Hello FreeSurfer experts,
I am getting this strange error when running selxavg3-sess. (in selxavg3 command I am calling the analysis file with: -a rtopyTR2.rh) When the system enters fast_selxavg3, it cannot read analysis.info, thus produces the following output:
#@# Sess05 ############################### /home/vm01/local/freesurfer/Project_bold/Sess05 ------------------------- $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $ ------------------------- outtop = /home/vm01/local/freesurfer/Project_bold Extension format = nii.gz ERROR: could not open rtopyTR2.rh/analysis.info else else echo "------------------------------------------" | tee -a $LF echo ------------------------------------------ tee -a /home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log ------------------------------------------ rm $MLF rm /tmp/selxavg3-sess-10173.m if ( ! -e $okfile ) then if ( ! -e /tmp/selxavg3-sess-10173.ok ) then echo "ERROR: fast_selxavg3() failed\n" ; echo ERROR: fast_selxavg3() failed\n ERROR: fast_selxavg3() failed\n exit 1 ; exit 1
The analysis folder it is referring to( rtopyTR2.rh) is in the directory from which I am calling selxavg3-sess. It has the analysis.info file in which doesn't have any restrictions. To troubleshoot, I moved the folder to inside the session's functional directory and inside the session folder and these didn't create any changes. I looked at the script and tried to debug there but didn't give any results. It gave a similar error when trying to open the config file of contrast in mkcontrast-sess. (I also don't have root access)Any help is appreciated!
Best, Idil
Does the file /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? If so, can you run it with -debug as the first option and send the terminal output?
On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:
Hello FreeSurfer experts,
I am getting this strange error when running selxavg3-sess. (in selxavg3 command I am calling the analysis file with: -a rtopyTR2.rh) When the system enters fast_selxavg3, it cannot read analysis.info, thus produces the following output:
#@# Sess05 ############################### /home/vm01/local/freesurfer/Project_bold/Sess05
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
outtop = /home/vm01/local/freesurfer/Project_bold Extension format = nii.gz ERROR: could not open rtopyTR2.rh/analysis.info else else echo "------------------------------------------" | tee -a $LF echo ------------------------------------------ tee -a /home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log
rm $MLF rm /tmp/selxavg3-sess-10173.m if ( ! -e $okfile ) then if ( ! -e /tmp/selxavg3-sess-10173.ok ) then echo "ERROR: fast_selxavg3() failed\n" ; echo ERROR: fast_selxavg3() failed\n ERROR: fast_selxavg3() failed\n exit 1 ; exit 1
The analysis folder it is referring to( rtopyTR2.rh) is in the directory from which I am calling selxavg3-sess. It has the analysis.info file in which doesn't have any restrictions. To troubleshoot, I moved the folder to inside the session's functional directory and inside the session folder and these didn't create any changes. I looked at the script and tried to debug there but didn't give any results. It gave a similar error when trying to open the config file of contrast in mkcontrast-sess. (I also don't have root access)Any help is appreciated!
Best, Idil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Dr. Greve,
Yes it exists. The output below was with debug option.
Best Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, January 30, 2018 8:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
Does the file /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? If so, can you run it with -debug as the first option and send the terminal output?
On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:
Hello FreeSurfer experts,
I am getting this strange error when running selxavg3-sess. (in selxavg3 command I am calling the analysis file with: -a rtopyTR2.rh) When the system enters fast_selxavg3, it cannot read analysis.info, thus produces the following output:
#@# Sess05 ############################### /home/vm01/local/freesurfer/Project_bold/Sess05 ------------------------- $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $ ------------------------- outtop = /home/vm01/local/freesurfer/Project_bold Extension format = nii.gz ERROR: could not open rtopyTR2.rh/analysis.info else else echo "------------------------------------------" | tee -a $LF echo ------------------------------------------ tee -a /home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log ------------------------------------------ rm $MLF rm /tmp/selxavg3-sess-10173.m if ( ! -e $okfile ) then if ( ! -e /tmp/selxavg3-sess-10173.ok ) then echo "ERROR: fast_selxavg3() failed\n" ; echo ERROR: fast_selxavg3() failed\n ERROR: fast_selxavg3() failed\n exit 1 ; exit 1
The analysis folder it is referring to( rtopyTR2.rh) is in the directory from which I am calling selxavg3-sess. It has the analysis.info file in which doesn't have any restrictions. To troubleshoot, I moved the folder to inside the session's functional directory and inside the session folder and these didn't create any changes. I looked at the script and tried to debug there but didn't give any results. It gave a similar error when trying to open the config file of contrast in mkcontrast-sess. (I also don't have root access)Any help is appreciated!
