Re: [Freesurfer] mris_label2annot: surf/rh.orig No such file or directory

2015-05-26 Thread Douglas N Greve 

The error is "ERROR: reading ./rh.unknown.label" meaning that it is 
expecting it as input. You need to create it or change the command to 
not expect it


On 05/26/2015 08:32 AM, Liu Y wrote:
> no ./rh.unknown.label was created.
> Yawu
>
> On Mon, May 25, 2015 at 7:22 PM, Douglas Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Is there a file called ./rh.unknown.label ?
>
>
>
> On 5/25/15 5:37 AM, Liu Y wrote:
>> Dear Freesurfers,
>> I tried to generate annotations by using the command
>> mris_label2annot --s K_TS66 --h rh --ctab aparc.annot.ctab --a
>> Liu --nhits nhits.mgh. But Could not succeed. Any helps would be
>> appreciated.
>>
>> --- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> FREESURFER_HOME   /home/Liu/freesurfer
>> FSFAST_HOME /home/Liu/freesurfer/fsfast
>> FSF_OUTPUT_FORMAT nii.gz
>> SUBJECTS_DIR /home/Liu/freesurfer/subjects
>> MNI_DIR /home/Liu/freesurfer/mni
>> FSL_DIR   /usr/local/fsl
>>
>> under folder /home/Liu/freesurfer/subjects/K_TS66/label, I run 
>> mris_label2annot --s K_TS66 --h rh --ctab aparc.annot.ctab --a
>> Liu --nhits nhits.mgh.
>>
>> output:
>> Reading ctab aparc.annot.ctab
>> Number of ctab entries 36
>> INFO: no labels specified, generating from ctab
>>  0 ./rh.unknown.label
>>  1 ./rh.bankssts.label
>>  2 ./rh.caudalanteriorcingulate.label
>>  3 ./rh.caudalmiddlefrontal.label
>>  4 ./rh.corpuscallosum.label
>>  5 ./rh.cuneus.label
>>  6 ./rh.entorhinal.label
>>  7 ./rh.fusiform.label
>>  8 ./rh.inferiorparietal.label
>>  9 ./rh.inferiortemporal.label
>> 10 ./rh.isthmuscingulate.label
>> 11 ./rh.lateraloccipital.label
>> 12 ./rh.lateralorbitofrontal.label
>> 13 ./rh.lingual.label
>> 14 ./rh.medialorbitofrontal.label
>> 15 ./rh.middletemporal.label
>> 16 ./rh.parahippocampal.label
>> 17 ./rh.paracentral.label
>> 18 ./rh.parsopercularis.label
>> 19 ./rh.parsorbitalis.label
>> 20 ./rh.parstriangularis.label
>> 21 ./rh.pericalcarine.label
>> 22 ./rh.postcentral.label
>> 23 ./rh.posteriorcingulate.label
>> 24 ./rh.precentral.label
>> 25 ./rh.precuneus.label
>> 26 ./rh.rostralanteriorcingulate.label
>> 27 ./rh.rostralmiddlefrontal.label
>> 28 ./rh.superiorfrontal.label
>> 29 ./rh.superiorparietal.label
>> 30 ./rh.superiortemporal.label
>> 31 ./rh.supramarginal.label
>> 32 ./rh.frontalpole.label
>> 33 ./rh.temporalpole.label
>> 34 ./rh.transversetemporal.label
>> 35 ./rh.insula.label
>>
>> $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
>> cwd /home/Liu/freesurfer/subjects/K_TS66/label
>> cmdline mris_label2annot --s K_TS66 --h rh --ctab
>> aparc.annot.ctab --a Liu --nhits nhits.mgh
>> sysname  Linux
>> hostname D4201Z
>> machine  x86_64
>> user Liu
>>
>> subject K_TS66
>> hemirh
>> SUBJECTS_DIR /home/Liu/freesurfer/subjects
>> ColorTable aparc.annot.ctab
>> AnnotName  Liu
>> NHitsFile nhits.mgh
>> nlables 36
>> LabelThresh 0 0.00
>> Loading /home/Liu/freesurfer/subjects/K_TS66/surf/rh.orig
>> No such file or directory
>> mris_label2annot: could not open label file ./rh.unknown.label
>> No such file or directory
>> ERROR: reading ./rh.unknown.label
>>
>> There is indeed a rh.orig file under
>> /home/Liu/freesurfer/subjects/K_TS66/surf/
>>
>> Thanks,
>> Yawu
>>
>>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu  
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] mris_label2annot: surf/rh.orig No such file or directory

2015-05-26 Thread Liu Y 
no ./rh.unknown.label was created.
Yawu

On Mon, May 25, 2015 at 7:22 PM, Douglas Greve 
wrote:

