Re: [Freesurfer] view retinotopy results in version 5
Hi Doug, It worked very well, thank you so much! For future references, these are the commands I put in with this new version of rtview (under the folder bold): Polar angle: rtview --lh --polar --real rtopy.self.lh/polar/real.nii.gz --imag rtopy.self.lh/polar/imag.nii.gz --fsig rtopy.self.lh/polar/fsig.nii.gz --s MySubjectNameInAnatomicalFolder --flat Eccentricity: rtview --lh --eccen --real rtopy.self.lh/eccen/real.nii.gz --imag rtopy.self.lh/eccen/imag.nii.gz --fsig rtopy.self.lh/eccen/fsig.nii.gz --s MySubjectNameInAnatomicalFolder --flat I compared the results from Version 5's rtview (see above) and Version 4's surf-sess from the same participant. The resulting maps were highly consistent. The only difference is that the colors were more scattered in Version 4, making it harder to identify the borders between regions. -Yuhong On Wed, Mar 27, 2013 at 2:35 PM, Douglas N Greve wrote: > Hi Yuhong, I put a new version that has a --flat and --patch option here: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview > > I have not tested it because I don't have any retinotopy handy. Can you > test it and let me know whether it works? > > doug > > > On 03/26/2013 03:00 PM, Y.V. Jiang wrote: > > Hi, > > > > I was able to view retinotopic mapping results using rtview in version > > 5. However, the display was on the inflated surface. Is there a way to > > view the results on the flattened occipital map, similar to version > > 4's surf-sess -flat? > > > > Thanks! > > > > -Yuhong > > > > > > ___ > > 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 > 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. > > ___ 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] view retinotopy results in version 5
Hi, I was able to view retinotopic mapping results using rtview in version 5. However, the display was on the inflated surface. Is there a way to view the results on the flattened occipital map, similar to version 4's surf-sess -flat? Thanks! -Yuhong ___ 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] preproc-sess -surface flag
Thanks Doug, this makes sense. What about retinotopic mapping? Should I use fsaverage or self? -Yuhong On Tue, Mar 26, 2013 at 10:56 AM, Douglas N Greve wrote: > > It should either be fsaverage, or self, or an average subject you have > created. The fMRI analysis is done such that the raw data are resampled > into the fsaverage space (unless you use self) and processed there in > anticipation of doing group analysis. > doug > > > On 03/26/2013 10:37 AM, Y.V. Jiang wrote: > > Hi, > > > > I wonder if you could help with a basic question for preproc-sess in > > Version 5.2.0. > > > > The flag "-surface subject hemi": what should be the entry to > > "subject?" The tutorial says fsaverage, but for first-level analysis, > > should it match subjectname? Or should it always be fsaverage? > > > > If it needs to match subjectname, then this command cannot be run in a > > batch (because different subjects have different input to that line), > > is that true? > > > > Thank you. > > > > -Yuhong > > > > > > ___ > > 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 > 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. > > ___ 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] preproc-sess -surface flag
Hi, I wonder if you could help with a basic question for preproc-sess in Version 5.2.0. The flag "-surface subject hemi": what should be the entry to "subject?" The tutorial says fsaverage, but for first-level analysis, should it match subjectname? Or should it always be fsaverage? If it needs to match subjectname, then this command cannot be run in a batch (because different subjects have different input to that line), is that true? Thank you. -Yuhong ___ 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] v5.2.0 preproc-sess failing on 3dvolreg.afni
