Re: [Freesurfer] Can't Remove WM
Hi Wade, You just need to adjust the min/mid/max settings for the wm on the sidebar under the Color map drop-down menu. Try using 0/100/255. How are you trying to erase? Either shift+left-click, or enable right-click erasing under Edit-Preferences. -Louis On Wed, 16 Jul 2014, Weber, Wade (weberw) wrote: Hi Surfers, I am running recon-all on some subjects and have run into a strange problem. When we go back to look at the WM voxels for editing, the wm.mgz layer has a light blue tint over the whole layer. When we try to edit the WM voxels, we can add , but we cannot delete any WM voxels. Also, all the WM voxels show up as yellow instead of red as we have set them to show up as red. We tried deleting all the FS files and re-doing the recon-all, but it still shows up like this. This has only happened on 3 or 4 subjects out of about 50. I’ve attached a picture of our problem Thanks in advance! Wade Weber, MS Clinical Research Manager Division of Bipolar Disorder Research Department of Psychiatry and Behavioral Neuroscience University of Cincinnati ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] exporting movies from freeview
Hi Pavitra, In Freeview, go to File - Save Movie Frames. For the fly through option select Frame. There is no command line option for this feature yet, but hopefully soon. -Louis On Fri, 11 Jul 2014, pavit...@nmr.mgh.harvard.edu wrote: Hi Freesurfer Team, I have a 4D volume mask of MRI mask values over time - which I can view frame by frame within Freeview. Is there any way to export this in movie form out of freeview so I can play it back independently of the interface? Thank you. Best Regards, Pavitra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Group analysis tutorial
Hi Qijing, Under the 'Freeview dev build' section on this wiki page you can download an updated version of freeview. http://freesurfer.net/fswiki/Download -Louis On Mon, 7 Jul 2014, Qijing Yu wrote: Hi Doug, By new version, do you mean v5.3.0? Qijing On Mon, Jul 7, 2014 at 11:31 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Yea, that is actually a feature in the new version On 07/02/2014 02:17 PM, Joshua S wrote: Hi all, I was following the group analysis tutorial when I got an error when trying to view the uncorrected significance map with freeview. I used the command freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gende r_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d. I removed the annot_outline=1, because it gave an error. Sig.mgh would not load, and I would get the attached image. I tried to manually add sig.mgh through add surface, but the program immediatley closed, and I got the message in the attached error.log. Text below. Thank you for any help, Josh Did not find any volume geometry information in the surface ???Tgreading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan _killiany.txt) colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan _killiany.txt) Did not find color table in track volume. [0]PETSC ERROR: [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si gnal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: - Error Message [0]PETSC ERROR: Signal received! [0]PETSC ERROR: [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: [0]PETSC ERROR: Unknown Name on a linux-gnu named farklemt.nmr.mgh.harvard.edu http://farklemt.nmr.mgh.harvard.edu by dc325 Wed Jul 2 11:35:56 2014 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src /petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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
Re: [Freesurfer] bad freesurfer segmentation
Hi Doety, Consider these options for uploading data: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html I think recon-all is expecting your wm.mgz to be conformed or 256^3. Something like: mri_convert wm.mgz wm.conform.mgz --conform You would need to rename wm.conform.mgz to wm.mgz, after renaming or saving a copy of the current non-conformed wm mask you got from FSL. -Louis On Thu, 10 Jul 2014, Doety Prins wrote: Hi Bruce, Thanks for your reply. In my previous e-mail I already tried to attach one of my subjects, but got the response that the message was too big, and therefore it was rejected. So how should I upload the image? The images are T1-weighted, 3D, acquired with a 3T scanner, resolution 256 256. I discovered that FSL does a proper segmentation on this subjects, so I was looking for a way to import these segments from FSL into the Freesurfer pipeline, but I didn't succeed so far. I used the white matter segment from FSL as wm.mgz (in a subject in which I already ran recon-all), I used mri_vol2vol to get this segment in the right space, and normalized with mri_normalize. Then I rerun recon-all with -autorecon2-wm. But it gives me the error message: 'ERROR: mri_segment-MRIcheckVolDims: volume1 depth=160 != volume2 depth=256.' So apparently, the wm.mgz still doesn't have the right size. Do you have any experience with this? Or any ideas about this? Best regards, Doety On 9 jul. 2014, at 15:00, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Doety yes, that looks pretty bad. Can you tell us about the acquisition? What resolution/field strength/scan type was it? If you upload the subject we will take a look cheers Bruce On Wed, 9 Jul 2014, Doety Prins wrote: Dear freesurfer experts, I experienced some problems with the segmentation of my T1 scans, as both the white surface and the pial surface are placed incorrectly (see attached images). This seems to me to be a too big difference with what it should look like, that I think could not be fixed with the standard troubleshooting strategies. Do you have any solutions for this? Is it for instance possible to make changes to the recon-all script to shift the surfaces? Thanks in advance, Doety ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer Help