>  Is there a file called ./rh.unknown.label ?
>
>
>
> On 5/25/15 5:37 AM, Liu Y wrote:
>
> Dear Freesurfers,
>  I tried to generate annotations by using the command mris_label2annot --s
> K_TS66 --h rh --ctab aparc.annot.ctab --a Liu --nhits nhits.mgh. But Could
> not succeed. Any helps would be appreciated.
>
>  --- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /home/Liu/freesurfer
> FSFAST_HOME   /home/Liu/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /home/Liu/freesurfer/subjects
> MNI_DIR   /home/Liu/freesurfer/mni
> FSL_DIR   /usr/local/fsl
>
>  under folder /home/Liu/freesurfer/subjects/K_TS66/label, I run
> mris_label2annot --s K_TS66 --h rh --ctab aparc.annot.ctab --a Liu --nhits
> nhits.mgh.
>
>  output:
> Reading ctab aparc.annot.ctab
> Number of ctab entries 36
> INFO: no labels specified, generating from ctab
>  0 ./rh.unknown.label
>  1 ./rh.bankssts.label
>  2 ./rh.caudalanteriorcingulate.label
>  3 ./rh.caudalmiddlefrontal.label
>  4 ./rh.corpuscallosum.label
>  5 ./rh.cuneus.label
>  6 ./rh.entorhinal.label
>  7 ./rh.fusiform.label
>  8 ./rh.inferiorparietal.label
>  9 ./rh.inferiortemporal.label
> 10 ./rh.isthmuscingulate.label
> 11 ./rh.lateraloccipital.label
> 12 ./rh.lateralorbitofrontal.label
> 13 ./rh.lingual.label
> 14 ./rh.medialorbitofrontal.label
> 15 ./rh.middletemporal.label
> 16 ./rh.parahippocampal.label
> 17 ./rh.paracentral.label
> 18 ./rh.parsopercularis.label
> 19 ./rh.parsorbitalis.label
> 20 ./rh.parstriangularis.label
> 21 ./rh.pericalcarine.label
> 22 ./rh.postcentral.label
> 23 ./rh.posteriorcingulate.label
> 24 ./rh.precentral.label
> 25 ./rh.precuneus.label
> 26 ./rh.rostralanteriorcingulate.label
> 27 ./rh.rostralmiddlefrontal.label
> 28 ./rh.superiorfrontal.label
> 29 ./rh.superiorparietal.label
> 30 ./rh.superiortemporal.label
> 31 ./rh.supramarginal.label
> 32 ./rh.frontalpole.label
> 33 ./rh.temporalpole.label
> 34 ./rh.transversetemporal.label
> 35 ./rh.insula.label
>
> $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
> cwd /home/Liu/freesurfer/subjects/K_TS66/label
> cmdline mris_label2annot --s K_TS66 --h rh --ctab aparc.annot.ctab --a Liu
> --nhits nhits.mgh
> sysname  Linux
> hostname D4201Z
> machine  x86_64
> user Liu
>
> subject K_TS66
> hemirh
> SUBJECTS_DIR /home/Liu/freesurfer/subjects
> ColorTable aparc.annot.ctab
> AnnotName  Liu
> NHitsFile nhits.mgh
> nlables 36
> LabelThresh 0 0.00
> Loading /home/Liu/freesurfer/subjects/K_TS66/surf/rh.orig
> No such file or directory
> mris_label2annot: could not open label file ./rh.unknown.label
> No such file or directory
> ERROR: reading ./rh.unknown.label
>
>  There is indeed a rh.orig file under
> /home/Liu/freesurfer/subjects/K_TS66/surf/
>
>  Thanks,
>  Yawu
>
>
>
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> 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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> properly
> dispose of the e-mail.
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Re: [Freesurfer] mris_label2annot: surf/rh.orig No such file or directory

2015-05-25 Thread Douglas Greve 

Is there a file called ./rh.unknown.label ?


On 5/25/15 5:37 AM, Liu Y wrote:

Dear Freesurfers,
I tried to generate annotations by using the command mris_label2annot 
--s K_TS66 --h rh --ctab aparc.annot.ctab --a Liu --nhits nhits.mgh. 
But Could not succeed. Any helps would be appreciated.


--- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /home/Liu/freesurfer
FSFAST_HOME   /home/Liu/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /home/Liu/freesurfer/subjects
MNI_DIR   /home/Liu/freesurfer/mni
FSL_DIR   /usr/local/fsl

under folder /home/Liu/freesurfer/subjects/K_TS66/label, I run  
mris_label2annot --s K_TS66 --h rh --ctab aparc.annot.ctab --a Liu 
--nhits nhits.mgh.


output:
Reading ctab aparc.annot.ctab
Number of ctab entries 36
INFO: no labels specified, generating from ctab
 0 ./rh.unknown.label
 1 ./rh.bankssts.label
 2 ./rh.caudalanteriorcingulate.label
 3 ./rh.caudalmiddlefrontal.label
 4 ./rh.corpuscallosum.label
 5 ./rh.cuneus.label
 6 ./rh.entorhinal.label
 7 ./rh.fusiform.label
 8 ./rh.inferiorparietal.label
 9 ./rh.inferiortemporal.label
10 ./rh.isthmuscingulate.label
11 ./rh.lateraloccipital.label
12 ./rh.lateralorbitofrontal.label
13 ./rh.lingual.label
14 ./rh.medialorbitofrontal.label
15 ./rh.middletemporal.label
16 ./rh.parahippocampal.label
17 ./rh.paracentral.label
18 ./rh.parsopercularis.label
19 ./rh.parsorbitalis.label
20 ./rh.parstriangularis.label
21 ./rh.pericalcarine.label
22 ./rh.postcentral.label
23 ./rh.posteriorcingulate.label
24 ./rh.precentral.label
25 ./rh.precuneus.label
26 ./rh.rostralanteriorcingulate.label
27 ./rh.rostralmiddlefrontal.label
28 ./rh.superiorfrontal.label
29 ./rh.superiorparietal.label
30 ./rh.superiortemporal.label
31 ./rh.supramarginal.label
32 ./rh.frontalpole.label
33 ./rh.temporalpole.label
34 ./rh.transversetemporal.label
35 ./rh.insula.label

