[Freesurfer] if: Expression Syntax
Hi there, When running selxavg for the following session: nmasa_031_130412 The following error message was generated: Error using MRIread (line 76) ERROR: cannot determine format of /autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm (MRIread) Error in fast_selxavg3 (line 146) runmask = MRIread(flac.maskfspec); I did some investigating and discovered that all the bold runs for this participant are missing the following files: .../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz So I ran: preproc-sess -s nmasa_031_130412 -fsd bold -stc up -surface fsaverage lhrh -min305 -fwhm 5 -per Which generated the following error message: if: Expression Syntax Do you have any idea what might be going wrong with this subject or what this error message (if: Expression Syntax) means? Thanks, Keji --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu ___ 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] if: Expression Syntax
Hi there, I’m running stable: source /usr/local/freesurfer/stable5_3_0 Thanks, Keji > On Jul 21, 2015, at 4:56 PM, Douglas Greve wrote: > > what environment are you running in? ie, dev or stable? > > On 7/21/15 2:12 PM, Morenikeji Adebayo wrote: >> Hi there, >> >> When running selxavg for the following session: >> >> >> >> nmasa_031_130412 >> >> >> >> The following >> error message was generated: >> >> >> >> Error using MRIread (line 76) >> ERROR: cannot determine format of >> /autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm >> (MRIread) >> >> >> >> Error in fast_selxavg3 (line 146) >> runmask = MRIread(flac.maskfspec); >> >> I did some investigating and discovered that all the bold runs for this >> participant are missing the following files: >> >> .../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm >> >> .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz >> .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz >> >> >> >> So I ran: >> >> >> >> preproc-sess -s >> nmasa_031_130412 -fsd bold -stc up -surface >> fsaverage lhrh -min305 -fwhm 5 -per >> >> >> >> >> >> >> Which generated the following error >> message: >> >> >> >> if: Expression Syntax >> >> Do you have any idea >> what might be going wrong with this subject or what >> this error message (if: Expression Syntax) means? >> >> >> >> >> >> >> Thanks, >> Keji >> --- >> Morenikeji Adebayo >> Clinical Research Coordinator >> Department of Psychiatric Neuroscience >> Massachusetts General Hospital >> (p) 617.643.6347 >> k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <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 --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu ___ 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] if: Expression Syntax
Hi Doug, When I run: preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface fsaverage lhrh -min305 -fwhm 5 -per* |& tee fordoug.log I get: preproc-sess: No match. Thanks, Keji > On Jul 22, 2015, at 3:37 PM, Douglas N Greve > wrote: > > * > Can you run the following > > preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface > fsaverage lhrh -min305 -fwhm 5 -per* |& tee fordoug.log > > and send me fordoug.log > > > > > On 07/22/2015 02:12 PM, Morenikeji Adebayo wrote: >> Hi there, >> >> I’m running stable: >> >> source /usr/local/freesurfer/stable5_3_0 >> >> Thanks, >> Keji >> >>> On Jul 21, 2015, at 4:56 PM, Douglas Greve >> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>> >>> what environment are you running in? ie, dev or stable? >>> >>> On 7/21/15 2:12 PM, Morenikeji Adebayo wrote: >>>> Hi there, >>>> >>>> *When running selxavg for the following session:* >>>> >>>> nmasa_031_130412 >>>> * >>>> * >>>> *The following error message was generated:* >>>> * >>>> * >>>> Error using MRIread (line 76) >>>> ERROR: cannot determine format of >>>> /autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm >>>> (MRIread) >>>> >>>> Error in fast_selxavg3 (line 146) >>>> runmask = MRIread(flac.maskfspec); >>>> * >>>> * >>>> *I did some investigating and discovered that all the bold runs for >>>> this participant are missing the following files:* >>>> * >>>> * >>>> .../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm >>>> .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz >>>> .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz >>>> * >>>> * >>>> * >>>> So I ran: >>>> >>>> preproc-sess -s nmasa_031_130412 -fsd bold -stc up -surface >>>> fsaverage lhrh -min305 -fwhm 5 -per >>>> >>>> * >>>> * >>>> * >>>> *Which generated the following error message:* >>>> >>>> if: Expression Syntax >>>> >>>> **Do you have any idea what might be going wrong with this subject >>>> or what this error message (**if: Expression Syntax) **means?** >>>> * >>>> * >>>> * >>>> * >>>> Thanks, >>>> Keji >>>> --- >>>> Morenikeji Adebayo >>>> Clinical Research Coordinator >>>> Department of Psychiatric Neuroscience >>>> Massachusetts General Hospital >>>> (p) 617.643.6347 >>>> k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu> >>>> >>>> >>>> >>>> ___ >>>> 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> --- >> Morenikeji Adebayo >> Clinical Research Coordinator >> Department of Psychiatric Neuroscience >> Massachusetts General Hospital >> (p) 617.643.6347 >> k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu> >> >> >> >> ___ >> 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 > > --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu ___ 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] if: Expression Syntax
No problem! Here you go. fordoug.log.docx Description: MS-Word 2007 document On Jul 22, 2015, at 4:30 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote:Sorry, there should not be a * at the end of -per. I was just trying to copy your command line with -debug as the first arg.On 07/22/2015 04:02 PM, Morenikeji Adebayo wrote:Hi Doug,When I run:preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface fsaverage lhrh -min305 -fwhm 5 -per* |& tee fordoug.logI get:preproc-sess: No match.Thanks,KejiOn Jul 22, 2015, at 3:37 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:*Can you run the followingpreproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surfacefsaverage lhrh -min305 -fwhm 5 -per* |& tee fordoug.logand send me fordoug.logOn 07/22/2015 02:12 PM, Morenikeji Adebayo wrote:Hi there,I’m running stable:source /usr/local/freesurfer/stable5_3_0Thanks,KejiOn Jul 21, 2015, at 4:56 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>> wrote:what environment are you running in? ie, dev or stable?On 7/21/15 2:12 PM, Morenikeji Adebayo wrote:Hi there,*When running selxavg for the following session:*nmasa_031_130412***The following error message was generated:***Error using MRIread (line 76)ERROR: cannot determine format of/autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm(MRIread)Error in fast_selxavg3 (line 146) runmask = MRIread(flac.maskfspec);***I did some investigating and discovered that all the bold runs forthis participant are missing the following files:***.../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm.../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz.../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz***So I ran:preproc-sess -s nmasa_031_130412 -fsd bold -stc up -surfacefsaverage lhrh -min305 -fwhm 5 -perWhich generated the following error message:*if: _expression_ Syntax**Do you have any idea what might be going wrong with this subjector what this error message (**if: _expression_ Syntax) **means?