Re: [Freesurfer] gtmseg getSignalBehindHead ERROR (no slices behind head)

2020-06-08 Thread Douglas N. Greve 

Get a new version of mri_seghead from here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_seghead
and copy it into $FREESURFER_HOME/bin
let me know if it works

On 6/5/2020 5:09 PM, Boris Rauchmann wrote:


External Email - Use Caution

thanks, the subj I sent you the logfile has a cut on the posterior 
part, I uploaded a similar case 098_S_4275_20181221.tar.gz

Is there any way to run gtmseg regardless?

Thanks

Am Fr., 5. Juni 2020 um 20:01 Uhr schrieb Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>:


Hmmm, not sure what is going on here. I'm guessing that the back
of the head was cut off (or wrapped around). Is that right? I'm
not sure why this would create an error. If you upload one of your
subjects, I'll take a look. See instructions below

From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu 
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.


On 6/4/2020 9:40 AM, Boris Rauchmann wrote:


External Email - Use Caution

Please find the logfile attached.

Thank you

Am Do., 4. Juni 2020 um 15:18 Uhr schrieb Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>>:

Can you send the log file?

On 6/4/2020 9:12 AM, Boris Rauchmann wrote:


External Email - Use Caution

Dear FS experts,

In my dataset I have 4 subjects where the T1 was acquired,
planning the FOV very close to the occipital lobe. I guess
that triggers the error: getSignalBehindHead ERROR (no
slices behind head) WARNING: only 0 < 7 slices behind head!
ERROR: xcerebralseg  and results in gtmseg exited with errors.
How can I fix this?

Best regards,
Boris

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Re: [Freesurfer] gtmseg getSignalBehindHead ERROR (no slices behind head)

2020-06-05 Thread Boris Rauchmann 
External Email - Use Caution

thanks, the subj I sent you the logfile has a cut on the posterior part, I
uploaded a similar case 098_S_4275_20181221.tar.gz
Is there any way to run gtmseg regardless?

Thanks

Am Fr., 5. Juni 2020 um 20:01 Uhr schrieb Douglas N. Greve <
dgr...@mgh.harvard.edu>:

> Hmmm, not sure what is going on here. I'm guessing that the back of the
> head was cut off (or wrapped around). Is that right? I'm not sure why this
> would create an error. If you upload one of your subjects, I'll take a
> look. See instructions below
>
> From the linux command line,
> Create the file you want to upload, eg,
> cd $SUBJECTS_DIR
> tar cvfz subject.tar.gz ./subject
> Now log  into our anonymous FTP site:
> ftp surfer.nmr.mgh.harvard.edu
> It will ask you for a user name: use "anonymous" (no quotes)
> It will ask you for a password: use "anonymous" (no quotes)
> cd transfer/incoming
> binary
> put subject.tar.gz
> Send an email that the file has been and the name of the file.
>
>
> On 6/4/2020 9:40 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
> Please find the logfile attached.
>
> Thank you
>
> Am Do., 4. Juni 2020 um 15:18 Uhr schrieb Douglas N. Greve <
> dgr...@mgh.harvard.edu>:
>
>> Can you send the log file?
>>
>> On 6/4/2020 9:12 AM, Boris Rauchmann wrote:
>>
>> External Email - Use Caution
>> Dear FS experts,
>>
>> In my dataset I have 4 subjects where the T1 was acquired, planning the
>> FOV very close to the occipital lobe. I guess that triggers the error:
>> getSignalBehindHead ERROR (no slices behind head) WARNING: only 0 < 7
>> slices behind head! ERROR: xcerebralseg  and results in gtmseg exited with
>> errors.
>> How can I fix this?
>>
>> Best regards,
>> Boris
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> 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] gtmseg getSignalBehindHead ERROR (no slices behind head)

2020-06-05 Thread Douglas N. Greve 
Hmmm, not sure what is going on here. I'm guessing that the back of the 
head was cut off (or wrapped around). Is that right? I'm not sure why 
this would create an error. If you upload one of your subjects, I'll 
take a look. See instructions below


From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.


On 6/4/2020 9:40 AM, Boris Rauchmann wrote:


External Email - Use Caution

Please find the logfile attached.

Thank you

Am Do., 4. Juni 2020 um 15:18 Uhr schrieb Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>:


Can you send the log file?

On 6/4/2020 9:12 AM, Boris Rauchmann wrote:


External Email - Use Caution

Dear FS experts,

In my dataset I have 4 subjects where the T1 was acquired,
planning the FOV very close to the occipital lobe. I guess that
triggers the error: getSignalBehindHead ERROR (no slices behind
head) WARNING: only 0 < 7 slices behind head! ERROR:
xcerebralseg  and results in gtmseg exited with errors.
How can I fix this?

Best regards,
Boris

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Re: [Freesurfer] gtmseg getSignalBehindHead ERROR (no slices behind head)

2020-06-04 Thread Boris Rauchmann 
External Email - Use Caution

Please find the logfile attached.

