Re: [Freesurfer] phase data overlay using fsaverage
Dear Doug, Thank you! I was able to display on the freesurfer surface from a matlab array to surface pipeline. However, only a portion of my voxels showed up on the surface, presumable owing that the others fall in the white matter ... My question is: is there any way to override this so that all the voxels are 'forced' to display on the surface? Many thanks, Jason. >-Original Message- >From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] >Sent: 09 February 2011 16:42 >To: Jason Connolly >Cc: 'freesurfer@nmr.mgh.harvard.edu' >Subject: Re: [Freesurfer] phase data overlay using fsaverage > >First, make sure that the volume you created is in register with the >template functional. Eg, > >tkmedit -f f.nii -ov f_LH12.mgz > >where f.nii is the functional that f_LH12.mgz was derived from. > >Once that is correct, run bbregister with the actual subject as the >target (not fsaverage), spec the --mov as f.nii, and use --init-fsl >instead of --init-header > >The vol2surf cmd is correct, though it will sample it on the subject's >surface (not that of fsaverage; you can change this with --trgsubject). > >The tksurfer cmd is correct, just make sure to use the correct subject. > >doug > >Jason Connolly wrote: >> >> Dear freesurfer experts, >> >> I have used the mri.vol and mri.analyzehdr.vol fields to encode my >> coordinates and phase values using MRIread and MRIwrite (f_LH12.mgz). >> >> I then brought these data into freesurfer using the following: >> >> >> bbregister --s fsaverage --mov >> /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg >> register12.dat --bold --init-header -t2 >> >> mri_vol2surf --mov >> /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg >> /Applications/freesurfer/subjects/fsaverage/surf/register12.dat --hemi >> lh --surf white --o >> /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh >> >> tksurfer fsaverage lh sphere --overlay >> /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh >> >> However, I do not see anything on the sphere (or fsaverage for that >> matter) ... >> >> Can you provide any hints? >> >> The phase values are normalized and range from 4 - 5 and I have >> converted to RAS space properly (I hope) ... >> >> Any tips would be a big help! >> >> Best wishes, >> >> Jason. >> >> -- >-- >> >> ___ >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > >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
Re: [Freesurfer] phase data overlay using fsaverage
Thank you for your advice Doug. Best wishes, -jason. >-Original Message- >From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] >Sent: 09 February 2011 16:42 >To: Jason Connolly >Cc: 'freesurfer@nmr.mgh.harvard.edu' >Subject: Re: [Freesurfer] phase data overlay using fsaverage > >First, make sure that the volume you created is in register with the >template functional. Eg, > >tkmedit -f f.nii -ov f_LH12.mgz > >where f.nii is the functional that f_LH12.mgz was derived from. > >Once that is correct, run bbregister with the actual subject as the >target (not fsaverage), spec the --mov as f.nii, and use --init-fsl >instead of --init-header > >The vol2surf cmd is correct, though it will sample it on the subject's >surface (not that of fsaverage; you can change this with --trgsubject). > >The tksurfer cmd is correct, just make sure to use the correct subject. > >doug > >Jason Connolly wrote: >> >> Dear freesurfer experts, >> >> I have used the mri.vol and mri.analyzehdr.vol fields to encode my >> coordinates and phase values using MRIread and MRIwrite (f_LH12.mgz). >> >> I then brought these data into freesurfer using the following: >> >> >> bbregister --s fsaverage --mov >> /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg >> register12.dat --bold --init-header -t2 >> >> mri_vol2surf --mov >> /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg >> /Applications/freesurfer/subjects/fsaverage/surf/register12.dat --hemi >> lh --surf white --o >> /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh >> >> tksurfer fsaverage lh sphere --overlay >> /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh >> >> However, I do not see anything on the sphere (or fsaverage for that >> matter) ... >> >> Can you provide any hints? >> >> The phase values are normalized and range from 4 - 5 and I have >> converted to RAS space properly (I hope) ... >> >> Any tips would be a big help! >> >> Best wishes, >> >> Jason. >> >> -- >-- >> >> ___ >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > >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] phase data overlay using fsaverage
Dear freesurfer experts, I have used the mri.vol and mri.analyzehdr.vol fields to encode my coordinates and phase values using MRIread and MRIwrite (f_LH12.mgz). I then brought these data into freesurfer using the following: bbregister --s fsaverage --mov /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg register12.dat --bold --init-header -t2 mri_vol2surf --mov /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg /Applications/freesurfer/subjects/fsaverage/surf/register12.dat --hemi lh --surf white --o /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh tksurfer fsaverage lh sphere --overlay /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh However, I do not see anything on the sphere (or fsaverage for that matter) ... Can you provide any hints? The phase values are normalized and range from 4 - 5 and I have converted to RAS space properly (I hope) ... Any tips would be a big help! Best wishes, Jason. ___ 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] two vol fields for retinotopic analysis?
