Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Talairach coordinates for Desikan gyral regions
by Robustelli, Briana (NIH/NIMH) [F] 22 Oct '10

22 Oct '10

Hi all, We are trying to depict spatial relations of each of the Desikan et. al (2006) gyral regions in a separate 3-D graph. To do this we need every regions' center Talairach coordinates in common space, not in relation to any particular group or subject. Is there a way to do this using Freesurfer? Thank you. Briana

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Freeview and Mac OS 10.6 - Snow Leopard
by Andreas Schindler 22 Oct '10

22 Oct '10

Dear Freesurfers Does anyone know if freeview already works on Mac OS Snow Leopard or when it will be patched? best wishes Andreas

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Postdoctoral Fellowship in multimodal developmental neuroimaging
by Michels Lars 22 Oct '10

22 Oct '10

Postdoctoral Fellowship in multimodal developmental neuroimaging Applications are invited for a 2-years postdoctoral fellowship in the human multimodal neuroimaging project "Linking the major system markers for typical and atypical brain development: a multimodal imaging and spectroscopy study" (http://www.zihp.uzh.ch/1610.php#45) funded by the Zürich Institute of Human Physiology. This study will investigate the major physiological markers of brain development, using a combination of advanced magnetic resonance imaging (e.g., functional MRI) and MR-spectroscopy methods. The initial phase of the study will establish baseline neurotransmitter levels, cerebral blood flow (e.g., perfusion MRI) and EEG frequency and power at rest across a range of age groups. Examining the interactions between these markers and the changes they demonstrate with age and hormone levels will allow to better understanding the global and regional processes underlying brain maturation. The later phases will investigate changes in these physiological markers with (a) cognitive tasks and (b) attention deficit hyperactivity disorder (ADHD). The starting date of the position is January 2011. The successful applicant will have a PhD research background in Cognitive Neuroscience, Neurophysiology, Psychology, Neuropsychology, or related fields. Fluency in English, good oral and written German, and the ability to work within a multidisciplinary team are essential. Applicants should be experienced at conducting fMRI and/or EEG studies and be familiar with analysis software, such as SPM/Matlab, BrainVoyager and/or FSL. Experience with stimulus presentation software (such as Presentation), UNIX, and programming languages a plus. Salaries are in accordance with the Swiss National Research Foundation (starting at around 80'000 CHF p.a.). APPLICATION INSTRUCTIONS: To apply by e-mail (max 5 MB), please send a curriculum vitae, a personal statement describing research interests, 3 letters of recommendations, and up to 5 article reprints/preprints to: Dr Lars Michels lars.michels(a)kispi.uzh.ch MR-Zentrum University Children's Hospital Steinwiesstrasse 75 Zürich 8032 Switzerland Reviews of applications will begin on the 7th of November and will continue until the positions are filled.

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Symbolic links generated
by Stephan Gerhard 21 Oct '10

21 Oct '10

Hi Freesurfer Team, I am running Freesurfer 5.0 on Ubuntu 64-bit. I want to change the SUBJECTS_DIR environment variable to point to an other location than inside the FREESURFER_HOME/subjects folder. When I do so, and run the recon-all command, 3 symbolic linked folders are generated for fsaverage/ lh.EC_average/ and rh.EC_average/. How can I avoid this behaviour? Thanks, Stephan

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exiting with errors
by Nathan Dankner 21 Oct '10

21 Oct '10

Hi all, I've run into a recurring error with some scans that I am running. It is duplicated below: ncopen: filename "./tmp.mri_nu_correct.mni.8091/0/nu1_residue.mnc": Not a netCD$ miopen: MINC package entry point nu_estimate_np_and_em: crashed while running mincmath (termination status=768) nu_correct: crashed while running nu_estimate_np_and_em (termination status=768) ERROR: nu_correct This is occuring very early in autorecon1. Any idea what's going wrong? Thanks, Nathan

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recon-all using cuda
by Jordi Delgado 20 Oct '10

