Freesurfer May 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

subcortical segmentation
by Richter, Julia 30 May '12

30 May '12

Dear FreeSurfer experts, I have a question regarding the subcortical segmentation. In the paper by Fischl et al (2002), I've read that the neuroanatomical labels are assigned to the voxels based on probabilistic information automatically estimated from a manually labeled training set. I don't understand which atlas is used though. Is it an atlas of the Center for Morphometric Analysis? How shall I cite it? Thank you very much for your help in advance, Julia

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read_surf - update
by Shay Ohayon 29 May '12

29 May '12

Hi again, OK. I managed to reverse engineer things back from mri_tessalate.c Here is the code snippet that should be added to read_surf to parse these new files: NEW_QUAD_FILE_MAGIC_NUMBER =16777213; elseif (magic == NEW_QUAD_FILE_MAGIC_NUMBER) vnum = fread3(fid); fnum = fread3(fid); vertex_coords = fread(fid, vnum*3, 'float32') ; tmp = fread(fid, fnum*3*3, 'uchar') ; tmp = reshape(tmp, 3, 3, fnum) ; faces = reshape(bitshift(tmp(1,:,:), 16) + bitshift(tmp(2,:,:),8) + tmp(3,:,:),3, fnum)'; end -- Shay

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read_surf and free surfer 5.0
by Shay Ohayon 29 May '12

29 May '12

Hi, I am trying to read a surface generated by mri_tessellate using matlab's API (read_surf.m) However, it seems like the function is not up-to-date, because the magic number in the surface file is 16777213, and the two magic-numbers recognized by read_surf are 16777214 and 16777215. Is there a newer version of read_surf.m out there? Thanks, -- Shay

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wmparc
by Christopher Bell 29 May '12

29 May '12

How much is the dilation (perpendicular to the cortical surface) for the creation of the white matter ROIs? Is there a citation for this? Chris Bell

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Does the fsaverage template belong to MNI space or Talairach space
by ZhiLiangLong 29 May '12

29 May '12

Hi all: In FS, does the fsaverage template belong to MNI space or Talairach space? Thanks!

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Re: [Freesurfer] Fw: wm surface does not follow wm.mgz
by Leon 25 May '12