**Thanks,Keji---Morenikeji AdebayoClinical Research CoordinatorDepartment of Psychiatric NeuroscienceMassachusetts General Hospital(p) 617.643.6347k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu> <mailto:k...@nmr.mgh.harvard.edu>___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer---Morenikeji AdebayoClinical Research CoordinatorDepartment of Psychiatric NeuroscienceMassachusetts General Hospital(p) 617.643.6347k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu> <mailto:k...@nmr.mgh.harvard.edu>___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>Phone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlOutgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer---Morenikeji AdebayoClinical Research CoordinatorDepartment of Psychiatric NeuroscienceMassachusetts General Hospital(p) 617.643.6347k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu>___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlOutgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ---Morenikeji AdebayoClinical Research CoordinatorDepartment of Psychiatric NeuroscienceMassachusetts General Hospital(p) 617.643.6347k...@nmr.mgh.harvard.edu ___ Freesurfer mailin
Re: [Freesurfer] if: Expression Syntax
I sure can. Hopefully. Is the what you need? fordoug.log Description: Binary data On Jul 22, 2015, at 5:01 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote:can you just send the log and not put it into a doc file?On 07/22/2015 04:46 PM, Morenikeji Adebayo wrote:No problem! Here you go.On Jul 22, 2015, at 4:30 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:Sorry, there should not be a * at the end of -per. I was just trying tocopy your command line with -debug as the first arg.On 07/22/2015 04:02 PM, Morenikeji Adebayo wrote:Hi Doug,When I run:preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surfacefsaverage lhrh -min305 -fwhm 5 -per* |& tee fordoug.logI get:preproc-sess: No match.Thanks,KejiOn Jul 22, 2015, at 3:37 PM, Douglas N Greve<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>> wrote:*Can you run the followingpreproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surfacefsaverage lhrh -min305 -fwhm 5 -per* |& tee fordoug.logand send me fordoug.logOn 07/22/2015 02:12 PM, Morenikeji Adebayo wrote:Hi there,I’m running stable:source /usr/local/freesurfer/stable5_3_0Thanks,KejiOn Jul 21, 2015, at 4:56 PM, Douglas Greve<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>> wrote:what environment are you running in? ie, dev or stable?On 7/21/15 2:12 PM, Morenikeji Adebayo wrote:Hi there,*When running selxavg for the following session:*nmasa_031_130412***The following error message was generated:***Error using MRIread (line 76)ERROR: cannot determine format of/autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm(MRIread)Error in fast_selxavg3 (line 146) runmask = MRIread(flac.maskfspec);***I did some investigating and discovered that all the bold runs forthis participant are missing the following files:***.../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm.../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz.../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz***So I ran:preproc-sess -s nmasa_031_130412 -fsd bold -stc up -surfacefsaverage lhrh -min305 -fwhm 5 -perWhich generated the following error message:*if: _expression_ Syntax**Do you have any idea what might be going wrong with this subjector what this error message (**if: _expression_ Syntax) **means?**Thanks,Keji---Morenikeji AdebayoClinical Research CoordinatorDepartment of Psychiatric NeuroscienceMassachusetts General Hospital(p) 617.643.6347k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu><mailto:k...@nmr.mgh.harvard.edu><mailto:k...@nmr.mgh.harvard.edu>___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer---Morenikeji AdebayoClinical Research CoordinatorDepartment of Psychiatric NeuroscienceMassachusetts General Hospital(p) 617.643.6347k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu><mailto:k...@nmr.mgh.harvard.edu><mailto:k...@nmr.mgh.harvard.edu>___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer--Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>Phone Number: 617-724-2358Fax: 617-726-7422Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer---Morenikeji AdebayoClinical Research CoordinatorDepartment of Psychiatric NeuroscienceMassachusetts General Hospital(p) 617.643.6347k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu><mailto:k...@nmr.mgh.harvard.edu>___Freesurfer mailing listFreesurfer@nmr.mg
Re: [Freesurfer] if: Expression Syntax
Just following up. Did i send the log in the correct format? Thanks, Keji On Jul 22, 2015, at 5:30 PM, Morenikeji Adebayo wrote: > I sure can. Hopefully. Is the what you need? > > > >> On Jul 22, 2015, at 5:01 PM, Douglas N Greve >> wrote: >> >> can you just send the log and not put it into a doc file? >> >> On 07/22/2015 04:46 PM, Morenikeji Adebayo wrote: >>> No problem! Here you go. >>> >>> >>> >>>> On Jul 22, 2015, at 4:30 PM, Douglas N Greve >>>> mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>>> >>>> Sorry, there should not be a * at the end of -per. I was just trying to >>>> copy your command line with -debug as the first arg. >>>> >>>> On 07/22/2015 04:02 PM, Morenikeji Adebayo wrote: >>>>> Hi Doug, >>>>> >>>>> When I run: >>>>> preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface >>>>> fsaverage lhrh -min305 -fwhm 5 -per* |& tee fordoug.log >>>>> >>>>> I get: >>>>> preproc-sess: No match. >>>>> >>>>> Thanks, >>>>> Keji >>>>> >>>>> >>>>>> On Jul 22, 2015, at 3:37 PM, Douglas N Greve >>>>>> >>>>> <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>> >>>>>> wrote: >>>>>> >>>>>> * >>>>>> Can you run the following >>>>>> >>>>>> preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface >>>>>> fsaverage lhrh -min305 -fwhm 5 -per* |& tee fordoug.log >>>>>> >>>>>> and send me fordoug.log >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 07/22/2015 