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Depth of sulci from ?h.sulc
by Lena Palaniyappan 13 Jun '10

13 Jun '10

I located some discussions but could noit figure out how can I obtain numerical depth values from ?h.sulc files. I need to find the sulcal dept of certain sulci as defined in aparc.a2009 Thanks in advance Lena This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Re: [Freesurfer] R: R: How means all the output file from a segmentation?
by Bruce Fischl 13 Jun '10

13 Jun '10

vol2surf won't work - that's for scalar maps. You need a tesselation I guess, which you can generate with mri_tesselate or mri_mc. If it's just for visualization though you could probably just load it into freeview and look at it as an isosurface of the volume. cheers Bruce On Sun, 13 Jun 2010, Leonardo Chesi wrote: > Hi bruce, > my goal is to obtain a 3D surface of the hippocampal region for a visual > comparison with a manual segmentation made by a neuroradiologist. Today I > managed to extract the volume with mri_binarize but I can't transform it in > a surface that tkurfer can visualize. For that I try to use mri_vol2surf but > I obtain a surface with 0 vertices. Can you help me?? > Cheers > Leonardo > > -----Messaggio originale----- > Da: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Inviato: domenica 13 giugno 2010 14.29 > A: Leonardo Chesi > Cc: freesurfer(a)nmr.mgh.harvard.edu; Ruopeng Wang > Oggetto: Re: R: [Freesurfer] How means all the output file from a > segmentation? > > Hi Leonardo, > > you just want to visualize it? Can you explain your goals a bit better? > You could view it in freeview as an isosurface if you wanted. Ruopeng: is > there wiki documentation for this? > > > cheers > Bruce > > > On Sun, 13 Jun 2010, Leonardo Chesi wrote: > >> >> Hi Bruce, Thanks for your attention, >> Can you write for me a sample line where I want to compute a 3D volume of >> the hippocampal? And I can show it with tksurfer? Thanks >> Leonardo >> >> -----Messaggio originale----- >> Da: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >> Inviato: sabato 12 giugno 2010 20.22 >> A: Leonardo Chesi >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Oggetto: Re: [Freesurfer] How means all the output file from a > segmentation? >> >> Hi Leonardo, >> >> the outputs are listed on our wiki. If you want to extract a single >> structure you can use mri_binarize using the indices in the >> $FREESURFER_HOME/FreeSurferColorLUT.txt file. >> >> cheers >> Bruce >> On Sat, 12 Jun 2010, Leonardo >> Chesi wrote: >> >>> Hi, after the segmentation process, we obtain a lots of file that I can't >>> understand what they represent. Infact I know the mean of the file >> aseg.mgz >>> (that is a mask of the segmentation) and norm.mgz but for example I can't >>> understand the difference between brainmask.mgz and brainmask_auto.mgz. >> Can >>> you help me with a list of the output? And can I obtain the volume >> rendering >>> of only one part of the segmented structure? (es. Hippocampal)?? >>> >>> Thanks for your help >>> >>> Leonardo >>> >>> >> >> >> 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. >> >> >> > > >

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standard deviation map
by Michael Scheel 13 Jun '10

13 Jun '10

Dear FS experts, I have a anatomical scan of a subject with a rare neurogenetical disorder. I'd like to compare this with a age matched control group. How can I visualize a z-score transform map of the cortical thickness, i.e. how would I compute and vizualize the number/amount of standard deviations that my subjects differs from the mean of the control group at each vertex? Thanks, Michael

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Re: [Freesurfer] R: How means all the output file from a segmentation?
by Bruce Fischl 13 Jun '10