Thank you

Am Do., 4. Juni 2020 um 15:18 Uhr schrieb Douglas N. Greve <
dgr...@mgh.harvard.edu>:

> Can you send the log file?
>
> On 6/4/2020 9:12 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
> Dear FS experts,
>
> In my dataset I have 4 subjects where the T1 was acquired, planning the
> FOV very close to the occipital lobe. I guess that triggers the error:
> getSignalBehindHead ERROR (no slices behind head) WARNING: only 0 < 7
> slices behind head! ERROR: xcerebralseg  and results in gtmseg exited with
> errors.
> How can I fix this?
>
> Best regards,
> Boris
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Log file for gtmseg
Thu Jun  4 14:40:20 CEST 2020

setenv SUBJECTS_DIR /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS
cd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS
/usr/local/freesurfer/bin/gtmseg --s 098_S_6655_20190107

freesurfer-linux-centos6_x86_64-dev-20180911-69aa645
$Id: gtmseg,v 1.19 2016/03/24 17:32:23 greve Exp $
Linux linuxrechner2 4.15.0-65-generic #74~16.04.1-Ubuntu SMP Wed Sep 18 09:51:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
xcerebralseg --s 098_S_6655_20190107
Thu Jun  4 14:40:20 CEST 2020

setenv SUBJECTS_DIR /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS
cd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS
/usr/local/freesurfer/bin/xcerebralseg --s 098_S_6655_20190107

freesurfer-linux-centos6_x86_64-dev-20180911-69aa645
$Id: xcerebralseg,v 1.12 2017/01/18 21:21:00 zkaufman Exp $
Linux linuxrechner2 4.15.0-65-generic #74~16.04.1-Ubuntu SMP Wed Sep 18 09:51:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
mri_ca_label -align -nobigventricles /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/nu.mgz /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/transforms/talairach.m3z /usr/local/freesurfer/average/aseg+spmhead+vermis+pons.ixi.gca /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg1.mgh
sysname  Linux
hostname linuxrechner2
machine  x86_64

setenv SUBJECTS_DIR /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS
cd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS
mri_ca_label -align -nobigventricles /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/nu.mgz /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/transforms/talairach.m3z /usr/local/freesurfer/average/aseg+spmhead+vermis+pons.ixi.gca /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg1.mgh 


== Number of threads available to mri_ca_label for OpenMP = 1 == 
renormalizing sequences with structure alignment, equivalent to:
	-renormalize
	-renormalize_mean 0.500
	-regularize 0.500
not handling expanded ventricles...
reading 1 input volumes
reading classifier array from /usr/local/freesurfer/average/aseg+spmhead+vermis+pons.ixi.gca
reading input volume from /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/nu.mgz
average std[0] = 20.4
reading transform from /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 7.01
Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca
average std = 20.4   using min determinant for regularization = 41.8
0 singular and 0 ill-conditioned covariance matrices regularized
labeling volume...
renormalizing by structure alignment
renormalizing input #0
gca peak = 0.24861 (36)
mri peak = 0.08632 (27)
Left_Lateral_Ventricle (4): linear fit = 0.69 x + 0.0 (14329 voxels, overlap=0.008)
Left_Lateral_Ventricle (4): linear fit = 0.69 x + 0.0 (14329 voxels, peak = 25), gca=25.0
gca peak = 0.29857 (37)
mri peak = 0.08013 (27)
Right_Lateral_Ventricle (43): linear fit = 0.64 x + 0.0 (12114 voxels, overlap=0.010)
Right_Lateral_Ventricle (43): linear fit = 0.64 x + 0.0 (12114 voxels, peak = 24), g

Re: [Freesurfer] gtmseg getSignalBehindHead ERROR (no slices behind head)

2020-06-04 Thread Douglas N. Greve 

Can you send the log file?

On 6/4/2020 9:12 AM, Boris Rauchmann wrote:


External Email - Use Caution

Dear FS experts,

In my dataset I have 4 subjects where the T1 was acquired, planning 
the FOV very close to the occipital lobe. I guess that triggers the 
error: getSignalBehindHead ERROR (no slices behind head) WARNING: only 
0 < 7 slices behind head! ERROR: xcerebralseg  and results in gtmseg 
exited with errors.

How can I fix this?

Best regards,
Boris

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[Freesurfer] gtmseg getSignalBehindHead ERROR (no slices behind head)

2020-06-04 Thread Boris Rauchmann 
External Email - Use Caution

Dear FS experts,

In my dataset I have 4 subjects where the T1 was acquired, planning the FOV
very close to the occipital lobe. I guess that triggers the error:
getSignalBehindHead ERROR (no slices behind head) WARNING: only 0 < 7
slices behind head! ERROR: xcerebralseg  and results in gtmseg exited with
errors.
How can I fix this?

Best regards,
Boris
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