02:12 PM, Morenikeji Adebayo wrote: >>>>>>> Hi there, >>>>>>> >>>>>>> I’m running stable: >>>>>>> >>>>>>> source /usr/local/freesurfer/stable5_3_0 >>>>>>> >>>>>>> Thanks, >>>>>>> Keji >>>>>>> >>>>>>>> On Jul 21, 2015, at 4:56 PM, Douglas Greve >>>>>>>> >>>>>>> <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu> >>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>>>>>>> >>>>>>>> what environment are you running in? ie, dev or stable? >>>>>>>> >>>>>>>> On 7/21/15 2:12 PM, Morenikeji Adebayo wrote: >>>>>>>>> Hi there, >>>>>>>>> >>>>>>>>> *When running selxavg for the following session:* >>>>>>>>> >>>>>>>>> nmasa_031_130412 >>>>>>>>> * >>>>>>>>> * >>>>>>>>> *The following error message was generated:* >>>>>>>>> * >>>>>>>>> * >>>>>>>>> Error using MRIread (line 76) >>>>>>>>> ERROR: cannot determine format of >>>>>>>>> /autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm >>>>>>>>> (MRIread) >>>>>>>>> >>>>>>>>> Error in fast_selxavg3 (line 146) >>>>>>>>> runmask = MRIread(flac.maskfspec); >>>>>>>>> * >>>>>>>>> * >>>>>>>>> *I did some investigating and discovered that all the bold runs for >>>>>>>>> this participant are missing the following files:* >>>>>>>>> * >>>>>>>>> * >>>>>>>>> .../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm >>>>>>>>> .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz >>>>>>>>> .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz >>>>>>>>> * >>>>>>>>> * >>>>>>>>> * >>>>>>>>> So I ran: >>>>>>>>> >>>>>>>>> preproc-sess -s nmasa_031_130
Re: [Freesurfer] if: Expression Syntax
Hi there,Attached is the log file from running:preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run |& tee fordoug.logI got more errors when I ran:preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per |& tee fordoug.logThanks,Keji fordoug (3).log Description: Binary data On Jul 23, 2015, at 6:05 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote:Yes, but you have a typo -min305 instead of -mni305On 07/22/2015 05:30 PM, Morenikeji Adebayo wrote:I sure can. Hopefully. Is the what you need?On Jul 22, 2015, at 5:01 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:can you just send the log and not put it into a doc file?On 07/22/2015 04:46 PM, Morenikeji Adebayo wrote:No problem! Here you go.On Jul 22, 2015, at 4:30 PM, Douglas N Greve<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> <mailto:gr...@nmr.mgh.harvard.edu>> wrote:Sorry, there should not be a * at the end of -per. I was just trying tocopy your command line with -debug as the first arg.On 07/22/2015 04:02 PM, Morenikeji Adebayo wrote:Hi Doug,When I run:preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surfacefsaverage lhrh -min305 -fwhm 5 -per* |& tee fordoug.logI get:preproc-sess: No match.Thanks,KejiOn Jul 22, 2015, at 3:37 PM, Douglas N Greve<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>> wrote:*Can you run the followingpreproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surfacefsaverage lhrh -min305 -fwhm 5 -per* |& tee fordoug.logand send me fordoug.logOn 07/22/2015 02:12 PM, Morenikeji Adebayo wrote:Hi there,I’m running stable:source /usr/local/freesurfer/stable5_3_0Thanks,KejiOn Jul 21, 2015, at 4:56 PM, Douglas Greve<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>> wrote:what environment are you running in? ie, dev or stable?On 7/21/15 2:12 PM, Morenikeji Adebayo wrote:Hi there,*When running selxavg for the following session:*nmasa_031_130412***The following error message was generated:***Error using MRIread (line 76)ERROR: cannot determine format of/autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm(MRIread)Error in fast_selxavg3 (line 146) runmask = MRIread(flac.maskfspec);***I did some investigating and discovered that all the bold runs forthis participant are missing the following files:***.../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm.../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz.../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz***So I ran:preproc-sess -s nmasa_031_130412 -fsd bold -stc up -surfacefsaverage lhrh -min305 -fwhm 5 -perWhich generated the following error message:*if: _expression_ Syntax**Do you have any idea what might be going wrong with this subjector what this error message (**if: _expression_ Syntax) **means?**Thanks,Keji---Morenikeji AdebayoClinical Research CoordinatorDepartment of Psychiatric NeuroscienceMassachusetts General Hospital(p) 617.643.6347k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu><mailto:k...@nmr.mgh.harvard.edu><mailto:k...@nmr.mgh.harvard.edu><mailto:k...@nmr.mgh.harvard.edu>___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer---Morenikeji AdebayoClinical Research CoordinatorDepartment of Psychiatric NeuroscienceMassachusetts General Hospital(p) 617.643.6347k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu><mailto:k...@nmr.mgh.harvard.edu><mailto:k...@nmr.mgh.harvard.edu><mailto:k...@nmr.mgh.harvard.edu>___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer--Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu><mailto:gr.
Re: [Freesurfer] if: Expression Syntax
Hi Doug,fordoug2 is attached.Thanks,Keji
fordoug2.log
Description: Binary data
On Jul 24, 2015, at 11:17 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote:
can you run
register-sess -debug -s nmasa_031_130412 -d
/autofs/cluster/iaslab/NMASA/mri/func/encoding -fsd bold -dof 6
-per-run -update |& tee fordoug2.log
and send me fourdoug2.log
doug
On 7/24/15 10:22 AM, Morenikeji Adebayo
wrote:
Hi there,
Attached is the log file from running:
preproc-sess
-debug -s nmasa_031_130412 -fsd bold -stc up -surface fsaverage lhrh -mni305
-fwhm 5 -per-run |& tee fordoug.log
I got more
errors when I ran:
preproc-sess
-debug -s nmasa_031_130412 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5
-per |& tee fordoug.log
Thanks,
Keji
On Jul 23, 2015, at 6:05 PM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu>
wrote:
Yes, but you have a typo -min305 instead of
-mni305
On 07/22/2015 05:30 PM, Morenikeji Adebayo wrote:
I sure can. Hopefully. Is
the what you need?
On Jul 22, 2015, at
5:01 PM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>
wrote:
can you just send the log and not put it into a doc
file?
On 07/22/2015 04:46 PM, Morenikeji Adebayo wrote:
No problem! Here you
go.
On Jul 22, 2015, at
4:30 PM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu>>
wrote:
Sorry, there should not be a * at the end of -per.
I was just trying to
copy your command line with -debug as the first
arg.
On 07/22/2015 04:02 PM, Morenikeji Adebayo wrote:
Hi Doug,
When I run:
preproc-sess -debug -s nmasa_031_130412 -fsd
bold -stc up -surface
fsaverage lhrh -min305 -fwhm 5 -per* |& tee
fordoug.log
I get:
preproc-sess: No match.