Best, Idil
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Strange. Can you send me the analysis.info file?
On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
Hello Dr. Greve,
Yes it exists. The output below was with debug option.
Best Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, January 30, 2018 8:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
Does the file /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? If so, can you run it with -debug as the first option and send the terminal output?
On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:
Hello FreeSurfer experts,
I am getting this strange error when running selxavg3-sess. (in selxavg3 command I am calling the analysis file with: -a rtopyTR2.rh) When the system enters fast_selxavg3, it cannot read analysis.info, thus produces the following output:
#@# Sess05 ############################### /home/vm01/local/freesurfer/Project_bold/Sess05
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
outtop = /home/vm01/local/freesurfer/Project_bold Extension format = nii.gz ERROR: could not open rtopyTR2.rh/analysis.info else else echo "------------------------------------------" | tee -a $LF echo ------------------------------------------ tee -a /home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log
rm $MLF rm /tmp/selxavg3-sess-10173.m if ( ! -e $okfile ) then if ( ! -e /tmp/selxavg3-sess-10173.ok ) then echo "ERROR: fast_selxavg3() failed\n" ; echo ERROR: fast_selxavg3() failed\n ERROR: fast_selxavg3() failed\n exit 1 ; exit 1
The analysis folder it is referring to( rtopyTR2.rh) is in the directory from which I am calling selxavg3-sess. It has the analysis.info file in which doesn't have any restrictions. To troubleshoot, I moved the folder to inside the session's functional directory and inside the session folder and these didn't create any changes. I looked at the script and tried to debug there but didn't give any results. It gave a similar error when trying to open the config file of contrast in mkcontrast-sess. (I also don't have root access)Any help is appreciated!
Best, Idil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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
Hello Dr. Greve,
The analysis.info file is below. I should also say that, when I am trying to create new analysis and contrast files, while creating the .config file for contrast, th system gives the same error saying that it cannot enter the file.
# FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c # MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $ # MKACMD /home/vm01/local/freesurfer/fsfast/bin/mkanalysis-sess -surface self lh -analysis rtopyTR2.lh -paradigm rtopy.par -TR 2 -nconditions 1 -event-related -fwhm 5 -per-run -fsd bold -refeventdur 10 -gammafit 2.25 1.25 -force # DATE Tue Jan 30 07:14:05 EST 2018
analysis rtopyTR2.lh mcstem fmcpr fsd bold TR 2 RegDOF 6 PerSession 0 RawSpace surface self lh mask brain RawFWHM 5 RawSTC none nSliceGroups 1 UseB0DC 0 ApplySubCortMask 1 inorm 100 acfbins 30 fixacf 1 acffwhm 20 acfsvd 0 designtype event-related nskip 0 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 nconditions 1 parname rtopy.par RefEventDur 10 timewindow 40.000000 prestim 0 TER 0.050000 gamma 2.25 1.25 2 0 stimulusdelay -1.00000000000000000000 Condition 1 Condition01
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Saturday, February 03, 2018 9:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
Strange. Can you send me the analysis.info file?
On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
Hello Dr. Greve,
Yes it exists. The output below was with debug option.
Best Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, January 30, 2018 8:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
Does the file /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? If so, can you run it with -debug as the first option and send the terminal output?
On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:
Hello FreeSurfer experts,
I am getting this strange error when running selxavg3-sess. (in selxavg3 command I am calling the analysis file with: -a rtopyTR2.rh) When the system enters fast_selxavg3, it cannot read analysis.info, thus produces the following output:
#@# Sess05 ############################### /home/vm01/local/freesurfer/Project_bold/Sess05
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
outtop = /home/vm01/local/freesurfer/Project_bold Extension format = nii.gz ERROR: could not open rtopyTR2.rh/analysis.info else else echo "------------------------------------------" | tee -a $LF echo ------------------------------------------ tee -a /home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log
rm $MLF rm /tmp/selxavg3-sess-10173.m if ( ! -e $okfile ) then if ( ! -e /tmp/selxavg3-sess-10173.ok ) then echo "ERROR: fast_selxavg3() failed\n" ; echo ERROR: fast_selxavg3() failed\n ERROR: fast_selxavg3() failed\n exit 1 ; exit 1
The analysis folder it is referring to( rtopyTR2.rh) is in the directory from which I am calling selxavg3-sess. It has the analysis.info file in which doesn't have any restrictions. To troubleshoot, I moved the folder to inside the session's functional directory and inside the session folder and these didn't create any changes. I looked at the script and tried to debug there but didn't give any results. It gave a similar error when trying to open the config file of contrast in mkcontrast-sess. (I also don't have root access)Any help is appreciated!