25 May '12

Hi, Sebastian I think you are right: the final wm surface not only considers wm.mgz and filled.mgz, but the brain.finalsurf.mgz as well. Even though I deleted these voxels with low intensity values in the wm.mgz, the lump at the precentral gyrus still show in the final wm surface. I assume this is due to the high variations of the subjects in this area, causing high intensity values in brain.finalsurf.mgz in these regions. Also, loading wm.mgz as a segmentation mask works for detecting the voxels with low values. Adjusting only the brightness and contrast seems not enough (see the attached file). Thank you! Leon ________________________________ From: Sebastian Moeller <sebastian.moeller1(a)rwth-aachen.de> To: Leon <leonado78(a)yahoo.com> Sent: Friday, May 25, 2012 2:15 PM Subject: Re: [Freesurfer] Fw: wm surface does not follow wm.mgz Hi Leon, On May 25, 2012, at 10:51 AM, Leon wrote: > Hi, Sebastian and Bruce > I think I have found the reason: there are low intensity values at the precentral region (~1) that are almost invisible when viewed using the gray color scheme in FS. When I converted the wm.mgz to nifti format and viewed it in FSL using red-yellow color scheme. They are readily shown there. Now that seems weird, as far as I know the wm.mgz should only contain values around 110. But that said, the orig surface looks fine so the wm.mgz is most likely not your problem. Please have a look at brain.mgz or brain.finalsurf.mgz and look for the intensities in that area. BTW https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable gives a nice overview aout the free surfer steps and the inputs and outputs My interpretation is that the whitematter surfaces take in the intensity gradients from brain.finalsurfs.mgz and refine the orig surface. But I have last used free surfer 4.5 for surface reconstruction so things might have changed. But please humor me and show that the brain.finalsurf.mgz at corresponding slices looks fine :) > > Is there any option in tkmedit that can show volume images with different color schemes such as red-yellow or blue, green? I found the option very helpful in detecting unwanted voxels with low intensity values when I am working on the data in FSL. The best workaround is to use Ctrl-b to open the brightness contrast dialog and set brightness to 0 and contrast to 30 (both sliders to the right), that way even values of 1 can be seen (to some degree). Best Sebastian > > Thank you for your help! > Leon > > From: Sebastian Moeller <sebastian.moeller1(a)rwth-aachen.de> > To: Leon <leonado78(a)yahoo.com> > Cc: FreeSurfer <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Friday, May 25, 2012 1:28 PM > Subject: Re: [Freesurfer] Fw: wm surface does not follow wm.mgz > > Hi Leon, > > if I recall correctly the wm surface is looking at intensity gradients in the brain.finalsurfs.mgz (I think). So please have a look at that file and see whether you have some weird issues in that file. The orig surface is created from the wm.mgz and so will reflect edit you made there. BTW I think the filled is created from wm.mgz, so I guess it is guaranteed to match the orig surface… I do wonder why your wm.mgz shows so much structure, as I am under the impression the wm.mgz should basically be of the wm voxel value (I am wondering about the basal ganglia /caudate intensity I guess) > > Best > Sebastian > > > On May 25, 2012, at 10:15 AM, Leon wrote: > > > Hi, FreeSurfer experts > > > > I am posting it here again since I still have not had the issue solved. Basically, I find that white matter surface does not follow the wm.mgz file (see the attached files). It is strange that such a problem is only located at the precentral gyrus. I checked the white matter original surface and the inflated surface and they look fine. I also went through wm.mgz slice by slice to see if there is abrupt gradient between slices and it doe not seem to have that either. I also checked the orig.nofix with defects_label overlaied as suggested by Bruce and I do not see red marks close to the region (see attached file). So I wonder if anyone would help on solving the issue. > > > > Many thanks in advance > > > > Leon > > > > ----- Forwarded Message ----- > > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > To: Leon <leonado78(a)yahoo.com> > > Sent: Friday, May 25, 2012 11:23 AM > > Subject: Re: [Freesurfer] wm surface does not follow wm.mgz > > > > Hi Leon > > > > can you cc the list so others can answer? I don't have any experience > > with monkey recons so I'm not going to be able to be all that helpful. > > Check the filled.mgz and see if the surface follows it, and if so we'll > > have to figure out why that region is being turned on in the filled > > cheers > > Bruce > > > > > > On Fri, 25 > > May 2012, Leon wrote: > > > > > Hi, Bruce > > > > > > I checked the orig.nofix and do not see any obvious defect there (see the > > > attached file). Do you have any suggestions on how I should check the > > > defects other than visual check? I loaded the defect_label and there is no > > > red label near this region. > > > > > > Thank you! > > > Leon > > > > > > ____________________________________________________________________________ > > > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > > To: Leon <leonado78(a)yahoo.com> > > > Sent: Wednesday, May 23, 2012 7:28 PM > > > Subject: Re: [Freesurfer] wm surface does not follow wm.mgz > > > > > > That almost certainly means there is a topological defect there. Check the > > > orig.nofix > > > > > > > > > Cheers > > > Bruce > > > > > > > > > > > > On May 23, 2012, at 2:49 PM, Leon <leonado78(a)yahoo.com> wrote: > > > > > > Hi, FreeSurfer experts > > > > > > I have seen similar posts before but did not think that I could solve > > > the issue based on the answers from the previous posts. So I am > > > posting it here again. Basically, I find that white matter surface > > > does not follow the wm.mgz file (see the attached file). It is strange > > > that such problem is only located at the precentral gyrus. I checked > > > the white matter original surface and the inflated surface and they > > > look fine. I also went through wm.mgz slice by slice to see if there > > > is abrupt gradient between slices and it doe not seem to have that > > > either. So I wonder if anyone would help on solving this issue. > > > > > > Thanks in advance! > > > Leon > > > > > > <RightPreCentralGyri.jpg> > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > 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. > > > > > > > > > > > > > > > > <OrigNoFix_vs_WM.jpg><RightPreCentralGyri.jpg>_______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > 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. > > -- > Sebastian Moeller > > telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 > fax: 626-395-8826 > German GSM: +49 - 15 77 - 1 90 31 41 > mobile: +1-626-325-8598 > +1-626-807-5242 > US CDMA: +1-626-807-5242 > moeller(a)caltech.edu > > Division of Biology > MC 114-96 > California Institute of Technology > 1200 East California Boulevard > CA 91125, Pasadena > USA > > > _______________________________________________ > 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 > > > 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. -- Sebastian Moeller telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 fax: 626-395-8826 German GSM: +49 - 15 77 - 1 90 31 41 mobile: +1-626-325-8598 +1-626-807-5242 US CDMA: +1-626-807-5242 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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Error during make_average_volume with --xform talairach.m3z
by Anne Bailey 25 May '12