Hi Paras, The tcsh warning is ok, but see this link for more info and a fix: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg28980.html The unrecognized flag error is because you have a space between the dash and subjid, just delete that space. -Louis On Thu, 3 Jul 2014, Paras Patel wrote: Dear Sir/Madam, I am a masters student at Newcastle University using Freesurfer to extract data from MRI scans. When trying to use the command lines in terminal, I seem to be getting an error message which I was wondering if you could help me with. The command line I am using is : recon-all -autorecon-all - subjid sam01 The error message displayed is: WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh ERROR: Flag - unrecognized. -autorecon-all -subjid try01 Linux xubuntu-VirtualBox 3.2.4-64-generic #97-Ubuntu SMP Wed Jun 4 22:03:48 UTC recon-all -s exited with ERRORs at Mon Jun 23 06:47:34 EDT 2014 I have tried the help guide which suggest to update the VM and I have tried to uninstall and re-install Freesurfer but I still get the same error message. I also get the same error message when trying with a different subjid . Please can you give me further guidance on how to fix this error so that I can continue working with Freesurfer. Thank You, Kind Regards, Paras Patel Newcastle University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] -normalization all black
Hi Teo, You might just need to adjust the contrast/brightness settings when viewing the volume in freeview. If you move your mouse around do any non-zero values appear in the bottom right voxel info panel? The T1.mgz for bert should be 4.6mb, so you can see if what you have matches that. Otherwise, could you send us the log file or terminal output from when you ran the normalization step? -Louis On Wed, 2 Jul 2014, Teo Gelles wrote: Hi Everyone, I would like to normalize some images. But even when I test the -normalize option with recon-all -s burt/ -normalization which from what I can see changes /burt/mri/nu.mgz (which came with the freesurfer download) to /burt/mri/T1.mgz, T1.mgz is entirely black. Is there a way to fix this issue? Thanks. Teo ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Voxels included in wm.mgz but not in white matter surface
Hi James, If you draw in 255 voxels on the wm.mgz to connect that stray blob of red voxels to the others, then the wm surf should include it on a rerun. Look through a couple slices in that area for any disconnected wm voxels since it may be occuring on multiple slices. -Louis On Thu, 3 Jul 2014, james pardon wrote: Hi, I'm working on some subjects with gray matter lesions, where usually these lesions happen at the boundary of GM and WM (mostly patients with MS). The problem is that Freesurfer can not follow the cortex past this areas. I have tried to use control points, white matter edits and even editing the problematic regions on orig.mgz volume with neighboring voxels and re running recon-all. My results have improved substantially, however I still have a problem where after white matter edit, and adding some new voxels to wm.mgz, the wm surface (and overlying pial surface) does not respect the wm.mgz. In the attached screenshot for example, I can see some areas that are part of wm.mgz (in red) but not included in WM surface. I was wondering whether anyone can give a hint on what recon-all steps I might need to re-run? Thanks James ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Fwd: surface to volume visualization
Hi James, It's not possible (currently?) to get snapshots with Freeview or the tktools without invoking X. I can post a link for the modified script which uses Freeview instead of the tktools. It's much slower though and until the movie frame capture is a commandline option, using the tktools is probably best. Just stumbled upon xvfb which might do the trick. http://en.wikipedia.org/wiki/Xvfb -Louis On Wed, 2 Jul 2014, james pardon wrote: Dear Louis, Thank you for your comprehensive response, the QA tools are certainly valuable tools. I'm very curious on how I could go about getting Freeview snapshots without invoking X. I was wondering whether you are happy to share your alternative version which gets snaps with freeview? Or perhaps more generally, how a programmer should approach this problem of not invoking X when getting the snapshot? Thanks James On Tue, Jul 1, 2014 at 10:30 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi James, Freeview has a Write Movie Frames option which will grab multiple screenshots throughout a volume. I recently requested a commandline option for this. I've run into the no X11 on cluster limitation as well, and I don't have a work-around at this point. The snapshot-to-html script is roughly implemented in the set of QATools scripts using tkmedit. I have an alternate version which gets snaps with freeview, but it runs faster with tkmedit at this point. https://surfer.nmr.mgh.harvard.edu/fswiki/QATools -Louis On Mon, 23 Jun 2014, Bruce Fischl wrote: Hi James Ruopeng is traveling and may not answer quickly, although Louis might be able to help Bruce On Mon, 23 Jun 2014, james pardon wrote: Sorry if you are receiving this for the second time , not really sure if this went through the first time I sent the email: Dear all, I'm looking for a way to automate surface on volume visualization, to check if the surface reconstruction have been successful on a very large number of subjects. Normally, I would use freeview with -f and -v flags to check and see if it is necessary to edit controls points, etc. As an example, one option to automate this process is to use freeview snapshot option and write a script that runs on several hundred subjects and then show all the resulting images in html format. Running freeview with snapshot option works really good, however, since every freeview run needs X11 there is an overhead here, especially when I'm running on a remote cluster with no X11, which makes running X11 almost impossible. I'm wondering whether any one has a better idea for this? Thanks James ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Longitudinal preprocessing troubleshooting
