External Email - Use Caution
Dear All,
I want to convert my .nii structural file to .mgz file. I tried using mri_convert however I got a permission denied message. Since I am not the administrator in the system, hence I cannot change the permissions at the moment, so I guess I will have to wait for IT to help me soon.
Instead, I wanted to try recon-all -i STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1 -subjid 10 [/bash] command. However, I am getting an "if: Expression Syntax" error. So I am not sure why might be the cause for that, though. So I might really appreciate your helps please.
I am using 4.4.0-139-generic #165-Ubuntu SMP Wed Oct 24 10:58:50 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux and bash.
I found a similar discussion from the archive ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-September/025691...) but there was no agreed solution I guess. So I wonder if there is any other way of converting the structural nii file to .mgz until these problems are solved?
Thank you very much for the help in advance
Kind regards
Isil
Hi Isil
can you send us the full command line and screen output of the commands you ran?
cheers Bruce On Sat, 19 Jan 2019, Isil Bilgin wrote:
External Email - Use Caution
Dear All,
I want to convert my .nii structural file to .mgz file. I tried using mri_convert however I got a permission denied message. Since I am not the administrator in the system, hence I cannot change the permissions at the moment, so I guess I will have to wait for IT to help me soon.
Instead, I wanted to try recon-all -i STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1 -subjid 10 [/bash] command. However, I am getting an "if: Expression Syntax" error. So I am not sure why might be the cause for that, though. So I might really appreciate your helps please.
I am using 4.4.0-139-generic #165-Ubuntu SMP Wed Oct 24 10:58:50 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux and bash.
I found a similar discussion from the archive (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-September/025691...) but there was no agreed solution I guess. So I wonder if there is any other way of converting the structural nii file to .mgz until these problems are solved?
Thank you very much for the help in advance
Kind regards
Isil
External Email - Use Caution
Dear Bruce,
thank you very much for replying promptly. Here are the commands they I use and the error messages that I get.
export SUBJECTS_DIR=/storage/shared/research/cinn/2017/SEMLRN/Data/Participant10/fMRIData/StructuralSegment export FREESURFER_HOME='/usr/share/freesurfer' source $FREESURFER_HOME/FreeSurferEnv.sh recon-all -i /storage/shared/research/cinn/2017/SEMLRN/Data/Participant10/fMRIData/StructuralSegment/1.3.12.2.1107.5.2.43.167013.2017120817330360897940188.0.0.0_0001_000001_1512762943b783.dcm -autorecon1 -subjid 10 *if: Expression Syntax.*
$FREESURFER_HOME/bin/mri_convert /storage/shared/research/cinn/2017/SEMLRN/Data/Participant10/fMRIData/StructuralSegment/sSEMLRN10-0001-00001-000128-01.nii *bash: /usr/share/freesurfer/bin/mri_convert: Permission denied*
I guess the second is more to be solved with IT, but I cannot understand the reason for the first error, so I would really appreciate if you could suggest a solution please.
Thank you very much for the help in advance
Isil
On Sat, Jan 19, 2019 at 8:04 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Isil
can you send us the full command line and screen output of the commands you ran?
cheers Bruce On Sat, 19 Jan 2019, Isil Bilgin wrote:
External Email - Use CautionDear All,
I want to convert my .nii structural file to .mgz file. I tried using
mri_convert however I got a permission denied
message. Since I am not the administrator in the system, hence I cannot
change the permissions at the moment, so I
guess I will have to wait for IT to help me soon.
Instead, I wanted to try recon-all -i STRUCT_FOLDER1/xxx.dcm -i
STRUCT_FOLDER2/xxx.dcm -autorecon1 -subjid 10
[/bash] command. However, I am getting an "if: Expression Syntax"
error. So I am not sure why might be the cause
for that, though. So I might really appreciate your helps please.
I am using 4.4.0-139-generic #165-Ubuntu SMP Wed Oct 24 10:58:50 UTC
2018 x86_64 x86_64 x86_64 GNU/Linux and bash.
I found a similar discussion from the archive (
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-September/025691...) but there was no agreed solution
I guess. So I wonder if there is any other way of converting the
structural nii file to .mgz until these problems
are solved?