Hi Doug, Here's the output from cat /proc/version: Linux version 2.6.32-45-generic (buildd@batsu) (gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5.1) ) #101-Ubuntu SMP Mon Dec 3 15:39:38 UTC 2012 This is the result of cat $FREESURFER_HOME/build-stamp.txt freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 Thanks. -Yuhong On Thu, Mar 21, 2013 at 1:12 PM, Douglas N Greve wrote: > which version of CentOS? Also, can you send me the result of > cat $FREESURFER_HOME/build-stamp.**txt > > > > On 03/21/2013 02:09 PM, Y.V. Jiang wrote: > >> Hi Doug, >> >> I am using Linux: x86_64 GNU/Linux. Thanks. >> >> -Yuhong >> >> On Thu, Mar 21, 2013 at 12:57 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu>> >> wrote: >> >> what platform are you using? >> >> >> On 03/21/2013 01:24 PM, Y.V. Jiang wrote: >> >> Hi Doug, >> >> Thanks for the reply. From the command line the command >> 3dvolreg.afni returned the following error: >> >> 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined >> symbol: afni_ncerr >> >> -Yuhong >> >> On Thu, Mar 21, 2013 at 12:08 PM, Douglas N Greve >> > <mailto:gr...@nmr.mgh.harvard.**edu >> > >> <mailto:gr...@nmr.mgh.harvard.**edu >> >> <mailto:gr...@nmr.mgh.harvard.**edu >>> >> wrote: >> >> >> Hi Yuhong, >> What happens when you run 3dvolreg.afni from the command >> line without >> any args? >> doug >> >> On 03/21/2013 12:38 PM, Y.V. Jiang wrote: >> > Hi Doug, >> > >> > I was running preproc-sess in the newly released >> freesurfer-5.2.0. The >> > command I used was: >> > >> > preproc-sess -sf sessid -df sessdir -fsd bold -surface >> fsaverage lhr >> > -mni305 -fwhm 6 -per-run >> > >> > The program failed with the following errors: >> > >> > 3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save >> > 004/fmcpr.mat -base >> 004/tmp.mc-afni2.29239/**tempvol.nii.gz -prefix >> > 004/tmp.mc-afni2.29239/outvol.**nii.gz >> 004/tmp.mc-afni2.29239/invol.**nii.gz >> > 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: >> undefined symbol: >> > afni_ncerr >> > ERROR: 3dvolreg.afni >> > Invalid null command. >> > >> > I have the file 3dvolreg.afni in $FREESURFER_HOME/bin. >> There is >> > another file of the same name under afni/bin. >> Preproc-sess is >> relying >> > on the version in $FREESURFER_HOME/bin. >> > >> > Do you know what the problem is? Should I replace >> freesurfer's >> copy of >> > 3dvolreg.afni with AFNI's copy of 3dvolreg.afni? >> > >> > Thanks. >> > >> > -Yuhong >> > >> > >> > __**_ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu >> > >> >> <mailto:freesur...@nmr.mgh.**harvard.edu >> >> >> <mailto:freesur...@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 > >> > >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fs
Re: [Freesurfer] v5.2.0 preproc-sess failing on 3dvolreg.afni
Hi Doug, I am using Linux: x86_64 GNU/Linux. Thanks. -Yuhong On Thu, Mar 21, 2013 at 12:57 PM, Douglas N Greve wrote: > what platform are you using? > > > On 03/21/2013 01:24 PM, Y.V. Jiang wrote: > >> Hi Doug, >> >> Thanks for the reply. From the command line the command 3dvolreg.afni >> returned the following error: >> >> 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: >> afni_ncerr >> >> -Yuhong >> >> On Thu, Mar 21, 2013 at 12:08 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu>> >> wrote: >> >> >> Hi Yuhong, >> What happens when you run 3dvolreg.afni from the command line without >> any args? >> doug >> >> On 03/21/2013 12:38 PM, Y.V. Jiang wrote: >> > Hi Doug, >> > >> > I was running preproc-sess in the newly released >> freesurfer-5.2.0. The >> > command I used was: >> > >> > preproc-sess -sf sessid -df sessdir -fsd bold -surface fsaverage lhr >> > -mni305 -fwhm 6 -per-run >> > >> > The program failed with the following errors: >> > >> > 3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save >> > 004/fmcpr.mat -base 004/tmp.mc-afni2.29239/**tempvol.nii.gz -prefix >> > 004/tmp.mc-afni2.29239/outvol.**nii.gz >> 004/tmp.mc-afni2.29239/invol.**nii.gz >> > 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: >> > afni_ncerr >> > ERROR: 3dvolreg.afni >> > Invalid null command. >> > >> > I have the file 3dvolreg.afni in $FREESURFER_HOME/bin. There is >> > another file of the same name under afni/bin. Preproc-sess is >> relying >> > on the version in $FREESURFER_HOME/bin. >> > >> > Do you know what the problem is? Should I replace freesurfer's >> copy of >> > 3dvolreg.afni with AFNI's copy of 3dvolreg.afni? >> > >> > Thanks. >> > >> > -Yuhong >> > >> > >> > __**_ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> <mailto:freesur...@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 >> > >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.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/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> __**_ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.** >> harvard.edu > >> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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 > g
