Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

3 button mouse for macintosh
by Rosso, Isabelle M. 29 Oct '10

29 Oct '10

Hello, Just getting started with Freesurfer. I'm hoping someone can recommend a 3-button mouse that works well with Freesurfer, on a Macintosh. I purchased a Logitech wireless mouse, but can't get it to work properly. Freesurfer does not seem to recognize the 2nd and 3rd buttons as any different than the 1st/left button. So I cannot get edits to work, for example, when trying to edit white matter. Any tips appreciated. -Isabelle --------------------------------------------------------------------- Isabelle M. Rosso, Ph.D. Assistant Professor of Psychology Licensed Psychologist -- Certified Health Service Provider McLean Hospital Neuroimaging Center 115 Mill Street Belmont, MA 02478 Phone: 617.855.2607 Fax: 617.855.2770 irosso(a)hms.harvard.edu ---------------------------------------------------------------------

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How to save a new label after cutting an existing label?
by 李瑾 28 Oct '10

28 Oct '10

Hi freesurfers, I'm trying to generate a new label, from cutting an existed label. The process was shown as attached, First I load a label on fsaverage, lh.inflated, then cut the label along the yellow line and keep the needed part by "cut plane". Now I hope to save the remained label shown in blue in the right pic, into a new label, and use it as my ROI. I tried many methods but they didn't work. Any help would be greatly appreciated. Thank you in advance.

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[Fwd: scientific programmer position with us]
by Douglas N Greve 28 Oct '10

28 Oct '10

Anyone interested should send email to Richard Baumgartner at richard_baumgartner(a)merck.com -------- Original Message -------- Hi Doug, we are urgently looking for a contractor position with us. The person should have good programming skills and some understanding of statistics. He/she will work with imaging, so some imaging experience would be welcome. If you know of someone who might be interested please let me know. Thanks, Richard. Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. -- 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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Re: [Freesurfer] Make functional ROI's from clusters
by Douglas N Greve 28 Oct '10

28 Oct '10

If the labels and data are surface, you can use the --slabel feature. doug Alice Albrecht wrote: > Thanks Doug, > > I have successfully made the labels, but now I want to use those > labels on other data as ROIs and that is where I am having trouble > using the mri_segstats function. I don't see where I can load in my > labels. > > -Alice > > On Thu, Oct 28, 2010 at 2:20 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > As Allison says, you can use the tools listed below. > Alternatively, there is an easier way to do it in tksurfer. > > 1. Click on cluster you want to convert into a label. > 2. Click on the "Custom Fill" button (little paint bucket pouring > into a blue blob). This will popup a window > 3. Click on the "Up to functional values below threshold" box, > then "Fill". The cluster will temporarily turn white, then it will > have a yellow border. You have just created a "label". > 4. Save this label using the File menu. > > doug > > > Allison Stevens wrote: > > Alice, > You might find this tutorial helpful: > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividu… > > and mri_volcluster or mri_surfcluster > > Allison > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@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> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center 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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Make functional ROI's from clusters
by Alice Albrecht 28 Oct '10

28 Oct '10

Hi Everyone, I'm new to freesurfer so I apologize if my question has already been answered previously (I searched the list archive and the website and couldn't find an answer). I would like to make functionally defined ROIs for each of my subjects based on a localizer I used. I would like to select several ROIs from one contrast. I have done that by simply drawing the ROI on the significant voxels using the "select voxels tool" and saving that out as a label. This process is rather painstaking though, and I was wondering if there was an easier way to do this- perhaps by selecting an entire cluster of voxels at once and saving that out to a label? If anyone has figured out a more efficient way to do this I would appreciate it. Thanks! -Alice

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Re: [Freesurfer] Retinotopic mapping of only polar data]
by f.leone＠donders.ru.nl 28 Oct '10