Thank you very much for the help in advance
Kind regards
Isil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Isil
I'll leave it to someone else to answer the first quesion, but if mri_convert is not executable I can't understand how recon-all can run at all, so you should probably get someone with root access to fix that first
cheers Bruce
On Sat, 19 Jan 2019, Isil Bilgin wrote:
External Email - Use Caution
Dear Bruce,
thank you very much for replying promptly. Here are the commands they I use and the error messages that I get.
export SUBJECTS_DIR=/storage/shared/research/cinn/2017/SEMLRN/Data/Participant10/fMRIData/StructuralSegment export FREESURFER_HOME='/usr/share/freesurfer' source $FREESURFER_HOME/FreeSurferEnv.sh recon-all -i/storage/shared/research/cinn/2017/SEMLRN/Data/Participant10/fMRIData/StructuralSegment/1.3.12.2.1107.5.2.43.16701 3.2017120817330360897940188.0.0.0_0001_000001_1512762943b783.dcm -autorecon1 -subjid 10 if: Expression Syntax.
$FREESURFER_HOME/bin/mri_convert /storage/shared/research/cinn/2017/SEMLRN/Data/Participant10/fMRIData/StructuralSegment/sSEMLRN10-0001-00001-00012 8-01.nii bash: /usr/share/freesurfer/bin/mri_convert: Permission denied
I guess the second is more to be solved with IT, but I cannot understand the reason for the first error, so I would really appreciate if you could suggest a solution please.
Thank you very much for the help in advance
Isil
On Sat, Jan 19, 2019 at 8:04 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Isil
can you send us the full command line and screen output of the commands you ran? cheers Bruce On Sat, 19 Jan 2019, Isil Bilgin wrote: > > External Email - Use Caution > > Dear All, > > I want to convert my .nii structural file to .mgz file. I tried using mri_convert however I got a permission denied > message. Since I am not the administrator in the system, hence I cannot change the permissions at the moment, so I > guess I will have to wait for IT to help me soon. > > Instead, I wanted to try recon-all -i STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1 -subjid 10 > [/bash] command. However, I am getting an "if: Expression Syntax" error. So I am not sure why might be the cause > for that, though. So I might really appreciate your helps please. > > > I am using 4.4.0-139-generic #165-Ubuntu SMP Wed Oct 24 10:58:50 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux and bash. > > I found a similar discussion from the archive > (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-September/025691.html) but there was no agreed solution > I guess. So I wonder if there is any other way of converting the structural nii file to .mgz until these problems > are solved? > > Thank you very much for the help in advance > > Kind regards > > Isil > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Isil, this issue might resolve itself once the executable permissions are taken care of, but if not, it's possible it's related to the dicom input. If you're still getting the error, can you run recon-all with the -debug flag and send us the output?
best, Andrew
On 1/22/19, 11:23 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Isil
I'll leave it to someone else to answer the first quesion, but if mri_convert is not executable I can't understand how recon-all can run at all, so you should probably get someone with root access to fix that first
cheers Bruce
On Sat, 19 Jan 2019, Isil Bilgin wrote:
> > External Email - Use Caution > > Dear Bruce, > > thank you very much for replying promptly. Here are the commands they I use and the error messages that I get. > > > export SUBJECTS_DIR=/storage/shared/research/cinn/2017/SEMLRN/Data/Participant10/fMRIData/StructuralSegment > export FREESURFER_HOME='/usr/share/freesurfer' > source $FREESURFER_HOME/FreeSurferEnv.sh > recon-all -i/storage/shared/research/cinn/2017/SEMLRN/Data/Participant10/fMRIData/StructuralSegment/1.3.12.2.1107.5.2.43.16701 > 3.2017120817330360897940188.0.0.0_0001_000001_1512762943b783.dcm -autorecon1 -subjid 10 > if: Expression Syntax. > > $FREESURFER_HOME/bin/mri_convert /storage/shared/research/cinn/2017/SEMLRN/Data/Participant10/fMRIData/StructuralSegment/sSEMLRN10-0001-00001-00012 > 8-01.nii > bash: /usr/share/freesurfer/bin/mri_convert: Permission denied > > I guess the second is more to be solved with IT, but I cannot understand the reason for the first error, so I would > really appreciate if you could suggest a solution please. > > Thank you very much for the help in advance > > Isil > > > > > > On Sat, Jan 19, 2019 at 8:04 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: > Hi Isil > > can you send us the full command line and screen output of the commands > you ran? > > cheers > Bruce > On Sat, 19 Jan 2019, Isil Bilgin wrote: > > > > > External Email - Use Caution > > > > Dear All, > > > > I want to convert my .nii structural file to .mgz file. I tried using mri_convert however