25 May '12

Hello, I am trying to run make_average_subject on my data using the --xform talairach.m3z option, but make_average_volume fails because I get an error during mri_vol2vol: ERROR: transforms/talairach.m3z does not start as 'MNI Transform File' Any suggestions? I can make an average subject perfectly fine using the talairach.xfm file. Thanks, Anne -- Anne Bailey, Ph.D. Candidate, C. Psych. Laboratory for Motor Learning and Neural Plasticity Concordia University 7141 Sherbrooke Ouest Montreal, Quebec H4R 1B6 (514) 848-2424 ext. 7567

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Fw: wm surface does not follow wm.mgz
by Leon 25 May '12

25 May '12

Hi, FreeSurfer experts I am posting it here again since I still have not had the issue solved. Basically, I find that white matter surface does not follow the wm.mgz file (see the attached files). It is strange that such a problem is only located at the precentral gyrus. I checked the white matter original surface and the inflated surface and they look fine. I also went through wm.mgz slice by slice to see if there is abrupt gradient between slices and it doe not seem to have that either. I also checked the orig.nofix with defects_label overlaied as suggested by Bruce and I do not see red marks close to the region (see attached file). So I wonder if anyone would help on solving the issue. Many thanks in advance Leon ----- Forwarded Message ----- From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> To: Leon <leonado78(a)yahoo.com> Sent: Friday, May 25, 2012 11:23 AM Subject: Re: [Freesurfer] wm surface does not follow wm.mgz Hi Leon can you cc the list so others can answer? I don't have any experience with monkey recons so I'm not going to be able to be all that helpful. Check the filled.mgz and see if the surface follows it, and if so we'll have to figure out why that region is being turned on in the filled cheers Bruce On Fri, 25 May 2012, Leon wrote: > Hi, Bruce > > I checked the orig.nofix and do not see any obvious defect there (see the > attached file). Do you have any suggestions on how I should check the > defects other than visual check? I loaded the defect_label and there is no > red label near this region. > > Thank you! > Leon > > ____________________________________________________________________________ > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: Leon <leonado78(a)yahoo.com> > Sent: Wednesday, May 23, 2012 7:28 PM > Subject: Re: [Freesurfer] wm surface does not follow wm.mgz > > That almost certainly means there is a topological defect there. Check the > orig.nofix > > > Cheers > Bruce > > > > On May 23, 2012, at 2:49 PM, Leon <leonado78(a)yahoo.com> wrote: > > Hi, FreeSurfer experts > > I have seen similar posts before but did not think that I could solve > the issue based on the answers from the previous posts. So I am > posting it here again. Basically, I find that white matter surface > does not follow the wm.mgz file (see the attached file). It is strange > that such problem is only located at the precentral gyrus. I checked > the white matter original surface and the inflated surface and they > look fine. I also went through wm.mgz slice by slice to see if there > is abrupt gradient between slices and it doe not seem to have that > either. So I wonder if anyone would help on solving this issue. > > Thanks in advance! > Leon > > <RightPreCentralGyri.jpg> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > 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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Longitudinal error follow up.
by Rashmi Singh 25 May '12

