Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Invitation to connect on LinkedIn
by Jose Angel Pineda Pardo via LinkedIn 19 Oct '10

19 Oct '10

LinkedIn ------------Jose Angel Pineda Pardo souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Freesurfer, I'd like to add you to my professional network on LinkedIn. - Jose Angel Accepter l'invitation de Jose Angel Pineda Pardo http://www.linkedin.com/e/-qq80um-gfggwd0p-13/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir l'invitation de Jose Angel Pineda Pardo http://www.linkedin.com/e/-qq80um-gfggwd0p-13/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… ------------------------------------------ SAVEZ-VOUS que LinkedIn peut vous aider à trouver les bons prestataires de services, parmi ceux que recommande votre réseau ? Grâce à LinkedIn, vous pouvez trouver et choisir des prestataires de services en consultant les recommandations écrites d'autres membres de votre réseau. http://www.linkedin.com/e/-qq80um-gfggwd0p-13/svp/inv-25/ -- (c) 2010, LinkedIn Corporation

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longitudinal processing
by Marie Schaer 18 Oct '10

18 Oct '10

Hi, I am planing to process a longitudinal dataset with 3 timepoints. Is it worthy to begin already the cross-sectional processing with version 5.0 and then wait version 5.1 to continue from the template part. Or would you advice me to wait the release of version 5.1 for the entire processing? Thank you for your help, Marie

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Re: [Freesurfer] bug in --projfrac-max?
by Douglas N Greve 18 Oct '10

18 Oct '10

The problem was in the way I documented the flag for mris_preproc. It should be mris_preproc "--projfrac-max Min Max Delta" instead of "Min Delta Max". I've updated the documentation, and that will be live on the next stable and/or dev update. But you can use the version that is there, just change the order of the Min, Max, and Delta. doug Marco Loggia, PhD wrote: > Sorry again, even in that email I hadn't mentioned the where the surfaces > are: > > > -----Original Message----- > From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Monday, October 18, 2010 11:06 AM > To: marco(a)nmr.mgh.harvard.edu > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] bug in --projfrac-max? > > 0.5.mgh and max.mgh do not exist in that directory. > > doug > > Marco Loggia wrote: > >> Dear all, >> >> Is it possible that the --projfrac-max has a bug (at least when used with >> mris_preproc)? >> >> I sampled the same volume using --projfrac 0.5 and --projfrac-max (see >> below) and, when I overimposed the two surfaces, I noticed that in some >> vertices the first surface (i.e., 0.5) appear to have a higher value than >> the second (i.e., max). >> >> Thanks! >> Marco >> >> >> dir_lbp=/autofs/cluster/randy/2/lbp/patients >> >> mris_preproc --target fsaverage --hemi lh --iv >> $dir_lbp/PH5/session1/data/pasl_RS2/cbf_24sept10.nii.gz >> $dir_lbp/PH5/session1/data/pasl_RS2/aslcal.reg --projfrac 0.5 --out >> 0.5.mgh >> >> mris_preproc --target fsaverage --hemi lh --iv >> $dir_lbp/PH5/session1/data/pasl_RS2/cbf_24sept10.nii.gz >> $dir_lbp/PH5/session1/data/pasl_RS2/aslcal.reg --projfrac-max 0 .1 1 --out >> max.mgh >> >> >> >> ______________________ >> >> Marco L. Loggia, PhD >> Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital >> Harvard Medical School >> >> Psychiatric Neuroimaging Research Program >> CNY Building 120, suite 100 >> Charlestown, Massachusetts 02129 >> Phone: (617) 643-7267 >> Fax: (617) 643-7340 >> marco(a)nmr.mgh.harvard.edu >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > > -- 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] Retinotopic mapping of only polar data]
by f.leone＠donders.ru.nl 18 Oct '10

18 Oct '10

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] -- 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

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bug in --projfrac-max?
by Marco Loggia 18 Oct '10