Best, Idil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 dispose of the e-mail.
I cannot replicate this. There must be some strange permission error. Can you try to make a new analysis with a different name and just see if fails?
On 2/4/18 12:50 PM, Yagmur Ozdemir 19 wrote:
Hello Dr. Greve,
The analysis.info file is below. I should also say that, when I am trying to create new analysis and contrast files, while creating the .config file for contrast, th system gives the same error saying that it cannot enter the file.
# FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c # MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $ # MKACMD /home/vm01/local/freesurfer/fsfast/bin/mkanalysis-sess -surface self lh -analysis rtopyTR2.lh -paradigm rtopy.par -TR 2 -nconditions 1 -event-related -fwhm 5 -per-run -fsd bold -refeventdur 10 -gammafit 2.25 1.25 -force # DATE Tue Jan 30 07:14:05 EST 2018
analysis rtopyTR2.lh mcstem fmcpr fsd bold TR 2 RegDOF 6 PerSession 0 RawSpace surface self lh mask brain RawFWHM 5 RawSTC none nSliceGroups 1 UseB0DC 0 ApplySubCortMask 1 inorm 100 acfbins 30 fixacf 1 acffwhm 20 acfsvd 0 designtype event-related nskip 0 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 nconditions 1 parname rtopy.par RefEventDur 10 timewindow 40.000000 prestim 0 TER 0.050000 gamma 2.25 1.25 2 0 stimulusdelay -1.00000000000000000000 Condition 1 Condition01
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Saturday, February 03, 2018 9:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
Strange. Can you send me the analysis.info file?
On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
Hello Dr. Greve,
Yes it exists. The output below was with debug option.
Best Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, January 30, 2018 8:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
Does the file /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? If so, can you run it with -debug as the first option and send the terminal output?
On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:
Hello FreeSurfer experts,
I am getting this strange error when running selxavg3-sess. (in selxavg3 command I am calling the analysis file with: -a rtopyTR2.rh) When the system enters fast_selxavg3, it cannot read analysis.info, thus produces the following output:
#@# Sess05 ############################### /home/vm01/local/freesurfer/Project_bold/Sess05
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
outtop = /home/vm01/local/freesurfer/Project_bold Extension format = nii.gz ERROR: could not open rtopyTR2.rh/analysis.info else else echo "------------------------------------------" | tee -a $LF echo ------------------------------------------ tee -a /home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log
rm $MLF rm /tmp/selxavg3-sess-10173.m if ( ! -e $okfile ) then if ( ! -e /tmp/selxavg3-sess-10173.ok ) then echo "ERROR: fast_selxavg3() failed\n" ; echo ERROR: fast_selxavg3() failed\n ERROR: fast_selxavg3() failed\n exit 1 ; exit 1
The analysis folder it is referring to( rtopyTR2.rh) is in the directory from which I am calling selxavg3-sess. It has the analysis.info file in which doesn't have any restrictions. To troubleshoot, I moved the folder to inside the session's functional directory and inside the session folder and these didn't create any changes. I looked at the script and tried to debug there but didn't give any results. It gave a similar error when trying to open the config file of contrast in mkcontrast-sess. (I also don't have root access)Any help is appreciated!
Best, Idil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dr. Greve,
Yes I have tried making new files. (I also gave the previous files and folders full permission with chmod which again didn't work) Mkanalysis-sess did not have any problems as expected, but mkcontrast-sess failed for the same reason of not being able to open the .config file that it should be creating under the analysis folder.
I am not the root user of the system, but maybe getting sudo access would be helpful? I can look into this.
Best Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, February 05, 2018 6:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
I cannot replicate this. There must be some strange permission error. Can you try to make a new analysis with a different name and just see if fails?
On 2/4/18 12:50 PM, Yagmur Ozdemir 19 wrote:
Hello Dr. Greve,
The analysis.info file is below. I should also say that, when I am trying to create new analysis and contrast files, while creating the .config file for contrast, th system gives the same error saying that it cannot enter the file.
# FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c # MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $ # MKACMD /home/vm01/local/freesurfer/fsfast/bin/mkanalysis-sess -surface self lh -analysis rtopyTR2.lh -paradigm rtopy.par -TR 2 -nconditions 1 -event-related -fwhm 5 -per-run -fsd bold -refeventdur 10 -gammafit 2.25 1.25 -force # DATE Tue Jan 30 07:14:05 EST 2018
analysis rtopyTR2.lh mcstem fmcpr fsd bold TR 2 RegDOF 6 PerSession 0 RawSpace surface self lh mask brain RawFWHM 5 RawSTC none nSliceGroups 1 UseB0DC 0 ApplySubCortMask 1 inorm 100 acfbins 30 fixacf 1 acffwhm 20 acfsvd 0 designtype event-related nskip 0 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 nconditions 1 parname rtopy.par RefEventDur 10 timewindow 40.000000 prestim 0 TER 0.050000 gamma 2.25 1.25 2 0 stimulusdelay -1.00000000000000000000 Condition 1 Condition01
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Saturday, February 03, 2018 9:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
Strange. Can you send me the analysis.info file?
