Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

fs450 Longitudinal edits, varied data, and other questions
by Jeff Sadino 20 Oct '10

20 Oct '10

Thank you for your feedback on my previous question regarding the surface area measurement. We found it very helpful to move forward. I am beginning (again) to do longitudinal processing using fs4.5.0, but I just want to make sure that I understand everything right before starting this time. We have about 150 subjects with timepoints varying from 2-7, for a total of somewhere around 750 scans. All have already been processed cross-sectionally. 1. Reading through the wiki, the main thing to check on the cross-sectional runs are the control points. I'm confused by this though because the base creation only needs the reconstruction ran through the norm.mgz step to start. But we won't know if we need to add control points to the cross-sectional scan until after the surfaces are made, later in the stream. So it seems like I need to run the cross-sectionals through the norm.mgz step to start the base creation, but then before I run the -long part, I need to run the cross-sectionals through the surface reconstruction so that I can check the control points so that they can be copied from the cross-sectional run to the -long run? Are there any other edits I need to look at before starting the -base run? The cross-sectional brainmasks? The brainmask QA is just to make sure that the skull and other things are correctly stripped away? What about intensity normalization and gm/wm contrast on the norm.mgz image? 2. Also, in http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12895.html, Martin says "the cross sectional asegs are 'fused' (probabilistic voting), to initialize the labeling in the longitudinal runs." Can someone explain what this 'fused' means? This is the only place I have read this besides the short description in recon-all --help. So it seems like I need to finish the cross-sectionals pretty much completely before doing the -long run. 3. Why is the brainmask from the -base run used in the -long run? I can see how this increases consistency between timepoints, but it seems like there would be a larger benefit of using the brainmask from the cross-sectional run? 4. I read that if the -base is stopped halfway through due to earthquakes, then it can be restarted from some point in the stream. I will just restart it from the beginning for ease of use. My question is what if the -long stops halfway through? I forget the command I use to restart from the last step in the cross-sectional stream (our cluster is down now), but can I do the same thing: recon-all -long tp1 longbase -restart_from_last_step_command? And then I had some questions specific to our data, if you would permit me =) 1. We have timepoints from the past 6 years, and so our scanning parameters have changed. Our old data is 1x1x1.4mm and 144 slices and our new data is 1x1x1mm and 160 slices. Some subjects have an acceleration of 2, while most have no acceleration. Our scanner is a Siemens 3T Trio. Will I need to exclude any of these timepoints? From both -base and -long? The thread http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14014.htmlsays that the new stream significantly reduces these effects, but I just wanted to doublecheck. 2. Because of the way our group is set up, sometimes subjects will have more than one mprage - from different days, say one week apart - for each timepoint. Even though I will only use one of these mprages for each -long timepoint, will the -base be better if I include all of them? As a tangential question, could I use these close together visits and average their mprages in the -motioncor step? My feeling would be no, that I could only do that if the subject does not move, but I wanted to check. Sorry for the long questions! Thank you for all of your great help all the time! Jeff Sadino

2 1

Re: [Freesurfer] Retinotopic mapping of only polar data]
by Douglas N Greve 20 Oct '10

