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 40.000000 >>> prestim 0 >>> TER 0.050000 >>> gamma 2.25 1.25 2 0 >>> stimulusdelay -1.00000000000000000000 >>> 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 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 > gr...@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 > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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