On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
Hello Dr. Greve,
Yes it exists. The output below was with debug option.
Best Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, January 30, 2018 8:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
Does the file /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? If so, can you run it with -debug as the first option and send the terminal output?
On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:
Hello FreeSurfer experts,
I am getting this strange error when running selxavg3-sess. (in selxavg3 command I am calling the analysis file with: -a rtopyTR2.rh) When the system enters fast_selxavg3, it cannot read analysis.info, thus produces the following output:
#@# Sess05 ############################### /home/vm01/local/freesurfer/Project_bold/Sess05
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
outtop = /home/vm01/local/freesurfer/Project_bold Extension format = nii.gz ERROR: could not open rtopyTR2.rh/analysis.info else else echo "------------------------------------------" | tee -a $LF echo ------------------------------------------ tee -a /home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log
rm $MLF rm /tmp/selxavg3-sess-10173.m if ( ! -e $okfile ) then if ( ! -e /tmp/selxavg3-sess-10173.ok ) then echo "ERROR: fast_selxavg3() failed\n" ; echo ERROR: fast_selxavg3() failed\n ERROR: fast_selxavg3() failed\n exit 1 ; exit 1
The analysis folder it is referring to( rtopyTR2.rh) is in the directory from which I am calling selxavg3-sess. It has the analysis.info file in which doesn't have any restrictions. To troubleshoot, I moved the folder to inside the session's functional directory and inside the session folder and these didn't create any changes. I looked at the script and tried to debug there but didn't give any results. It gave a similar error when trying to open the config file of contrast in mkcontrast-sess. (I also don't have root access)Any help is appreciated!
Best, Idil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 dispose of the e-mail.
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
I don't know, it is all very weird. What platform are you using?
On 02/05/2018 01:27 PM, Yagmur Ozdemir 19 wrote:
Dr. Greve,
Yes I have tried making new files. (I also gave the previous files and folders full permission with chmod which again didn't work) Mkanalysis-sess did not have any problems as expected, but mkcontrast-sess failed for the same reason of not being able to open the .config file that it should be creating under the analysis folder.
I am not the root user of the system, but maybe getting sudo access would be helpful? I can look into this.
Best Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, February 05, 2018 6:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
I cannot replicate this. There must be some strange permission error. Can you try to make a new analysis with a different name and just see if fails?
On 2/4/18 12:50 PM, Yagmur Ozdemir 19 wrote:
Hello Dr. Greve,
The analysis.info file is below. I should also say that, when I am trying to create new analysis and contrast files, while creating the .config file for contrast, th system gives the same error saying that it cannot enter the file.
# FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c # MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $ # MKACMD /home/vm01/local/freesurfer/fsfast/bin/mkanalysis-sess -surface self lh -analysis rtopyTR2.lh -paradigm rtopy.par -TR 2 -nconditions 1 -event-related -fwhm 5 -per-run -fsd bold -refeventdur 10 -gammafit 2.25 1.25 -force # DATE Tue Jan 30 07:14:05 EST 2018
analysis rtopyTR2.lh mcstem fmcpr fsd bold TR 2 RegDOF 6 PerSession 0 RawSpace surface self lh mask brain RawFWHM 5 RawSTC none nSliceGroups 1 UseB0DC 0 ApplySubCortMask 1 inorm 100 acfbins 30 fixacf 1 acffwhm 20 acfsvd 0 designtype event-related nskip 0 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 nconditions 1 parname rtopy.par RefEventDur 10 timewindow 40.000000 prestim 0 TER 0.050000 gamma 2.25 1.25 2 0 stimulusdelay -1.00000000000000000000 Condition 1 Condition01
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Saturday, February 03, 2018 9:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
Strange. Can you send me the analysis.info file?
On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
Hello Dr. Greve,
Yes it exists. The output below was with debug option.
Best Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, January 30, 2018 8:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
Does the file /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? If so, can you run it with -debug as the first option and send the terminal output?