20 Oct '10

Oh, I see now. I did not read your subject line carefully. You have to have both eccen and polar to run the retinotopy. One way around it is to just copy the polar data and call it eccen. This is a bit of an annoyance, I'll try to fix it in the next version. doug f.leone(a)donders.ru.nl wrote: > Yup, sure, thanks for the quick reply. See attached, > > Frank > > ----- Original Message ----- > From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > To: "Frank Leoné" <f.leone(a)donders.ru.nl> > Sent: Tuesday, October 19, 2010 9:06:38 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna > Subject: Re: [Freesurfer] Retinotopic mapping of only polar data] > > Can you send me the Xtmp.mat? > > f.leone(a)donders.ru.nl wrote: > >> Hi Doug, >> >> Sure I can. I bump into problems though, exactly the same problems as mentioned before (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14953.html) >> >> Found 136019/147456 (92.2) voxels in mask >> Creating Design Matrix >> ... creation time = 0.010 sec >> DoMCFit = 1 >> ntptot = 686, nX = 42, DOF = 644 >> Saving X matrix to /home/action/fraleo/Data/Exp1_Saccades_phase/S1_FS/bold/rtopy.S1_FS.rh/Xtmp.mat >> ??? Error using ==> svd >> Input to SVD must not contain NaN or Inf. >> >> Error in ==> cond at 40 >> s = svd(A); >> >> Error in ==> fast_selxavg3 at 247 >> XCond = cond(XtX); >> >> Any ideas why this is/how I can solve this? Same result for multiple subjects, not sure where it comes from. >> >> Thanks a lot in advance, >> >> kind regards, >> >> Frank >> ----- Original Message ----- >> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >> To: "Frank Leoné" <f.leone(a)donders.ru.nl> >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Sent: Monday, October 18, 2010 5:08:42 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna >> Subject: Re: [Freesurfer] Retinotopic mapping of only polar data] >> >> Can you let me know when you have processed a set with the new tools? >> It's going to be a lot easier for me to instruct you on how to do those >> things. >> >> doug >> >> f.leone(a)donders.ru.nl wrote: >> >> >>> Dear Doug, >>> >>> Thanks a lot for the reply, that really helps. I see that the new function is more integrated with the rest of the standard analyses, so it now also wants to do motion correction ed. it seems, so didn't run the full thing yet. Still, if I make the pictures using the new functions, but an old h.nii, I get the same kind of pictures, so can you maybe also help me with the interpretation questions: >>> >>> - How to interpret the color codes / values on the inflatedsurface? >>> - How to threshold them on significance? >>> (Third one: how to interpolate them to get away from the patchy representation?) >>> >>> You suggest to smooth the data btw, thought that wasn't standard procedure when doing retinotopic mapping, at least not with a fwhm of 5. >>> >>> Thanks again, >>> >>> kind regards, >>> >>> Frank >>> >>> >>> ----- Oorspronkelijk bericht ----- >>> Van: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>> Aan: "Frank Leoné" <f.leone(a)donders.ru.nl> >>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>> Verzonden: Donderdag 14 oktober 2010 22:52:21 GMT +01:00 Amsterdam / Berlijn / Bern / Rome / Stockholm / Wenen >>> Onderwerp: Re: [Freesurfer] Retinotopic mapping of only polar data] >>> >>> >>> Hi Frank, sfa-sess does not exist in version 5 of FreeSurfer because >>> its functions have been incorporated into selxavg3-sess. It will be a >>> lot easier to support you if you move to version 5. Unfortunately, I >>> have been slow in getting it documented. Having said that, I think the >>> new version is a lot easier to use. It is very similar to regular task >>> studies, which is pretty well documented (see >>> http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt) >>> >>> For retinotopy, there are only a few deviations: >>> 1.a. When you create the analysis, specify something like: >>> mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -fwhm 5 >>> -retinotopy 30 -paradigm rtopy.par >>> where "-retinotopy 30" means that it is a retinotopy study with a >>> period of 30 sec >>> 1.b Run selxavg3-sess (instead of sfa-sess) >>> 1.c Run tksurfer-sess, like >>> tksurfer-sess -s sess -a rtopy.self.lh >>> This will show you the eccen and polor contrasts >>> 2.a Create a field sign (with an occipital patch) with: >>> fieldsign-sess -a rtopy.lh -s sess -occip >>> 2.b View the fieldsign >>> tksurfer-sess -s sess -a rtopy.self.lh -fieldsign >>> >>> The above assumes that you want to analyze the data on the subject's >>> left hemi. Make and run anther analysis for the right hemi >>> >>> doug >>> >>> >>> f.leone(a)donders.ru.nl wrote: >>> >>> >>> >>>> Hi everyone, >>>> >>>> The e-mail included below I sent some time ago, maybe it slipped through. In the mean time I did find out I can plot the results with tksurfer-sess like >>>> >>>> tksurfer-sess -s S2_FS -h rh -analysis rtopy -c polar -map h >>>> >>>> But then two big questions remain: >>>> - How to interpret these color codes? >>>> - How to threshold them on significance? >>>> (Third one: how to interpolate them to get away from the patchy representation?) >>>> >>>> The other questions stated below are also still relevant. >>>> >>>> Asked this before, but can we add stuff ourselves to the wiki? Found out quite a bit about the retinotopic inner workings which I wasn't able to find anywhere else, might help some others. >>>> >>>> kind regards, >>>> >>>> Frank >>>> >>>> Old topic, but it is directly related, so I'll just continue it here. >>>> >>>> In the end I have the spots on the right place, but now it's not clear >>>> to me how to