Re: [Freesurfer] question retinotopic mapping
Hi Julia, I don't think it looks terrible (unfortunately:). You might try increasing the smoothing level (maybe 10 fwhm). doug On 12/12/2012 08:02 AM, Julia Foecker wrote: Hey Doug, thanks for your reply. I tried now the polar angle mapping for the left hemisphere and I got the figure attached. It is difficult to see the typical polar maps in that figure and I am wondering how to change the settings so that I will receive a typical polar angle map. I had a 180 deg. wedge. One cycle took 38.4 sec. There were 8 cycles. The first 5 volumes had to be deleted. I did the follwing analysis. mkanalysis-sess analysis rtopy.self.lh -surface self lh -TR 1.2 -retnotopy 38.4 -fsd bold -fwhm 5 -paradigm rtopy.par -tpef tp-exclude.txt Do you have any advices what to change so that it looks more like polar angle maps? Thanks so much for any further advices, best Julia On Mon, 10 Dec 2012 12:27:13 -0500 Douglas N Greve gr...@nmr.mgh.harvard.eduwrote Hi Julia, that command is fine. It will not use the fieldsign or eccen. doug On 12/10/2012 10:17 AM, Julia Foecker wrote: Dear Doug, I tried version 5 with the commands suggested on the webside and this is working (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis) . However, I have only polar angle runs and I am not sure if the rtview commands is only referring to polar angle maps (because the field signs are included and I think that they consist of eccentricity maps as well which do not have a meaning in my analysis). How do I have to change the command below so that it is just referring to polar maps? rtview --s VGP01 --lh --polar --real polar/real.nii.gz --imag polar/imag.nii.gz --fsig polar/fsig.nii.gz Many thanks for further suggestions, Julia -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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 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
Re: [Freesurfer] question retinotopic mapping
Hi Julia, that command is fine. It will not use the fieldsign or eccen. doug On 12/10/2012 10:17 AM, Julia Foecker wrote: Dear Doug, I tried version 5 with the commands suggested on the webside and this is working (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis). However, I have only polar angle runs and I am not sure if the rtview commands is only referring to polar angle maps (because the field signs are included and I think that they consist of eccentricity maps as well which do not have a meaning in my analysis). How do I have to change the command below so that it is just referring to polar maps? rtview --s VGP01 --lh --polar --real polar/real.nii.gz --imag polar/imag.nii.gz --fsig polar/fsig.nii.gz Many thanks for further suggestions, Julia -- 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 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 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] question retinotopic mapping
Julia, what version of FS are you using? It looks like pre-5.0. Can you upgrade to 5.1? There were a lot of changes in going from 4 to 5, and it is becoming increasingly hard to support version 4. doug On 12/06/2012 02:45 AM, Julia Foecker wrote: thanks. attached the info file. When I run the surf-sess command after that, it shows the functional on a surface (see attached but the values at the occip regions show inf. (see figure 1 attached). Moreover, when I try to load the occipital patch it shows me the attached file (fig.3) and I cannot use the command - configure - overlay to change settings. I have used fake ecc. runs (I have recorded only polar runs). Would you have any further suggestions? Thanks, Julia On Wed, 05 Dec 2012 17:03:31 -0500 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote It should automatically detect that this was a retinotopy analysis and then load the polar and eccen. Was this configured as a retinotopy analysis? Can you send me the $ANALYSIS_PHASE/analysis.info file? doug On 12/05/2012 04:12 PM, Julia Foecker wrote: Hi Doug, I tried now several ways to get the maps on the surface: 1. When I am deleting -retinotopy flag and type in: tksurfer-sess -debug -s $SESSIONNAME -hemi lh -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE I got the message:no contrast has been specified (I do not have any contrasts in the analysis, just use polar angle maps) 2. I tried to use the commands on the website you referred to, but I do not have -surface in the preproc-sess (see attached) The other commands depend on this preproc-sess command. 3. I tried the following command paint-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE and I got the errors listed below... I am not sure how to procede. Would you have any further suggestions? Many thanks, Julia Thanks, Julia 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 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