On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:
Hello FreeSurfer experts,
I am getting this strange error when running selxavg3-sess. (in selxavg3 command I am calling the analysis file with: -a rtopyTR2.rh) When the system enters fast_selxavg3, it cannot read analysis.info, thus produces the following output:
#@# Sess05 ############################### /home/vm01/local/freesurfer/Project_bold/Sess05
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
outtop = /home/vm01/local/freesurfer/Project_bold Extension format = nii.gz ERROR: could not open rtopyTR2.rh/analysis.info else else echo "------------------------------------------" | tee -a $LF echo ------------------------------------------ tee -a /home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log
rm $MLF rm /tmp/selxavg3-sess-10173.m if ( ! -e $okfile ) then if ( ! -e /tmp/selxavg3-sess-10173.ok ) then echo "ERROR: fast_selxavg3() failed\n" ; echo ERROR: fast_selxavg3() failed\n ERROR: fast_selxavg3() failed\n exit 1 ; exit 1
The analysis folder it is referring to( rtopyTR2.rh) is in the directory from which I am calling selxavg3-sess. It has the analysis.info file in which doesn't have any restrictions. To troubleshoot, I moved the folder to inside the session's functional directory and inside the session folder and these didn't create any changes. I looked at the script and tried to debug there but didn't give any results. It gave a similar error when trying to open the config file of contrast in mkcontrast-sess. (I also don't have root access)Any help is appreciated!
Best, Idil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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
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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 dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Dr. Greve,
I tried with root access and it still gave the same error. I am using a virtual machine from our server that I connect with VCN, and it has freesurfer and matlab installed and setup in its shell. The VM has Ubuntu 16.04 (Xenial), Freesurfer v.6, and Matlab R2016b. I appreciate your help.
Best Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, February 05, 2018 8:34 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
I don't know, it is all very weird. What platform are you using?
On 02/05/2018 01:27 PM, Yagmur Ozdemir 19 wrote:
Dr. Greve,
Yes I have tried making new files. (I also gave the previous files and folders full permission with chmod which again didn't work) Mkanalysis-sess did not have any problems as expected, but mkcontrast-sess failed for the same reason of not being able to open the .config file that it should be creating under the analysis folder.
I am not the root user of the system, but maybe getting sudo access would be helpful? I can look into this.
Best Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, February 05, 2018 6:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
I cannot replicate this. There must be some strange permission error. Can you try to make a new analysis with a different name and just see if fails?
On 2/4/18 12:50 PM, Yagmur Ozdemir 19 wrote:
Hello Dr. Greve,
The analysis.info file is below. I should also say that, when I am trying to create new analysis and contrast files, while creating the .config file for contrast, th system gives the same error saying that it cannot enter the file.
# FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c # MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $ # MKACMD /home/vm01/local/freesurfer/fsfast/bin/mkanalysis-sess -surface self lh -analysis rtopyTR2.lh -paradigm rtopy.par -TR 2 -nconditions 1 -event-related -fwhm 5 -per-run -fsd bold -refeventdur 10 -gammafit 2.25 1.25 -force # DATE Tue Jan 30 07:14:05 EST 2018
analysis rtopyTR2.lh mcstem fmcpr fsd bold TR 2 RegDOF 6 PerSession 0 RawSpace surface self lh mask brain RawFWHM 5 RawSTC none nSliceGroups 1 UseB0DC 0 ApplySubCortMask 1 inorm 100 acfbins 30 fixacf 1 acffwhm 20 acfsvd 0 designtype event-related nskip 0 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 nconditions 1 parname rtopy.par RefEventDur 10 timewindow 40.000000 prestim 0 TER 0.050000 gamma 2.25 1.25 2 0 stimulusdelay -1.00000000000000000000 Condition 1 Condition01
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Saturday, February 03, 2018 9:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
Strange. Can you send me the analysis.info file?
On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
Hello Dr. Greve,
Yes it exists. The output below was with debug option.
Best Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, January 30, 2018 8:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
Does the file /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? If so, can you run it with -debug as the first option and send the terminal output?
On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:
Hello FreeSurfer experts,
I am getting this strange error when running selxavg3-sess. (in selxavg3 command I am calling the analysis file with: -a rtopyTR2.rh) When the system enters fast_selxavg3, it cannot read analysis.info, thus produces the following output:
#@# Sess05 ############################### /home/vm01/local/freesurfer/Project_bold/Sess05
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
outtop = /home/vm01/local/freesurfer/Project_bold Extension format = nii.gz ERROR: could not open rtopyTR2.rh/analysis.info else else echo "------------------------------------------" | tee -a $LF echo ------------------------------------------ tee -a /home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log
rm $MLF rm /tmp/selxavg3-sess-10173.m if ( ! -e $okfile ) then if ( ! -e /tmp/selxavg3-sess-10173.ok ) then echo "ERROR: fast_selxavg3() failed\n" ; echo ERROR: fast_selxavg3() failed\n ERROR: fast_selxavg3() failed\n exit 1 ; exit 1
The analysis folder it is referring to( rtopyTR2.rh) is in the directory from which I am calling selxavg3-sess. It has the analysis.info file in which doesn't have any restrictions. To troubleshoot, I moved the folder to inside the session's functional directory and inside the session folder and these didn't create any changes. I looked at the script and tried to debug there but didn't give any results. It gave a similar error when trying to open the config file of contrast in mkcontrast-sess. (I also don't have root access)Any help is appreciated!