interpret the map. I have created three overlays (sign, >>>> log10 * sin, log10 * cos, like mentioned in selfreq.pdf) and loaded them >>>> all three in tksurfer. Most important question now: how to relate these >>>> three to get one figure instead of three separate? >>>> >>>> Other more minor questions: >>>> - What do the values actually mean? Apparently I can threshold on the >>>> basis of them, but that does't make sense to do, because the direction >>>> info is also in there, right? I should probably threshold the F-values >>>> first, before overlaying them on the inflated brain. >>>> - What happened to sfa-sess in the new version of freesurfer? I can't >>>> seem to find it. >>>> - Why does the sfa-sess script check whether amp data is present? >>>> Looking at the script, the line that checks whether there is amplitude >>>> data can safely be removed. >>>> - Just like the original Sereno paper, I have 20s pre and post stimulus >>>> presentation time. I now only use the data where the convolved DM >>>> predicts there will be signal, so discarding the first 20s and, due to >>>> the HRF, keeping almost the entire second 20s. Is this the correct thing >>>> to do, or should I rather keep everything / make sure I have an exact >>>> number of periods for each stimulus? >>>> >>>> Thanks a lot in advance, >>>> >>>> kind regards, >>>> >>>> Frank >>>> >>>> >>>> On Mon, 2010-01-18 at 17:32 -0500, Douglas N Greve wrote: >>>> >>>> >>>> >>>> >>>>> If the activation is showing up in the wrong places, then that probably >>>>> means that the registration is off. Have you checked the registration. >>>>> >>>>> doug >>>>> >>>>> f.leone(a)donders.ru.nl wrote: >>>>> >>>>> >>>>> >>>>> >>>>>> Probably my e-mail just slipped through, so just a short notice that I still have the problem with the overlay mentioned in the last e-mail: >>>>>> >>>>>> "I now have a polar map overlayed on my inflated brain. But something seems to be amiss, because it plots it mainly on the temporal lobe, with nothing on the most dorsal slices, while actually I only scanned the 18 most dorsal (oriented along the occipital-parietal axis), sot here shouldn't be anything in the temporal or inferior frontal lobe. How can this be/where is it going wrong? >>>>>> >>>>>> Moreover, I'm not sure on the format used by the polar map: the scale bar states it ranges from 1.18 to 1.18, but I don't see the sense in that. What will come out? Radians I pressume?" >>>>>> >>>>>> Is it possible to edit the wikipages ourselves btw? I could add some more / update the info on the retinotopic mapping to help other people when I got it all figured out. >>>>>> >>>>>> kind regards, thanks in advance, >>>>>> >>>>>> Frank >>>>>> >>>>>> ----- Original Message ----- >>>>>> From: "f.leone(a)donders.ru.nl" <f.leone(a)fcdonders.ru.nl> >>>>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>>>> Sent: Monday, January 11, 2010 9:15:43 AM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna >>>>>> Subject: Re: [Freesurfer] Retinotopic mapping of only polar data >>>>>> >>>>>> Hi everyone, >>>>>> >>>>>> Doug: thanks a lot for the reply, that indeed worked, I now have a polar map overlayed on my inflated brain. But something seems to be amiss, because it plots it mainly on the temporal lobe, with nothing on the most dorsal slices, while actually I only scanned the 18 most dorsal (oriented along the occipital-parietal axis), sot here shouldn't be anything in the temporal or inferior frontal lobe. How can this be/where is it going wrong? >>>>>> >>>>>> Moreover, I'm not sure on the format used by the polar map: the scale bar states it ranges from 1.18 to 1.18, but I don't see the sense in that. What will come out? Radians I pressume? >>>>>> >>>>>> kind regards, thanks a lot in advance, >>>>>> >>>>>> Frank >>>>>> >>>>>> ----- Original Message ----- >>>>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>> To: "Frank Leoné" <f.leone(a)donders.ru.nl> >>>>>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>>>>> Sent: Friday, January 8, 2010 4:26:21 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna >>>>>> Subject: Re: [Freesurfer] Retinotopic mapping of only polar data >>>>>> >>>>>> You can generate a register.dat with either fslregister-sess or >>>>>> spmregister-sess, or, if you have it in your version, use bbregister >>>>>> (note that there is not a -sess version for this yet). >>>>>> >>>>>> You can then use mri_vol2surf to resample the h.nii file to the surface, >>>>>> then view it in tksurfer. You can also extract certain frames with >>>>>> mri_convert with the --frame option. >>>>>> >>>>>> doug >>>>>> >>>>>> f.leone(a)donders.ru.nl wrote: >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>> Hi everyone, >>>>>>> >>>>>>> Still not working fully, partly because I'm missing some info on the file formats. What I now did was a run of selfreqavg with four input polar sessions, which ran succesfully. This gives me the expected h.nii. Now I either want to >>>>>>> >>>>>>> - use this h file directly, using paint-sess (get message register.dat is missing) and sliceview-sess (get message it can't determine format h-offset, which makes sense, because it doesn't exist) >>>>>>> - or extract w files from the first three layers of the nii files and superimpose them in tksurfer. I don't know how I should extract them though. Can use the SPM surfrend functions, but I can't imagine that is the way, or is it? >>>>>>> >>>>>>> Hopefully someone can help me along either of the two paths, I'm really eager to see whether the retinotopic analysis worked. Thanks a lot in advance! >>>>>>> >>>>>>> kind regards, >>>>>>> >>>>>>> Frank >>>>>>> >>>>>>> ----- Original