Hi Bryan, Re: 1a) Did you run the case all the way through recon-all? Even if the skullstripping looks poor, it's possible that the surfaces will turn out ok and might only require some pial edits. Otherwise, this site has some helpful info on rerunning the skullstripping step: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview Re: 1b) If you are referring to voxels located in dura being labelled as cerebral cortex in the aseg then this can be ignored. The cerebral cortex labeled voxels are not used to calculate the morphometry stats. https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats Re: 3) You probably just need to adjust the contrast and brightness, using the window and level sliders on the left in freeview. Re: 4) Could you send a snapshot (or two) of that? -Louis On Thu, 26 Jun 2014, Martin Reuter wrote: Hi Bryan, I can answer the longitudinal question (2), the rest is about cross sectional editing and can probably better be answered by someone else. So yes, I would run the base and check brainmask and surfaces there before going too deep into editing the cross. Best Martin Sent via my smartphone, please excuse brevity. Original message From: Chiu, Bryan (PHTH) Date:06/26/2014 8:06 PM (GMT+01:00) To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal preprocessing troubleshooting Hi all, I have a set of data with ~75 subjects with up to 4 timepoints of scans. The structure of the data indicates that it would be best processed using a longitudinal design. I have recon-all most of the scans. There are a few scans that I am worried about and wondering how to treat each case. I do one sanity check with freeview using a modified version of bert's command: freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red 1a) Skull strip or underanalysis errors: I have attached one screenshot of a very severe case of an underanalysis. How should I treat this case? I have recently read about Editing a Recon in Freeview, but I'm not sure how to proceed with this. b) Skull strip errors -- Some scans have a very small amount of cerebral cortex labelling into the dura mater/ skull. Does this warrant the manual removal via freeview of the skull? 2) Since I am running this through the longitudinal processing, could I be able to skip #1 hoping that the averaging of the timepoints into a 'base' will remove these issues? 3) I have 2 brains that are completely whited out in Freeview (see attached). However the analysis went through and it looks good to me. Opening the raw Nifti file in mricroGL does not show this at all. What is going on and should I be concerned? 4) I have 2 other brains that failed the recon-all. One of them is a Talairach fail and the other one failed mri_watershed. Looking at these brains in mricroGL shows a dark shadow being cast over the brain running diagonally from the front of the head to the back. I think this is the root of the problem. Is there a way to fix this or should I consider these scans problematic and exclude them? Regards, - Bryan ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Fwd: surface to volume visualization
Hi James, Freeview has a Write Movie Frames option which will grab multiple screenshots throughout a volume. I recently requested a commandline option for this. I've run into the no X11 on cluster limitation as well, and I don't have a work-around at this point. The snapshot-to-html script is roughly implemented in the set of QATools scripts using tkmedit. I have an alternate version which gets snaps with freeview, but it runs faster with tkmedit at this point. https://surfer.nmr.mgh.harvard.edu/fswiki/QATools -Louis On Mon, 23 Jun 2014, Bruce Fischl wrote: Hi James Ruopeng is traveling and may not answer quickly, although Louis might be able to help Bruce On Mon, 23 Jun 2014, james pardon wrote: Sorry if you are receiving this for the second time , not really sure if this went through the first time I sent the email: Dear all, I'm looking for a way to automate surface on volume visualization, to check if the surface reconstruction have been successful on a very large number of subjects. Normally, I would use freeview with -f and -v flags to check and see if it is necessary to edit controls points, etc. As an example, one option to automate this process is to use freeview snapshot option and write a script that runs on several hundred subjects and then show all the resulting images in html format. Running freeview with snapshot option works really good, however, since every freeview run needs X11 there is an overhead here, especially when I'm running on a remote cluster with no X11, which makes running X11 almost impossible. I'm wondering whether any one has a better idea for this? Thanks James ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Edits, where art thou?