Best, Idil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 dispose of the e-mail.
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Try running selxavg3-sess with -monly sxa3.m
Then start matlab and run sxa3.m
On 02/05/2018 02:02 PM, Yagmur Ozdemir 19 wrote:
Dr. Greve,
I tried with root access and it still gave the same error. I am using a virtual machine from our server that I connect with VCN, and it has freesurfer and matlab installed and setup in its shell. The VM has Ubuntu 16.04 (Xenial), Freesurfer v.6, and Matlab R2016b. I appreciate your help.
Best Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, February 05, 2018 8:34 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
I don't know, it is all very weird. What platform are you using?
On 02/05/2018 01:27 PM, Yagmur Ozdemir 19 wrote:
Dr. Greve,
Yes I have tried making new files. (I also gave the previous files and folders full permission with chmod which again didn't work) Mkanalysis-sess did not have any problems as expected, but mkcontrast-sess failed for the same reason of not being able to open the .config file that it should be creating under the analysis folder.
I am not the root user of the system, but maybe getting sudo access would be helpful? I can look into this.
Best Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, February 05, 2018 6:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
I cannot replicate this. There must be some strange permission error. Can you try to make a new analysis with a different name and just see if fails?
On 2/4/18 12:50 PM, Yagmur Ozdemir 19 wrote:
Hello Dr. Greve,
The analysis.info file is below. I should also say that, when I am trying to create new analysis and contrast files, while creating the .config file for contrast, th system gives the same error saying that it cannot enter the file.
# FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c # MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $ # MKACMD /home/vm01/local/freesurfer/fsfast/bin/mkanalysis-sess -surface self lh -analysis rtopyTR2.lh -paradigm rtopy.par -TR 2 -nconditions 1 -event-related -fwhm 5 -per-run -fsd bold -refeventdur 10 -gammafit 2.25 1.25 -force # DATE Tue Jan 30 07:14:05 EST 2018
analysis rtopyTR2.lh mcstem fmcpr fsd bold TR 2 RegDOF 6 PerSession 0 RawSpace surface self lh mask brain RawFWHM 5 RawSTC none nSliceGroups 1 UseB0DC 0 ApplySubCortMask 1 inorm 100 acfbins 30 fixacf 1 acffwhm 20 acfsvd 0 designtype event-related nskip 0 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 nconditions 1 parname rtopy.par RefEventDur 10 timewindow 40.000000 prestim 0 TER 0.050000 gamma 2.25 1.25 2 0 stimulusdelay -1.00000000000000000000 Condition 1 Condition01
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Saturday, February 03, 2018 9:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
Strange. Can you send me the analysis.info file?
On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
Hello Dr. Greve,
Yes it exists. The output below was with debug option.
Best Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, January 30, 2018 8:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
Does the file /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? If so, can you run it with -debug as the first option and send the terminal output?
On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:
Hello FreeSurfer experts,
I am getting this strange error when running selxavg3-sess. (in selxavg3 command I am calling the analysis file with: -a rtopyTR2.rh) When the system enters fast_selxavg3, it cannot read analysis.info, thus produces the following output:
#@# Sess05 ############################### /home/vm01/local/freesurfer/Project_bold/Sess05
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
outtop = /home/vm01/local/freesurfer/Project_bold Extension format = nii.gz ERROR: could not open rtopyTR2.rh/analysis.info else else echo "------------------------------------------" | tee -a $LF echo ------------------------------------------ tee -a /home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log
rm $MLF rm /tmp/selxavg3-sess-10173.m if ( ! -e $okfile ) then if ( ! -e /tmp/selxavg3-sess-10173.ok ) then echo "ERROR: fast_selxavg3() failed\n" ; echo ERROR: fast_selxavg3() failed\n ERROR: fast_selxavg3() failed\n exit 1 ; exit 1
The analysis folder it is referring to( rtopyTR2.rh) is in the directory from which I am calling selxavg3-sess. It has the analysis.info file in which doesn't have any restrictions. To troubleshoot, I moved the folder to inside the session's functional directory and inside the session folder and these didn't create any changes. I looked at the script and tried to debug there but didn't give any results. It gave a similar error when trying to open the config file of contrast in mkcontrast-sess. (I also don't have root access)Any help is appreciated!