Message ----- >>>>>>> From: "f.leone(a)donders.ru.nl" <f.leone(a)fcdonders.ru.nl> >>>>>>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>>>>>> Sent: Monday, January 4, 2010 9:35:51 AM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna >>>>>>> Subject: Re: [Freesurfer] Retinotopic mapping of only polar data >>>>>>> >>>>>>> Hi everyone, >>>>>>> >>>>>>> I fixed it with the help of Jascha: when using the full path, e.g. /home/frank/etc.../007/f.nii it does find them. So it is now running. Thanks for the help! >>>>>>> >>>>>>> kind regards, >>>>>>> >>>>>>> Frank >>>>>>> >>>>>>> ----- Original Message ----- >>>>>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>> To: "Frank Leoné" <f.leone(a)donders.ru.nl> >>>>>>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>>>>>> Sent: Tuesday, December 22, 2009 7:58:23 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna >>>>>>> Subject: Re: [Freesurfer] Retinotopic mapping of only polar data >>>>>>> >>>>>>> Do you have read permissions to the file? If so, can you send the log >>>>>>> file created by sfa-sess? >>>>>>> >>>>>>> f.leone(a)donders.ru.nl wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>> Thanks a lot for the reply. I now bump into different problems though: it doesn't understand my f.nii file, see below. I run: >>>>>>>> >>>>>>>> frank@frank-desktop:~/PhD/data/Exp1_Saccades_phase$ sfa-sess -a rtopy -s FSFAST_S1/ >>>>>>>> >>>>>>>> and I think the main error line is: >>>>>>>> >>>>>>>> ERROR: cannot determine format of 007/f >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>>> ??? Attempt to reference field of non-structure array. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>> 007 is my first session (is a dir) and in there is one f.nii, which includes all the scans of that run. . Previously I tried it with separate scan files, but that didn't work either. So what does it expect? And will it work with data preprocessed in SPM instead in FreeSurfer? The rest of the dir structure is setup as specified in the guide >>>>>>>> >>>>>>>> Hopefully someone can help me, thanks a lot in advance, >>>>>>>> >>>>>>>> kind regards, >>>>>>>> >>>>>>>> Frank >>>>>>>> >>>>>>>> frank@frank-desktop:~/PhD/data/Exp1_Saccades_phase$ mkanalysis-sess.new -force -a rtopy -TR 2.12 -designtype retinotopy -paradigm rtopy.par -funcstem f -ncycles 8 >>>>>>>> INFO: analysis rtopy exists, but overwrite forced by user. >>>>>>>> Completed successfully >>>>>>>> frank@frank-desktop:~/PhD/data/Exp1_Saccades_phase$ sfa-sess -a rtopy -s FSFAST_S1/ >>>>>>>> -------------------------------------------------------------- >>>>>>>> sfa-sess logfile is /home/frank/PhD/data/Exp1_Saccades_phase/log/sfa-sess-bold-rtopy-0912221252.log >>>>>>>> -------------------------------------------------------------- >>>>>>>> ------------------------------------------- >>>>>>>> /home/frank/PhD/data/Exp1_Saccades_phase/FSFAST_S1 >>>>>>>> Tue Dec 22 12:52:30 CET 2009 >>>>>>>> INFO (FSFAST_S1): RunList = 007 008 009 010 011 >>>>>>>> -------------------------------------------------- >>>>>>>> /home/frank/PhD/data/Exp1_Saccades_phase/FSFAST_S1/bold >>>>>>>> selfreqavg -TR 2.12 -o rtopy/polar/h -i 007/f -i 008/f -i 009/f -i 010/f -cfg /home/frank/PhD/data/Exp1_Saccades_phase/rtopy/analysis.cfg -parname rtopy.par >>>>>>>> -------------------------------------------------- >>>>>>>> --- Parsing Config File: /home/frank/PhD/data/Exp1_Saccades_phase/rtopy/analysis.cfg ---- >>>>>>>> -ncycles 8 -delay 0 -nskip 0 -fwhm 0 >>>>>>>> DirectionList: +1 +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 007/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 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>> Could not open rtopy/polar/h.sfa for writing >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>> quiting matlab >>>>>>>> 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 >>>>>>>> >>>>>>>> ----- Original Message ----- >>>>>>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>>> To: "Frank Leoné" <f.leone(a)donders.ru.nl> >>>>>>>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> Sent: Wednesday, December 16, 2009 5:12:41 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna >>>>>>>> Subject: Re: [Freesurfer] Retinotopic mapping of only polar data >>>>>>>> >>>>>>>> If you run the retinotopy analysis, it will expect eccen. If it stops >>>>>>>> without doing the polar analysis, you can "fool" it by copying the polar >>>>>>>> data into the eccen directory. >>>>>>>> >>>>>>>> doug >>>>>>>> >>>>>>>> f.leone(a)donders.ru.nl wrote: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> Dear all, >>>>>>>>> >>>>>>>>> I just started using FreeSurfer, specifically for retinotopic data, on the moment only polar data. So I followed the guide as mentioned on http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis . This does seem to work to some extend, except that it complains that I don't have eccentricity data. He is right about that, but is the analysis also doable with the eccentricity data? I really hope so, thanks a lot in advance, >>>>>>>>> >>>>>>>>> kind regards, >>>>>>>>> >>>>>>>>> Frank >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>> ----- Oorspronkelijk bericht ----- >>>> Van: "Frank Leone" <f.leone(a)donders.ru.nl> >>>> Aan: "f leone" <f.leone(a)donders.ru.nl> >>>> Verzonden: Woensdag 6 oktober 2010 17:16:43 GMT +01:00 Amsterdam / Berlijn / Bern / Rome / Stockholm / Wenen >>>> Onderwerp: [Fwd: Re: [Freesurfer] Retinotopic mapping of only polar data] >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>> >>> >>> >> >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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

