Re: [Freesurfer] FreeSurfer Errors (2)

[Sparsh Jain]

External Email - Use Caution

I attached that to the previous email, but it got rejected by the moderator
for some reason!

Sparsh

On Tue, Oct 16, 2018 at 1:03 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> can you send the command-line output as text?
>
> On 10/16/2018 11:12 AM, Sparsh Jain wrote:
> >
> > External Email - Use Caution
> >
> > Hey!
> > I sent two responses on Friday. The second response was bigger than 1
> > MB so it awaited moderator approval. I don't know if you received it
> > eventually.
> >
> > Following up to that mail, my reconstruction on the subject with 176
> > images crashed after about 32 hours of execution with the error 'could
> > not read label' and 'too many symbolic links' in fsaverage. I have
> > attached the entire command line output. Please help me understand
> > what I'm doing wrong !
> >
> > Thanks
> >
> > Sparsh
> >
> >
> >
> >
> > ___
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>
>
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Re: [Freesurfer] FreeSurfer Errors (2)

[Greve, Douglas N.,Ph.D.]

can you send the command-line output as text?

On 10/16/2018 11:12 AM, Sparsh Jain wrote:
>
> External Email - Use Caution
>
> Hey!
> I sent two responses on Friday. The second response was bigger than 1 
> MB so it awaited moderator approval. I don't know if you received it 
> eventually.
>
> Following up to that mail, my reconstruction on the subject with 176 
> images crashed after about 32 hours of execution with the error 'could 
> not read label' and 'too many symbolic links' in fsaverage. I have 
> attached the entire command line output. Please help me understand 
> what I'm doing wrong !
>
> Thanks
>
> Sparsh
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] FreeSurfer Errors

[Greve, Douglas N.,Ph.D.]

On 10/11/18 1:58 PM, Sparsh Jain wrote:

External Email - Use Caution

Hey!

I have recently started using FreeSurfer. I have encountered multiple errors 
over the past few days, and I would like to mention them all.

1. While testing the installation, the code ran for roughly 4-6 hours and 
generated the T1 and wm output images. The brainmask image failed to load even 
after multiple attempts.
what does "failed to load" mean? Please be more specific, supplying command 
lines and terminal output
2. We have patient data from a Seimens 1.5 T MRI machine. They are DICOM images 
(about 120-145 images). Running dcmunpack on the directory to locate the 
suitable T1 weighted image (to pass as the input image to freesurfer) returns 
an error message 'Element not found'. It fails to generate a list of usable 
input images. The log file also only mentions the error message. Basically, I 
am having trouble working with DICOM images using Freesurfer. Please advise me 
on how to go about it.
This usually means that some part of the DICOM that dcmunpack expects is not 
there. Again, command line and terminal output would be helpful.
3. I tried using the dcm2nii tool on the DICOM images. The software gave out 
three (nearly identical) nii.gz files as output, each about 7 MB in size. I 
tried running reconstruction on all three one by one. Only the 'compressed' 
version output underwent reconstruction for a long time without giving any 
errors. However, the reconstruction process went on for 150 hours without 
completion. There were no errors during this time, and the mris_fix_topo 
process went on for about 74 hours until tonight. It was working on 'correcting 
defect 48' for most of this time, and then the PC suddenly stopped responding. 
The process had been utilizing 100% of the CPU and 87% of the RAM for a long 
time, but the computer was always responding. However it suddenly stopped 
responding after about 74 hours of mris_fix_topology process. My machine has 8 
GB RAM and more than 3.4 GHz processing speed (Acer Veriton).
I don't know what is going on here. Did you look at the nii.gz file in freeview 
to make sure that it looks ok. What is the size of the volume?
4. Previously, I tried running reconstruction on a different subject's data 
after converting it to nifti using dcm2niix. After 70 hours of execution, it 
terminated with an error which showed that the fsaverage folder was 
inaccessible. Further digging revealed that the folder  was somehow pointing to 
itself. The original error said failed to read from the label file.
 I had to eventually reinstall FreeSurfer.
I don't know how that happened.
5. I tried running iElvis pipeline. After some time I got an error which said 
that the sphere.reg file couldn't be opened. I tried fixing this but nothing 
worked. I kept getting the error that lh.sphere.reg file could not be opened 
and so on.
I don't know anything about iElvis

Please help. I have been trying to run it for weeks now. I hope you will be 
able to address each of these problems soon.

Thank You

Sparsh



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[Freesurfer] FreeSurfer Errors

[Sparsh Jain]

External Email - Use Caution

Hey!

I have recently started using FreeSurfer. I have encountered multiple
errors over the past few days, and I would like to mention them all.