25 May '12

Thanks Martin, I deleted the older runs for base run and started a new run with -use–mritotal flag in the command line: Following is my script for base run for the subjects ( AA543 and AA550) that were giving me errors other than AA510.T1 #!/bin/bash SUBJECTS_DIR=~/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/FreeSurfer export SUBJECTS_DIR recon-all -base AA543.long1 -tp AA543.T0 -tp AA543.T2 -tp AA543.T3 -use-mritotal -all </dev/null&> FSAA543.long1 & recon-all -base AA550.long1 -tp AA550.T1 -tp AA550.T2 -tp AA550.T3 -use-mritotal -all </dev/null&> FSAA550.long1 & The base runs for AA453, AA550 and AA510 completed without error, So I ran the long run for each time point. My script for that was #!/bin/bash SUBJECTS_DIR=~/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/FreeSurfer export SUBJECTS_DIR recon-all -long AA543.T0 AA543.long1 -use-mritotal -all </dev/null&> FSAA543.T0long & recon-all -long AA543.T2 AA543.long1 -use-mritotal -all </dev/null&> FSAA543.T2long & recon-all -long AA543.T3 AA543.long1 -use-mritotal -all </dev/null&> FSAA543.T3long & recon-all -long AA550.T1 AA550.long1 -use-mritotal -all </dev/null&> FSAA550.T1long & recon-all -long AA550.T2 AA550.long1 -use-mritotal -all </dev/null&> FSAA550.T2long & recon-all -long AA550.T3 AA550.long1 -use-mritotal -all </dev/null&> FSAA550.T3long & recon-all -long AA510.T1 AA510.long1 -use-mritotal -all </dev/null&> FSAA550.T1long & recon-all -long AA510.T2 AA510.long1 -use-mritotal -all </dev/null&> FSAA550.T2long & recon-all -long AA510.T7 AA510.long1 -use-mritotal -all </dev/null&> FSAA550.T1long & The long run for All AA510 time points and AA543.T2 and AA550.T1 and .T3 were completed without error, however surprisingly AA550.T2, AA543.T1 and AA543.T3 exited with error, the srcipt log didn't define any error other than suggesting the error to be reported. All incomplete runs exited at the same point. Attached are the script log of the runs that exited with error. I am also atatching the log file for AA543.T2 which completed the long run Message: 7 Date: Thu, 24 May 2012 18:42:17 -0400 From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu<mailto:mreuter@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] error longitudinal processing To: Rashmi Singh <rsingh(a)laureateinstitute.org<mailto:rsingh@laureateinstitute.org>> Cc: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <1337899337.19912.95.camel(a)riemann.nmr.mgh.harvard.edu<mailto:1337899337.19912.95.camel@riemann.nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=utf-8 Hi Rashmi, the command line for running the base (subject-template) should be: recon-all -base AA510 -tp AA510.T1 -tp AA510.T2 -tp AA510.T7 -all we usually don't put the '.long' after the base. I don't think this is causing your problem however. In your case for some reason the talairach transform fails. It could be that something earlier fails. You should - check the .....AA510.long/mri/norm_template.mgz if it looks OK (it is the average of your time points). also the .....AA510.long/mri/orig.mgz should look good. if they are OK, you need to find out why the talairach reg is failing .....AA510.long/mri/transforms/talairach.xfm forgot the command for it, but it is the same as in cross sectional processing. What is weird is your log says this: "INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm" So probably you have an old talairach.xfm there. I think deleting the AA510.long and rerunning the base from scratch may fix everything. So maybe you want to try that first. Best, Martin On Tue, 2012-05-22 at 15:00 +0000, Rashmi Singh wrote: Hello, I ran longitudinal processing which exited with errors. I am attaching the output file. Please advise why this error occurred. The recon ?all run ran perfectly for all the time points for this subject. My command was as follows: recon-all -base AA510.long -tp AA510.T1 -tp AA510.T2 -tp AA510.T7 -all </dev/null&> FSAA510.long & My all other subjects longitudinal run completed without error. Thanks, Rashmi ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

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To what extend will brain.mgz affect final surfaces
by Leon 25 May '12

25 May '12

Hi, FreeSurfer experts I apologize for so many questions, but I am fairly new to FreeSurfer and do need some help on reconstructing surfaces. I noticed that in many areas, such as the subcortical regions with low signal intensity, even if they are filled in the wm.mgz and filled.mgz files, they are still excluded in the final surface files (see the attached file where the crossing hair is located). So, I wonder which file actually decides a voxel will be included in the final surface or not, wm.mgz, filled.mgz, brain.mgz or all of them combined? Hope this will help when I modify the mgz files for fixing some topological defects. Thank you in advance for the help. Leon

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Freesurfer May 2012