Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@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-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >> [gr...@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-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve >>> [gr...@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 40.00 >>>> prestim 0 >>>> TER 0.05 >>>> gamma 2.25 1.25 2 0 >>>> stimulusdela
Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
That works, thank you! Best Idil From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@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-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve >> [gr...@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 40.00 >>> prestim 0 >>> TER 0.05 >>> gamma 2.25 1.25 2 0 >>> stimulusdelay -1. >>> Condition 1 Condition01 >>> >>> Best, >>> Idil >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve >>> [gr...@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, >&g
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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@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-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve >> [gr...@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 40.00 >>> prestim 0 >>> TER 0.05 >>> gamma 2.25 1.25 2 0 >>> stimulusdelay -1. >>> Condition 1 Condition01 >>> >>> Best, >>> Idil >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve >>> [gr...@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-boun...@nmr.mgh.harvard.edu >>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve >&g
Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve > [gr...@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 40.00 >> prestim 0 >> TER 0.05 >> gamma 2.25 1.25 2 0 >> stimulusdelay -1.000000000000 >> Condition 1 Condition01 >> >> Best, >> Idil >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve >> [gr...@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-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve >>> [gr...@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 th
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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve > [gr...@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 40.00 >> prestim 0 >> TER 0.05 >> gamma 2.25 1.25 2 0 >> stimulusdelay -1.000000000000 >> Condition 1 Condition01 >> >> Best, >> Idil >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve >> [gr...@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-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve >>> [gr...@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 =
Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@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 40.00 > prestim 0 > TER 0.05 > gamma 2.25 1.25 2 0 > stimulusdelay -1. > Condition 1 Condition01 > > Best, > Idil > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve > [gr...@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-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve >> [gr...@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_selxa
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 40.00 > prestim 0 > TER 0.05 > gamma 2.25 1.25 2 0 > stimulusdelay -1. > Condition 1 Condition01 > > Best, > Idil > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve > [gr...@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-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve >> [gr...@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 >> >> >> &
Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
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 40.00 prestim 0 TER 0.05 gamma 2.25 1.25 2 0 stimulusdelay -1. Condition 1 Condition01 Best, Idil From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve > [gr...@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.edu<mailto: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 th
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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve > [gr...@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.edu<mailto: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.
Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
Hello Dr. Greve, Yes it exists. The output below was with debug option. Best Idil From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@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.edu<mailto: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.
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.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.