Thanks,
Keji
On Jul 22,
2015, at 3:37 PM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>>
wrote:
*
Can you run the following
preproc-sess -debug -s nmasa_031_130412 -fsd
bold -stc up -surface
fsaverage lhrh -min305 -fwhm 5 -per* |&
tee fordoug.log
and send me fordoug.log
On 07/22/2015 02:12 PM, Morenikeji Adebayo
wrote:
Hi there,
I’m running stable:
source /usr/local/freesurfer/stable5_3_0
Thanks,
Keji
On Jul 21,
2015, at 4:56 PM, Douglas Greve
<gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu&
Re: [Freesurfer] if: Expression Syntax
Oh excellent, you are correct! I’ll update the file and try re-running selxavg. Thanks, Keji > On Jul 24, 2015, at 12:06 PM, Douglas Greve wrote: > > I think there is something wrong with the contents of > /autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/subjectname > > It looks like it is "cd nmasa_031_130412", probably it should be > "nmasa_031_130412" ? > > > > On 7/24/15 11:58 AM, Morenikeji Adebayo wrote: >> Hi Doug, >> >> fordoug2 is attached. >> >> Thanks, >> Keji >> >> >> >> >>> On Jul 24, 2015, at 11:17 AM, Douglas Greve >> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>> >>> >>> can you run >>> register-sess -debug -s nmasa_031_130412 -d >>> /autofs/cluster/iaslab/NMASA/mri/func/encoding -fsd bold -dof 6 -per-run >>> -update |& tee fordoug2.log >>> >>> and send me fourdoug2.log >>> >>> doug >>> >>> >>> On 7/24/15 10:22 AM, Morenikeji Adebayo wrote: >>>> Hi there, >>>> >>>> Attached is the log file from running: >>>> >>>> preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface >>>> fsaverage lhrh -mni305 -fwhm 5 -per-run |& tee fordoug.log >>>> >>>> I got more errors when I ran: >>>> >>>> preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface >>>> fsaverage lhrh -mni305 -fwhm 5 -per |& tee fordoug.log >>>> >>>> >>>> Thanks, >>>> Keji >>>> >>>> >>>> >>>>> On Jul 23, 2015, at 6:05 PM, Douglas N Greve >>>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>>>> >>>>> Yes, but you have a typo -min305 instead of -mni305 >>>>> >>>>> >>>>> >>>>> On 07/22/2015 05:30 PM, Morenikeji Adebayo wrote: >>>>>> I sure can. Hopefully. Is the what you need? >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>> On Jul 22, 2015, at 5:01 PM, Douglas N Greve >>>>>>> mailto:gr...@nmr.mgh.harvard.edu> >>>>>>> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>> >>>>>>> wrote: >>>>>>> >>>>>>> can you just send the log and not put it into a doc file? >>>>>>> >>>>>>> On 07/22/2015 04:46 PM, Morenikeji Adebayo wrote: >>>>>>>> No problem! Here you go. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> On Jul 22, 2015, at 4:30 PM, Douglas N Greve >>>>>>>>> mailto:gr...@nmr.mgh.harvard.edu> >>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> >>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu >>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: >>>>>>>>> >>>>>>>>> Sorry, there should not be a * at the end of -per. I was just trying >>>>>>>>> to >>>>>>>>> copy your command line with -debug as the first arg. >>>>>>>>> >>>>>>>>> On 07/22/2015 04:02 PM, Morenikeji Adebayo wrote: >>>>>>>>>> Hi Doug, >>>>>>>>>> >>>>>>>>>> When I run: >>>>>>>>>> preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface >>>>>>>>>> fsaverage lhrh -min305 -fwhm 5 -per* |& tee fordoug.log >>>>>>>>>> >>>>>>>>>> I get: >>>>>>>>>> preproc-sess: No match. >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> Keji >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> On Jul 22, 2015, at 3:37 PM, Douglas N Greve >>>>>>>>>>> mailto:gr...@nmr.mgh.harvard.edu> >>>>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu >>>>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu>> >>>>>>
Re: [Freesurfer] if: Expression Syntax
That fixed it! Thanks for all your help - I appreciate it. Keji > On Jul 24, 2015, at 12:17 PM, Morenikeji Adebayo > wrote: > > Oh excellent, you are correct! I’ll update the file and try re-running > selxavg. > > Thanks, > Keji > >> On Jul 24, 2015, at 12:06 PM, Douglas Greve > <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> I think there is something wrong with the contents of >> /autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/subjectname >> >> It looks like it is "cd nmasa_031_130412", probably it should be >> "nmasa_031_130412" ? >> >> >> >> On 7/24/15 11:58 AM, Morenikeji Adebayo wrote: >>> Hi Doug, >>> >>> fordoug2 is attached. >>> >>> Thanks, >>> Keji >>> >>> >>> >>> >>>> On Jul 24, 2015, at 11:17 AM, Douglas Greve >>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>>> >>>> >>>> can you run >>>> register-sess -debug -s nmasa_031_130412 -d >>>> /autofs/cluster/iaslab/NMASA/mri/func/encoding -fsd bold -dof 6 -per-run >>>> -update |& tee fordoug2.log >>>> >>>> and send me fourdoug2.log >>>> >>>> doug >>>> >>>> >>>> On 7/24/15 10:22 AM, Morenikeji Adebayo wrote: >>>>> Hi there, >>>>> >>>>> Attached is the log file from running: >>>>> >>>>> preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface >>>>> fsaverage lhrh -mni305 -fwhm 5 -per-run |& tee fordoug.log >>>>> >>>>> I got more errors when I ran: >>>>> >>>>> preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface >>>>> fsaverage lhrh -mni305 -fwhm 5 -per |& tee fordoug.log >>>>> >>>>> >>>>> Thanks, >>>>> Keji >>>>> >>>>> >>>>> >>>>>> On Jul 23, 2015, at 6:05 PM, Douglas N Greve >>>>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>>>>> >>>>>> Yes, but you have a typo -min305 instead of -mni305 >>>>>> >>>>>> >>>>>> >>>>>> On 07/22/2015 05:30 PM, Morenikeji Adebayo wrote: >>>>>>> I sure can. Hopefully. Is the what you need? >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>> On Jul 22, 2015, at 5:01 PM, Douglas N Greve >>>>>>>> mailto:gr...@nmr.mgh.harvard.edu> >>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>> >>>>>>>> wrote: >>>>>>>> >>>>>>>> can you just send the log and not put it into a doc file? >>>>>>>> >>>>>>>> On 07/22/2015 04:46 PM, Morenikeji Adebayo wrote: >>>>>>>>> No problem! Here you go. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> On Jul 22, 2015, at 4:30 PM, Douglas N Greve >>>>>>>>>> mailto:gr...@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu >>>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu>> >>>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu >>>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: >>>>>>>>>> >>>>>>>>>> Sorry, there should not be a * at the end of -per. I was just trying >>>>>>>>>> to >>>>>>>>>> copy your command line with -debug as the first arg. >>>>>>>>>> >>>>>>>>>> On 07/22/2015 04:02 PM, Morenikeji Adebayo wrote: >>>>>>>>>>> Hi Doug, >>>>>>>>>>> >>>>>>>>>>> When I run: >>>>>>>>>>> preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface >>>>>>>>>>> fsaverage lhrh -min305 -fwhm 5 -per* |& tee fordoug.log >>>>>>>>>>> >>>>>>>>>>> I get: >&
[Freesurfer] mri_volcluster