Re: [Freesurfer] question retinotopic mapping
The problem is that you have a version 4 analysis that you are trying to view with version 5 tools. To use version 5 visualization, you'll need to remake the analysis in version 5 and then reanalyze. Otherwise, you'll have to use the version 4 stream (instructions attached). It is somewhat difficult for me to support the version 4 stream because it is so old. doug On 12/06/2012 03:27 PM, Julia Foecker wrote: I have the two versions 4 and 5 , but I am receiving the same error messages with 5.1 For example when I type in preproc-see there is no -surface as well. Isn't there any other possibility to solve that issue? It may have also sth. to do with the computer. I have a new Mac, not sure if this may be the reason. As I said, I do not think this is due to the version...I just tried that and similar requirements are missing when I am doing that with 5.1 Thanks again for further advices, Julia On 12/6/12 11:56 AM, Douglas N Greve wrote: Julia, what version of FS are you using? It looks like pre-5.0. Can you upgrade to 5.1? There were a lot of changes in going from 4 to 5, and it is becoming increasingly hard to support version 4. doug On 12/06/2012 02:45 AM, Julia Foecker wrote: thanks. attached the info file. When I run the surf-sess command after that, it shows the functional on a surface (see attached but the values at the occip regions show inf. (see figure 1 attached). Moreover, when I try to load the occipital patch it shows me the attached file (fig.3) and I cannot use the command - configure - overlay to change settings. I have used fake ecc. runs (I have recorded only polar runs). Would you have any further suggestions? Thanks, Julia On Wed, 05 Dec 2012 17:03:31 -0500 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote It should automatically detect that this was a retinotopy analysis and then load the polar and eccen. Was this configured as a retinotopy analysis? Can you send me the $ANALYSIS_PHASE/analysis.info file? doug On 12/05/2012 04:12 PM, Julia Foecker wrote: Hi Doug, I tried now several ways to get the maps on the surface: 1. When I am deleting -retinotopy flag and type in: tksurfer-sess -debug -s $SESSIONNAME -hemi lh -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE I got the message:no contrast has been specified (I do not have any contrasts in the analysis, just use polar angle maps) 2. I tried to use the commands on the website you referred to, but I do not have -surface in the preproc-sess (see attached) The other commands depend on this preproc-sess command. 3. I tried the following command paint-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE and I got the errors listed below... I am not sure how to procede. Would you have any further suggestions? Many thanks, Julia Thanks, Julia 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ Retinotopy analysis in FS-FAST For each session, create retinotopy paradigm files in each of the run directories. These paradigm files are different than an event-related or block paradigm (which list which stimulus was presented when). A retinotopy paradigm file has information about whether the run was an eccentricity or polar stimulus and in what direction the stimulus was presented. For polar, the direction is indicates whether the spoke was traveling clockwise or counter-clockwise. For eccen, the direction is indicates whether the ring was expanding or contracting. The definition of what's positive and what's negative is arbitrary, though it must be consistent. If you don't have both directions, just use positive. For example, if there were four runs (001, 002, 003, 004), two eccen and two polar, both in the positive and negative directions. Create a file (eg, rtopy.par) in each run. Assuming run 001 was eccen in the negative direction, then the rtopy.par for run 001 would look like: cut here stimtype eccen direction neg cut here If needed, create a run-list file with the all retinotopy runs (regardless of whether it was eccen or polar). Create the analysis: mkanalysis-sess \ -a rtopy \ -TR 2 \ -designtype retinotopy \ -paradigm rtopy.par \ -funcstem fmcsm5 \ -ncycles 8 Preprocess preproc-sess -s avdk -fwhm 8 Run the
Re: [Freesurfer] question retinotopic mapping