Best, Idil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 dispose of the e-mail.
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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
That works, thank you!
Best Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, February 05, 2018 9:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
Try running selxavg3-sess with -monly sxa3.m
Then start matlab and run sxa3.m
On 02/05/2018 02:02 PM, Yagmur Ozdemir 19 wrote:
Dr. Greve,
I tried with root access and it still gave the same error. I am using a virtual machine from our server that I connect with VCN, and it has freesurfer and matlab installed and setup in its shell. The VM has Ubuntu 16.04 (Xenial), Freesurfer v.6, and Matlab R2016b. I appreciate your help.
Best Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, February 05, 2018 8:34 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
I don't know, it is all very weird. What platform are you using?
On 02/05/2018 01:27 PM, Yagmur Ozdemir 19 wrote:
Dr. Greve,
Yes I have tried making new files. (I also gave the previous files and folders full permission with chmod which again didn't work) Mkanalysis-sess did not have any problems as expected, but mkcontrast-sess failed for the same reason of not being able to open the .config file that it should be creating under the analysis folder.
I am not the root user of the system, but maybe getting sudo access would be helpful? I can look into this.
Best Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, February 05, 2018 6:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
I cannot replicate this. There must be some strange permission error. Can you try to make a new analysis with a different name and just see if fails?
On 2/4/18 12:50 PM, Yagmur Ozdemir 19 wrote:
Hello Dr. Greve,
The analysis.info file is below. I should also say that, when I am trying to create new analysis and contrast files, while creating the .config file for contrast, th system gives the same error saying that it cannot enter the file.
# FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c # MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $ # MKACMD /home/vm01/local/freesurfer/fsfast/bin/mkanalysis-sess -surface self lh -analysis rtopyTR2.lh -paradigm rtopy.par -TR 2 -nconditions 1 -event-related -fwhm 5 -per-run -fsd bold -refeventdur 10 -gammafit 2.25 1.25 -force # DATE Tue Jan 30 07:14:05 EST 2018
analysis rtopyTR2.lh mcstem fmcpr fsd bold TR 2 RegDOF 6 PerSession 0 RawSpace surface self lh mask brain RawFWHM 5 RawSTC none nSliceGroups 1 UseB0DC 0 ApplySubCortMask 1 inorm 100 acfbins 30 fixacf 1 acffwhm 20 acfsvd 0 designtype event-related nskip 0 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 nconditions 1 parname rtopy.par RefEventDur 10 timewindow 40.000000 prestim 0 TER 0.050000 gamma 2.25 1.25 2 0 stimulusdelay -1.00000000000000000000 Condition 1 Condition01
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Saturday, February 03, 2018 9:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
Strange. Can you send me the analysis.info file?
On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
Hello Dr. Greve,
Yes it exists. The output below was with debug option.
Best Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, January 30, 2018 8:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
Does the file /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? If so, can you run it with -debug as the first option and send the terminal output?
On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:
Hello FreeSurfer experts,
I am getting this strange error when running selxavg3-sess. (in selxavg3 command I am calling the analysis file with: -a rtopyTR2.rh) When the system enters fast_selxavg3, it cannot read analysis.info, thus produces the following output:
#@# Sess05 ############################### /home/vm01/local/freesurfer/Project_bold/Sess05
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
outtop = /home/vm01/local/freesurfer/Project_bold Extension format = nii.gz ERROR: could not open rtopyTR2.rh/analysis.info else else echo "------------------------------------------" | tee -a $LF echo ------------------------------------------ tee -a /home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log
rm $MLF rm /tmp/selxavg3-sess-10173.m if ( ! -e $okfile ) then if ( ! -e /tmp/selxavg3-sess-10173.ok ) then echo "ERROR: fast_selxavg3() failed\n" ; echo ERROR: fast_selxavg3() failed\n ERROR: fast_selxavg3() failed\n exit 1 ; exit 1
The analysis folder it is referring to( rtopyTR2.rh) is in the directory from which I am calling selxavg3-sess. It has the analysis.info file in which doesn't have any restrictions. To troubleshoot, I moved the folder to inside the session's functional directory and inside the session folder and these didn't create any changes. I looked at the script and tried to debug there but didn't give any results. It gave a similar error when trying to open the config file of contrast in mkcontrast-sess. (I also don't have root access)Any help is appreciated!