1. While testing the installation, the code ran for roughly 4-6 hours and
generated the T1 and wm output images. The brainmask image failed to load
even after multiple attempts.
2. We have patient data from a Seimens 1.5 T MRI machine. They are DICOM
images (about 120-145 images). Running dcmunpack on the directory to locate
the suitable T1 weighted image (to pass as the input image to freesurfer)
returns an error message 'Element not found'. It fails to generate a list
of usable input images. The log file also only mentions the error message.
Basically, I am having trouble working with DICOM images using Freesurfer.
Please advise me on how to go about it.
3. I tried using the dcm2nii tool on the DICOM images. The software gave
out three (nearly identical) nii.gz files as output, each about 7 MB in
size. I tried running reconstruction on all three one by one. Only the
'compressed' version output underwent reconstruction for a long time
without giving any errors. However, the reconstruction process went on for
150 hours without completion. There were no errors during this time, and
the mris_fix_topo process went on for about 74 hours until tonight. It was
working on 'correcting defect 48' for most of this time, and then the PC
suddenly stopped responding. The process had been utilizing 100% of the CPU
and 87% of the RAM for a long time, but the computer was always responding.
However it suddenly stopped responding after about 74 hours of
mris_fix_topology process. My machine has 8 GB RAM and more than 3.4 GHz
processing speed (Acer Veriton).
4. Previously, I tried running reconstruction on a different subject's data
after converting it to nifti using dcm2niix. After 70 hours of execution,
it terminated with an error which showed that the fsaverage folder was
inaccessible. Further digging revealed that the folder  was somehow
pointing to itself. The original error said failed to read from the label
file.
 I had to eventually reinstall FreeSurfer.
5. I tried running iElvis pipeline. After some time I got an error which
said that the sphere.reg file couldn't be opened. I tried fixing this but
nothing worked. I kept getting the error that lh.sphere.reg file could not
be opened and so on.

Please help. I have been trying to run it for weeks now. I hope you will be
able to address each of these problems soon.

Thank You

Sparsh
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Re: [Freesurfer] freesurfer errors-windows bash

[Iglesias Gonzalez, Eugenio]

Dear Alexandre,
It seems that problem is that you need the latest dev version to use this 
feature.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: Alexandre Obert 
Date: Thursday, 26 October 2017 at 16:31
To: "freesurfer@nmr.mgh.harvard.edu" , 
"Iglesias Gonzalez, Eugenio" 
Subject: Re: freesurfer errors-windows bash

Dear Eugenio,

The freesurfer version commands tells me that I run the 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c version.
Before using segmentHA_T1.sh command, I run the recon-all -all -s bert one and 
it worked.
Of course, recon-all also worked, telling be how to use it properly.

Regards,

Alexandre

2017-10-26 17:08 GMT+02:00 Alexandre Obert 
>:
Dear all,

I'm would like to run a hippocampal segmentation on my data.
However, I'm a beginner with freesurfer thus, I juste try to run the commands 
with subject training data.
I first try to run commands following the recent development 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).
 However, terminal says that the command segmentHA.sh doesn't exist.

I guess that it could be linked to the fact that I used bash in Windows but I 
can't find a way to check this..;

Any idea ?

Regards,

Alexandre

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Re: [Freesurfer] freesurfer errors-windows bash

[Alexandre Obert]

Dear Eugenio,

The freesurfer version commands tells me that I run
the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c version.
Before using segmentHA_T1.sh command, I run the recon-all -all -s bert one
and it worked.
Of course, recon-all also worked, telling be how to use it properly.

Regards,

Alexandre

2017-10-26 17:08 GMT+02:00 Alexandre Obert :

> Dear all,
>
> I'm would like to run a hippocampal segmentation on my data.
> However, I'm a beginner with freesurfer thus, I juste try to run the
> commands with subject training data.
> I first try to run commands following the recent development (
> https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiO
> fAmygdala). However, terminal says that the command segmentHA.sh doesn't
> exist.
>
> I guess that it could be linked to the fact that I used bash in Windows
> but I can't find a way to check this..;
>
> Any idea ?
>
> Regards,
>
> Alexandre
>
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Re: [Freesurfer] freesurfer errors-windows bash

[Iglesias Gonzalez, Eugenio]

Dear Alexandre,
You need to download the latest dev version to have access to the new 
hippocampus/amygdala segmentation.
The other potential problem is that FreeSurfer is not sourced properly. Do 
other FreeSurfer commands work? E.g. do you get an output when you type:  
recon-all
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alexandre Obert 
<obert.alexan...@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, 26 October 2017 at 16:10
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] freesurfer errors-windows bash

Dear all,

I'm would like to run a hippocampal segmentation on my data.
However, I'm a beginner with freesurfer thus, I juste try to run the commands 
with subject training data.
I first try to run commands following the recent development 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).
 However, terminal says that the command segmentHA.sh doesn't exist.

I guess that it could be linked to the fact that I used bash in Windows but I 
can't find a way to check this..;

Any idea ?