Dear freesurfer experts: I noticed that there are two 'vol' fields when I use MRIread. 1) mri.vol 2) mri.analyzehdr.vol My question is: I have two arrays, one with 3D coordinates and a second 1 dimensional array with corresponding phase values. Which 'vol' field do I put the 3D coordinates in and which do I put the phase values in? Many thanks! -jason. ___ 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] Inverse projection query
Hello, I think that the problem may lie with MRIread. I have 1 x 82 Array of phase volumes. I also then have a separate 3 x 82 array of coordinates (that correspond to each of the normalized 0 to 1 phase values above. My question is: if I input the phases in vol, what field do I place the coordinates for the phase values in? Many thanks, Jason. On 05/02/2011 01:03, "Bruce Fischl" wrote: try one '-' in '-overlay', not two On Sat, 5 Feb 2011, Jason Connolly wrote: > Hi Bruce, > > I used mri_vol2surf, but there appears to be no overlay colours ... Here is > the output ... > > Any ideas would be great ... > > tksurfer bert rh inflated --overlay > /Applications/fesurfer/subjects/bert/surf/test_LH.mgh > WARNING: flag --overlay unrecognized > WARNING: flag /Applications/freesurfer/subjects/bert/surf/test_LH.mgh > unrecognized > subject is bert > hemiis rh > surface is inflated > surfer: current subjects dir: /Applications/freesurfer/subjects > surfer: not in "scripts" dir ==> using cwd for session root > surfer: session root data dir ($session) set to: > surfer: /Applications/freesurfer/subjects/bert/mri > surfer: can't create file surfer.log in cwd > surfer: surfer.log created in /tmp > surfer: session root data dir ($session) reset to: > surfer: /tmp > Reading image info (/Applications/freesurfer/subjects/bert) > Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz > surfer: Reading header info from > /Applications/freesurfer/subjects/bert/mri/orig.mgz > ltMNIreadEx: could not open file > /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm > Permission denied > surfer: Talairach xform file not found (ignored) > surfer: vertices=131547, faces=263090 > surfer: single buffered window > surfer: tkoInitWindow(bert) > surfer: using interface /Applications/freesurfer/lib/tcl/tksurfer.tcl > Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl > Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl > Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl > Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl > Successfully parsed tksurfer.tcl > reading white matter vertex locations... > > > On 05/02/2011 00:32, "Bruce Fischl" wrote: > > no, you can use it to sample volume data onto the surface using > mri_vol2surf > > On Sat, 5 Feb 2011, Jason > Connolly wrote: > >> Can I display register.dat in tksurfer? >> >> Thanks, -j. >> >> >> On 05/02/2011 00:21, "Bruce Fischl" wrote: >> >> that writes the file named register.dat that has the affine registration >> matrix (and some other things) >> >> On >> Sat, 5 Feb 2011, Jason Connolly wrote: >> >>> Hi Bruce, >>> >>> Here it is: >>> >>> bbregister --s bert --mov >>> /Applications/freesurfer/subjects/bert/mri/f_RH.mgz --reg register.dat >>> --bold --init-header >>> >>> -jason. >>> >>> On 05/02/2011 00:18, "Bruce Fischl" wrote: >>> >>> can you send us your command line? >>> On Sat, 5 Feb 2011, Jason Connolly wrote: >>> >>>> Hi Doug, >>>> >>>> I am now at the bbregister stage ... I ran this but it is not clear to me >>>> where the output is? I don't see an output flag ... >>>> >>>> Can you tell me where to look for my output? >>>> >>>> Almost there! >>>> >>>> Many thanks, Jason. >>>> >>>> >>>> On 04/02/2011 23:49, "Jason Connolly" >>>> wrote: >>>> >>>> Thank you. -jason. >>>> >>>> >>>> On 04/02/2011 23:48, "Douglas N Greve" wrote: >>>> >>>> You can load in the functional with MRIread since you are going to be >>>> replacing all the pixel data anyway with your single time point. Just >>>> use the single argument. The second is if you dont want to read in the >>>> pixel data. >>>> >>>> Jason Connolly wrote: >>>>> Thanks. >>>>> >>>>> So, to clarify, I am trying to just make an overlay. So do I use MRIread >>>>> with a functional .img as input? >>>>> >>>>> Is the second argument in MRIread my scanCoords for my phase-value pixels? >>>>> >>>>> Almost there ... >>>>> >>>>> >>>>> >>>>> >>>>> On 04/02/2011 23:35, "Douglas N Greve" wrote: >&
Re: [Freesurfer] Inverse projection query
Final question: My values are normalized: from 0 to 1 ... How do I change the overlay colours so that this is scaled correctly? I am assuming I have to make a file of some sort ... Thanks, I think I am almost there ... -jason. On 05/02/2011 01:03, "Bruce Fischl" wrote: try one '-' in '-overlay', not two On Sat, 5 Feb 2011, Jason Connolly wrote: > Hi Bruce, > > I used mri_vol2surf, but there appears to be no overlay colours ... Here is > the output ... > > Any ideas would be great ... > > tksurfer bert rh inflated --overlay > /Applications/fesurfer/subjects/bert/surf/test_LH.mgh > WARNING: flag --overlay unrecognized > WARNING: flag /Applications/freesurfer/subjects/bert/surf/test_LH.mgh > unrecognized > subject is bert > hemiis rh > surface is inflated > surfer: current subjects dir: /Applications/freesurfer/subjects > surfer: not in "scripts" dir ==> using cwd for session root > surfer: session root data dir ($session) set to: > surfer: /Applications/freesurfer/subjects/bert/mri > surfer: can't create file surfer.log in cwd > surfer: surfer.log created in /tmp > surfer: session root data dir ($session) reset to: > surfer: /tmp > Reading image info (/Applications/freesurfer/subjects/bert) > Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz > surfer: Reading header info from > /Applications/freesurfer/subjects/bert/mri/orig.mgz > ltMNIreadEx: could not open file > /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm > Permission denied > surfer: Talairach xform file not found (ignored) > surfer: vertices=131547, faces=263090 > surfer: single buffered window > surfer: tkoInitWindow(bert) > surfer: using interface /Applications/freesurfer/lib/tcl/tksurfer.tcl > Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl > Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl > Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl > Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl > Successfully parsed tksurfer.tcl > reading white matter vertex locations... > > > On 05/02/2011 00:32, "Bruce Fischl" wrote: > > no, you can use it to sample volume data onto the surface using > mri_vol2surf > > On Sat, 5 Feb 2011, Jason > Connolly wrote: > >> Can I display register.dat in tksurfer? >> >> Thanks, -j. >> >> >> On 05/02/2011 00:21, "Bruce Fischl" wrote: >> >> that writes the file named register.dat that has the affine registration >> matrix (and some other things) >> >> On >> Sat, 5 Feb 2011, Jason Connolly wrote: >> >>> Hi Bruce, >>> >>> Here it is: >>> >>> bbregister --s bert --mov >>> /Applications/freesurfer/subjects/bert/mri/f_RH.mgz --reg register.dat >>> --bold --init-header >>> >>> -jason. >>> >>> On 05/02/2011 00:18, "Bruce Fischl" wrote: >>> >>> can you send us your command line? >>> On Sat, 5 Feb 2011, Jason Connolly wrote: >>> >>>> Hi Doug, >>>> >>>> I am now at the bbregister stage ... I ran this but it is not clear to me >>>> where the output is? I don't see an output flag ... >>>> >>>> Can you tell me where to look for my output? >>>> >>>> Almost there! >>>> >>>> Many thanks, Jason. >>>> >>>> >>>> On 04/02/2011 23:49, "Jason Connolly" >>>> wrote: >>>> >>>> Thank you. -jason. >>>> >>>> >>>> On 04/02/2011 23:48, "Douglas N Greve" wrote: >>>> >>>> You can load in the functional with MRIread since you are going to be >>>> replacing all the pixel data anyway with your single time point. Just >>>> use the single argument. The second is if you dont want to read in the >>>> pixel data. >>>> >>>> Jason Connolly wrote: >>>>> Thanks. >>>>> >>>>> So, to clarify, I am trying to just make an overlay. So do I use MRIread >>>>> with a functional .img as input? >>>>> >>>>> Is the second argument in MRIread my scanCoords for my phase-value pixels? >>>>> >>>>> Almost there ... >>>>> >>>>> >>>>> >>>>> >>>>> On 04/02/2011 23:35, "Douglas N Greve" wrote: >>>>> >>>>> It's the vol field. >>>>> doug >>>>> >>>>>
Re: [Freesurfer] Inverse projection query
Hi Bruce, I used mri_vol2surf, but there appears to be no overlay colours ... Here is the output ... Any ideas would be great ... tksurfer bert rh inflated --overlay /Applications/fesurfer/subjects/bert/surf/test_LH.mgh WARNING: flag --overlay unrecognized WARNING: flag /Applications/freesurfer/subjects/bert/surf/test_LH.mgh unrecognized subject is bert hemiis rh surface is inflated surfer: current subjects dir: /Applications/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Applications/freesurfer/subjects/bert/mri surfer: can't create file surfer.log in cwd surfer: surfer.log created in /tmp surfer: session root data dir ($session) reset to: surfer: /tmp Reading image info (/Applications/freesurfer/subjects/bert) Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /Applications/freesurfer/subjects/bert/mri/orig.mgz ltMNIreadEx: could not open file /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm Permission denied surfer: Talairach xform file not found (ignored) surfer: vertices=131547, faces=263090 surfer: single buffered window surfer: tkoInitWindow(bert) surfer: using interface /Applications/freesurfer/lib/tcl/tksurfer.tcl Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... On 05/02/2011 00:32, "Bruce Fischl" wrote: no, you can use it to sample volume data onto the surface using mri_vol2surf On Sat, 5 Feb 2011, Jason Connolly wrote: > Can I display register.dat in tksurfer? > > Thanks, -j. > > > On 05/02/2011 00:21, "Bruce Fischl" wrote: > > that writes the file named register.dat that has the affine registration > matrix (and some other things) > > On > Sat, 5 Feb 2011, Jason Connolly wrote: > >> Hi Bruce, >> >> Here it is: >> >> bbregister --s bert --mov >> /Applications/freesurfer/subjects/bert/mri/f_RH.mgz --reg register.dat >> --bold --init-header >> >> -jason. >> >> On 05/02/2011 00:18, "Bruce Fischl" wrote: >> >> can you send us your command line? >> On Sat, 5 Feb 2011, Jason Connolly wrote: >> >>> Hi Doug, >>> >>> I am now at the bbregister stage ... I ran this but it is not clear to me >>> where the output is? I don't see an output flag ... >>> >>> Can you tell me where to look for my output? >>> >>> Almost there! >>> >>> Many thanks, Jason. >>> >>> >>> On 