Hi there, I have a a couple of question related to the output generated by the ‘mri_volcluster' command. 1) It seems that the command automatically assumes that my voxels are 8 mm^3. Is there a way to specify my voxel size when I run the command? 2) The output is given in Talairach coordinates. Is there a way to specify the output in MNI coordinates? Thanks, Keji --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu ___ 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] mri_volcluster
Hi there, The command I submitted is: mri_volcluster --in merged_encode_Young_NEUT_hit_V_miss_n41.nii.gz --thmin 1.3 --minsizevox 5 --sign neg --sum adebayo_young_neut_p.05 —fsaverage How would I: 1) Specify the voxel size 2) Have the results output in MNI? Thanks, Keji > On Aug 10, 2015, at 11:32 AM, Douglas N Greve > wrote: > > > > On 08/10/2015 10:47 AM, Morenikeji Adebayo wrote: >> Hi there, >> >> I have a a couple of question related to the output generated by the >> ‘mri_volcluster' command. >> >> 1) It seems that the command automatically assumes that my voxels are >> 8 mm^3. Is there a way to specify my voxel size when I run the command? > It should use whatever the voxel size of the input is. Remember to > include a command line. >> >> 2) The output is given in Talairach coordinates. Is there a way to >> specify the output in MNI coordinates? > Can tell without your command line >> >> >> Thanks, >> Keji >> >> --- >> Morenikeji Adebayo >> Clinical Research Coordinator >> Department of Psychiatric Neuroscience >> Massachusetts General Hospital >> (p) 617.643.6347 >> k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu> >> >> >> >> ___ >> 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 > > --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu ___ 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] mri_volcluster
Hi there, Just following up. Any advice would be much appreciated! Thanks, Keji > On Aug 10, 2015, at 1:50 PM, Morenikeji Adebayo > wrote: > > Hi there, > > The command I submitted is: > mri_volcluster --in merged_encode_Young_NEUT_hit_V_miss_n41.nii.gz --thmin > 1.3 --minsizevox 5 --sign neg --sum adebayo_young_neut_p.05 —fsaverage > > How would I: > > 1) Specify the voxel size > 2) Have the results output in MNI? > > > Thanks, > Keji > > >> On Aug 10, 2015, at 11:32 AM, Douglas N Greve > <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> >> >> On 08/10/2015 10:47 AM, Morenikeji Adebayo wrote: >>> Hi there, >>> >>> I have a a couple of question related to the output generated by the >>> ‘mri_volcluster' command. >>> >>> 1) It seems that the command automatically assumes that my voxels are >>> 8 mm^3. Is there a way to specify my voxel size when I run the command? >> It should use whatever the voxel size of the input is. Remember to >> include a command line. >>> >>> 2) The output is given in Talairach coordinates. Is there a way to >>> specify the output in MNI coordinates? >> Can tell without your command line >>> >>> >>> Thanks, >>> Keji >>> >>> --- >>> Morenikeji Adebayo >>> Clinical Research Coordinator >>> Department of Psychiatric Neuroscience >>> Massachusetts General Hospital >>> (p) 617.643.6347 >>> k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu> >>> <mailto:k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu>> >>> >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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 >> >> > > --- > Morenikeji Adebayo > Clinical Research Coordinator > Department of Psychiatric Neuroscience > Massachusetts General Hospital > (p) 617.643.6347 > k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu ___ 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] Error using selexavg3-sess
Hi there, I’m running into difficulty executing the “selexavg3-sess” command for a few participants. For example, when I run the command: foreach c(lh rh mni305) selxavg3-sess -analysis analysis_encoding_stimXmem.$c -s nmasa_045_130621 -d . -no-preproc end I get the following error: Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 36) s = svd(A); Error in fast_selxavg3 (line 279) XCond = cond(XtX); Any help on this error would be much appreciated! Thanks, Keji --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu ___ 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] Using mri_glmfit to generate R (correlation) maps
Hello Freesurfers, I'm interested in creating a group map where each vertex represents the correlation (as a correlation coefficient) between a task-related BOLD contrast value (ces.nii.gz) and a single covariate. This is analogous to a cortical thickness GLM with one group and one covariate, but I'd want an r-map instead of a sig-map. How might I accomplish this? It appears that mri_glmfit generates sig-maps, gamma-maps, etc, but not r-maps. Thanks in advance, Keji ___ 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] Using mri_glmfit to generate R (correlation) maps
Thanks, Doug!! I’ll give it a whirl. > On Nov 17, 2016, at 6:40 PM, Douglas N Greve > wrote: > > Use this version of mri_glmfit. It will create a file called pcc.mgh. > This is the partial correlation coefficient > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit > > > > On 11/17/2016 06:20 PM, Morenikeji Adebayo wrote: >> Hello Freesurfers, >> >> I'm interested in creating a group map where each vertex represents the >> correlation (as a correlation coefficient) between a task-related BOLD >> contrast value (ces.nii.gz) and a single covariate. This is analogous to a >> cortical thickness GLM with one group and one covariate, but I'd want an >> r-map instead of a sig-map. How might I accomplish this? It appears that >> mri_glmfit generates sig-maps, gamma-maps, etc, but not r-maps. >> >> >> >> Thanks in advance, >> Keji >> >> >> >> ___ >> 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 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] Using mri_glmfit to generate R (correlation) maps
Hi there, I’m having trouble running the script. Should I place the script in the $FSFAST/bin directory? Any advice on how to run the this version of mri_glmfit would be much appreciated. Thanks, Keji > On Nov 17, 2016, at 6:48 PM, Morenikeji Adebayo > wrote: > > Thanks, Doug!! I’ll give it a whirl. > >> On Nov 17, 2016, at 6:40 PM, Douglas N Greve >> wrote: >> >> Use this version of mri_glmfit. It will create a file called pcc.mgh. >> This is the partial correlation coefficient >> >> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit >> >> >> >> On 11/17/2016 06:20 PM, Morenikeji Adebayo wrote: >>> Hello Freesurfers, >>> >>> I'm interested in creating a group map where each vertex represents the >>> correlation (as a correlation coefficient) between a task-related BOLD >>> contrast value (ces.nii.gz) and a single covariate. This is analogous to a >>> cortical thickness GLM with one group and one covariate, but I'd want an >>> r-map instead of a sig-map. How might I accomplish this? It appears that >>> mri_glmfit generates sig-maps, gamma-maps, etc, but not r-maps. >>> >>> >>> >>> Thanks in advance, >>> Keji >>> >>> >>> >>> ___ >>> 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 > > ___ 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] Using mri_glmfit to generate R (correlation) maps