Regards,

Alexandre
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] freesurfer errors-windows bash

[Alexandre Obert]

Dear all,

I'm would like to run a hippocampal segmentation on my data.
However, I'm a beginner with freesurfer thus, I juste try to run the
commands with subject training data.
I first try to run commands following the recent development (
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).
However, terminal says that the command segmentHA.sh doesn't exist.

I guess that it could be linked to the fact that I used bash in Windows but
I can't find a way to check this..;

Any idea ?

Regards,

Alexandre
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[Freesurfer] Freesurfer errors on using .nii images

[Atif Adam]

Good afternoon,



We are trying to use Freesurfer to work out NifTi images are on using recon 
script run into this error message below. .



It doesn't seem to move past motion correction in the run.



Any input will be greatly appreciated!



Adam



 [mcarlsonspronew:/] m_carlson% recon-all -i 
$SUBJECTS_DIR/23/Follow-UpIII/MPRAGE/fMPragecorSENSE.nii -subjid 23test22 -all

Subject Stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0

Current Stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /Applications/freesurfer/data/test

Actual FREESURFER_HOME /Applications/freesurfer

Darwin mcarlsonspronew.sph.ad.jhsph.edu 13.2.0 Darwin Kernel Version 13.2.0: 
Thu Apr 17 23:03:13 PDT 2014; root:xnu-2422.100.13~1/RELEASE_X86_64 x86_64

/Applications/freesurfer/data/test/23test22

\n mri_convert 
/Applications/freesurfer/data/test/23/Follow-UpIII/MPRAGE/fMPragecorSENSE.nii 
/Applications/freesurfer/data/test/23test22/mri/orig/001.mgz \n

mri_convert 
/Applications/freesurfer/data/test/23/Follow-UpIII/MPRAGE/fMPragecorSENSE.nii 
/Applications/freesurfer/data/test/23test22/mri/orig/001.mgz

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from 
/Applications/freesurfer/data/test/23/Follow-UpIII/MPRAGE/fMPragecorSENSE.nii...

TR=8.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-0.998364, 0, 0.0571858)

j_ras = (0.0555427, -0.237979, 0.969681)

k_ras = (-0.0136096, -0.97127, -0.23759)

writing to /Applications/freesurfer/data/test/23test22/mri/orig/001.mgz...

#

#@# MotionCor Tue Apr 21 15:35:44 EDT 2015

Found 1 runs

/Applications/freesurfer/data/test/23test22/mri/orig/001.mgz

Checking for (invalid) multi-frame inputs...

WARNING: only one run found. This is OK, but motion

correction cannot be performed on one run, so I'll

copy the run to rawavg and continue.

\n cp /Applications/freesurfer/data/test/23test22/mri/orig/001.mgz 
/Applications/freesurfer/data/test/23test22/mri/rawavg.mgz \n

/Applications/freesurfer/data/test/23test22

\n mri_convert /Applications/freesurfer/data/test/23test22/mri/rawavg.mgz 
/Applications/freesurfer/data/test/23test22/mri/orig.mgz --conform \n

mri_convert /Applications/freesurfer/data/test/23test22/mri/rawavg.mgz 
/Applications/freesurfer/data/test/23test22/mri/orig.mgz --conform

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from /Applications/freesurfer/data/test/23test22/mri/rawavg.mgz...

TR=8.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-0.998364, 0, 0.0571858)

j_ras = (0.0555427, -0.237979, 0.969681)

k_ras = (-0.0136096, -0.97127, -0.23759)

Original Data has (1, 1, 1) mm size and (256, 256, 200) voxels.

Data is conformed to 1 mm size and 256 voxels for all directions

changing data type from float to uchar (noscale = 0)...

MRIchangeType: Building histogram

Reslicing using trilinear interpolation

writing to /Applications/freesurfer/data/test/23test22/mri/orig.mgz...

\n mri_add_xform_to_header -c 
/Applications/freesurfer/data/test/23test22/mri/transforms/talairach.xfm 
/Applications/freesurfer/data/test/23test22/mri/orig.mgz 
/Applications/freesurfer/data/test/23test22/mri/orig.mgz \n

INFO: extension is mgz

#

#@# Talairach Tue Apr 21 15:35:55 EDT 2015

/Applications/freesurfer/data/test/23test22/mri

\n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz \n

Darwin mcarlsonspronew.sph.ad.jhsph.edu 13.2.0 Darwin Kernel Version 13.2.0: 
Thu Apr 17 23:03:13 PDT 2014; root:xnu-2422.100.13~1/RELEASE_X86_64 x86_64



recon-all -s 23test22 exited with ERRORS at Tue Apr 21 15:35:58 EDT 2015



For more details, see the log file 
/Applications/freesurfer/data/test/23test22/scripts/recon-all.log

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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