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Error with mris_volmask.bin
by Jordi Casals 20 Oct '10

20 Oct '10

Hello everybody. There is a few days I try to run a recon-all process with one subject and there is some problem that can't let the process finish correctly. The command I want to run is the next one: *recon-all -autorecon2-wm -force -i /nfs/arpon/PROJCT/DEPR/orig/DICOM/T13D/GMI_544/GMI_544_0002 -s GMI_544 -qcache* And the final errors I get are the next ones: */nfs/arpon/PROJCT/DEPR/proc/FREESURFER/OutPBS/AAA_000/mri* * * * mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41* *--label_right_ribbon 42 --save_ribbon --save_distance AAA_000* * * *mris_volmask.bin: symbol lookup error: /usr/lib/nvidia/libGL.so.1: undefined symbol: _nv000049gl* *Linux machine.domain 2.6.18-164.11.1.el5 #1 SMP Wed Jan 20 00:57:09 EST 2010 x86_64 x86_64 x86_64 GNU/Linux* * * *recon-all exited with ERRORS at Sun Oct 17 06:58:15 CEST 2010* I wanted to know if these errors are caused by the execution of the subject or if it's my work environment. Thank you, Jordi Casals

2 2

brain stem volume
by Thesen, Thomas 20 Oct '10

20 Oct '10

Dear Freesurfers, I am curious as to how accurate the brain stem and ventral DC volumes are? In particular, how does FS decide where to stop in the inferior direction, i.e. where does it draw the junction between brain stem and spinal cord? Are there FS options to segment the brain stem any further, e.g. into midbrain and hindbrain? Thank you, Thomas ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================

2 1

Lenroot, Rhoshel is out of the office.
by Rhoshel Lenroot 19 Oct '10

19 Oct '10

I will be out of the office starting 18/10/2010 and will not return until 25/10/2010. I will be checking email intermittently during this time. For urgent matters please contact Julia Hill, julia.hill(a)neura.edu.au, 9399 1268

1 0

Question about rotating the segmentation
by Timour Al-Khindi 19 Oct '10

19 Oct '10

Hello, Several of our scans are slightly misaligned along the horizontal plane, and we are currently looking for a way to align them using tkmedit. We've tried using the "Rotate volume" function. However, when we do this, our segmentation (aseg.mgz) does not rotate along with the anatomical image. Is there any way to rotate the segmentation along with the volume file (e.g. a coregistration function)? Also, has anyone found a benefit to aligning scans with the horizontal plane for manual segmentation of subcortical regions (we are segmenting hippocampal volumes into anterior and posterior regions using the tkmedit tool)? Would rotation improve or distort the volume measurements? Thanks, Tim Al-Khindi

1 0

Re: [Freesurfer] Retinotopic mapping of only polar data]
by f.leone＠donders.ru.nl 19 Oct '10