04/02/2011 23:49, "Jason Connolly" >>> wrote: >>> >>> Thank you. -jason. >>> >>> >>> On 04/02/2011 23:48, "Douglas N Greve" wrote: >>> >>> You can load in the functional with MRIread since you are going to be >>> replacing all the pixel data anyway with your single time point. Just >>> use the single argument. The second is if you dont want to read in the >>> pixel data. >>> >>> Jason Connolly wrote: >>>> Thanks. >>>> >>>> So, to clarify, I am trying to just make an overlay. So do I use MRIread >>>> with a functional .img as input? >>>> >>>> Is the second argument in MRIread my scanCoords for my phase-value pixels? >>>> >>>> Almost there ... >>>> >>>> >>>> >>>> >>>> On 04/02/2011 23:35, "Douglas N Greve" wrote: >>>> >>>> It's the vol field. >>>> doug >>>> >>>> Jason Connolly wrote: >>>> >>>>> Hi Doug, >>>>> >>>>> You state: >>>>> >>>>> "then replace the pixel data with your >>>>> analyzed data" >>>>> >>>>> I cannot seem to find the field for the pixel data. Can you tell me >>>>> where to position these values? >>>>> >>>>> Thanks! -jason. >>>>> >>>>> >>>>> On 04/02/2011 18:15, "Douglas N Greve" wrote: >>>>> >>>>> You should save it out as nifti (see MRIwrite.m and MRIread.m). I would >>>>> suggest using MRIread.m to read in your file in order to create the >>>>> proper header information, then replace the pixel data with your >>>>> ana
Re: [Freesurfer] Inverse projection query
Can I display register.dat in tksurfer? Thanks, -j. On 05/02/2011 00:21, "Bruce Fischl" wrote: that writes the file named register.dat that has the affine registration matrix (and some other things) On Sat, 5 Feb 2011, Jason Connolly wrote: > Hi Bruce, > > Here it is: > > bbregister --s bert --mov /Applications/freesurfer/subjects/bert/mri/f_RH.mgz > --reg register.dat --bold --init-header > > -jason. > > On 05/02/2011 00:18, "Bruce Fischl" wrote: > > can you send us your command line? > On Sat, 5 Feb 2011, Jason Connolly wrote: > >> Hi Doug, >> >> I am now at the bbregister stage ... I ran this but it is not clear to me >> where the output is? I don't see an output flag ... >> >> Can you tell me where to look for my output? >> >> Almost there! >> >> Many thanks, Jason. >> >> >> On 04/02/2011 23:49, "Jason Connolly" wrote: >> >> Thank you. -jason. >> >> >> On 04/02/2011 23:48, "Douglas N Greve" wrote: >> >> You can load in the functional with MRIread since you are going to be >> replacing all the pixel data anyway with your single time point. Just >> use the single argument. The second is if you dont want to read in the >> pixel data. >> >> Jason Connolly wrote: >>> Thanks. >>> >>> So, to clarify, I am trying to just make an overlay. So do I use MRIread >>> with a functional .img as input? >>> >>> Is the second argument in MRIread my scanCoords for my phase-value pixels? >>> >>> Almost there ... >>> >>> >>> >>> >>> On 04/02/2011 23:35, "Douglas N Greve" wrote: >>> >>> It's the vol field. >>> doug >>> >>> Jason Connolly wrote: >>> >>>> Hi Doug, >>>> >>>> You state: >>>> >>>> "then replace the pixel data with your >>>> analyzed data" >>>> >>>> I cannot seem to find the field for the pixel data. Can you tell me where >>>> to position these values? >>>> >>>> Thanks! -jason. >>>> >>>> >>>> On 04/02/2011 18:15, "Douglas N Greve" wrote: >>>> >>>> You should save it out as nifti (see MRIwrite.m and MRIread.m). I would >>>> suggest using MRIread.m to read in your file in order to create the >>>> proper header information, then replace the pixel data with your >>>> analyzed data, then use MRIwrite.m to save it out. Then use bbregister >>>> to register this volume to the anatomical, then use mri_vol2surf to >>>> sample it to the surface (either native anatomical or to some other >>>> subject). >>>> >>>> doug >>>> >>>> Jason Connolly wrote: >>>> >>>> >>>>> Dear freesurfer experts: >>>>> >>>>> I have been using matlab to analyze a retinotopic dataset. >>>>> >>>>> However, the 3D volumes are not in standardized space (and I wish to >>>>> display multiple maps from different subjects on one surface). >>>>> >>>>> Although the initial segmentations were done in freesurfer, my question >>>>> is: >>>>> >>>>> Is it possible to take matlab arrays that contain 3D space anatomical >>>>> coordinates and phase information (on a voxel by voxel basis) and display >>>>> these on a standardized inflated freesurfer-generated surface? >>>>> >>>>> If so, is the pipeline documented? >>>>> >>>>> Many thanks, >>>>> >>>>> Jason. >>>>> >>>>> ___ >>>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> >>>> >>>> >>>> The information in this e-mail is
Re: [Freesurfer] Inverse projection query