$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
cwd /home/Liu/freesurfer/subjects/K_TS66/label
cmdline mris_label2annot --s K_TS66 --h rh --ctab aparc.annot.ctab --a 
Liu --nhits nhits.mgh

sysname  Linux
hostname D4201Z
machine  x86_64
user Liu

subject K_TS66
hemirh
SUBJECTS_DIR /home/Liu/freesurfer/subjects
ColorTable aparc.annot.ctab
AnnotName  Liu
NHitsFile nhits.mgh
nlables 36
LabelThresh 0 0.00
Loading /home/Liu/freesurfer/subjects/K_TS66/surf/rh.orig
No such file or directory
mris_label2annot: could not open label file ./rh.unknown.label
No such file or directory
ERROR: reading ./rh.unknown.label

There is indeed a rh.orig file under 
/home/Liu/freesurfer/subjects/K_TS66/surf/


Thanks,
Yawu





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[Freesurfer] mris_label2annot: surf/rh.orig No such file or directory

2015-05-25 Thread Liu Y 
Dear Freesurfers,
I tried to generate annotations by using the command mris_label2annot --s
K_TS66 --h rh --ctab aparc.annot.ctab --a Liu --nhits nhits.mgh. But Could
not succeed. Any helps would be appreciated.

--- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /home/Liu/freesurfer
FSFAST_HOME   /home/Liu/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /home/Liu/freesurfer/subjects
MNI_DIR   /home/Liu/freesurfer/mni
FSL_DIR   /usr/local/fsl

under folder /home/Liu/freesurfer/subjects/K_TS66/label, I run
mris_label2annot --s K_TS66 --h rh --ctab aparc.annot.ctab --a Liu --nhits
nhits.mgh.

output:
Reading ctab aparc.annot.ctab
Number of ctab entries 36
INFO: no labels specified, generating from ctab
 0 ./rh.unknown.label
 1 ./rh.bankssts.label
 2 ./rh.caudalanteriorcingulate.label
 3 ./rh.caudalmiddlefrontal.label
 4 ./rh.corpuscallosum.label
 5 ./rh.cuneus.label
 6 ./rh.entorhinal.label
 7 ./rh.fusiform.label
 8 ./rh.inferiorparietal.label
 9 ./rh.inferiortemporal.label
10 ./rh.isthmuscingulate.label
11 ./rh.lateraloccipital.label
12 ./rh.lateralorbitofrontal.label
13 ./rh.lingual.label
14 ./rh.medialorbitofrontal.label
15 ./rh.middletemporal.label
16 ./rh.parahippocampal.label
17 ./rh.paracentral.label
18 ./rh.parsopercularis.label
19 ./rh.parsorbitalis.label
20 ./rh.parstriangularis.label
21 ./rh.pericalcarine.label
22 ./rh.postcentral.label
23 ./rh.posteriorcingulate.label
24 ./rh.precentral.label
25 ./rh.precuneus.label
26 ./rh.rostralanteriorcingulate.label
27 ./rh.rostralmiddlefrontal.label
28 ./rh.superiorfrontal.label
29 ./rh.superiorparietal.label
30 ./rh.superiortemporal.label
31 ./rh.supramarginal.label
32 ./rh.frontalpole.label
33 ./rh.temporalpole.label
34 ./rh.transversetemporal.label
35 ./rh.insula.label

$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
cwd /home/Liu/freesurfer/subjects/K_TS66/label
cmdline mris_label2annot --s K_TS66 --h rh --ctab aparc.annot.ctab --a Liu
--nhits nhits.mgh
sysname  Linux
hostname D4201Z
machine  x86_64
user Liu

subject K_TS66
hemirh
SUBJECTS_DIR /home/Liu/freesurfer/subjects
ColorTable aparc.annot.ctab
AnnotName  Liu
NHitsFile nhits.mgh
nlables 36
LabelThresh 0 0.00
Loading /home/Liu/freesurfer/subjects/K_TS66/surf/rh.orig
No such file or directory
mris_label2annot: could not open label file ./rh.unknown.label
No such file or directory
ERROR: reading ./rh.unknown.label

There is indeed a rh.orig file under
/home/Liu/freesurfer/subjects/K_TS66/surf/

Thanks,
Yawu
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The information in this e-mail is intended only for the person to whom it is
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
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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