19 Oct '10

Hi Doug, Sure I can. I bump into problems though, exactly the same problems as mentioned before (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14953.html) Found 136019/147456 (92.2) voxels in mask Creating Design Matrix ... creation time = 0.010 sec DoMCFit = 1 ntptot = 686, nX = 42, DOF = 644 Saving X matrix to /home/action/fraleo/Data/Exp1_Saccades_phase/S1_FS/bold/rtopy.S1_FS.rh/Xtmp.mat ??? Error using ==> svd Input to SVD must not contain NaN or Inf. Error in ==> cond at 40 s = svd(A); Error in ==> fast_selxavg3 at 247 XCond = cond(XtX); Any ideas why this is/how I can solve this? Same result for multiple subjects, not sure where it comes from. Thanks a lot in advance, kind regards, Frank ----- Original Message ----- From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> To: "Frank Leoné" <f.leone(a)donders.ru.nl> Cc: freesurfer(a)nmr.mgh.harvard.edu Sent: Monday, October 18, 2010 5:08:42 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: Re: [Freesurfer] Retinotopic mapping of only polar data] Can you let me know when you have processed a set with the new tools? It's going to be a lot easier for me to instruct you on how to do those things. doug f.leone(a)donders.ru.nl wrote: > Dear Doug, > > Thanks a lot for the reply, that really helps. I see that the new function is more integrated with the rest of the standard analyses, so it now also wants to do motion correction ed. it seems, so didn't run the full thing yet. Still, if I make the pictures using the new functions, but an old h.nii, I get the same kind of pictures, so can you maybe also help me with the interpretation questions: > > - How to interpret the color codes / values on the inflatedsurface? > - How to threshold them on significance? > (Third one: how to interpolate them to get away from the patchy representation?) > > You suggest to smooth the data btw, thought that wasn't standard procedure when doing retinotopic mapping, at least not with a fwhm of 5. > > Thanks again, > > kind regards, > > Frank > > > ----- Oorspronkelijk bericht ----- > Van: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > Aan: "Frank Leoné" <f.leone(a)donders.ru.nl> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Verzonden: Donderdag 14 oktober 2010 22:52:21 GMT +01:00 Amsterdam / Berlijn / Bern / Rome / Stockholm / Wenen > Onderwerp: Re: [Freesurfer] Retinotopic mapping of only polar data] > > > Hi Frank, sfa-sess does not exist in version 5 of FreeSurfer because > its functions have been incorporated into selxavg3-sess. It will be a > lot easier to support you if you move to version 5. Unfortunately, I > have been slow in getting it documented. Having said that, I think the > new version is a lot easier to use. It is very similar to regular task > studies, which is pretty well documented (see > http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt) > > For retinotopy, there are only a few deviations: > 1.a. When you create the analysis, specify something like: > mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -fwhm 5 > -retinotopy 30 -paradigm rtopy.par > where "-retinotopy 30" means that it is a retinotopy study with a > period of 30 sec > 1.b Run selxavg3-sess (instead of sfa-sess) > 1.c Run tksurfer-sess, like > tksurfer-sess -s sess -a rtopy.self.lh > This will show you the eccen and polor contrasts > 2.a Create a field sign (with an occipital patch) with: > fieldsign-sess -a rtopy.lh -s sess -occip > 2.b View the fieldsign > tksurfer-sess -s sess -a rtopy.self.lh -fieldsign > > The above assumes that you want to analyze the data on the subject's > left hemi. Make and run anther analysis for the right hemi > > doug > > > f.leone(a)donders.ru.nl wrote: > >> Hi everyone, >> >> The e-mail included below I sent some time ago, maybe it slipped through. In the mean time I did find out I can plot the results with tksurfer-sess like >> >> tksurfer-sess -s S2_FS -h rh -analysis rtopy -c polar -map h >> >> But then two big questions remain: >> - How to interpret these color codes? >> - How to threshold them on significance? >> (Third one: how to interpolate them to get away from the patchy representation?) >> >> The other questions stated below are also still relevant. >> >> Asked this before, but can we add stuff ourselves to the wiki? Found out quite a bit about the retinotopic inner workings which I wasn't able to find anywhere else, might help some others. >> >> kind regards, >> >> Frank >> >> Old topic, but it is directly related, so I'll just continue it here. >> >> In the end I have the spots on the right place, but now it's not clear >> to me how to interpret the map. I have created three overlays (sign, >> log10 * sin, log10 * cos, like mentioned in selfreq.pdf) and loaded them >> all three in tksurfer. Most important question now: how to relate these >> three to get one figure instead of three separate? >> >> Other more minor questions: >> - What do the values actually mean? Apparently I can threshold on the >> basis of them, but that does't make sense to do, because the direction >> info is also in there, right? I should probably threshold the F-values >> first, before overlaying them on the inflated brain. >> - What happened to sfa-sess in the new version of freesurfer? I can't >> seem to find it. >> - Why does the sfa-sess script check whether amp data is present? >> Looking at the script, the line that checks whether there is amplitude >> data can safely be removed. >> - Just like the original Sereno paper, I have 20s pre and post stimulus >> presentation time. I now only use the data where the convolved DM >> predicts there will be signal, so discarding the first 20s and, due to >> the HRF, keeping almost the entire second 20s. Is this the correct thing >> to do, or should I rather keep everything / make sure I have an exact >> number of periods for each stimulus? >> >> Thanks a lot in advance, >> >> kind regards, >> >> Frank >> >> >> On Mon, 2010-01-18 at 17:32 -0500, Douglas N Greve wrote: >> >> >>> If the activation is showing up in the wrong places, then that probably >>> means that the registration is off. Have you checked the registration. >>> >>> doug >>> >>> f.leone(a)donders.ru.nl wrote: >>> >>> >>>> Probably my e-mail just slipped through, so just a short notice that I still have the problem with the overlay mentioned in the last e-mail: >>>> >>>> "I now have a polar map overlayed on my inflated brain. But something seems to be amiss, because it plots it mainly on the temporal lobe, with nothing on the most dorsal slices, while actually I only scanned the 18 most dorsal (oriented along the occipital-parietal axis), sot here shouldn't be anything in the temporal or inferior frontal lobe. How can this be/where is it going wrong? >>>> >>>> Moreover, I'm not sure on the format used by the polar map: the scale bar states it ranges from 1.18 to 1.18, but I don't see the sense in that. What will come out? Radians I pressume?" >>>> >>>> Is it possible to edit the wikipages ourselves btw? I could add some more / update the info on the retinotopic mapping to help other people when I got it all figured out. >>>> >>>> kind regards, thanks in advance, >>>> >>>> Frank >>>> >>>> ----- Original Message ----- >>>> From: "f.leone(a)donders.ru.nl" <f.leone(a)fcdonders.ru.nl> >>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>> Sent: Monday, January 11, 2010 9:15:43 AM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna >>>> Subject: Re: [Freesurfer] Retinotopic mapping of only polar data >>>> >>>> Hi everyone, >>>> >>>> Doug: thanks a lot for the reply, that indeed worked, I now have a polar map overlayed on my inflated brain. But something seems to be amiss, because it plots it mainly on the temporal lobe, with nothing on the most dorsal slices, while actually I only scanned the 18 most