Hi there, The new mri_glmfit script that I was directed to doesn’t create a file called “pcc.mgh.” It does create a file called “z.nii.gz” (as far as I can tell this file is the only difference between the old and new mri_glm fit scripts). Is there another script that I should be using to generate the Pearson correlation maps? Thanks! Keji --- Morenikeji Adebayo Junior Research Fellow Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu> > >> On Nov 17, 2016, at 6:48 PM, Morenikeji Adebayo > <mailto:k...@nmr.mgh.harvard.edu>> wrote: >> >> Thanks, Doug!! I’ll give it a whirl. >> >>> On Nov 17, 2016, at 6:40 PM, Douglas N Greve >> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>> >>> Use this version of mri_glmfit. It will create a file called pcc.mgh. >>> This is the partial correlation coefficient >>> >>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit >>> <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit> >>> >>> >>> >>> On 11/17/2016 06:20 PM, Morenikeji Adebayo wrote: >>>> Hello Freesurfers, >>>> >>>> I'm interested in creating a group map where each vertex represents the >>>> correlation (as a correlation coefficient) between a task-related BOLD >>>> contrast value (ces.nii.gz) and a single covariate. This is analogous to a >>>> cortical thickness GLM with one group and one covariate, but I'd want an >>>> r-map instead of a sig-map. How might I accomplish this? It appears that >>>> mri_glmfit generates sig-maps, gamma-maps, etc, but not r-maps. >>>> >>>> >>>> >>>> Thanks in advance, >>>> Keji >>>> >>>> >>>> >>>> ___ >>>> 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 <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] Using mri_glmfit to generate R (correlation) maps
Hi, I’m not sure if this is what you’re looking for but this is the command I ran: /autofs/space/fatfriar_002/cluster/iaslab/NMASA/mri/func/encoding/adebayo/mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --fsgd /autofs/space/fatfriar_001/cluster/iaslab/NMASA/mri/func/encoding/adebayo/allVfix/fsgd_files/All_n109_NEUT_dassoc --surface fsaverage lh --glmdir glm_AvF_vs_dassoc_R --nii.gz --C /autofs/space/fatfriar_001/cluster/iaslab/NMASA/mri/func/encoding/adebayo/allVfix/group_contrasts/1_group_1cov_slope.group.m And this is what’s in the output directory: C.dat cnr.nii.gz efficiency.dat F.nii.gz gamma.nii.gz gammavar.nii.gz maxvox.dat sig.nii.gz z.nii.gz Thanks, Keji --- Morenikeji Adebayo Junior Research Fellow Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu> > On Nov 29, 2016, at 1:39 PM, Douglas N Greve > wrote: > > what is your command line and terminal output? > > > On 11/29/2016 01:24 PM, Morenikeji Adebayo wrote: >> Hi there, >> >> The new mri_glmfit script that I was directed to doesn’t create a file >> called “pcc.mgh.” It does create a file called “z.nii.gz” (as far as >> I can tell this file is the only difference between the old and new >> mri_glm fit scripts). >> >> Is there another script that I should be using to generate the Pearson >> correlation maps? >> >> Thanks! >> Keji >> >> --- >> Morenikeji Adebayo >> Junior Research Fellow >> Department of Psychiatric Neuroscience >> Massachusetts General Hospital >> (p) 617.643.6347 >> k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu> >> <mailto:k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu>> >> >> >> >>> >>>> On Nov 17, 2016, at 6:48 PM, Morenikeji Adebayo >>>> mailto:k...@nmr.mgh.harvard.edu> >>>> <mailto:k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu>>> wrote: >>>> >>>> Thanks, Doug!! I’ll give it a whirl. >>>> >>>>> On Nov 17, 2016, at 6:40 PM, Douglas N Greve >>>>> mailto:gr...@nmr.mgh.harvard.edu> >>>>> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>> >>>>> wrote: >>>>> >>>>> Use this version of mri_glmfit. It will create a file called pcc.mgh. >>>>> This is the partial correlation coefficient >>>>> >>>>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit >>>>> <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit> >>>>> >>>>> >>>>> >>>>> On 11/17/2016 06:20 PM, Morenikeji Adebayo wrote: >>>>>> Hello Freesurfers, >>>>>> >>>>>> I'm interested in creating a group map where each vertex >>>>>> represents the correlation (as a correlation coefficient) between >>>>>> a task-related BOLD contrast value (ces.nii.gz) and a single >>>>>> covariate. This is analogous to a cortical thickness GLM with one >>>>>> group and one covariate, but I'd want an r-map instead of a >>>>>> sig-map. How might I accomplish this? It appears that mri_glmfit >>>>>> generates sig-maps, gamma-maps, etc, but not r-maps. >>>>>> >>>>>> >>>>>> >>>>>> Thanks in advance, >>>>>> Keji >>>>>> >>>>>> >>>>>> >>>>>> ___ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>>>> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> &
Re: [Freesurfer] Using mri_glmfit to generate R (correlation) maps
Ok - no problem. I’ll run again without -wls. Thanks! Keji --- Morenikeji Adebayo Junior Research Fellow Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu> > On Nov 29, 2016, at 2:52 PM, Douglas N Greve > wrote: > > The pcc calculation is turned off with --wls. I can't remember why I did > it that way. > > > On 11/29/2016 02:50 PM, Morenikeji Adebayo wrote: >> Hi, >> >> I’m not sure if this is what you’re looking for but this is the >> command I ran: >> >> /autofs/space/fatfriar_002/cluster/iaslab/NMASA/mri/func/encoding/adebayo/mri_glmfit >> >> --y ces.nii.gz --wls cesvar.nii.gz --fsgd >> /autofs/space/fatfriar_001/cluster/iaslab/NMASA/mri/func/encoding/adebayo/allVfix/fsgd_files/All_n109_NEUT_dassoc--surface >> >> fsaverage lh--glmdir glm_AvF_vs_dassoc_R --nii.gz --C >> /autofs/space/fatfriar_001/cluster/iaslab/NMASA/mri/func/encoding/adebayo/allVfix/group_contrasts/1_group_1cov_slope.group.m >> >> And this is what’s in the output directory: >> >> C.dat >> cnr.nii.gz >> efficiency.dat >> F.nii.gz >> gamma.nii.gz >> gammavar.nii.gz >> maxvox.dat >> sig.nii.gz >> z.nii.gz >> >> >> >> >> Thanks, >> Keji >> >> >> --- >> Morenikeji Adebayo >> Junior Research Fellow >> Department of Psychiatric Neuroscience >> Massachusetts General Hospital >> (p) 617.643.6347 >> k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu> >> <mailto:k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu>> >> >> >> >>> On Nov 29, 2016, at 1:39 PM, Douglas N Greve >>> mailto:gr...