20 Oct '10

Hi FS experts, I'm currently testing FS v5 with cuda support. I'm using Centos 5.5 x86_64 on a DELL XPS with 4GB RAM, Intel Core 2 Extreme Processor QX9650 @ 3.67GHz and three GPUS Geforce 9800 GT. Every GPU has 512 GDDR3 memory, 256-BIT Memory Bus, 112 Stream Processing Units, 2x 400MHz RAMDACs and PCI Express 2.0 suport. The SDK examples runs perfect but when I run the following script: export FREESURFER_HOME=/home/neuro/freesurfer source /home/neuro/freesurfer/SetUpFreeSurfer.sh export SUBJECTS_DIR=/home/neuro/proc/OutPBS_GPU recon-all -all -force -i /home/neuro/orig/ACR_103/ACR_103_0002 -s ACR_103 -qcache *-use-cuda* I obtain the following error message: *** glibc detected *** mri_em_register: malloc(): memory corruption: 0x00000000315dfdc0 *** ======= Backtrace: ========= /lib64/libc.so.6[0x3304072fae] /lib64/libc.so.6(__libc_calloc+0xcd)[0x330407495d] mri_em_register[0x42efad] mri_em_register[0x40e80d] /lib64/libc.so.6(__libc_start_main+0xf4)[0x330401d994] mri_em_register(__gxx_personality_v0+0x16a)[0x40b16a] ======= Memory map: ======== 00400000-00b55000 r-xp 00400000 00:00 0 00b55000-00c54000 ---p 00b55000 00:00 0 00c54000-02627000 rwxp 00c54000 00:00 0 1ef6f000-3c61e000 rwxp 1ef6f000 00:00 0 [heap] 3303c00000-3303c1c000 r-xp 00000000 08:03 79331333 /lib64/ld-2.5.so 3303c1c000-3303e1b000 ---p 3303c1c000 00:00 0 3303e1b000-3303e1c000 r-xp 0001b000 08:03 79331333 /lib64/ld-2.5.so 3303e1c000-3303e1d000 rwxp 0001c000 08:03 79331333 /lib64/ld-2.5.so 3304000000-330414e000 r-xp 00000000 08:03 79331340 /lib64/libc-2.5.so 330414e000-330434d000 ---p 0014e000 08:03 79331340 /lib64/libc-2.5.so 330434d000-3304351000 r-xp 0014d000 08:03 79331340 /lib64/libc-2.5.so 3304351000-3304352000 rwxp 00151000 08:03 79331340 /lib64/libc-2.5.so 3304352000-3304357000 rwxp 3304352000 00:00 0 3304400000-3304402000 r-xp 00000000 08:03 79331344 /lib64/libdl-2.5.so 3304402000-3304602000 ---p 00002000 08:03 79331344 /lib64/libdl-2.5.so 3304602000-3304603000 r-xp 00002000 08:03 79331344 /lib64/libdl-2.5.so 3304603000-3304604000 rwxp 00003000 08:03 79331344 /lib64/libdl-2.5.so 3304800000-3304882000 r-xp 00000000 08:03 79331372 /lib64/libm-2.5.so 3304882000-3304a81000 ---p 00082000 08:03 79331372 /lib64/libm-2.5.so 3304a81000-3304a82000 r-xp 00081000 08:03 79331372 /lib64/libm-2.5.so 3304a82000-3304a83000 rwxp 00082000 08:03 79331372 /lib64/libm-2.5.so 3304c00000-3304c16000 r-xp 00000000 08:03 79331354 /lib64/libpthread-2.5.so 3304c16000-3304e15000 ---p 00016000 08:03 79331354 /lib64/libpthread-2.5.so 3304e15000-3304e16000 r-xp 00015000 08:03 79331354 /lib64/libpthread-2.5.so 3304e16000-3304e17000 rwxp 00016000 08:03 79331354 /lib64/libpthread-2.5.so 3304e17000-3304e1b000 rwxp 3304e17000 00:00 0 3305000000-3305014000 r-xp 00000000 08:03 12817044 /usr/lib64/libz.so.1.2.3 3305014000-3305213000 ---p 00014000 08:03 12817044 /usr/lib64/libz.so.1.2.3 3305213000-3305214000 rwxp 00013000 08:03 12817044 /usr/lib64/libz.so.1.2.3 3306400000-3306409000 r-xp 00000000 08:03 79331382 /lib64/libcrypt-2.5.so 3306409000-3306608000 ---p 00009000 08:03 79331382 /lib64/libcrypt-2.5.so 3306608000-3306609000 r-xp 00008000 08:03 79331382 /lib64/libcrypt-2.5.so 3306609000-330660a000 rwxp 00009000 08:03 79331382 /lib64/libcrypt-2.5.so 330660a000-3306638000 rwxp 330660a000 00:00 0 3309c00000-3309c0d000 r-xp 00000000 08:03 79331394 /lib64/libgcc_s-4.1.2-20080825.so.1 3309c0d000-3309e0d000 ---p 0000d000 08:03 79331394 /lib64/libgcc_s-4.1.2-20080825.so.1 3309e0d000-3309e0e000 rwxp 0000d000 08:03 79331394 /lib64/libgcc_s-4.1.2-20080825.so.1 330b400000-330b4e6000 r-xp 00000000 08:03 12824478 /usr/lib64/libstdc++.so.6.0.8 330b4e6000-330b6e5000 ---p 000e6000 08:03 12824478 /usr/lib64/libstdc++.so.6.0.8 330b6e5000-330b6eb000 r-xp 000e5000 08:03 12824478 /usr/lib64/libstdc++.so.6.0.8 330b6eb000-330b6ee000 rwxp 000eb000 08:03 12824478 /usr/lib64/libstdc++.so.6.0.8 330b6ee000-330b700000 rwxp 330b6ee000 00:00 0 2b2d46aaa000-2b2d46aad000 rwxp 2b2d46aaa000 00:00 0 2b2d46ab9000-2b2d47f2e000 rwxp 2b2d46ab9000 00:00 0 2b2d48000000-2b2d48021000 rwxp 2b2d48000000 00:00 0 2b2d48021000-2b2d4c000000 ---p 2b2d48021000 00:00 0 7fff73ffe000-7fff741f2000 rwxp 7fffffe0a000 00:00 0 [stack] ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vdso] I attached the output log of the execution. Any idea will be apreciated! Thank you in advance!! -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html

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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

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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

1 0

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

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