[Freesurfer] XL defect in recon-all

[Devika K]

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Hi,

I am running recon-all on Freesurfer version 6. Few of my subject's
have XL  defect error as shown below.

CORRECTING DEFECT 0 (vertices=18408, convex hull=3300, v0=0)
XL defect detected...

This has been running for more than a day.

How can I fix this error?
 Please give me some commands to solve this issue.

Looking forward to hearing from you


Thanks and Regards
Devika K
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Re: [Freesurfer] medial wall metric file

[Alexopoulos, Dimitrios]

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Having difficulty with how to use label2label for this purpose. Just need a 
binary mask of medial wall (vertex number and 0 or 1s) on native surface. 
What's would this command be?

On Jan 28, 2020 5:42 PM, "Greve, Douglas N.,Ph.D."  
wrote:

Attention: This email originated from outside the university.

Do you mean you want a binary mask of the medial wall?
You can create a mask of the cortical label (?h.cortex.label) with 
mri_label2label
You can then invert that with something like
fscalc lh.cortex.mask.mgz not -o lh.medialwall.mask.mgz


On 1/28/2020 6:31 PM, Alexopoulos, Dimitrios wrote:

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Is there a freesurfer file that contains metric info that delineates the medial 
wall in the native surface output for an individual?

It appears to be associated with the ?lh.aparc.annot file (below).

I’d like to be able to export the medial wall metric into Worbench.



Thanks.

Jim





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Re: [Freesurfer] Error Bad CPU

[Hoopes, Andrew]

Just to add on to this: you should use freeview, which runs smoothly on 
Catalina, for visualizing registration quality
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of fsbuild 

Sent: Thursday, January 30, 2020 12:32 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: philipp.bar...@uni-konstanz.de
Subject: Re: [Freesurfer] Error Bad CPU

External Email - Use Caution

Hello Phillip,

If you run the following command on that file - which is from the 6.0.0 
freesurfer release,

$ file /Applications/freesurfer/tktools/tkregister2.bin

I think you will see that it reports it is a i386 binary - which is 32 bit - 
and cannot run on Catalina.  That is also why you get bad CPU type,

% file tkregister2.bin
tkregister2.bin: Mach-O executable i386

% ./tkregister2.bin
./tkregister2.bin: Bad CPU type in executable.

The last version of MacOS that can run 32 bit binaries is 10.14, Mojave, but 
with Mac OS 10.15 (Catalina) none of the old 32 bit binaries will run.   So if 
you need to be compatible with running the 6.0.0 freesurfer release, then I 
suggest you look into reverting back to the previous version of the OS you were 
running before the upgrade, i.e., hopefully you made a backup before upgrading. 
 Or if you have 10.13 (High Sierra), 10.12 (Sierra), or older, etc., that would 
work as well.

- R.



On Jan 30, 2020, at 10:50, Philipp Barzyk  
wrote:

   External Email - Use Caution

Tanks for the quick reply.

what exactly do you mean by all FS executables? It happens for various commands 
I am using but they all work on my Imac.

I am working from a 2019 macbook air using catalina, and installed it myself. 
The imac where it works is from 2013 and runs on Mojave.

Greets,
Philipp

On 30.01.20, 16:31, "Bruce Fischl"  wrote:

   Hi Philipp

   does this happen for all the FS executables? What kind of machine are you
   trying it from and who installed it? Sounds like you are on a mac and
   maybe trying to use a version installed for a different kind of computer

   cheers
   Bruce
   On Thu, 30 Jan 2020, Philipp Barzyk
   wrote:


   External Email - Use Caution

Hello,
I am new to freesurfer and currently analysing and working on fMRI Data for
my master thesis. I’ve come to an issue, that I can’t seem to solve.

The following error occurs and I cannot find a threat or forum entry that
solves it.

/Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type in
executable.


It would be great if you could help me figure out a solution.

Thanks in advance,

Philipp Barzyk




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Re: [Freesurfer] Error Bad CPU

[fsbuild]

External Email - Use Caution

Hello Phillip,
If you run the following command on that file - which is from the 6.0.0 
freesurfer release,
$ file /Applications/freesurfer/tktools/tkregister2.bin
I think you will see that it reports it is a i386 binary - which is 32 bit - 
and cannot run on Catalina.  That is also why you get bad CPU type,
% file tkregister2.bin
tkregister2.bin: Mach-O executable i386
% ./tkregister2.bin
../tkregister2.bin: Bad CPU type in executable.