Hi Bruce, Here it is: bbregister --s bert --mov /Applications/freesurfer/subjects/bert/mri/f_RH.mgz --reg register.dat --bold --init-header -jason. On 05/02/2011 00:18, "Bruce Fischl" wrote: can you send us your command line? On Sat, 5 Feb 2011, Jason Connolly wrote: > Hi Doug, > > I am now at the bbregister stage ... I ran this but it is not clear to me > where the output is? I don't see an output flag ... > > Can you tell me where to look for my output? > > Almost there! > > Many thanks, Jason. > > > On 04/02/2011 23:49, "Jason Connolly" wrote: > > Thank you. -jason. > > > On 04/02/2011 23:48, "Douglas N Greve" wrote: > > You can load in the functional with MRIread since you are going to be > replacing all the pixel data anyway with your single time point. Just > use the single argument. The second is if you dont want to read in the > pixel data. > > Jason Connolly wrote: >> Thanks. >> >> So, to clarify, I am trying to just make an overlay. So do I use MRIread >> with a functional .img as input? >> >> Is the second argument in MRIread my scanCoords for my phase-value pixels? >> >> Almost there ... >> >> >> >> >> On 04/02/2011 23:35, "Douglas N Greve" wrote: >> >> It's the vol field. >> doug >> >> Jason Connolly wrote: >> >>> Hi Doug, >>> >>> You state: >>> >>> "then replace the pixel data with your >>> analyzed data" >>> >>> I cannot seem to find the field for the pixel data. Can you tell me where >>> to position these values? >>> >>> Thanks! -jason. >>> >>> >>> On 04/02/2011 18:15, "Douglas N Greve" wrote: >>> >>> You should save it out as nifti (see MRIwrite.m and MRIread.m). I would >>> suggest using MRIread.m to read in your file in order to create the >>> proper header information, then replace the pixel data with your >>> analyzed data, then use MRIwrite.m to save it out. Then use bbregister >>> to register this volume to the anatomical, then use mri_vol2surf to >>> sample it to the surface (either native anatomical or to some other >>> subject). >>> >>> doug >>> >>> Jason Connolly wrote: >>> >>> >>>> Dear freesurfer experts: >>>> >>>> I have been using matlab to analyze a retinotopic dataset. >>>> >>>> However, the 3D volumes are not in standardized space (and I wish to >>>> display multiple maps from different subjects on one surface). >>>> >>>> Although the initial segmentations were done in freesurfer, my question is: >>>> >>>> Is it possible to take matlab arrays that contain 3D space anatomical >>>> coordinates and phase information (on a voxel by voxel basis) and display >>>> these on a standardized inflated freesurfer-generated surface? >>>> >>>> If so, is the pipeline documented? >>>> >>>> Many thanks, >>>> >>>> Jason. >>>> >>>> ___ >>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >>> >>> >>> 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. >>> >>> >>> >>> >>> >>> >> >> -- >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >> >> >> > > -- > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > ___ > 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
Re: [Freesurfer] Inverse projection query
Hi Doug, I am now at the bbregister stage ... I ran this but it is not clear to me where the output is? I don't see an output flag ... Can you tell me where to look for my output? Almost there! Many thanks, Jason. On 04/02/2011 23:49, "Jason Connolly" wrote: Thank you. -jason. On 04/02/2011 23:48, "Douglas N Greve" wrote: You can load in the functional with MRIread since you are going to be replacing all the pixel data anyway with your single time point. Just use the single argument. The second is if you dont want to read in the pixel data. Jason Connolly wrote: > Thanks. > > So, to clarify, I am trying to just make an overlay. So do I use MRIread > with a functional .img as input? > > Is the second argument in MRIread my scanCoords for my phase-value pixels? > > Almost there ... > > > > > On 04/02/2011 23:35, "Douglas N Greve" wrote: > > It's the vol field. > doug > > Jason Connolly wrote: > >> Hi Doug, >> >> You state: >> >> "then replace the pixel data with your >> analyzed data" >> >> I cannot seem to find the field for the pixel data. Can you tell me where >> to position these values? >> >> Thanks! -jason. >> >> >> On 04/02/2011 18:15, "Douglas N Greve" wrote: >> >> You should save it out as nifti (see MRIwrite.m and MRIread.m). I would >> suggest using MRIread.m to read in your file in order to create the >> proper header information, then replace the pixel data with your >> analyzed data, then use MRIwrite.m to save it out. Then use bbregister >> to register this volume to the anatomical, then use mri_vol2surf to >> sample it to the surface (either native anatomical or to some other >> subject). >> >> doug >> >> Jason Connolly wrote: >> >> >>> Dear freesurfer experts: >>> >>> I have been using matlab to analyze a retinotopic dataset. >>> >>> However, the 3D volumes are not in standardized space (and I wish to >>> display multiple maps from different subjects on one surface). >>> >>> Although the initial segmentations were done in freesurfer, my question is: >>> >>> Is it possible to take matlab arrays that contain 3D space anatomical >>> coordinates and phase information (on a voxel by voxel basis) and display >>> these on a standardized inflated freesurfer-generated surface? >>> >>> If so, is the pipeline documented? >>> >>> Many thanks, >>> >>> Jason. >>> >>> ___ >>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >> >> 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. >> >> >> >> >> >> > > -- > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Inverse projection query