Re: [Freesurfer] v5.2.0 preproc-sess failing on 3dvolreg.afni
Hi Doug, Thanks for the reply. From the command line the command 3dvolreg.afni returned the following error: 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr -Yuhong On Thu, Mar 21, 2013 at 12:08 PM, Douglas N Greve wrote: > > Hi Yuhong, > What happens when you run 3dvolreg.afni from the command line without > any args? > doug > > On 03/21/2013 12:38 PM, Y.V. Jiang wrote: > > Hi Doug, > > > > I was running preproc-sess in the newly released freesurfer-5.2.0. The > > command I used was: > > > > preproc-sess -sf sessid -df sessdir -fsd bold -surface fsaverage lhr > > -mni305 -fwhm 6 -per-run > > > > The program failed with the following errors: > > > > 3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save > > 004/fmcpr.mat -base 004/tmp.mc-afni2.29239/tempvol.nii.gz -prefix > > 004/tmp.mc-afni2.29239/outvol.nii.gz 004/tmp.mc-afni2.29239/invol.nii.gz > > 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: > > afni_ncerr > > ERROR: 3dvolreg.afni > > Invalid null command. > > > > I have the file 3dvolreg.afni in $FREESURFER_HOME/bin. There is > > another file of the same name under afni/bin. Preproc-sess is relying > > on the version in $FREESURFER_HOME/bin. > > > > Do you know what the problem is? Should I replace freesurfer's copy of > > 3dvolreg.afni with AFNI's copy of 3dvolreg.afni? > > > > Thanks. > > > > -Yuhong > > > > > > ___ > > 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 > 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. > > ___ 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] v5.2.0 preproc-sess failing on 3dvolreg.afni
Hi Doug, I was running preproc-sess in the newly released freesurfer-5.2.0. The command I used was: preproc-sess -sf sessid -df sessdir -fsd bold -surface fsaverage lhr -mni305 -fwhm 6 -per-run The program failed with the following errors: 3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save 004/fmcpr.mat -base 004/tmp.mc-afni2.29239/tempvol.nii.gz -prefix 004/tmp.mc-afni2.29239/outvol.nii.gz 004/tmp.mc-afni2.29239/invol.nii.gz 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr ERROR: 3dvolreg.afni Invalid null command. I have the file 3dvolreg.afni in $FREESURFER_HOME/bin. There is another file of the same name under afni/bin. Preproc-sess is relying on the version in $FREESURFER_HOME/bin. Do you know what the problem is? Should I replace freesurfer's copy of 3dvolreg.afni with AFNI's copy of 3dvolreg.afni? Thanks. -Yuhong ___ 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] vidualizing fcseed results
Hi Doug, I ran fcseed-sess in Freesurfer 5.1, all the way through selxavg3-sess. How can the results be visualized, given that no contrast was specified? In the freesurfer wiki, it is said that "a contrast does not need to be made because one is automatically created with an -taskreg". But without a contrast I am not sure what the data can be visualized?? Thank you. -Yuhong ___ 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] problem with spmregister on mac
It depends on which version of SPM you're running. It's either the file called spm_defaults.m, or on my system it's file called spm_flip_analyze_images.m. There is a line that says: flip = 1; (or flip = 0). For my kind of scans I need to set flip = 0, whereas the spm defaults tend to come with flip = 1 (which turns your radiology images into neurology images). -Yuhong On Fri, Feb 4, 2011 at 10:30 AM, Katie Bettencourt wrote: > Can you tell me how to check that because I"m having the same problem with > spmregister-sess with my linux as well and I've never used SPM at all, and > honestly can't even figure out how to open it. > > Katie > > On Thu, Feb 3, 2011 at 11:21 PM, Y.V. Jiang wrote: > >> Hi Maryam, >> >> You should check your spm defaults to see whether it uses radiology or >> neurology convention. Most likely your spm has flipped your image, and the >> spmregister-sess is trying to match the left hemisphere of your functionals >> to the right hemisphere of your anatomical. >> >> -Yuhong >> >> On Thu, Feb 3, 2011 at 9:59 PM, Maryam Vaziri Pashkam < >> mvazir...