18 Oct '10

Dear all, Is it possible that the --projfrac-max has a bug (at least when used with mris_preproc)? I sampled the same volume using --projfrac 0.5 and --projfrac-max (see below) and, when I overimposed the two surfaces, I noticed that in some vertices the first surface (i.e., 0.5) appear to have a higher value than the second (i.e., max). Thanks! Marco dir_lbp=/autofs/cluster/randy/2/lbp/patients mris_preproc --target fsaverage --hemi lh --iv $dir_lbp/PH5/session1/data/pasl_RS2/cbf_24sept10.nii.gz $dir_lbp/PH5/session1/data/pasl_RS2/aslcal.reg --projfrac 0.5 --out 0.5.mgh mris_preproc --target fsaverage --hemi lh --iv $dir_lbp/PH5/session1/data/pasl_RS2/cbf_24sept10.nii.gz $dir_lbp/PH5/session1/data/pasl_RS2/aslcal.reg --projfrac-max 0 .1 1 --out max.mgh ______________________ Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School Psychiatric Neuroimaging Research Program CNY Building 120, suite 100 Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco(a)nmr.mgh.harvard.edu

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Re: [Freesurfer] montecarlo
by Douglas N Greve 18 Oct '10

18 Oct '10

Hi Marco, I'm copying the list on this because this is a good question about an aspect that is not well documented. The answer to the question has to do with the sign of the test. By default, mri_glmfit produces p-values that are for unsigned tests. The p-value for a signed test if half that of the signed test (ie, it is more significant). When the p-value is expressed as -log10(p), then the signed test will be 0.301 higher than the unsigned test. Eg, if you have a p-value of .01, the value in the sig.mgh file will be 2.0, but for a signed test it would be .005, making the value in the sig.mgh file 2.3. When you run mri_glmfit-sim and specify a signed test (ie, --sim-sign pos or --sim-sign neg), it lowers the threshold to account for this. So below you specified 1.3 as the threshold and --sim-sign pos, so it lowered the threshold to 1.0. hope this is clear doug Marco Loggia, PhD wrote: > Sorry Doug, > > Below are directory and command line. Also attached is a screenshot showing > a vertex located on a significant cluster, but below threshold in the > sig.mgh. > > Thanks! > Marco > > dir=/autofs/cluster/randy/2/lbp/freesurfer/patients+controls/analyses/lh.lbp > +ctrl.session1.asl2-asl1_30sept10_sm7_03mm_masked_projfrac-max_P=0.05.glmdir > /lbp_only_24sept10 > > > pbsubmit -c "mri_glmfit-sim --glmdir > lh.lbp+ctrl.session1.asl2-asl1_30sept10_sm7_03mm_masked_projfrac-max_P=0.05. > glmdir > --sim perm 10000 1.30103 perm.positive --sim-sign pos --overwrite" > > > > -----Original Message----- > From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Monday, October 18, 2010 10:34 AM > To: Marco Loggia, PhD > Subject: Re: montecarlo > > Hi Marco, can you send the command-line and directory that you ran it > from? In general, it is always a good idea to send this ... > > doug > > Marco Loggia, PhD wrote: > >> Hello Doug, >> >> >> >> I have one question about the montecarlo simulation. >> >> >> >> When I compare the mc-z.positive.sig.cluster.mgh and the >> mc-z.positive.sig.masked.mgh, I notice that the significant clusters >> include also some vertices that are below the cluster forming >> threshold. Is this normal? Why is that? >> >> >> >> Thanks, >> >> >> >> Marco >> >> >> _____________________ >> >> >> >> Marco L. Loggia, PhD >> >> Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital >> >> Harvard Medical School >> >> >> >> CNY Building 120, suite 101E >> >> Charlestown, Massachusetts 02129 >> >> Phone: (617) 643-7267 >> >> Fax: (617) 643-7340 marco(a)nmr.mgh.harvard.edu >> >> >> >> > > > > ------------------------------------------------------------------------ > -- 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] 答复: Problem with intensity normalization
by Douglas N Greve 18 Oct '10

