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