Hi Julia, what is your command line when you give it the hemisphere? Also, when you run it, put -debug as the first argument and send me the terminal output. doug On 12/05/2012 10:55 AM, Julia Foecker wrote: Hi Doug, I tried now several things to use the tksurfer command but it does not seem to work. tksurfer-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE -retinotopy polar when I run the command and just replace tksurfer, it is asking for the hemisphere ERROR: no hemisphere specified When I am specifying the hemisphere it does not find the command... I think the problem according to the colortables has been already posted in the forum, but I cannot see any reply to that. It has been mentioned under a different topic though (see link below). Thanks a lot for any advices, Julia https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-April/007556.html On Tue, 04 Dec 2012 12:00:50 -0500 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote Hi Julia, I meant tksurfer-sess (not surf-sess) doug On 12/04/2012 05:39 AM, Julia Foecker wrote: Hi Doug, thanks for your reply. I got the following messages when running the surf-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE -retinotopy polar and there was also this kind of message: GL window already open: can't open second % tksurfer: polar-views.tcl: save rgb's saveviews.tcl: nosave setenv'd = nothing will be saved invalid command name dontsave_rgb_named% surfer: dmin=0.2470, vno=45600, I am still not sure what I can do so that this issue will not occur. Do you have another advice? Thanks! Julia WARNING: No colortable found! invalid command name urfer/subjects] % invalid command name WARNING: % invalid command name WARNING: % invalid command name surfer: % invalid command name surfer: % invalid command name surfer: % invalid command name surfer: % invalid command name surfer: % invalid command name surfer: % invalid command name mrisReadTriangleFile(/Users/foecker/Documents/Data/FMRI/Freesurfer/subjects/ VGP01/surf/lh.sphere.reg): % % invalid command name mrisReadTriangleFile % % % % invalid command name WARNING: % % e buffered window surfer: tkoInitWindow(VGP01) surfer: using interface /Users/foecker/Documents/freesurfer4/lib/tcl/tksurfer.tcl Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkm_common.tcl Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkm_wrappers.tcl Reading /Users/foecker/Documents/freesurfer4/lib/tcl/fsgdfPlot.tcl Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % invalid command name surfer: % invalid command name surfer: % invalid command name surfer: % invalid command name Reading % invalid command name Reading % invalid command name Reading % invalid command name Reading % invalid command name Successfully % invalid command name reading % invalid command name % % % exit [4157-JF-MACPRO1:FMRI/Freesurfer/subjects] foecker% tksurfer usage: tksurfer subject hemisphere surface [options] subject: a subject directory in the SUBJECTS_DIR path hemipshere : rh or lh surface: a surface file name relative to the subject's surf directory Options -title title : set window title to title. Def is subject name. -reassign : resample labels onto surface (set vnos=-1) -sdir path : sets the subjects directory path -orig suffix : sets the orig suffix string -sphere suffix:sets the sphere.reg suffix string -patch filename : load a patch -tcl filename : run a script -annotation filename : load an annotation -aparc : set annotation to aparc.annot and use outline mode -colortable filename : load a color table file -labels-under : display labels under any overlay -label-outline : draw labels as outlines -curv : automatically load ?h.curv -gray : automatically load ?h.curv and make it gray -overlay filename : load an overlay volume -overlay-reg filename : use a file for the overlay registration -overlay-reg-find: look in the data directory for a register.dat : file -overlay-reg-identity: calculate an identity transform for registration -mni152reg : for use with average subject when overlay is mni152 -zm : remove mean from overlays -fslope value : set the overlay threshold slope value -fmid value: set the overlay threshold midpoint value -fthresh value : set the overlay threshold minimum value -foffset value : set the overlay threshold offset value -colscalebarflag 1|0 : display color scale bar -colscaletext 1|0 : display text in color scale bar -truncphaseflag 1|0: truncate the overlay display -revphaseflag 1|0 : reverse the overlay display -invphaseflag 1|0 : invert the
Re: [Freesurfer] question retinotopic mapping
It should automatically detect that this was a retinotopy analysis and then load the polar and eccen. Was this configured as a retinotopy analysis? Can you send me the $ANALYSIS_PHASE/analysis.info file? doug On 12/05/2012 04:12 PM, Julia Foecker wrote: Hi Doug, I tried now several ways to get the maps on the surface: 1. When I am deleting -retinotopy flag and type in: tksurfer-sess -debug -s $SESSIONNAME -hemi lh -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE I got the message:no contrast has been specified (I do not have any contrasts in the analysis, just use polar angle maps) 2. I tried to use the commands on the website you referred to, but I do not have -surface in the preproc-sess (see attached) The other commands depend on this preproc-sess command. 3. I tried the following command paint-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE and I got the errors listed below... I am not sure how to procede. Would you have any further suggestions? Many thanks, Julia Thanks, Julia ___ 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] question retinotopic mapping