Thank you. -jason. On 04/02/2011 23:48, "Douglas N Greve" wrote: You can load in the functional with MRIread since you are going to be replacing all the pixel data anyway with your single time point. Just use the single argument. The second is if you dont want to read in the pixel data. Jason Connolly wrote: > Thanks. > > So, to clarify, I am trying to just make an overlay. So do I use MRIread > with a functional .img as input? > > Is the second argument in MRIread my scanCoords for my phase-value pixels? > > Almost there ... > > > > > On 04/02/2011 23:35, "Douglas N Greve" wrote: > > It's the vol field. > doug > > Jason Connolly wrote: > >> Hi Doug, >> >> You state: >> >> "then replace the pixel data with your >> analyzed data" >> >> I cannot seem to find the field for the pixel data. Can you tell me where >> to position these values? >> >> Thanks! -jason. >> >> >> On 04/02/2011 18:15, "Douglas N Greve" wrote: >> >> You should save it out as nifti (see MRIwrite.m and MRIread.m). I would >> suggest using MRIread.m to read in your file in order to create the >> proper header information, then replace the pixel data with your >> analyzed data, then use MRIwrite.m to save it out. Then use bbregister >> to register this volume to the anatomical, then use mri_vol2surf to >> sample it to the surface (either native anatomical or to some other >> subject). >> >> doug >> >> Jason Connolly wrote: >> >> >>> Dear freesurfer experts: >>> >>> I have been using matlab to analyze a retinotopic dataset. >>> >>> However, the 3D volumes are not in standardized space (and I wish to >>> display multiple maps from different subjects on one surface). >>> >>> Although the initial segmentations were done in freesurfer, my question is: >>> >>> Is it possible to take matlab arrays that contain 3D space anatomical >>> coordinates and phase information (on a voxel by voxel basis) and display >>> these on a standardized inflated freesurfer-generated surface? >>> >>> If so, is the pipeline documented? >>> >>> Many thanks, >>> >>> Jason. >>> >>> ___ >>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >> >> 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. >> >> >> >> >> >> > > -- > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Inverse projection query
Thanks. So, to clarify, I am trying to just make an overlay. So do I use MRIread with a functional .img as input? Is the second argument in MRIread my scanCoords for my phase-value pixels? Almost there ... On 04/02/2011 23:35, "Douglas N Greve" wrote: It's the vol field. doug Jason Connolly wrote: > Hi Doug, > > You state: > > "then replace the pixel data with your > analyzed data" > > I cannot seem to find the field for the pixel data. Can you tell me where to > position these values? > > Thanks! -jason. > > > On 04/02/2011 18:15, "Douglas N Greve" wrote: > > You should save it out as nifti (see MRIwrite.m and MRIread.m). I would > suggest using MRIread.m to read in your file in order to create the > proper header information, then replace the pixel data with your > analyzed data, then use MRIwrite.m to save it out. Then use bbregister > to register this volume to the anatomical, then use mri_vol2surf to > sample it to the surface (either native anatomical or to some other > subject). > > doug > > Jason Connolly wrote: > >> Dear freesurfer experts: >> >> I have been using matlab to analyze a retinotopic dataset. >> >> However, the 3D volumes are not in standardized space (and I wish to display >> multiple maps from different subjects on one surface). >> >> Although the initial segmentations were done in freesurfer, my question is: >> >> Is it possible to take matlab arrays that contain 3D space anatomical >> coordinates and phase information (on a voxel by voxel basis) and display >> these on a standardized inflated freesurfer-generated surface? >> >> If so, is the pipeline documented? >> >> Many thanks, >> >> Jason. >> >> ___ >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > 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. > > > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Inverse projection query
Hi Doug, You state: "then replace the pixel data with your analyzed data" I cannot seem to find the field for the pixel data. Can you tell me where to position these values? Thanks! -jason. On 04/02/2011 18:15, "Douglas N Greve" wrote: You should save it out as nifti (see MRIwrite.m and MRIread.m). I would suggest using MRIread.m to read in your file in order to create the proper header information, then replace the pixel data with your analyzed data, then use MRIwrite.m to save it out. Then use bbregister to register this volume to the anatomical, then use mri_vol2surf to sample it to the surface (either native anatomical or to some other subject). doug Jason Connolly wrote: > Dear freesurfer experts: > > I have been using matlab to analyze a retinotopic dataset. > > However, the 3D volumes are not in standardized space (and I wish to display > multiple maps from different subjects on one surface). > > Although the initial segmentations were done in freesurfer, my question is: > > Is it possible to take matlab arrays that contain 3D space anatomical > coordinates and phase information (on a voxel by voxel basis) and display > these on a standardized inflated freesurfer-generated surface? > > If so, is the pipeline documented? > > Many thanks, > > Jason. > > ___ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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
Re: [Freesurfer] Inverse projection query