Hi Max, Could you send a snapshot of an area where your wm edits did not have an effect? Keep in mind the wm voxels you add to the wm.mgz should be well connected to the rest of the wm mask, or else it will tend to get pruned off. You can look at the ?h.orig.nofix surfaces to see if the intial surface model includes your wm edits. -Louis On Mon, 23 Jun 2014, Max Svensson wrote: Hi! When I edit my data, for instance wm editing, I do not see the changes applied to the original image. To make you understand what I do: Open up freeview, load the image, Wm and brainmask, with wm at the top. Then I go into voxel edit, press recon edit, and start filling in topographical defects and do some wm editing. HOWEVER, after I run recon all (recon-all -autorecon2 -autorecon3 -subjid anon)and it's finished without problems, I do not see the edits done on my image. Sure, I see the yellow colour which I filled some spots with, but I was thinking that I would see an edited image, that is with pia (topographical defects) and wm surface going out to the areas I edited. Not only yellow filling which was there before since I edited. Am I doing something wrong? Is the reconprocessed images hidden out there somewhere? Freesurfer team, please help! Best, MAX ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Skull-Stripping Atlas Usage
Hi Teo, Yes it does, but you can use the -no-wsgcaatlas flag. You can also try using gcut which doesn't use an atlas (almost certain). Link with skullstripping info: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview -Louis On Fri, 27 Jun 2014, Teo Gelles wrote: Hi Everyone, I am trying to skullstrip an mri image without using an atlas. Does the following command use an atlas at any point? If so, is there a way to run the skullstripping algorithm without using information from an atlas? recon-all -s bert/ -clean-bm -skullstrip Thanks. Teo Gelles ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] free surfer
Hi Sam, With the voxel edit tool in freeview, you can select the flood fill tool (paint bucket icon), and check the box labeled Flood fill multiple slices at a time. You might have to play with the tolerance percentage to get a good rough-start segmentation of the tumor tissue. -Louis On Wed, 25 Jun 2014, Bruce Fischl wrote: Hi Sam no, I don't think there is anything we have that will do tumor segmentation. I think there are some tools for manually segmenting structures and propagating segmentations from one slice to the next. Perhaps Ruopeng or some other power freeview user can comment? cheers Bruce On Wed, 25 Jun 2014, Sam Raby wrote: Hi, Would someone kindly let me know that, in order to segment a tumor in brain, how/whether I can segment only one slice so it propagates through the adjacent slices and cover up the tumor? thanks, -S On Tue, Jun 24, 2014 at 8:31 PM, Sam Raby rabysa...@gmail.com wrote: Thanks. I would like to start learning and using freesurfer. I have a DICOM MRI of the brain which has a tumor in it. I would like to segment this tumor as automatically as possible. Can I segment only one slice so it propagates through the adjacent slices? Which tool in freesurfer do I need to use to achieve this? Thanks, -S On Tue, Jun 17, 2014 at 5:51 PM, Markus Gschwind markus.gschw...@gmail.com wrote: Hi, You can see here what to do: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall no 4., 5 and 6 especailly. Cheers, M 2014-06-18 0:45 GMT+02:00 Sam Raby rabysa...@gmail.com: I have downloaded the following file freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz and have extracted the contained files, and I was wondering where the binary file is so that I can open the freesurfer with? thanks -S ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] editing aseg
Hi Andrea, To regenerate the aseg.stats file after aseg edits you can run: recon-all -segstats -s subjID -Louis On Wed, 25 Jun 2014, Andrea Horváth wrote: Dear All, After running recon-all and checked all the required steps, some part of the right cerebral white matter was still segmented as right cerebral cortex in the aseg.mgz as seen in the attached pictures (red cross). I would like to edit these two labels in aseg which is OK, but how can I get the correct values in the aseg.stats file? Thank you for your help! Andrea Szövegközi kép 4 Szövegközi kép 3 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Problem with freeview