The last version of MacOS that can run 32 bit binaries is 10.14, Mojave, but 
with Mac OS 10.15 (Catalina) none of the old 32 bit binaries will run.   
So if you need to be compatible with running the 6.0.0 freesurfer release, then 
I suggest you look into reverting back to the previous version of the OS you 
were running before the upgrade, i.e., hopefully you made a backup before 
upgrading.  Or if you have 10.13 (High Sierra), 10.12 (Sierra), or older, 
etc., that would work as well.
- R.


On Jan 30, 2020, at 10:50, Philipp Barzyk 
 
wrote:   External Email - Use Caution 
   Tanks for the quick reply.what 
exactly do you mean by all FS executables? It happens for various commands I am 
using but they all work on my Imac.I am working from a 2019 macbook air using 
catalina, and installed it myself. The imac where it works is from 2013 and 
runs on Mojave.Greets,PhilippOn 30.01.20, 16:31, "Bruce Fischl" 
 wrote:   Hi 
Philipp   does this happen for all the FS executables? What kind 
of machine are youtrying it from and who installed it? 
Sounds like you are on a mac andmaybe trying to use a 
version installed for a different kind of 
computer   cheers   Bruce   On 
Thu, 30 Jan 2020, Philipp 
Barzykwrote:   External
 Email - Use Caution    Hello,I am new 
to freesurfer and currently analysing and working on fMRI Data formy master 
thesis. I’ve come to an issue, that I can’t seem to solve.The following error 
occurs and I cannot find a threat or forum entry thatsolves 
it. /Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type 
inexecutable.It would be great if you could help me figure out a 
solution. Thanks in advance,Philipp 
Barzyk___   Freesurfer
 mailing 
list   Freesurfer@nmr.mgh.harvard.edu   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] (no subject)

[fsbuild]

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Hello Phillip,
If you run the following command on that file - which is from the 6.0.0 
freesurfer release,
$ file /Applications/freesurfer/tktools/tkregister2.bin
I think you will see that it reports it is a i386 binary - which is 32 bit - 
and cannot run on Catalina.  That is also why you get bad CPU type,
% file tkregister2.bin
tkregister2.bin: Mach-O executable i386
% ./tkregister2.bin
../tkregister2.bin: Bad CPU type in executable.

The last version of MacOS that can run 32 bit binaries is 10.14, Mojave, but 
with Mac OS 10.15 (Catalina) none of the old 32 bit binaries will run.   
So if you need to be compatible with running the 6.0.0 freesurfer release, then 
I suggest you look into reverting back to the previous version of the OS you 
were running before the upgrade, i.e., hopefully you made a backup before 
upgrading.  Or if you have 10.13 (High Sierra), 10.12 (Sierra), or older, 
etc., that would work as well.
- R.


On Jan 30, 2020, at 10:50, Philipp Barzyk 
 
wrote:   External Email - Use Caution 
   Tanks for the quick reply.what 
exactly do you mean by all FS executables? It happens for various commands I am 
using but they all work on my Imac.I am working from a 2019 macbook air using 
catalina, and installed it myself. The imac where it works is from 2013 and 
runs on Mojave.Greets,PhilippOn 30.01.20, 16:31, "Bruce Fischl" 
 wrote:   Hi 
Philipp   does this happen for all the FS executables? What kind 
of machine are youtrying it from and who installed it? 
Sounds like you are on a mac andmaybe trying to use a 
version installed for a different kind of 
computer   cheers   Bruce   On 
Thu, 30 Jan 2020, Philipp 
Barzykwrote:   External
 Email - Use Caution    Hello,I am new 
to freesurfer and currently analysing and working on fMRI Data formy master 
thesis. I’ve come to an issue, that I can’t seem to solve.The following error 
occurs and I cannot find a threat or forum entry thatsolves 
it. /Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type 
inexecutable.It would be great if you could help me figure out a 
solution. Thanks in advance,Philipp 
Barzyk___   Freesurfer
 mailing 
list   Freesurfer@nmr.mgh.harvard.edu   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] format bvalues bvectors tracula

[Yendiki, Anastasia]

Hi Renew - I think it's just because of using "/" instead of "\" at the end of 
lines for bveclist and bvallist. If the problem persists after you change that, 
let us know.

a.y

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Renew Andrade 

Sent: Wednesday, January 29, 2020 11:54 AM
To: Freesurfer Support List 
Subject: [Freesurfer] format bvalues bvectors tracula


External Email - Use Caution

Dear FreeSurfer experts:
I have tried to run tracula -prep but I cannot get to no where for the moment. 
I keep receiving this error. I assumed numbers had to be aligned in rows and 
columns. But none either that or one space in between seems to work. I don't 
know what format means with respect to bvalues o bvectors. It is not clear 
enough to me in the tutorial how do I have to fix the issue.