I got a > permission denied > > message. Since I am not the administrator in the system, hence I cannot change the permissions at the > moment, so I > > guess I will have to wait for IT to help me soon. > > > > Instead, I wanted to try recon-all -i STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1 > -subjid 10 > > [/bash] command. However, I am getting an "if: Expression Syntax" error. So I am not sure why might > be the cause > > for that, though. So I might really appreciate your helps please. > > > > > > I am using 4.4.0-139-generic #165-Ubuntu SMP Wed Oct 24 10:58:50 UTC 2018 x86_64 x86_64 x86_64 > GNU/Linux and bash. > > > > I found a similar discussion from the archive > > (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-September/025691...) but there was no > agreed solution > > I guess. So I wonder if there is any other way of converting the structural nii file to .mgz until > these problems > > are solved? > > > > Thank you very much for the help in advance > > > > Kind regards > > > > Isil > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >
External Email - Use Caution
Dear both,
thank you so much for your help and recommendations. I talked to our IT and they gave me all the necessary permissions, so everything seems working now.
Thank you very much indeed,
Kind regards
Isil
On Tue, Jan 22, 2019 at 4:52 PM Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:
Hi Isil, this issue might resolve itself once the executable permissions are taken care of, but if not, it's possible it's related to the dicom input. If you're still getting the error, can you run recon-all with the -debug flag and send us the output?
best, Andrew
On 1/22/19, 11:23 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Isil I'll leave it to someone else to answer the first quesion, but if mri_convert is not executable I can't understand how recon-all can runat all, so you should probably get someone with root access to fix that first
cheers Bruce On Sat, 19 Jan 2019, Isil Bilgin wrote: > > External Email - Use Caution > > Dear Bruce, > > thank you very much for replying promptly. Here are the commandsthey I use and the error messages that I get. > > > export SUBJECTS_DIR=/storage/shared/research/cinn/2017/SEMLRN/Data/Participant10/fMRIData/StructuralSegment > export FREESURFER_HOME='/usr/share/freesurfer' > source $FREESURFER_HOME/FreeSurferEnv.sh > recon-all -i/storage/shared/research/cinn/2017/SEMLRN/Data/Participant10/fMRIData/StructuralSegment/ 1.3.12.2.1107.5.2.43.16701 > 3.2017120817330360897940188.0.0.0_0001_000001_1512762943b783.dcm -autorecon1 -subjid 10 > if: Expression Syntax. > > $FREESURFER_HOME/bin/mri_convert /storage/shared/research/cinn/2017/SEMLRN/Data/Participant10/fMRIData/StructuralSegment/sSEMLRN10-0001-00001-00012 > 8-01.nii > bash: /usr/share/freesurfer/bin/mri_convert: Permission denied > > I guess the second is more to be solved with IT, but I cannot understand the reason for the first error, so I would > really appreciate if you could suggest a solution please. > > Thank you very much for the help in advance > > Isil > > > > > > On Sat, Jan 19, 2019 at 8:04 PM Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: > Hi Isil > > can you send us the full command line and screen output of the commands > you ran? > > cheers > Bruce > On Sat, 19 Jan 2019, Isil Bilgin wrote: > > > > > External Email - Use Caution > > > > Dear All, > > > > I want to convert my .nii structural file to .mgz file. I tried using mri_convert however I got a > permission denied > > message. Since I am not the administrator in the system, hence I cannot change the permissions at the > moment, so I > > guess I will have to wait for IT to help me soon. > > > > Instead, I wanted to try recon-all -i STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1 > -subjid 10 > > [/bash] command. However, I am getting an "if: Expression Syntax" error. So I am not sure why might > be the cause > > for that, though. So I might really appreciate your helps please. > > > > > > I am using 4.4.0-139-generic #165-Ubuntu SMP Wed Oct 24 10:58:50 UTC 2018 x86_64 x86_64 x86_64 > GNU/Linux and bash. > > > > I found a similar discussion from the archive > > ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-September/025691...) but there was no > agreed solution > > I guess. So I wonder if there is any other way of converting the structural nii file to .mgz until > these problems > > are solved? > > > > Thank you very much for the help in advance > > > > Kind regards > > > > Isil > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://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
glad to hear it worked out Bruce On Tue, 22 Jan 2019, Isil Bilgin wrote:
External Email - Use Caution
Dear both, thank you so much for your help and recommendations. I talked to our IT and they gave me all the necessary permissions, so everything seems working now.