Best, Idil
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good, but that is not a long-term solution. I don't know why that is working but it does not work when you run it from the shell. There must be some kind of permission or id change when you run it from the shell. I don't know.
On 2/6/18 8:55 AM, Yagmur Ozdemir 19 wrote:
That works, thank you!
Best Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, February 05, 2018 9:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
Try running selxavg3-sess with -monly sxa3.m
Then start matlab and run sxa3.m
On 02/05/2018 02:02 PM, Yagmur Ozdemir 19 wrote:
Dr. Greve,
I tried with root access and it still gave the same error. I am using a virtual machine from our server that I connect with VCN, and it has freesurfer and matlab installed and setup in its shell. The VM has Ubuntu 16.04 (Xenial), Freesurfer v.6, and Matlab R2016b. I appreciate your help.
Best Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, February 05, 2018 8:34 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
I don't know, it is all very weird. What platform are you using?
On 02/05/2018 01:27 PM, Yagmur Ozdemir 19 wrote:
Dr. Greve,
Yes I have tried making new files. (I also gave the previous files and folders full permission with chmod which again didn't work) Mkanalysis-sess did not have any problems as expected, but mkcontrast-sess failed for the same reason of not being able to open the .config file that it should be creating under the analysis folder.
I am not the root user of the system, but maybe getting sudo access would be helpful? I can look into this.
Best Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, February 05, 2018 6:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
I cannot replicate this. There must be some strange permission error. Can you try to make a new analysis with a different name and just see if fails?
On 2/4/18 12:50 PM, Yagmur Ozdemir 19 wrote:
Hello Dr. Greve,
The analysis.info file is below. I should also say that, when I am trying to create new analysis and contrast files, while creating the .config file for contrast, th system gives the same error saying that it cannot enter the file.
# FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c # MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $ # MKACMD /home/vm01/local/freesurfer/fsfast/bin/mkanalysis-sess -surface self lh -analysis rtopyTR2.lh -paradigm rtopy.par -TR 2 -nconditions 1 -event-related -fwhm 5 -per-run -fsd bold -refeventdur 10 -gammafit 2.25 1.25 -force # DATE Tue Jan 30 07:14:05 EST 2018
analysis rtopyTR2.lh mcstem fmcpr fsd bold TR 2 RegDOF 6 PerSession 0 RawSpace surface self lh mask brain RawFWHM 5 RawSTC none nSliceGroups 1 UseB0DC 0 ApplySubCortMask 1 inorm 100 acfbins 30 fixacf 1 acffwhm 20 acfsvd 0 designtype event-related nskip 0 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 nconditions 1 parname rtopy.par RefEventDur 10 timewindow 40.000000 prestim 0 TER 0.050000 gamma 2.25 1.25 2 0 stimulusdelay -1.00000000000000000000 Condition 1 Condition01
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Saturday, February 03, 2018 9:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
Strange. Can you send me the analysis.info file?
On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
Hello Dr. Greve,
Yes it exists. The output below was with debug option.
Best Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, January 30, 2018 8:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
Does the file /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? If so, can you run it with -debug as the first option and send the terminal output?
On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:
Hello FreeSurfer experts,
I am getting this strange error when running selxavg3-sess. (in selxavg3 command I am calling the analysis file with: -a rtopyTR2.rh) When the system enters fast_selxavg3, it cannot read analysis.info, thus produces the following output:
#@# Sess05 ############################### /home/vm01/local/freesurfer/Project_bold/Sess05
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
outtop = /home/vm01/local/freesurfer/Project_bold Extension format = nii.gz ERROR: could not open rtopyTR2.rh/analysis.info else else echo "------------------------------------------" | tee -a $LF echo ------------------------------------------ tee -a /home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log
rm $MLF rm /tmp/selxavg3-sess-10173.m if ( ! -e $okfile ) then if ( ! -e /tmp/selxavg3-sess-10173.ok ) then echo "ERROR: fast_selxavg3() failed\n" ; echo ERROR: fast_selxavg3() failed\n ERROR: fast_selxavg3() failed\n exit 1 ; exit 1
The analysis folder it is referring to( rtopyTR2.rh) is in the directory from which I am calling selxavg3-sess. It has the analysis.info file in which doesn't have any restrictions. To troubleshoot, I moved the folder to inside the session's functional directory and inside the session folder and these didn't create any changes. I looked at the script and tried to debug there but didn't give any results. It gave a similar error when trying to open the config file of contrast in mkcontrast-sess. (I also don't have root access)Any help is appreciated!
Best, Idil
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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 dispose of the e-mail.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Yagmur Ozdemir 19