13 Jun '10

Hi Leonardo, you just want to visualize it? Can you explain your goals a bit better? You could view it in freeview as an isosurface if you wanted. Ruopeng: is there wiki documentation for this? cheers Bruce On Sun, 13 Jun 2010, Leonardo Chesi wrote: > > Hi Bruce, Thanks for your attention, > Can you write for me a sample line where I want to compute a 3D volume of > the hippocampal? And I can show it with tksurfer? Thanks > Leonardo > > -----Messaggio originale----- > Da: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Inviato: sabato 12 giugno 2010 20.22 > A: Leonardo Chesi > Cc: freesurfer(a)nmr.mgh.harvard.edu > Oggetto: Re: [Freesurfer] How means all the output file from a segmentation? > > Hi Leonardo, > > the outputs are listed on our wiki. If you want to extract a single > structure you can use mri_binarize using the indices in the > $FREESURFER_HOME/FreeSurferColorLUT.txt file. > > cheers > Bruce > On Sat, 12 Jun 2010, Leonardo > Chesi wrote: > >> Hi, after the segmentation process, we obtain a lots of file that I can't >> understand what they represent. Infact I know the mean of the file > aseg.mgz >> (that is a mask of the segmentation) and norm.mgz but for example I can't >> understand the difference between brainmask.mgz and brainmask_auto.mgz. > Can >> you help me with a list of the output? And can I obtain the volume > rendering >> of only one part of the segmented structure? (es. Hippocampal)?? >> >> Thanks for your help >> >> Leonardo >> >> > > > 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. > > >

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Processing need more time using freesurfer
by Zhangyuanchao 13 Jun '10

13 Jun '10

Hi, expert, I used freesurfer on a 32bit ubuntu operation system some days ago. For one subject, the "recon-all -s $filename -all" command need 30 hours or less. I changed it to 64bit Centos operation system, however, the precessing time needed for one subject seems longer than on 32bit system, It needs nearly 40 hours. I do not know what the matter is. Thanks!

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Re: [Freesurfer] How means all the output file from a segmentation?
by Bruce Fischl 13 Jun '10

13 Jun '10

Hi Leonardo, the outputs are listed on our wiki. If you want to extract a single structure you can use mri_binarize using the indices in the $FREESURFER_HOME/FreeSurferColorLUT.txt file. cheers Bruce On Sat, 12 Jun 2010, Leonardo Chesi wrote: > Hi, after the segmentation process, we obtain a lots of file that I can't > understand what they represent. Infact I know the mean of the file aseg.mgz > (that is a mask of the segmentation) and norm.mgz but for example I can't > understand the difference between brainmask.mgz and brainmask_auto.mgz. Can > you help me with a list of the output? And can I obtain the volume rendering > of only one part of the segmented structure? (es. Hippocampal)?? > > Thanks for your help > > Leonardo > >

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manual entry for mri_concat
by Michael Scheel 13 Jun '10

13 Jun '10

Dear FS experts, I recognized that there is no manual entry for mri_concat and fslcalc.fsl. Although there is an extensive help text just typing the command I would find a manual entry (man mri_concat) including exmaples very helpful (or an entry on the freesurfer command site). Thanks, Michael

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sorry for repeating, PFC question
by Ahmed, F, Me <fahmed＠sun.ac.za> 12 Jun '10

12 Jun '10

Sorry for repeating myself, but I'm unsure if my first post got through successfully. My post is detailed below: I require values (total volume) for the prefrontal cortex. I see labels for "G_frontal_middle" and "G_frontal_superior" in the lh.aparc.annot files - are these correct to use? If so, could I add up the values for these to get one total volume for the PFC? Thank you, Fatima

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tksurfer issue
by Gad Klein 12 Jun '10

12 Jun '10

I am having a problem using tksurfer. It does not appear to be the same issue that others have had in the past with NVIDIA drivers etc. When I try to load a surface file the entire process freezes and eventually if I let it run, I will get the following error: gklein@gklein-NSPC:~$ tksurfer CL lh full.flat.patch.3d surfer: current subjects dir: /home/gklein/fssubjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/gklein surfer: Reading header info from /home/gklein/fssubjects/CL/mri/T1.mgz /home/gklein/fssubjects/CL/surf/lh.full.flat.patch.3d: face[0].v[0] = 0, but face 0 not in vertex 0 face list Cannot allocate memory As I am new to FS, any help would be appreciated. Thanks. -Gad

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Label files for the Cortical Ribbon
by Tina Jeon 12 Jun '10

12 Jun '10

Hello freesurfers! After creating some labeling files from aparc.a2005s.annot, I noticed that my sulci and gyri volumes generated from the .label files (i.e., after running mri_annotation2label and mri_label2vol) were only representing the outer layer of the white surface. Is there any way to generate .label files that include the entire cortical ribbon? Thanks, any help would be appreciated. Tina Jeon

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