18 Oct '10

Hi Jing, I'm reposting to the group in case someone else has any suggestions. I've answered some of your questions below 1) all of our outputs are "conformed" meaning that they are resampled to 1mm3 256^3. To convert back to native anatomical space search for "native" on our wiki. 2) Don't know 3) Don't know doug Huo, Jing wrote: > Hi Douglas, > > Thanks a lot for your reply!!! > I am doing brain tumor segmentation with voxel-based classification. We have images from all difference scanners. To have good performance in the training stage, I need to normalize the intensity into the same range... > And after segmentation, I need to compare the ground truth and the automated results. > I don't have a choice here...:( > > -Jing > ________________________________________ > 发件人: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > 发送时间: 2010年10月14日 15:12 > 收件人: Huo, Jing > 抄送: freesurfer(a)nmr.mgh.harvard.edu > 主题: Re: [Freesurfer] Problem with intensity normalization > > Jing, why are you running these commands by hand instead of just running > recon-all? These are very complicated steps and don't lend themselves to > running by hand. > > doug > > Huo, Jing wrote: > >> Hi, >> >> I have a problem with using mri_normalize for intensity normalization for T1w+contrast 3D volumes. >> >> What I ran: >> mri_convert t1.hdr t1.mgz >> mri_normalize -g 1 t1.mgz t1_norm.mgz >> mri_convert t1_norm.mgz t1_norm.hdr >> >> (1) The first problem is that all volumes are 256*256*256 as output. Why are there dummy slices? Is there an automatic way to get rid of the dummy slices? >> >> (2) For 1/3 of the 50 cases, I observed a spatial shift for some voxels. I was wondering whether this comes from the spatial registration, but it is wierd coz the rest 2/3 of the cases are pretty OK visually. Anyone has similar experience before? That would be very helpful. Thanks. >> >> (3) For 4 cases, the brain white matter was normalized to 59 instead of 110. I dunno why... >> >> Thanks! I will really appreciate if anyone could help here! >> >> Best, >> Jing >> >> IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > > -- > 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. > > > IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. > > > -- 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

1 0

Nifti data storage type 0?
by Luis Lafer-Sousa 18 Oct '10

18 Oct '10

We have anatomical NHP data that we unpack and preprocess using freesurfer and fsl (using Sebastian's scripts). An end product is a skull stripped brain in .mgz format, that I then convert to .nii using mri_convert. I am trying to use this to register to a McLaren template using jip-align, but always get an error: Error: the Nifti data storage type 0 is not supported. The only difference I have noticed between our files and files that successfully register are, when using mri_info: type: UCHAR (0) instead of type: FLOAT (3) Pulling up the .nii files in MatLab, I get the following: >> castor = load_nii('091017Castor_SkullStripped_unregistered.nii') castor = hdr: [1x1 struct] filetype: 2 fileprefix: '091017Castor_SkullStripped_unregistered' machine: 'ieee-le' img: [256x256x256 uint8] original: [1x1 struct] >> castor.filetype ans = 2 >> castor.hdr.hist ans = descrip: 'FreeSurfer Aug 11 2009' aux_file: '' qform_code: 0 sform_code: 0 quatern_b: 0 quatern_c: 0.7071 quatern_d: -0.7071 qoffset_x: 116.0951 qoffset_y: -115.1852 qoffset_z: 143.2094 srow_x: [-1 0 0 116.0951] srow_y: [0 0 1 -115.1852] srow_z: [0 -1 0 143.2094] intent_name: '' magic: 'n+1' originator: [139.9049 116.1852 112.7906 -3328 13572] rot_orient: [1 3 2] flip_orient: [3 0 3] >> castor.hdr ans = hk: [1x1 struct] dime: [1x1 struct] hist: [1x1 struct] Any ideas why we are getting this error? Or if I should be posting the problem in a differen't forum? Thanks, Luis

2 1

ERROR: mpr2mni305 failed
by Maria Luisa Mandelli 18 Oct '10

18 Oct '10

Hi! I get this error running recon_all Applications/freesurfer/bin/talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log parameter 1 1.219086 -> -0.500000 qaram 1.5209 imgrege: no voxels in register ERROR: 'imgreg_4dfp /data/henry4/Applications/freesurfer/average/711-2C_as_mni_average_305 /data/henry4/Applications/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254 ERROR: mpr2mni305 execution aborted Have someone some ideas about this error? thank you! -- Maria Luisa Mandelli Postdoctoral Fellow Center for Functional and Molecular Imaging UCSF Department of Radiology and Biomedical Imaging China Basin Landing 185 Berry Street, Suite 350 San Francisco, CA 94107 phone (415) 353-9419

2 1

qdec plots
by Khalid Hamandi 17 Oct '10

17 Oct '10

(How) Can I modify the plots produced using the Ctrl click on a vertex of interest in the brain map on the qdec GUI? I have two groups, 12 subjects each, currently using the Ctrl Click I get the measure of interest on the y-axis, and my subjects along the x-axis. I would like just two abcissae - patients and controls (with means shown for each!?) on my x-axis instead? if not easily modified, where are these values found? many thanks Khalid

2 1

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