Hi Bruce, I guess the problem I have at hand is how to map them to fsaverage. Do I have to convert the arrays somehow to nifti format first? I tried looking this up on the web but couldn't find a solution ... Many thanks, Jason. On 04/02/2011 13:48, "Bruce Fischl" wrote: Hi Jason why not map them all to fsaverage and display them on a common surface? cheers Bruce On Fri, 4 Feb 2011, Jason Connolly wrote: > Dear freesurfer experts: > > I have been using matlab to analyze a retinotopic dataset. > > However, the 3D volumes are not in standardized space (and I wish to display > multiple maps from different subjects on one surface). > > Although the initial segmentations were done in freesurfer, my question is: > > Is it possible to take matlab arrays that contain 3D space anatomical > coordinates and phase information (on a voxel by voxel basis) and display > these on a standardized inflated freesurfer-generated surface? > > If so, is the pipeline documented? > > Many thanks, > > Jason. > > ___ > 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] Inverse projection query
Dear freesurfer experts: I have been using matlab to analyze a retinotopic dataset. However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface). Although the initial segmentations were done in freesurfer, my question is: Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface? If so, is the pipeline documented? Many thanks, Jason. ___ 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] compatibility question
Dear Free Surfers, I'm having a problem I've seen posts about in the archive, but have not been able to see the solution to it. If I start tksurfer bert rh pial (as the example says), the display only shows a small fraction of the brain and nothing more. I've tried some of the suggestions such as zooming, the 'Auto redraw' option, but to no use. I have tried on two of our Linux machines, with CentOS 5, either logged in locally or remotely with NoMachines. I've got external video cards and the GLX gears works fine at ~100 FPS (remotely) and ~1000FPS (locally). The machines have 8 processors, are 64 bit, 500 GB+ hard drives and 4GB of RAM, and external NVIDIA compatible video cards. A colleague who is running Fedora 11 has no problems. Is this an OS type problem and any way to fix it? Thanks in advance for your help Best wishes, -Jason ___ 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] monkey segmentation error query
Dear Freesurfer experts, We are attempting to segment a template monkey brain. The following is the command line input: recon-all -i /usr/local/freesurfer/subjects/template_2/mri/orig/MonkTempl_w81096_T1.nii.gz -s template -all -notal-check -force -noaseg It runs for a few hours and then we get the following error: "cannot find seed region for corpus collosum" Do we have to manually mark this somehow in tkmedit? Any advice would be appreciated! Thank you, Jason. ___ 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] freesurfer recon-all running in a few seconds without error?
Thanks. It's working now. J >-Original Message- >From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] >Sent: 13 May 2010 15:12 >To: Jason Connolly >Cc: 'freesurfer@nmr.mgh.harvard.edu' >Subject: Re: [Freesurfer] freesurfer recon-all running in a few seconds >without error? > >Hi Jason, > >you have to tell it do do something (e.g. -autorecon2, -all, etc...) > >cheers >Bruce > >On Thu, >13 May 2010, Jason Connolly wrote: > >> Dear freesurfer experts: >> >> Recon-all is running in a few seconds (obvious error). >> >> I am getting the following screen output on Linux, when I run recon- >all: >> >> >> recon-all -i >/usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img -s arlene - >force >> INFO: /usr/local/freesurfer/subjects/arlene exists with -i, but -force >specified. >> Deleting any previous source volumes >> Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 >> Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 >> INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects >> Actual FREESURFER_HOME /usr/local/freesurfer >> -rw-rw-r-- 1 lab root 59398 May 13 15:07 >/usr/local/freesurfer/subjects/arlene/scripts/recon-all.log >> Linux ionimagelab1 2.6.30.5-43.fc11.x86_64 #1 SMP Thu Aug 27 21:39:52 >EDT 2009 x86_64 x86_64 x86_64 GNU/Linux >> /usr/local/freesurfer/subjects/arlene >> >> mri_convert >/usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img >/usr/local/freesurfer/subjects/arlene/mri/orig/001.mgz >> >> mri_convert >/usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img >/usr/local/freesurfer/subjects/arlene/mri/orig/001.mgz >> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ >> reading from >/usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img... >> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (-0.998356, -0.0445698, 0.0360538) >> j_ras = (0.0395912, -0.0812138, 0.99591) >> k_ras = (0.0414595, -0.9957, -0.0828448) >> writing to /usr/local/freesurfer/subjects/arlene/mri/orig/001.mgz... >> >> #-- >> >> recon-all finished without error at Thu May 13 15:08:08 BST 2010 >> >> The TR, flig angle etc. are all 0.00 ... Do you have any ideas? >> >> Many thanks, Jason. >> >> ___ >> 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] freesurfer recon-all running in a few seconds without error?