@nmr.mgh.harvard.edu> >>> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>> >>> wrote: >>> >>> what is your command line and terminal output? >>> >>> >>> On 11/29/2016 01:24 PM, Morenikeji Adebayo wrote: >>>> Hi there, >>>> >>>> The new mri_glmfit script that I was directed to doesn’t create a file >>>> called “pcc.mgh.” It does create a file called “z.nii.gz” (as far as >>>> I can tell this file is the only difference between the old and new >>>> mri_glm fit scripts). >>>> >>>> Is there another script that I should be using to generate the Pearson >>>> correlation maps? >>>> >>>> Thanks! >>>> Keji >>>> >>>> --- >>>> Morenikeji Adebayo >>>> Junior Research Fellow >>>> Department of Psychiatric Neuroscience >>>> Massachusetts General Hospital >>>> (p) 617.643.6347 >>>> k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu> >>>> <mailto:k...@nmr.mgh.harvard.edu >>>> <mailto:k...@nmr.mgh.harvard.edu>><mailto:k...@nmr.mgh.harvard.edu >>>> <mailto:k...@nmr.mgh.harvard.edu>> >>>> >>>> >>>> >>>>> >>>>>> On Nov 17, 2016, at 6:48 PM, Morenikeji Adebayo >>>>>> mailto:k...@nmr.mgh.harvard.edu> >>>>>> <mailto:k...@nmr.mgh.harvard.edu >>>>>> <mailto:k...@nmr.mgh.harvard.edu>><mailto:k...@nmr.mgh.harvard.edu >>>>>> <mailto:k...@nmr.mgh.harvard.edu>>> >>>>>> wrote: >>>>>> >>>>>> Thanks, Doug!! I’ll give it a whirl. >>>>>> >>>>>>> On Nov 17, 2016, at 6:40 PM, Douglas N Greve >>>>>>> mailto:gr...@nmr.mgh.harvard.edu> >>>>>>> <mailto:gr...@nmr.mgh.harvard.edu >>>>>>> <mailto:gr...@nmr.mgh.harvard.edu>><mailto:gr...@nmr.mgh.harvard.edu >>>>>>> <mailto:gr...@nmr.mgh.harvard.edu>>> >>>>>>> wrote: >>>>>>> >>>>>>> Use this version of mri_glmfit. It will create a file called pcc.mgh. >>>>>>> This is the partial correlation coefficient >>>>>>> >>>>>>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit >>>>>>> <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 11/17/2016 06:20 PM, Morenikeji Adebayo wrote: >>>>>>>
Re: [Freesurfer] Error using selexavg3-sess
Just following up on this - thanks! > On Sep 29, 2015, at 1:29 PM, Morenikeji Adebayo > wrote: > > Hi there, > > I’m running into difficulty executing the “selexavg3-sess” command for a few > participants. For example, when I run the command: > > foreach c(lh rh mni305) > selxavg3-sess -analysis analysis_encoding_stimXmem.$c -s nmasa_045_130621 -d > . -no-preproc > end > > > I get the following error: > > > Error using svd > Input to SVD must not contain NaN or Inf. > > Error in cond (line 36) > s = svd(A); > > Error in fast_selxavg3 (line 279) > XCond = cond(XtX); > > Any help on this error would be much appreciated! > > Thanks, > Keji > > --- > Morenikeji Adebayo > Clinical Research Coordinator > Department of Psychiatric Neuroscience > Massachusetts General Hospital > (p) 617.643.6347 > k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu ___ 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] Funcroi-Table-Sess Error
Hi there, I ran the following analysis commands: mri_cor2label --c /autofs/cluster/iaslab/NMASA/mri/recon/$s/mri/aparc.a2009s+aseg.mgz --id 11106 --l /autofs/cluster/iaslab/NMASA/mri/recon/$s/label/labl_ACC_lh.label funcroi-config -label labl_ACC_lh.label -analysis analysis_induc_block.lh -roi roiconfig_ACC_lh funcroi-table-sess -analysis analysis_induc_block.lh -contrast contrast_neg_V_neut -roi roiconfig_ACC_lh -sf sublist_All_SHORT_n111 -o sumtable_ACC_lh.dat After running the 'funcroi-table-sess’ command I got the following error: ERROR: There is a vertex in the label that cannot be matched to the surface. This usually occurs when the label and surface are from different subjects or hemispheres of the surface has been changed since the label was created. It seems that the problem might be that the command is using my participant (in this case, nmasa_001) as the source subject BUT it’s using fsaverage as the target subject. I want the target subject to be my participant as well (not fsaverage). Is there a way that I can specify the target subjects? Or is there a more efficient way do what I’m trying to do (ie: 1. generate labels for each participant based on their aparc+aseg file and 2. calculate the mean contrast signal from each ROI for each participant). Thanks, Keji --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu ___ 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] Funcroi-Table-Sess Error
Hi there, Just following up on this. Any help would much appreciated! Thanks, Keji > On Oct 23, 2015, at 1:46 PM, Morenikeji Adebayo > wrote: > > Hi there, > > I ran the following analysis commands: > > mri_cor2label --c > /autofs/cluster/iaslab/NMASA/mri/recon/$s/mri/aparc.a2009s+aseg.mgz --id > 11106 --l /autofs/cluster/iaslab/NMASA/mri/recon/$s/label/labl_ACC_lh.label > funcroi-config -label labl_ACC_lh.label -analysis analysis_induc_block.lh > -roi roiconfig_ACC_lh > funcroi-table-sess -analysis analysis_induc_block.lh -contrast > contrast_neg_V_neut -roi roiconfig_ACC_lh -sf sublist_All_SHORT_n111 -o > sumtable_ACC_lh.dat > > After running the 'funcroi-table-sess’ command I got the following error: > > ERROR: There is a vertex in the label that cannot be matched to the surface. > This usually occurs when the label and surface are from different subjects or > hemispheres of the surface has been changed since the label was created. > > It seems that the problem might be that the command is using my participant > (in this case, nmasa_001) as the source subject BUT it’s using fsaverage as > the target subject. I want the target subject to be my participant as well > (not fsaverage). > > Is there a way that I can specify the target subjects? Or is there a more > efficient way do what I’m trying to do (ie: 1. generate labels for each > participant based on their aparc+aseg file and 2. calculate the mean contrast > signal from each ROI for each participant). > > > Thanks, > Keji > > > > --- > Morenikeji Adebayo > Clinical Research Coordinator > Department of Psychiatric Neuroscience > Massachusetts General Hospital > (p) 617.643.6347 > k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu> > ___________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu ___ 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] Funcroi-Table-Sess Error