@gmail.com> wrote: >> >>> Hi, >>> >>> >>> I am new to freesurfer and I am analyzing fmri data on a Mac OSX 10.5.8 >>> computer using freesurfer 4.5. I have SPM 8 and FSL also installed. >>> >>> >>> I have two versions of matlab (matlab R2009b & R2008a) on my computer. I >>> think spm runs through the R2009b on my computer. I have added the SPM path >>> to the startup.m of both matlabs by adding the following line (they both >>> point to the same startup.m ): >>> >>> path(path,'/Applications/spm8'); >>> >>> >>> I run preprocessing on the data using the following command: >>> >>> preproc-sess -nosmooth -sf retino-sess -df retino.dir >>> >>> >>> then I run automatic registration with the following command: >>> >>> spmregister-sess -sf retino-sess -df retino.dir >>> >>> >>> It runs smoothly and there seems to be no errors. But when I try to check >>> the registration with this command: >>> >>> >>> tkregister-sess -sf retino-sess -df retino.dir -inorm >>> >>> >>> what I see is not a good registration. Isn't spm register supposed to do >>> a good job in automatic registration? The one that I get still needs a lot >>> of manual adjustment. Am I doing something wrong? I have attached the log >>> files for spmregister and tkregister and a screen shot of the image that I >>> get after running tkregister. I would appreciate any help in this matter. >>> >>> >>> >>> Thanks, >>> >>> Maryam >>> >>> >>> >>> ___ >>> 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. >>> >>> >> >> >> -- >> -- >> Yuhong Vanessa Jiang, PhD, >> Associate Professor & McKnight Presidential Fellow >> Department of Psychology, Univ of Minnesota >> jiang...@umn.edu, 612-625-7003 >> https://sites.google.com/site/jiang166/ >> -- >> >> ___ >> 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 a
Re: [Freesurfer] problem with spmregister on mac
Hi Maryam, You should check your spm defaults to see whether it uses radiology or neurology convention. Most likely your spm has flipped your image, and the spmregister-sess is trying to match the left hemisphere of your functionals to the right hemisphere of your anatomical. -Yuhong On Thu, Feb 3, 2011 at 9:59 PM, Maryam Vaziri Pashkam wrote: > Hi, > > > I am new to freesurfer and I am analyzing fmri data on a Mac OSX 10.5.8 > computer using freesurfer 4.5. I have SPM 8 and FSL also installed. > > > I have two versions of matlab (matlab R2009b & R2008a) on my computer. I > think spm runs through the R2009b on my computer. I have added the SPM path > to the startup.m of both matlabs by adding the following line (they both > point to the same startup.m ): > > path(path,'/Applications/spm8'); > > > I run preprocessing on the data using the following command: > > preproc-sess -nosmooth -sf retino-sess -df retino.dir > > > then I run automatic registration with the following command: > > spmregister-sess -sf retino-sess -df retino.dir > > > It runs smoothly and there seems to be no errors. But when I try to check > the registration with this command: > > > tkregister-sess -sf retino-sess -df retino.dir -inorm > > > what I see is not a good registration. Isn't spm register supposed to do a > good job in automatic registration? The one that I get still needs a lot of > manual adjustment. Am I doing something wrong? I have attached the log files > for spmregister and tkregister and a screen shot of the image that I get > after running tkregister. I would appreciate any help in this matter. > > > > Thanks, > > Maryam > > > > ___ > 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. > > -- -- Yuhong Vanessa Jiang, PhD, Associate Professor & McKnight Presidential Fellow Department of Psychology, Univ of Minnesota jiang...@umn.edu, 612-625-7003 https://sites.google.com/site/jiang166/ -- ___ 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] retinotopic mapping with bowtie vs. wedge
Dear Doug and other Freesurferers, We are considering using rotating bowtie-shaped stimuli rather than rotating wedges for retinotopic mapping. The bowties are essentially two symmetriccal wedges, but unlike horizontal/vertical meridian mapping, they do rotate around (rather that stay at horizontal/vertical meridian). Is Freesurfer's retinotopic mapping program capable of handling data analysis of bowtie retinotopy? Do we need to make changes to the analysis stream (e.g., when entering the number of cycles, should this be twice as frequent?) Would this mess up with color maps? Thanks for your feedback. -Yuhong -- Yuhong Vanessa Jiang, PhD, Department of Psychology, Univ of Minnesota jiang...@umn.edu, 612-625-7003 -- ___ 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.