Dear freesurfer experts: Recon-all is running in a few seconds (obvious error). I am getting the following screen output on Linux, when I run recon-all: recon-all -i /usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img -s arlene -force INFO: /usr/local/freesurfer/subjects/arlene exists with -i, but -force specified. Deleting any previous source volumes Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 lab root 59398 May 13 15:07 /usr/local/freesurfer/subjects/arlene/scripts/recon-all.log Linux ionimagelab1 2.6.30.5-43.fc11.x86_64 #1 SMP Thu Aug 27 21:39:52 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/arlene mri_convert /usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img /usr/local/freesurfer/subjects/arlene/mri/orig/001.mgz mri_convert /usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img /usr/local/freesurfer/subjects/arlene/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998356, -0.0445698, 0.0360538) j_ras = (0.0395912, -0.0812138, 0.99591) k_ras = (0.0414595, -0.9957, -0.0828448) writing to /usr/local/freesurfer/subjects/arlene/mri/orig/001.mgz... #-- recon-all finished without error at Thu May 13 15:08:08 BST 2010 The TR, flig angle etc. are all 0.00 ... Do you have any ideas? Many thanks, Jason. ___ 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] fs-fast sfa-sess retinotopy error
Dear freesurfer experts: I am new to fs-fast and I am currently running sfa-sess on some retinotopy data and I think the main error is "cannot determine format of 005/f" I read in a previous post related to retinotopy that you need to add the full path to the .nii files and then it will work. My question is: where do you add the full path? Many thanks, Jason. Error message: sfa-sess -analysis rtopy -s jason-functional -- sfa-sess logfile is /usr/local/freesurfer/subjects/jason/brainmapper/log/sfa-sess-bold-rtopy-1001181608.log -- --- /usr/local/freesurfer/subjects/jason/brainmapper/jason-functional Mon Jan 18 16:08:48 GMT 2010 INFO (jason-functional): RunList = 005 007 012 013 -- /usr/local/freesurfer/subjects/jason/brainmapper/jason-functional/bold selfreqavg -TR 1.5 -o rtopy/polar/h -i 005/f -i 007/f -i 012/f -cfg /usr/local/freesurfer/subjects/jason/brainmapper/rtopy/analysis.cfg -parname rtopy.par -- --- Parsing Config File: /usr/local/freesurfer/subjects/jason/brainmapper/rtopy/analysis.cfg -ncycles 15 -delay 0 -nskip 0 -fwhm 0 DirectionList: +1 -1 +1 Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2009 The MathWorks, Inc. Version 7.8.0.347 (R2009a) 64-bit (glnxa64) February 12, 2009 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> Extension format = >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> nii >> >> >> >> >> >> >> hanrad = 0 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ERROR: cannot determine >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> format of 005/f >> ??? Attempt to reference field of non-structure array. >> ??? Attempt to reference field of non-structure array. >> ??? Attempt to reference field of non-structure array. >> >> ??? Attempt to reference field of non-structure array. >> >> ??? Undefined function or variable 'lastslice'. >> ??? Attempt to reference field of non-structure array. >> >> >> ??? Attempt to reference field of non-structure array. >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ??? Index >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> exceeds matrix >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> dimensions. >> >> >> >> >> ??? Attempted to access tmp(NaN); index must be a positive >> >> >> >> >> integer or logical. >> ??? Attempted to access tmp(NaN); index must be a positive integer or >> logical. >> ??? Attempted to access tmp(NaN); index must be a positive integer or >> logical. >> ??? Attempted to access tmp(NaN); index must be a positive integer or >> logical. >> ??? Attempted to access tmp(NaN); index must be a positive integer or >> logical. >> ??? Attempted to access tmp(NaN); index must be a positive integer or >> logical. >> >> >> >> >> >> >> >> >> >> >> >> >> Slice >> ??? Undefined function or >> >> >> >> >> >> >> >> >> >> >> >> >> variable 'lastslice'. >> >> >> >> ??? Attempt to reference field of non-structure array. Error in ==> MRIwrite at 94 hdr.dim = [mri.volsize(2) mri.volsize(1) mri.volsize(3) mri.nframes]; >> >> >> ??? Attempt to reference field of non-structure array. Error in ==> MRIwrite at 94 hdr.dim = [mri.volsize(2) mri.volsize(1) mri.volsize(3) mri.nframes]; >> >> >> ??? Attempt to reference field of non-structure array. Error in ==> MRIwrite at 94 hdr.dim = [mri.volsize(2) mri.volsize(1) mri.volsize(3) mri.nframes]; >> >> >> >> Saving header to rtopy/polar/h >> >> >> selfreqavg COMPLETED mri_convert rtopy/polar/h.nii -o rtopy/polar/h-offset.nii --frame 10 mri_convert rtopy/polar/h.nii -o rtopy/polar/h-offset.nii --frame 10 niiRead(): error opening file rtopy/polar/h.nii $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from rtopy/polar/h.nii... ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