Thank you very much indeed,
Kind regards
Isil
On Tue, Jan 22, 2019 at 4:52 PM Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote: Hi Isil, this issue might resolve itself once the executable permissions are taken care of, but if not, it's possible it's related to the dicom input. If you're still getting the error, can you run recon-all with the -debug flag and send us the output?
best, Andrew On 1/22/19, 11:23 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote: Hi Isil I'll leave it to someone else to answer the first quesion, but if mri_convert is not executable I can't understand how recon-all can run at all, so you should probably get someone with root access to fix that first cheers Bruce On Sat, 19 Jan 2019, Isil Bilgin wrote: > > External Email - Use Caution > > Dear Bruce, > > thank you very much for replying promptly. Here are the commands they I use and the error messages that I get. > > > export SUBJECTS_DIR=/storage/shared/research/cinn/2017/SEMLRN/Data/Participant10/fMRIData/StructuralSegment > export FREESURFER_HOME='/usr/share/freesurfer' > source $FREESURFER_HOME/FreeSurferEnv.sh > recon-all -i/storage/shared/research/cinn/2017/SEMLRN/Data/Participant10/fMRIData/StructuralSegment/MailScanner has detected a possible fraud attempt from "1.3.12.2" claiming to be MailScanner warning: numerical links are often malicious: 1.3.12.2.1107.5.2.43.16701 > 3.2017120817330360897940188.0.0.0_0001_000001_1512762943b783.dcm -autorecon1 -subjid 10 > if: Expression Syntax. > > $FREESURFER_HOME/bin/mri_convert/storage/shared/research/cinn/2017/SEMLRN/Data/Participant10/fMRIData/StructuralSegment/sSEMLRN10-0001-00001-00012 > 8-01.nii > bash: /usr/share/freesurfer/bin/mri_convert: Permission denied > > I guess the second is more to be solved with IT, but I cannot understand the reason for the first error, so I would > really appreciate if you could suggest a solution please. > > Thank you very much for the help in advance > > Isil > > > > > > On Sat, Jan 19, 2019 at 8:04 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > Hi Isil > > can you send us the full command line and screen output of the commands > you ran? > > cheers > Bruce > On Sat, 19 Jan 2019, Isil Bilgin wrote: > > > > > External Email - Use Caution > > > > Dear All, > > > > I want to convert my .nii structural file to .mgz file. I tried using mri_convert however I got a > permission denied > > message. Since I am not the administrator in the system, hence I cannot change the permissions at the > moment, so I > > guess I will have to wait for IT to help me soon. > > > > Instead, I wanted to try recon-all -i STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1 > -subjid 10 > > [/bash] command. However, I am getting an "if: Expression Syntax" error. So I am not sure why might > be the cause > > for that, though. So I might really appreciate your helps please. > > > > > > I am using 4.4.0-139-generic #165-Ubuntu SMP Wed Oct 24 10:58:50 UTC 2018 x86_64 x86_64 x86_64 > GNU/Linux and bash. > > > > I found a similar discussion from the archive > > (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-September/025691.html) but there was no > agreed solution > > I guess. So I wonder if there is any other way of converting the structural nii file to .mgz until > these problems > > are solved? > > > > Thank you very much for the help in advance > > > > Kind regards > > > > Isil > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Hoopes, Andrew -
Isil Bilgin