Hi Julia, I meant tksurfer-sess (not surf-sess) doug On 12/04/2012 05:39 AM, Julia Foecker wrote: Hi Doug, thanks for your reply. I got the following messages when running the surf-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE -retinotopy polar and there was also this kind of message: GL window already open: can't open second % tksurfer: polar-views.tcl: save rgb's saveviews.tcl: nosave setenv'd = nothing will be saved invalid command name dontsave_rgb_named% surfer: dmin=0.2470, vno=45600, I am still not sure what I can do so that this issue will not occur. Do you have another advice? Thanks! Julia WARNING: No colortable found! invalid command name urfer/subjects] % invalid command name WARNING: % invalid command name WARNING: % invalid command name surfer: % invalid command name surfer: % invalid command name surfer: % invalid command name surfer: % invalid command name surfer: % invalid command name surfer: % invalid command name mrisReadTriangleFile(/Users/foecker/Documents/Data/FMRI/Freesurfer/subjects/VGP01/surf/lh.sphere.reg): % % invalid command name mrisReadTriangleFile % % % % invalid command name WARNING: % % e buffered window surfer: tkoInitWindow(VGP01) surfer: using interface /Users/foecker/Documents/freesurfer4/lib/tcl/tksurfer.tcl Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkm_common.tcl Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkm_wrappers.tcl Reading /Users/foecker/Documents/freesurfer4/lib/tcl/fsgdfPlot.tcl Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % invalid command name surfer: % invalid command name surfer: % invalid command name surfer: % invalid command name Reading % invalid command name Reading % invalid command name Reading % invalid command name Reading % invalid command name Successfully % invalid command name reading % invalid command name % % % exit [4157-JF-MACPRO1:FMRI/Freesurfer/subjects] foecker% tksurfer usage: tksurfer subject hemisphere surface [options] subject: a subject directory in the SUBJECTS_DIR path hemipshere : rh or lh surface: a surface file name relative to the subject's surf directory Options -title title : set window title to title. Def is subject name. -reassign : resample labels onto surface (set vnos=-1) -sdir path : sets the subjects directory path -orig suffix : sets the orig suffix string -sphere suffix:sets the sphere.reg suffix string -patch filename : load a patch -tcl filename : run a script -annotation filename : load an annotation -aparc : set annotation to aparc.annot and use outline mode -colortable filename : load a color table file -labels-under : display labels under any overlay -label-outline : draw labels as outlines -curv : automatically load ?h.curv -gray : automatically load ?h.curv and make it gray -overlay filename : load an overlay volume -overlay-reg filename : use a file for the overlay registration -overlay-reg-find: look in the data directory for a register.dat : file -overlay-reg-identity: calculate an identity transform for registration -mni152reg : for use with average subject when overlay is mni152 -zm : remove mean from overlays -fslope value : set the overlay threshold slope value -fmid value: set the overlay threshold midpoint value -fthresh value : set the overlay threshold minimum value -foffset value : set the overlay threshold offset value -colscalebarflag 1|0 : display color scale bar -colscaletext 1|0 : display text in color scale bar -truncphaseflag 1|0: truncate the overlay display -revphaseflag 1|0 : reverse the overlay display -invphaseflag 1|0 : invert the overlay display -timecourse filename: load an timecourse volume -timecourse-reg filename: use a file for the timecourse : registration -timecourse-reg-find : look in the data directory for a : register.dat file -timecourse-reg-identity : calculate an identity transform for : regisrtation -timecourse-offset filename : load an timecourse offset volume -timecourse-offset-reg-file filename : use a file for the timecourse offset : registration -timecourse-offset-reg-find: look in the data directory for a : register.dat file -timecourse-offset-reg-identity: calculate an identity transform for : registration -delink : do not move tool window with image window -scalebarflag 1|0
