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problems aligning fsfast functional to anatomical..
by Srihasam, Krishna 28 May '09

28 May '09

Hi, I am having trouble overlaying my functional data generate by FSFAST stream onto the surfaces which I generated using Freesurfer. The registration is going haywire. I used spmregister-sess and the output registers coronal sections of the anatomical to horizontal sections of the fMRI data. So, I tried using the original anatomical image, not the surfaces I generated from it, the registration looks great. I used mri_info to check the difference between the images and my original anatomical image is 256x256x240 in size and its resolution is 0.5x0.5x0.5mm. The data seems to be stored as float. The brainmask.mgz in the mri directory of where I created the surfaces has different stats: 256x256x256 ; resolution: 1x1x1 and the data is in UCHAR. BTw, I am working on data from monkey rain. Any help will be more that appreciated.. -Krishna

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Re: Freesurfer Digest, Vol 63, Issue 48
by Sebastian Moeller 28 May '09

28 May '09

Hi Falk, On May 28, 2009, at 3:50 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 4 > Date: Thu, 28 May 2009 11:56:51 +0200 > From: Falk L?sebrink <falk.luese(a)gmx.net> > Subject: [Freesurfer] Troubleshooting > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <001501c9df7a$9fe15a40$dfa40ec0$@luese@gmx.net> > Content-Type: text/plain; charset="iso-8859-1" > > Hello, > > > > Im having trouble to generate a correct aseg.mgz for one volume of > mine. > The nu_noneck.mgz is also incorrect and therefore I think the -careg > stage > of autorecon2 might fail. Is there a way to do some kind quality > check, like > the tal-check during autorecon1, to see whether the talairach.m3z is > incorrect? Are there some kind of instructions like fixing the bad > output > from the talairach registration? Or are there some parameters which > can be > adjusted to get better results? > > > > If none of this is possible in some way, would it be advisable to > use the > -noaseg flag? Im actually in no need for the subcortical > segmentation, it > would just be a plus, but the aseg.mgz is needed during the - > segmentation > stage to remove the cerebellum and brain stem. Maybe there even is > another > way to remove these structures automatically? Well, I can offer a very rough method that seems to work with my monkey data (where I always use -noaseg), I never tried it with humans. I edit the wm.mgz and delete two slices worth of midbrain above the upper connection of the cerebellum to the midbrain. It seems important that there are no connections from cerebellum left to white matter (if there are connection above the cut I always delete the cerebellar part of those, but I do not care about the cerebellum currently). Then I pick a point on the pons in the segment above the cut. I use this point, as well as a point picked somewhere in the middle of the corpus callosum to feed into further recon-all steps (see below). This probably is rather unclean, but it seems to work okay, at least with monkey data... Here my actual script for that step (replace the values in CC_string and PONS_string with your real values picked from tkmedit of wm.mgz): # set the target directory and file_name set targ_dir = ../mri set src_vol = wm.mgz #set brain = brain.mgz set targ_vol = filled.mgz set controlpoints = ../tmp/control.dat set cur_dir = `pwd` # ATTENTION please specify the cutting planes for the pons and the corpus callosum # define the raw voxel coordinates for CC and PONS set CC_string = "128 110 132" set PONS_string = "128 136 125"#"127 129 112" # do an initial filling to check the cutting planes set check_filling = 0 cd .. set tmp_subj = 0?????* cd ${cur_dir} if (${check_filling} == 1) then echo "Testing the CC and Pons coordinates, if the filled volume is okay rerun this script with set check_filling = 0" #mri_fill -CV 127 128 128 -PV 127 154 128 ${src_dir}/${src_vol} $ {targ_dir}/${targ_vol} mri_fill -a ../scripts/ponscc.cut.log -PV ${PONS_string} -CV $ {CC_string} ${src_dir}/wm.mgz ${src_dir}/filled.mgz # check the results, left and right white matter should be colored differently and the cerebellum should be excluded tkmedit -f ${src_dir}/filled.mgz -aux ${src_dir}/T1.mgz exit 0 endif # 20060224 recon-all -autorecon2-wm \ -subjid ${tmp_subj} \ -cc-crs ${CC_string} \ -pons-crs ${PONS_string} \ -noaseg \ -xopts-use > > > > > Thanks in advance, > > Regards, > > Falk I hope this helps Sebastian -- Sebastian Moeller telephone: 626-395-6713 German GSM: 0 15 77 - 1 90 31 41 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

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Using tmpfs to speed up recon-all
by Luke Robot Hospadaruk 28 May '09

28 May '09

Hi, I've noticed recon-all (-all) doesn't really grind my cpu as intensely as it might, which makes me wonder if it might be more I/O limited, which further makes me wonder if I could get any kind of speedup using a tmpfs to store the subject's directory while running recon-all, and then copying the results back to disk when I'm done. Does anyone know how I/O limited recon-all is (I realize it consists of many tasks, but if even some of them would be significantly sped up by putting their data in memory, it'd be worth my time). Also, do all recon-all components store their scratch data (if they have it) in the subject directory? or do they go somewhere else (like /tmp or /var)? Thanks for the help --Luke Hospadaruk

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Projecting 3-D voxel data onto the cortical surface
by m.e.kirlangic＠fz-juelich.de 28 May '09