Hi Fabio, I don't believe the 5.1 version of freeview had that flag. The tutorial instructions are written for 5.3 version of freeview. You can download a more recent version of freeview here (under Other Downloads Info): https://surfer.nmr.mgh.harvard.edu/fswiki/Download You may want to make a backup of your current freeview.bin file. -Louis On Thu, 19 Jun 2014, Bernardoni, Fabio wrote: Dear all, trying to follow the freesurfer longitudinal tutorial I encounter the following problem. Commands I digit in a new shell: ~tcsh ~source $FREESURFER_HOME/SetUpFreeSurfer.csh ~setenv SUBJECTS_DIR freesurfer_tutorial/long-tutorial/ ~cd $SUBJECTS_DIR ~freeview -f OAS2_0001/surf/lh.pial:overlay=OAS2_0001/surf/lh.long.thickness-avg.fwhm15.mgh:overlay_threshold=0,3.5:overlay=OAS2_0001/surf/lh.long.thickness-stack.mgh:annot=OAS2_0001/label/lh.aparc.annot:annot_outline=1 --timecourse --colorscale Output: Option 'timecourse' not recognized. Run 'freeview -h' for more information. 1- If I remove the timecourse option together with another 3 the command executes correctly. 2- As output of the bugr command I get: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: wheezy/sid Kernel info: Linux 3.2.0-64-generic x86_64 Could anybody please telle me what's my problem? Thanks Fabio ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] neocortical gray matter
Hi Elisabetta, The cortex measure (surface-based) reported in the aseg.stats file would be best. See this site for details on various morphometry measures: https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats -Louis On Thu, 5 Jun 2014, Elisabetta del Re wrote: Dear Freesurfer team,what is the best measure for neocortical gray matter from the FS output? Thank you so much, best, Elisabetta ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Unpacking Problem
Hi Emad, In your recon-all command what does 03551671 correspond to? I don't see 03551671 in the scan.info file corresponding to any of the runs. I think you want to use 03557285. Also, run 26 apparently has 176 frames which shouldn't be the case. -Louis On Wed, 4 Jun 2014, Emad Ahmadi wrote: Hello, I’m trying to unpack and run recon-all on a set of MEMPRAGE images we’ve obtained in Lunder 6 scanner (Siemens Skyra), but recon-all is giving me errors. I’ve attached for the scan.info file (outputted by unpacksdcmdir), the unpack.config file that I used to unpack the MEMPRAGE images, and the recon-all.log file containing the error that recon-all command gives me. I’m running recon-all on in MEMPRAGE3 folder containing MEMPRAGE_IPAT3 RMS images. Please let me know if I have to provide any further info about this problem. Thank you very much for your help, Emad Emad Ahmadi, MD --- Postdoc Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Control point error
Hi Victor, This recon was originally processed with FS5.3, but when you reran it with autorecon2-cp -autorecon3 you used FS5.1. Could you try rerunning this case again with the same (314) control points using FS5.3 instead and see if the right frontal area of the wm surface is severely underestimated again? -Louis On Fri, 30 May 2014, Victor Kovac wrote: Hello, I ran recon-all on few subjects but noticed that much of the temporal lobes were excluded from segmentation, so I added control points to missed white matter voxels in this area, and subsequently ran recon-all -autorecon2-cp -autorecon3. The control points fixed much of the segmentation errors in the temporal lobes; however, errors in segmentation of other areas of the brain -- far from where I had placed control points -- were introduced. Attached are images of the same subject and same coronal slice, before and after running -autorecon2-cp -autorecon3, and, as you can see, much of the right superior frontal lobe is now missed. Is there any way to fix this, other than by simply adding more control points to the newly missed areas? One note is that the cores I am running these subjects on have a memory limit of 3.75 GB and I see that the recommended memory per subject is at least 4.0 GB. Could this be the problem? Also attached is the recon-all log. Thank you! Victor ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] FW: WG: WG: [Fwd: WG: missing temporal lobes], calculation CSF
Hi Kristina, Sorry, I misread your email slightly. I don't believe it is possible to get total CSF without some additional non-T1-weighted scans. The closest you can get is adding up all the ventricular volumes. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg26258.html http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg15514.html -Louis On Tue, 27 May 2014, Mayer Kristina wrote: Dear Louis, I got my information from the same page. As eTIV is a totally different algorithm, I am not sure if it is faisible to calculate total CSF from this parameters. As eTIV isn't representing voxels should I rather use the following: eTIV - BrainSegNotVentSurf = total intracranial CSF Or is there a more sophisticated method (sorry I did not find anything described on the freesurfer wiki about it)? Thanks in advance, Kristina -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Louis Nicholas Vinke Sent: Tuesday, May 27, 2014 3:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] FW: WG: WG: [Fwd: WG: missing temporal lobes], calculation CSF Hi Kristina, This page has the details I believe you are looking for: https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats -Louis On Tue, 27 May 2014, Mayer Kristina wrote: Oh, I see. So in the calculation of total GM in aseg.stats does it include the hippocampus, although it is not showing on the masks for surface of GM or PIAL? I also tried to calculate total intracranial CSF (ventricles + outer liquor spaces). Is following calculation correct: e TIV - BrainSegNotVent = total intracranial CSF These calculations are voxels based. I rather prefer a surface based calculation of total intracranial CSF. Is this faisible with freesurfer? Thanks a lot! Cheers, Kristina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Tuesday, May 27, 2014 2:24 PM To: Mayer Kristina Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: WG: [Freesurfer] WG: [Fwd: WG: missing temporal lobes] Hi Kristina can you please post to the list so others can answer? If you add control points to the temporal WM where you are missing gm it should recover most if not all of it. Hippocampus is not neocortical and isn't supposed to be included. The surfaces are somewhat arbitrary there, and excluded from all subsequent calculations (like total cortical area/volume) cheers Bruce On Tue, 27 May 2014, Mayer Kristina wrote: Dear Bruce How can I get the Hippocampus and the missing parts of GM of the temporal lobe into the PIAL (sufrace mask)? How can I convince freesurfer those parts are belonging to gray matter? Cheers, Kristina Von: Mayer Kristina Gesendet: Freitag, 23. Mai 2014 16:11 An: Freesurfer support list; freesurfer-boun...@nmr.mgh.harvard.edu Betreff: AW: [Freesurfer] WG: [Fwd: WG: missing temporal lobes] Von: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]quot; im Auftrag von quot;Bruce Fischl [fis...@nmr.mgh.harvard.edu] Gesendet: Freitag, 23. Mai 2014 14:52 An: Freesurfer support list Betreff: Re: [Freesurfer] WG: [Fwd: WG: missing temporal lobes] Hi Kristina don't add CPs to the gray matter - that will mess everything up! Bruce On Fri, 23 May 2014, Mayer Kristina wrote: Dear Bruce My dataset is very young (around 2 years of age), I suppose the contrast and size is just different from the default-template of freesurfer. Is there a way to exchange the template (I am thinking of a probabilistic map) without creating an own atlas first? Attached you find screenshots of my work and the recon-log of the same subject. I first run all recon-all steps. Then I added CP where WM was missing. I also added CP in GM region where lost of GM was missing (temporal lobe) to get the pial right. Then I tried to remove the WM which came out too much, for I placed CP in GM regions. Is there another way for it? Best, Kristina log 0001339: Fri May 16 08:50:00 CEST 2014 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer /media/n-NAS_MRI/freesurfer-subjects-dir/0001336 setenv SUBJECTS_DIR /media/n-NAS_MRI/freesurfer-subjects-dir -autorecon2-cp -autorecon3 -subjid 0001336 Linux cs2.kispi.int 3.13.5-103.fc19.x86_64 #1 SMP Mon Mar 3 18:46:36 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 maxlocks unlimited maxsignal514103 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited FSL_BIN=/usr/local/fsl/bin SSH_AGENT_PID=4883 XDG_SESSION_ID=35 HOSTNAME=cs2.kispi.int SELINUX_ROLE_REQUESTED= FS_OVERRIDE=0 GPG_AGENT_INFO=/home
Re: [Freesurfer] FW: WG: WG: [Fwd: WG: missing temporal lobes], calculation CSF
Hi Kristina, This page has the details I believe you are looking for: https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats -Louis On Tue, 27 May 2014, Mayer Kristina wrote: Oh, I see. So in the calculation of total GM in aseg.stats does it include the hippocampus, although it is not showing on the masks for surface of GM or PIAL? I also tried to calculate total intracranial CSF (ventricles + outer liquor spaces). Is following calculation correct: e TIV - BrainSegNotVent = total intracranial CSF These calculations are voxels based. I rather prefer a surface based calculation of total intracranial CSF. Is this faisible with freesurfer? Thanks a lot! Cheers, Kristina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Tuesday, May 27, 2014 2:24 PM To: Mayer Kristina Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: WG: [Freesurfer] WG: [Fwd: WG: missing temporal lobes] Hi Kristina can you please post to the list so others can answer? If you add control points to the temporal WM where you are missing gm it should recover most if not all of it. Hippocampus is not neocortical and isn't supposed to be included. The surfaces are somewhat arbitrary there, and excluded from all subsequent calculations (like total cortical area/volume) cheers Bruce On Tue, 27 May 2014, Mayer Kristina wrote: Dear Bruce How can I get the Hippocampus and the missing parts of GM of the temporal lobe into the PIAL (sufrace mask)? How can I convince freesurfer those parts are belonging to gray matter? Cheers, Kristina Von: Mayer Kristina Gesendet: Freitag, 23. Mai 2014 16:11 An: Freesurfer support list; freesurfer-boun...