dorsal (oriented along the occipital-parietal axis), sot here shouldn't be anything in the temporal or inferior frontal lobe. How can this be/where is it going wrong? >>>> >>>> Moreover, I'm not sure on the format used by the polar map: the scale bar states it ranges from 1.18 to 1.18, but I don't see the sense in that. What will come out? Radians I pressume? >>>> >>>> kind regards, thanks a lot in advance, >>>> >>>> Frank >>>> >>>> ----- Original Message ----- >>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>> To: "Frank Leoné" <f.leone(a)donders.ru.nl> >>>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>>> Sent: Friday, January 8, 2010 4:26:21 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna >>>> Subject: Re: [Freesurfer] Retinotopic mapping of only polar data >>>> >>>> You can generate a register.dat with either fslregister-sess or >>>> spmregister-sess, or, if you have it in your version, use bbregister >>>> (note that there is not a -sess version for this yet). >>>> >>>> You can then use mri_vol2surf to resample the h.nii file to the surface, >>>> then view it in tksurfer. You can also extract certain frames with >>>> mri_convert with the --frame option. >>>> >>>> doug >>>> >>>> f.leone(a)donders.ru.nl wrote: >>>> >>>> >>>> >>>>> Hi everyone, >>>>> >>>>> Still not working fully, partly because I'm missing some info on the file formats. What I now did was a run of selfreqavg with four input polar sessions, which ran succesfully. This gives me the expected h.nii. Now I either want to >>>>> >>>>> - use this h file directly, using paint-sess (get message register.dat is missing) and sliceview-sess (get message it can't determine format h-offset, which makes sense, because it doesn't exist) >>>>> - or extract w files from the first three layers of the nii files and superimpose them in tksurfer. I don't know how I should extract them though. Can use the SPM surfrend functions, but I can't imagine that is the way, or is it? >>>>> >>>>> Hopefully someone can help me along either of the two paths, I'm really eager to see whether the retinotopic analysis worked. Thanks a lot in advance! >>>>> >>>>> kind regards, >>>>> >>>>> Frank >>>>> >>>>> ----- Original Message ----- >>>>> From: "f.leone(a)donders.ru.nl" <f.leone(a)fcdonders.ru.nl> >>>>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>>>> Sent: Monday, January 4, 2010 9:35:51 AM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna >>>>> Subject: Re: [Freesurfer] Retinotopic mapping of only polar data >>>>> >>>>> Hi everyone, >>>>> >>>>> I fixed it with the help of Jascha: when using the full path, e.g. /home/frank/etc.../007/f.nii it does find them. So it is now running. Thanks for the help! >>>>> >>>>> kind regards, >>>>> >>>>> Frank >>>>> >>>>> ----- Original Message ----- >>>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>> To: "Frank Leoné" <f.leone(a)donders.ru.nl> >>>>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>>>> Sent: Tuesday, December 22, 2009 7:58:23 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna >>>>> Subject: Re: [Freesurfer] Retinotopic mapping of only polar data >>>>> >>>>> Do you have read permissions to the file? If so, can you send the log >>>>> file created by sfa-sess? >>>>> >>>>> f.leone(a)donders.ru.nl wrote: >>>>> >>>>> >>>>> >>>>> >>>>>> Thanks a lot for the reply. I now bump into different problems though: it doesn't understand my f.nii file, see below. I run: >>>>>> >>>>>> frank@frank-desktop:~/PhD/data/Exp1_Saccades_phase$ sfa-sess -a rtopy -s FSFAST_S1/ >>>>>> >>>>>> and I think the main error line is: >>>>>> >>>>>> ERROR: cannot determine format of 007/f >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>>> ??? Attempt to reference field of non-structure array. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>> 007 is my first session (is a dir) and in there is one f.nii, which includes all the scans of that run. . Previously I tried it with separate scan files, but that didn't work either. So what does it expect? And will it work with data preprocessed in SPM instead in FreeSurfer? The rest of the dir structure is setup as specified in the guide >>>>>> >>>>>> Hopefully someone can help me, thanks a lot in advance, >>>>>> >>>>>> kind regards, >>>>>> >>>>>> Frank >>>>>> >>>>>> frank@frank-desktop:~/PhD/data/Exp1_Saccades_phase$ mkanalysis-sess.new -force -a rtopy -TR 2.12 -designtype retinotopy -paradigm rtopy.par -funcstem f -ncycles 8 >>>>>> INFO: analysis rtopy exists, but overwrite forced by user. >>>>>> Completed successfully >>>>>> frank@frank-desktop:~/PhD/data/Exp1_Saccades_phase$ sfa-sess -a rtopy -s FSFAST_S1/ >>>>>> -------------------------------------------------------------- >>>>>> sfa-sess logfile is /home/frank/PhD/data/Exp1_Saccades_phase/log/sfa-sess-bold-rtopy-0912221252.log >>>>>> -------------------------------------------------------------- >>>>>> ------------------------------------------- >>>>>> /home/frank/PhD/data/Exp1_Saccades_phase/FSFAST_S1 >>>>>> Tue Dec 22 12:52:30 CET 2009 >>>>>> INFO (FSFAST_S1): RunList = 007 008 009 010 011 >>>>>> -------------------------------------------------- >>>>>> /home/frank/PhD/data/Exp1_Saccades_phase/FSFAST_S1/bold >>>>>> selfreqavg -TR 2.12 -o rtopy/polar/h -i 007/f -i 008/f -i 009/f -i 010/f -cfg /home/frank/PhD/data/Exp1_Saccades_phase/rtopy/analysis.cfg -parname rtopy.par >>>>>> -------------------------------------------------- >>>>>> --- Parsing Config File: /home/frank/PhD/data/Exp1_Saccades_phase/rtopy/analysis.cfg ---- >>>>>> -ncycles 8 -delay 0 -nskip 0 -fwhm 0 >>>>>> DirectionList: +1 +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 007/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 >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>> Could not open rtopy/polar/h.sfa for writing >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>> quiting matlab >>>>>> 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 >>>>>> >>>>>> ----- Original Message ----- >>>>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>> To: "Frank Leoné" <f.leone(a)donders.ru.nl> >>>>>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>>>>> Sent: Wednesday, December 16, 2009 5:12:41 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna >>>>>> Subject: Re: [Freesurfer] Retinotopic mapping of only polar data >>>>>> >>>>>> If you run the retinotopy analysis, it will expect eccen. If it stops >>>>>> without doing the polar analysis, you can "fool" it by copying the polar >>>>>> data into the eccen directory. >>>>>> >>>>>> doug >>>>>> >>>>>> f.leone(a)donders.ru.nl wrote: >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>> Dear all, >>>>>>> >>>>>>> I just started using FreeSurfer, specifically for retinotopic data, on the moment only polar data. So I followed the guide as mentioned on http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis . This does seem to work to some extend, except that it complains that I don't have eccentricity data. He is right about that, but is the analysis also doable with the eccentricity data? I really hope so, thanks a lot in advance, >>>>>>> >>>>>>> kind regards, >>>>>>> >>>>>>> Frank >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> >> ----- Oorspronkelijk bericht ----- >> Van: "Frank Leone" <f.leone(a)donders.ru.nl> >> Aan: "f leone" <f.leone(a)donders.ru.nl> >> Verzonden: Woensdag 6 oktober 2010 17:16:43 GMT +01:00 Amsterdam / Berlijn / Bern / Rome / Stockholm / Wenen >> Onderwerp: [Fwd: Re: [Freesurfer] Retinotopic mapping of only polar data] >> >> >> >> >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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. -- Frank T.M. Leoné, MSc Graduate student | Donders Institute for Brain, Cognition and Behaviour f.leone(a)donders.ru.nl | +31 24 36 12542 / +31 24 36 68388 | Room B.1.31 / Room 1.34