28 Oct '10

Hi Douglas, Thanks a lot, I made dummy data for the eccen and that worked. Last problem: when I try to overlay the data on an inflated brain, the registration is off (patches are frontal and in parts I didn't scan, while they for sure should be posterior and within my actually scanned scans). I did create a register.dat using bbregister and it seems alright when I check it with tkregister2. Is there anything different for the register.dat in v5? I don't see it being referred now. I do see it refer to two other files, which actually don't exist: tkmedit: Trying to open /home/action/fraleo/Data/Exp1_Saccades_phase/S1_FS/bold/rtopy.S1_FS.rh/tksconcat.dat surfer: Interpreting overlay volume /home/action/fraleo/Data/Exp1_Saccades_phase/S1_FS/bold/rtopy.S1_FS.rh/tksconcat.nii Also, when running the analysis, it automatically looks for a brain.S1_FS.rh in the 001/masks directory. It isn't there though, only an brain.fsaverage.rh.nii, so that's what I now used, but that might be the reason it's going wrong. What should I use there? The coregistered structural? Thanks a lot in advance, hope to be able to solve this last little prob fast, Frank ----- Original Message ----- From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> To: "Frank Leoné" <f.leone(a)donders.ru.nl>, "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> Sent: Wednesday, October 20, 2010 7:51:06 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: Re: [Freesurfer] Retinotopic mapping of only polar data] 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 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

2 1

Subcortical Labelling correction
by antonio cerasa 28 Oct '10

28 Oct '10

Dear FS experts, I 've question concerning the automatic subcortical labelling provided by FS. Is it possible to manually correct the output? That is, if hippocampal segmentation results inaccurate, can I modified the aseg.mgz file ? Thanks for your attention. ---------------------------------------------------------------------- Antonio Cerasa, PhD Neuroimaging Research Unit, National Research Council, Catanzaro, 88100 Italy. Part-time Lecturer Unversity "Magna Graecia" Germaneto (CZ), Italy http://docenti.unicz.it/sito/cerasa.php phone: +39 0984 9801766 Cell: +39 333 9633511 Fax: +39 0984 9801791 / 969306

3 2

subcortical structure coordinates
by Aya Ben Yakov 28 Oct '10

28 Oct '10

Hi I used FreeSurfer to automatically segment subcortical structures, and I would now like to transfer the data to Matlab. I am looking for a way to load the coordinates of all structures (or, if it isn't possible, for each structure, by its number) to Matlab, in Talairach coordinates. Is this possible? If so - how can it be done? I use BrainVoyager, not FSL, for analysis, and I would like to somehow use the segmentation from FreeSurfer for analysis in Matlab, in combination with data I have from BrainVoyager (the functional data). I don't necessarily need talairach coordinates, but otherwise I'm not sure how it would be possible to convert between FreeSurfer and BrainVoyager. Any suggestions? Thanks! Aya