Hi Doug, Thanks for the help! So, you’re saying that: By specifying a volume file (ie: aparc.a2009s+aseg.mgz) when using mri_cor2label, I’ve created volume labels The commands ‘funcroi-config' and 'funcroi-table-sess' accept only labels created on the surface. Is this correct? Thanks, Keji > On Oct 27, 2015, at 11:38 AM, Douglas Greve wrote: > > I think the problem is probably that you created the label from a volume > whereas funcroi expects the label to come from a surface. Instead of using > mri_cor2label and -label for funcroi-config, try using something like > > funcroi-config -annot aparc.a2009s G_and_S_cingul-Ant -analysis > analysis_induc_block.lh -roi roiconfig_ACC_lh > > > > On 10/23/15 1:46 PM, Morenikeji Adebayo wrote: >> Hi there, >> >> I ran the following analysis commands: >> >> mri_cor2label --c >> /autofs/cluster/iaslab/NMASA/mri/recon/$s/mri/aparc.a2009s+aseg.mgz --id >> 11106 --l /autofs/cluster/iaslab/NMASA/mri/recon/$s/label/labl_ACC_lh.label >> funcroi-config -label labl_ACC_lh.label -analysis analysis_induc_block.lh >> -roi roiconfig_ACC_lh >> funcroi-table-sess -analysis analysis_induc_block.lh -contrast >> contrast_neg_V_neut -roi roiconfig_ACC_lh -sf sublist_All_SHORT_n111 -o >> sumtable_ACC_lh.dat >> >> After running the 'funcroi-table-sess’ command I got the following error: >> >> ERROR: There is a vertex in the label that cannot be matched to the surface. >> This usually occurs when the label and surface are from different subjects >> or hemispheres of the surface has been changed since the label was created. >> >> It seems that the problem might be that the command is using my participant >> (in this case, nmasa_001) as the source subject BUT it’s using fsaverage as >> the target subject. I want the target subject to be my participant as well >> (not fsaverage). >> >> Is there a way that I can specify the target subjects? Or is there a more >> efficient way do what I’m trying to do (ie: 1. generate labels for each >> participant based on their aparc+aseg file and 2. calculate the mean >> contrast signal from each ROI for each participant). >> >> >> Thanks, >> Keji >> >> >> >> --- Morenikeji Adebayo Clinical Research Coordinator Department of >> Psychiatric Neuroscience >> Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu >> <mailto:k...@nmr.mgh.harvard.edu> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <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 --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu ___ 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] Funcroi-Table-Sess Error
Thanks!! > On Oct 27, 2015, at 1:18 PM, Douglas Greve wrote: > > > > On 10/27/15 1:09 PM, Morenikeji Adebayo wrote: >> Hi Doug, >> >> Thanks for the help! So, you’re saying that: >> >> By specifying a volume file (ie: aparc.a2009s+aseg.mgz) when using >> mri_cor2label, I’ve created volume labels > Correct >> The commands ‘funcroi-config' and 'funcroi-table-sess' accept only labels >> created on the surface. > It takes either. But the analysis you use is a surface-based analysis, so you > need a surface-based label. > doug > >> >> Is this correct? >> >> Thanks, >> Keji >> >> >>> On Oct 27, 2015, at 11:38 AM, Douglas Greve >> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>> >>> I think the problem is probably that you created the label from a volume >>> whereas funcroi expects the label to come from a surface. Instead of using >>> mri_cor2label and -label for funcroi-config, try using something like >>> >>> funcroi-config -annot aparc.a2009s G_and_S_cingul-Ant -analysis >>> analysis_induc_block.lh -roi roiconfig_ACC_lh >>> >>> >>> >>> On 10/23/15 1:46 PM, Morenikeji Adebayo wrote: >>>> Hi there, >>>> >>>> I ran the following analysis commands: >>>> >>>> mri_cor2label --c >>>> /autofs/cluster/iaslab/NMASA/mri/recon/$s/mri/aparc.a2009s+aseg.mgz --id >>>> 11106 --l /autofs/cluster/iaslab/NMASA/mri/recon/$s/label/labl_ACC_lh.label >>>> funcroi-config -label labl_ACC_lh.label -analysis analysis_induc_block.lh >>>> -roi roiconfig_ACC_lh >>>> funcroi-table-sess -analysis analysis_induc_block.lh -contrast >>>> contrast_neg_V_neut -roi roiconfig_ACC_lh -sf sublist_All_SHORT_n111 -o >>>> sumtable_ACC_lh.dat >>>> >>>> After running the 'funcroi-table-sess’ command I got the following error: >>>> >>>> ERROR: There is a vertex in the label that cannot be matched to the >>>> surface. This usually occurs when the label and surface are from different >>>> subjects or hemispheres of the surface has been changed since the label >>>> was created. >>>> >>>> It seems that the problem might be that the command is using my >>>> participant (in this case, nmasa_001) as the source subject BUT it’s >>>> using fsaverage as the target subject. I want the target subject to be my >>>> participant as well (not fsaverage). >>>> >>>> Is there a way that I can specify the target subjects? Or is there a more >>>> efficient way do what I’m trying to do (ie: 1. generate labels for each >>>> participant based on their aparc+aseg file and 2. calculate the mean >>>> contrast signal from each ROI for each participant). >>>> >>>> >>>> Thanks, >>>> Keji >>>> >>>> >>>> >>>> --- Morenikeji Adebayo Clinical Research Coordinator Department of >>>> Psychiatric Neuroscience >>>> Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu >>>> <mailto:k...@nmr.mgh.harvard.edu> >>>> ___ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>___ >>>> Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> --- Morenikeji Adebayo Clinical Research Coordinator Department of >> Psychiatric Neuroscience >> Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu >> <mailto:k...@nmr.mgh.harvard.edu> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu ___ 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] R-Map
Hello Freesurfers, I'm interested in creating a group map where each vertex/voxel represents the correlation (as a correlation coefficient) between a task-related BOLD contrast values (ces.nii.gz) and a single covariate. This is analogous to a cortical thickness GLM with one group and one covariate, but I'd want an r-map instead of a log10p-map. How exactly might I do this? I’m trying to accomplish this using mri_glmfit, but I’m having generating output that is interpretable in terms of a correlation coefficient and in particular, the direction of the effect. Thanks, Keji --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu ___ 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] funcroi-table-sess error, \"set: Variable name must begin with a letter\"
Hi there, I'm having the same problem referenced in this thread from last year. When I send the command: funcroi-table-sess -roi l_ant_cingulate_allVfix.roicfg -analysis NMASA_induction.lh -contrast allVfix -sf induction_all2.lst -o l_ant_cingulate_induction_FIR_f0.dat -frame 0 I get the following error: set: Variable name must begin with a letter. I was wondering if there was any resolution to this issue when it came up last year or if you have any advice on how I should proceed now. I do have a folder named "log" in the directory I'm running the command from. Thanks, Keji --- Morenikeji Adebayo Clinical Research Coordinator Interdisciplinary Affective Science Lab Massachusetts General Hospital Department of Psychiatric Neuroscience (p) 617.643.6347 (f) 617.726.5760 k...@nmr.mgh.harvard.edu ___ 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.