1 0

mri_vol2surf error
by Don Hagler 19 Oct '10

19 Oct '10

Using version 4.5.0, I get this error message with mri_vol2surf: INFO: Source volume detected as selxavg format number of frames is incorrect (0,1) This error does not happen with version 3.0.5, and it only happens for input volumes with particular file names. This fails: mri_vol2surf \ --src /space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTcalc/DTI5_corr_resDTI_DT_minb1000_FA.mgz \ --src_type mgh \ --srcreg /space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTanalysis/rh-tmpreg.dat \ --hemi lh \ --surf white \ --out /space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTanalysis/DTI5_corr_resDTI_DT_minb1000_FA_pdist-1.0-lh.mgh \ --out_type mgh \ --trgsubject FREESURFERRECON_EPDTI_epd34_101002_20101002.185011_1 \ --projdist -1.000 \ --noreshape But this works: mri_vol2surf \ --src /space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTcalc/DTI5_corr_resDTI_DT_minb1000_FA2.mgz \ --src_type mgh \ --srcreg /space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTanalysis/rh-tmpreg.dat \ --hemi lh \ --surf white \ --out /space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTanalysis/DTI5_corr_resDTI_DT_minb1000_FA_pdist-1.0-lh.mgh \ --out_type mgh \ --trgsubject FREESURFERRECON_EPDTI_epd34_101002_20101002.185011_1 \ --projdist -1.000 \ --noreshape In the second case, the input file is a direct copy of the input file for the first case. It also works if the input file is copied to another location. The complete messages when it fails: srcvol = /space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTcalc/DTI5_corr_resDTI_DT_minb1000_FA.mgz srctype = mgh srcreg = /space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTanalysis/rh-tmpreg.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = FREESURFERRECON_EPDTI_epd34_101002_20101002.185011_1 surfreg = sphere.reg ProjDist = -1 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume INFO: Source volume detected as selxavg format number of frames is incorrect (0,1) Complete messages when it succeeds (second case): srcvol = /space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTcalc/DTI5_corr_resDTI_DT_minb1000_FA2.mgz srctype = mgh srcreg = /space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTanalysis/rh-tmpreg.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = FREESURFERRECON_EPDTI_epd34_101002_20101002.185011_1 surfreg = sphere.reg ProjDist = -1 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Reading surface /space/md4/5/halgdev/epiproj/FSRECONS/FREESURFERRECON_EPDTI_epd34_101002_20101002.185011_1/surf/lh.white Done reading source surface Reading thickness /space/md4/5/halgdev/epiproj/FSRECONS/FREESURFERRECON_EPDTI_epd34_101002_20101002.185011_1/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 Done mapping volume to surface Number of source voxels hit = 28720 Writing to /space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTanalysis/DTI5_corr_resDTI_DT_minb1000_FA_pdist-1.0-lh.mgh Dim: 145736 1 1 FYI: FREESURFER_HOME: /usr/pubsw/packages/freesurfer/RH4-x86_64-R450 Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 RedHat release: CentOS release 5.5 (Final) Kernel info: Linux 2.6.18-194.8.1.el5 x86_64

2 2

Statistical doubt
by Gabriel Go.Es. 19 Oct '10

19 Oct '10

Dear Freesurfers I would like to perform regression analysis between volume of subcortical structures (obtained from aseg) and psychometric scores removing effects of age and gender. Is there any way to do it with FS? Gabriel

2 1

Adding new contrasts to an analysis
by Adam Nitenson 19 Oct '10

19 Oct '10

Hello Freesurfers, I recently used mkcontrast-sess to create a new contrast within an already made analysis: mkcontrast-sess -analysis caitlin_prep -contrast EasyAndHard_vs_Error.mat -a 1 -a 2 -c 4 Is there a way that I can use selxavg3-sess to analyze this new contract for my subjects (who all already have a caitlin_prep folder with older contrasts) without having to completely overwrite the entire analysis folder? I tried using a command such as: selxavg3-sess -s RMCON003 -analysis caitlin_prep -c EasyAndHard_vs_Error.....but receive an error ERROR: analysis RM_caitlin_prep already exists. You must specify whether to -skip or -overwrite ...even though that specific contrast does not yet exist within that folder. Any ideas? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

2 1

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