do not match

There may be something wrong with the demo dmrirc.tutorial configuration
file, which is attached to the email. Please help me with how to fix
the problem.

Thank you very much.
Best regards
Xin


dmrirc.tutorial
Description: Binary data
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Re: [Freesurfer] mri_label2vol with fill-ribbon option

2022-06-14 Thread Huang, Yujing 
Hi Junjie,

Can you specify the Freesurfer version you are running?

Thanks.

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Wu, Junjie
Sent: Saturday, June 11, 2022 11:15 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_label2vol with fill-ribbon option


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Dear Freesurfer experts,,

I tried to use mri_label2vol with fill-ribbon option to covert the 
surface-based label of perirhinal cortex into the volume (an ROI in mgz file). 
However, when I typed "mri_label2vol --fill-ribbon --label 
lh.entorhinal_exvivo.thresh.label --o lh.entorhinal_exvivo.thresh.nii 
--identity" in the command line, an error popped up, saying "ERROR: Option 
--fill-ribbon unknown". Do you have any solution in order to make it work?

Thanks,
Junjie
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