@nmr.mgh.harvard.edu Betreff: AW: [Freesurfer] WG: [Fwd: WG: missing temporal lobes] Von: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]quot; im Auftrag von quot;Bruce Fischl [fis...@nmr.mgh.harvard.edu] Gesendet: Freitag, 23. Mai 2014 14:52 An: Freesurfer support list Betreff: Re: [Freesurfer] WG: [Fwd: WG: missing temporal lobes] Hi Kristina don't add CPs to the gray matter - that will mess everything up! Bruce On Fri, 23 May 2014, Mayer Kristina wrote: Dear Bruce My dataset is very young (around 2 years of age), I suppose the contrast and size is just different from the default-template of freesurfer. Is there a way to exchange the template (I am thinking of a probabilistic map) without creating an own atlas first? Attached you find screenshots of my work and the recon-log of the same subject. I first run all recon-all steps. Then I added CP where WM was missing. I also added CP in GM region where lost of GM was missing (temporal lobe) to get the pial right. Then I tried to remove the WM which came out too much, for I placed CP in GM regions. Is there another way for it? Best, Kristina log 0001339: Fri May 16 08:50:00 CEST 2014 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer /media/n-NAS_MRI/freesurfer-subjects-dir/0001336 setenv SUBJECTS_DIR /media/n-NAS_MRI/freesurfer-subjects-dir -autorecon2-cp -autorecon3 -subjid 0001336 Linux cs2.kispi.int 3.13.5-103.fc19.x86_64 #1 SMP Mon Mar 3 18:46:36 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 maxlocks unlimited maxsignal514103 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited FSL_BIN=/usr/local/fsl/bin SSH_AGENT_PID=4883 XDG_SESSION_ID=35 HOSTNAME=cs2.kispi.int SELINUX_ROLE_REQUESTED= FS_OVERRIDE=0 GPG_AGENT_INFO=/home/maykr/.gnupg/S.gpg-agent:4883:1 GLADE_PIXMAP_PATH=: TERM=xterm-256color XDG_MENU_PREFIX=xfce- SHELL=/bin/bash HISTSIZE=1000 SSH_CLIENT=127.0.0.1 40762 22 FSLMULTIFILEQUIT=TRUE PERL5LIB=/media/n-NAS_MRI/Fontan/programs/ibeat/tools:/media/n-NAS_MRI/Fontan/programs/ibeat/tools:/media/n-NAS_MRI/Fontan/programs/ibeat/tools:/usr/local/freesurfer/mni/lib/perl5/5.8.5 SELINUX_USE_CURRENT_RANGE= WINDOWID=46782934 OS=Linux XAPPLRESDIR=/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/X11/app-defaults QT_GRAPHICSSYSTEM_CHECKED=1 http_proxy=http://proxy.uzh.ch:3128/ LOCAL_DIR=/usr/local/freesurfer/local USER=maykr
Re: [Freesurfer] mri_vol2vol memory error
Hi Ben, There should be a procsurffast flag called -volproj_lowmem which avoids this mri_vol2vol memory issue. -Louis On Wed, 21 May 2014, Douglas N Greve wrote: mri_vol2vol when used in this way does not manage memory very well. It resamples the time series into a 256^3 volume of floats. Even for a small number of time points, this becomes unmanagebly huge On 05/21/2014 06:06 PM, Ben Mooneyham wrote: Hello all, I am doing pre-processing for resting-state fMRI volumes, but I have encountered an error and am unsure of how to correct it: I have previously determined the nonlinear warping transformations from my subjects' anatomical (T1) space to the 2mm MNI template using ANTs. At the end of my pre-processing pipeline, I am trying to transform my subjects' functional volumes (206 TRs of 2sec) into this MNI space by 1) transforming the functional volumes into subject T1 space using mri_vol2vol, and 2) applying the nonlinear warp (from ANTs) to the volumes in subject-T1 space to ultimately have my subjects' functional data in MNI space. However, I am getting an error while running mri_vol2vol, where it cannot allocate region. I gather from looking around online that this is a memory issue, but I am not sure how to fix it. Thoughts? It is crucial that I be able to translate my functional data into common MNI space before performing second-level analyses... I do not encounter this issue when performing this transformation on functional connectivity maps (where I take an ROI defined in MNI space, transform it into T1, and then subject-EPI space, calculate the FC with the rest of the brain, and then invert the process by transforming back into T1, and finally MNI space). How can I get this to work with a larger file? Thank you in advance for your help, Ben Mooneyham -- Graduate Student UCSB - Department of Psychological Brain Sciences Building 429 Room 102 (210) 912-6076 bwmooney...@gmail.com mailto:bwmooney...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] change background color in tksurfer