Sincerely,
Andrade.


root@andraderenew:/home/andraderenew# trac-all -prep -c 
'/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/dmrirc.IXI'
Too many ('s.
INFO: SUBJECTS_DIR is 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed
INFO: Diffusion root is 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed
Actual FREESURFER_HOME /usr/local/freesurfer
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /usr/local/freesurfer
Previous: /Applications/freesurfer
trac-preproc -c 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/dmrirc.local
 -log 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/trac-all.log
 -cmd 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/trac-all.cmd
#-
/usr/local/freesurfer/bin/trac-preproc
#-
#@# Image corrections mié ene 29 17:42:22 CET 2020
mri_convert --bvec-voxel 
/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz
 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel 
/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz
 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 
/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998725, -0.0503472, 0.00377193)
j_ras = (-0.0504772, 0.994141, -0.0955763)
k_ras = (-0.00106217, 0.0956448, 0.995415)
writing to 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz...
cp 
/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/bvec/gradients.txt
 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.bvecs
ERROR: Must specify input table of b-values
Linux andraderenew 5.0.0-37-generic #40~18.04.1-Ubuntu SMP Thu Nov 14 12:06:39 
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at mié ene 29 17:42:22 CET 2020







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Re: [Freesurfer] Error Bad CPU

[Philipp Barzyk]

External Email - Use Caution

Tanks for the quick reply.

what exactly do you mean by all FS executables? It happens for various commands 
I am using but they all work on my Imac.

I am working from a 2019 macbook air using catalina, and installed it myself. 
The imac where it works is from 2013 and runs on Mojave.

Greets,
Philipp

On 30.01.20, 16:31, "Bruce Fischl"  wrote:

Hi Philipp

does this happen for all the FS executables? What kind of machine are you 
trying it from and who installed it? Sounds like you are on a mac and 
maybe trying to use a version installed for a different kind of computer

cheers
Bruce
On Thu, 30 Jan 2020, Philipp Barzyk 
wrote:

> 
> External Email - Use Caution
> 
> Hello,
> I am new to freesurfer and currently analysing and working on fMRI Data 
for
> my master thesis. I’ve come to an issue, that I can’t seem to solve.
> 
> The following error occurs and I cannot find a threat or forum entry that
> solves it. 
> 
> /Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type in
> executable.
> 
> 
> It would be great if you could help me figure out a solution. 
> 
> Thanks in advance,
> 
> Philipp Barzyk
> 
>  
> 
> 
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Re: [Freesurfer] Error Bad CPU

[Bruce Fischl]

Hi Philipp

does this happen for all the FS executables? What kind of machine are you 
trying it from and who installed it? Sounds like you are on a mac and 
maybe trying to use a version installed for a different kind of computer


cheers
Bruce
On Thu, 30 Jan 2020, Philipp Barzyk 
wrote:




External Email - Use Caution

Hello,
I am new to freesurfer and currently analysing and working on fMRI Data for
my master thesis. I’ve come to an issue, that I can’t seem to solve.

The following error occurs and I cannot find a threat or forum entry that
solves it. 

/Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type in
executable.


It would be great if you could help me figure out a solution. 

Thanks in advance,

Philipp Barzyk

 


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[Freesurfer] Error Bad CPU

[Philipp Barzyk]

External Email - Use Caution

Hello,
I am new to freesurfer and currently analysing and working on fMRI Data for my 
master thesis. I’ve come to an issue, that I can’t seem to solve.

The following error occurs and I cannot find a threat or forum entry that 
solves it. 

/Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type in executable.


It would be great if you could help me figure out a solution. 

Thanks in advance,

Philipp Barzyk

 

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Re: [Freesurfer] PetSurfer questions

[Soo-Jong Kim]

External Email - Use Caution

I ran gtmseg for my partial volume correction

1. but I have a question. What regions are for the detail??
in this option.

mri_gtmpvc --default-seg-merge.

I searched mri_gtmpvc --help
but it is default schema for merging ROIs.
So I wanna know what regions you use as default. for example, in
FreeSurferLUT. 1000, 1010, etc..

Can you tell me what regions freesurfer uses.

2. In general, After PVC (i.e.MG or RBV),  Does some smoothing kernel apply
to pv-corrected images from rbv as rbv.nii.gz?

If then, how large smoothing kernel?

Best,
Soo
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