3 6

Re: [Freesurfer] Total GM and WM volumes
by Ed Gronenschild 27 Oct '10

27 Oct '10

Hi Allison, Thanks. It is still confusing: for the gm the aseg.stats lists cortical as well as subcortical and the total volumes (being the sum of both). But for wm only cortical volumes are present. Is there no subcortical wm volume present or defined? Ed On 27 Oct 2010, at 15:58, Allison Stevens wrote: > Ed, > I would use the values in the aseg.stats. I'm not sure why there is > this > difference (Doug might be able to elaborate on how the values in > aseg.stats are calculated) but for v5.0, we went over how all the > stats > were being calculated and make sure the values in the aseg.stats > were the > most accurate. > Allison > > -- > > On Wed, 27 Oct 2010, Ed Gronenschild wrote: > >> Dear Bruce/Allison, >> >> Could you please try to give response to my question >> which wm and gm volumes I shoud use, see my >> today's submission below. >> >> Ed >> >> On 27 Oct 2010, at 14:41, freesurfer-request(a)nmr.mgh.harvard.edu >> wrote: >> >>> Dear Christian, >>> >>> Thanks for your suggestion. I followed the instructions to derive >>> the >>> GM and WM volumes. Here are the (rounded-off) results for one >>> example: >>> >>> mris_volume lh.pial: 532767 >>> mris_volume rh.pial: 536127 >>> >>> mris_wm_volume lh: 251139 >>> mris_wm_volume rh: 254730 >>> >>> Accordingly: >>> gm lh = 532767 - 251139 = 281628 >>> gm rh = 536127 - 254730 = 281397 >>> >>> Left + right: >>> total = 1068894 >>> wm = 505869 >>> gm = 563025 >>> >>> ------------ >>> >>> The aseg.stats file lists the following results: >>> >>> cortical wm lh: 251139 >>> cortical wm rh: 254730 >>> total wm: 505869 >>> >>> cortical gm lh: 263888 >>> cortical gm rh: 265231 >>> total cortical gm: 529119 >>> subcortical gm: 181270 >>> total gm: 710389 >>> >>> -------------- >>> >>> For wm both results are equal but for gm they are not. >>> >>> So now my question still exists: which wm and gm volumes should I >>> take? >>> >>> Ed >>> >>> >>> On 26 Oct 2010, at 20:40, freesurfer-request(a)nmr.mgh.harvard.edu >>> wrote: >>> >>>> Dear Ed, >>>> >>>> to my knowledge, "mris_wm_volume" is the best option to determine >>>> the >>>> white matter volume. >>>> >>>> See this wiki page for usage: >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats >>>> >>>> Best wishes, >>>> Christian >>>> >>>> >>>> --- >>>> Christian Scheel >>>> Department of Psychiatry >>>> University of Cologne >>>> >>>> >>>> >>>> >>>> Am 26.10.2010 15:22, schrieb Ed Gronenschild: >>>>> Hi, >>>>> >>>>> I post this once again because I didn't get any response. >>>>> >>>>> In the v5.0.0 aseg.stats file I can find the following volumes: >>>>> >>>>> - left/right cortical gray matter >>>>> - subcortical gray matter >>>>> - total cortical gray matter >>>>> - total gray matter volume >>>>> and >>>>> - left/right cortical white matter >>>>> - total cortical white matter >>>>> >>>>> How can I derive the total white matter volume? >>>>> >>>>> Ed >>>> >>> >> > > > 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. >

2 1

Re: [Freesurfer] Longitudinal processing
by Martin Reuter 27 Oct '10

27 Oct '10

Hi Sandra, (and the list, I think this might be interesting for others) 1. the longitudinal ?h.thickness files are in registration (within subject) so in order to compute the difference or the rate you can simply use: mris_calc -o lh.outdiff sdir2/surf/lh.thickness sdir1/surf/lh.thickness and for the rate, you can divide by time 1 thickness or by the average thickness. If the time points are not equally spaced across subjects, you can also divide by difference in time. It is best to smooth the thickness files before you do all this (i.e. within time point smooth the ?h.thickness files with mri_surf2surf). 2. then map everything to your template (e.g. fsaverage) with mri_surf2surf 3. there you can stack the thick-differences or thick-rates with mri_concat 4. do the glm Beste Gruesse, Martin On Tue, 2010-06-29 at 21:50 +0200, Sandra Duezel wrote: > Hi Martin > > I just have got your answer to the longitudinal processing question > from Michele and have some other questions regarding the output data > from the longitudinal stream. > Our study contains MRI scans of 45 elderly subjects from 2 timepoints. > I have done all steps from the longitudinal stream and it worked > without any problems. > > Now I would like calculate the thickness difference maps between the > prae and post scans, which are already longitudinally processed. > > I have tried the thickdiffmap-script using the <tp1>.long and > <tp2>.long data. It creates a .mgz file in each subject but also a new > folder "groupstudy" > with the prae/post data resampled to fsaverage (its an .mgh file) > > Is this the right way to calculate the difference for longitudinal data? > > Do I also need to proceed with GLM analysis as suggestet in http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > or do I need to handle the longitudial data in a different way? > > Thank you very much for your help and answers! > > Best regards > > Sandra > > > > > > > > > Am 29.06.2010 um 17:24 schrieb Martin Reuter: > > > There is a step by step description on the longitudinal stream. > > It basically means: > > 1. to process your two time points individually through freesurfer > > (standard processing). > > 2. to create a template for each subjects from these processed time > > points > > 3. to run the two time points again (passing it the template) to > > compute > > better longitudinal results (less variability, more accuracy). > >

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