28 May '09

Dear Freesurfer Community, I am quite new in freesurfer, getting just acquainted with the tools. What I am currently trying to do is, projecting 3-D voxel data (i.e. postmortem probability maps of Prof. Katrin Amunts and Prof. Karl Zilles in Research Center Juelich -Germany) onto the cortical surface. For the time being, I assume that both types of data are registered to a reference space (e.g., Collin27-brain). Which functions I would/could need for the calculations and visualization? Which data format(s) is/are required in order to be able to make use of the available freesurfer functions? Any guidance and all tips are very welcome :-) And sorry for any inconvenience using the terminology! Thanks, Eylem Kirlangic ------------------------------------------------------------------- ------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------- -------------------------------------------------------------------

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RE: [Freesurfer] Troubleshooting
by Bruce Fischl 28 May '09

28 May '09

Hi Falk, you can check the transforms via: cd $SUBJECTS_DIR/$subject/mri mri_convert -rt nearest aseg.mgz -rl $FREESURFER_HOME/average/RB_all_2008-03-26.gca -at transforms/talairach.m3z aseg_in_atlas.mgz freeview -v aseg_in_atlas.mgz:colormap=lut /homes/4/fischl/dev/freesurfer/average/RB_all_2008-03-26.gca#1:colormap=lut the mri_convert applies the nonlinear warp to the aseg and reslices it into the same voxel space as the atlas (you could use the talairach.lta to check it instead if you want, or apply it to the norm without the -rt nearest switch). Then freeview loads them both and you can switch back and forth with alt-c to see if they are in register. The #1 at the end of the gca means frame index 1, which is by convention the label with the highest prior at that location in the atlas (frame index 0 is the mean intensity of the most probably class). cheers, Bruce On Thu, 28 May 2009, Falk Lüsebrink wrote: > Hi Martin, > > Thanks for the input, but I think you got me wrong. The talairach > registration and talairach check during -autorecon1 is fine. I think the > -careg stage during -autorecon2 might fail, which "generates a > multi-dimensinal talairach transform" (mri_ca_register). And I was looking > for something like the tutorials you mentioned, however not for the > talairach registration during -autorecon1, but for mri_ca_register. > > Regards, > Falk > > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Martin Kavec > Sent: Thursday, May 28, 2009 1:31 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Troubleshooting > > Hi Falk, > > On Thursday 28 May 2009 11:56:51 Falk Lüsebrink wrote: >> Hello, >> >> >> >> Im having trouble to generate a correct aseg.mgz for one volume of mine. >> The nu_noneck.mgz is also incorrect and therefore I think the -careg stage >> of autorecon2 might fail. Is there a way to do some kind quality check, >> like the tal-check during autorecon1, to see whether the talairach.m3z is >> incorrect? Are there some kind of instructions like fixing the bad output >> from the talairach registration? > > For this you can follow instruction on > > http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction > > and more specifically > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > Hope some of that may lead you to successful reconstruction. > > Best, > > Martin > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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Re: [Freesurfer] Troubleshooting
by Martin Kavec 28 May '09

28 May '09

Hi Falk, On Thursday 28 May 2009 11:56:51 Falk Lüsebrink wrote: > Hello, > > > > Im having trouble to generate a correct aseg.mgz for one volume of mine. > The nu_noneck.mgz is also incorrect and therefore I think the -careg stage > of autorecon2 might fail. Is there a way to do some kind quality check, > like the tal-check during autorecon1, to see whether the talairach.m3z is > incorrect? Are there some kind of instructions like fixing the bad output > from the talairach registration? For this you can follow instruction on http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction and more specifically http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Hope some of that may lead you to successful reconstruction. Best, Martin

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export cortical/subcortical regions to nii
by Jose Luis Cantero Lorente 28 May '09

28 May '09

Dear Freesurfers, Is it possible to export to nii format specific regions previously segmented with FS? If yes, how should I proceed with this task in the case of cortical and subcortical regions? Are they exported in the MNI space, Talairach,...? Thanks in advance. Best regards, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/

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recon-all : brainmasl.mgz missing
by Iwo Bohr 28 May '09

28 May '09

Dear Freesurfer experts, When I run recon-all batch command it did not produce all the files normally kept in subject/mri folder. Importantly brainmask.mgz file is missing, so I can't run reg-feat2anat command. Please advise me what I can do. Many thanks, Iwo Bohr, PhD School of Computing Science University of Newcastle, UK

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Troubleshooting
by Falk Lüsebrink 28 May '09

28 May '09

Hello, Im having trouble to generate a correct aseg.mgz for one volume of mine. The nu_noneck.mgz is also incorrect and therefore I think the -careg stage of autorecon2 might fail. Is there a way to do some kind quality check, like the tal-check during autorecon1, to see whether the talairach.m3z is incorrect? Are there some kind of instructions like fixing the bad output from the talairach registration? Or are there some parameters which can be adjusted to get better results? If none of this is possible in some way, would it be advisable to use the -noaseg flag? Im actually in no need for the subcortical segmentation, it would just be a plus, but the aseg.mgz is needed during the -segmentation stage to remove the cerebellum and brain stem. Maybe there even is another way to remove these structures automatically? Thanks in advance, Regards, Falk

1 0

ROI
by Kelly Silva 28 May '09

28 May '09

Hello, I would like to know how can I create a ROI from one subcortical structure? Thanks in advance, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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