Hi Rujing, If you load the surface up in freeview you can change the background color. -Louis On Wed, 14 May 2014, charujing123 wrote: Hi Bruce and Doug, Ok, I see. That's all right. All the best. Rujing Zha 2014-05-14 charujing123 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2014-05-14 20:22 主题：Re: [Freesurfer] change background color in tksurfer 收件人：Freesurfer support listfreesurfer@nmr.mgh.harvard.edu 抄送： Sorry Rujing, I don't think we ever implemented that (although we should) On Wed, 14 May 2014, charujing123 wrote: Hi FS experts and users I want to change the background color of tksurfer from black to white. However I cannot find the drop-down list. Is there anyone who can tell me to desolve this? Thanks. All the best. Rujing Zha 2014-05-14 charujing123 ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Coomand not found
Hi Francesca, Are you trying to run the tkmedit command in the same terminal window you have sourced freesurfer? You'll need to source freesurfer in any new terminal window you open before being able to run any freesurfer commands. It's possible to set it up so that freesurfer is sourced automatically when opening a new terminal or setting up an alias to make the process quicker. -Louis On Sat, 10 May 2014, Francesca Strappini wrote: Hi, I'm just starting out with freesurfer. I downloaded CentOS6_x86_64 and I have Ubuntu 12.04 LTS. I have set up the licence file and configured freesurfer: tcsh setenv FREESURFER_HOME /media/Shared_Data/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /media/Shared_Data/freesurfer FSFAST_HOME /media/Shared_Data/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /media/Shared_Data/freesurfer/subjects MNI_DIR /media/Shared_Data/freesurfer/mni When I try to run any type of command, like tkmedit bert orig.mgz, I get this error: command not found. Thanks for the help! Francesca ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Coomand not found
Ok, could you send the entire terminal output? Thanks. -Louis On Mon, 12 May 2014, Francesca Strappini wrote: Thanks Louis! Yes, I did run tkmedit from the same terminal window I have sourced freesurfer... Francesca 2014-05-12 16:57 GMT+03:00 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu: Hi Francesca, Are you trying to run the tkmedit command in the same terminal window you have sourced freesurfer? You'll need to source freesurfer in any new terminal window you open before being able to run any freesurfer commands. It's possible to set it up so that freesurfer is sourced automatically when opening a new terminal or setting up an alias to make the process quicker. -Louis On Sat, 10 May 2014, Francesca Strappini wrote: Hi, I'm just starting out with freesurfer. I downloaded CentOS6_x86_64 and I have Ubuntu 12.04 LTS. I have set up the licence file and configured freesurfer: tcsh setenv FREESURFER_HOME /media/Shared_Data/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /media/Shared_Data/freesurfer FSFAST_HOME /media/Shared_Data/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /media/Shared_Data/freesurfer/subjects MNI_DIR /media/Shared_Data/freesurfer/mni When I try to run any type of command, like tkmedit bert orig.mgz, I get this error: command not found. Thanks for the help! Francesca ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] installing freesurfer on mac
Hi Charmaine, Sounds like you just need to change the folder permissions for, /Applications/freesurfer/ before attempting to copy the .license file to that location. -Louis On Thu, 1 May 2014, Demanuele, Charmaine wrote: Hi, I am trying to install freesurfer on my mac, and I got a license key, which I need to save as .license file. However, the mac is not allowing me to do so. I tried saving the file in linux and importing to the mac but this failed too. I also tried saving it as freesurfer.license instead of just .license but I get the error: [Charmaines-MacBook-Pro:/Applications/freesurfer] Charm% tkmedit bert orig.mgz Couldn't create output file .xdebug_tkmedit-- ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. Any ideas? Thanks very much, Best, Charmaine --- Charmaine Demanuele, Ph.D. Psychiatric Neuroimaging Athinoula A. Martinos Center for Biomedical Imaging Harvard Medical School 149 13th Street Charlestown Navy Yard Charlestown, MA 02129 phone: +1617-724-3170 email: cha...@nmr.mgh.harvard.edu ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] wm and pial edits - what to correct and what not?
Hi Markus, You can try running mri_gcut with a slightly higher T value, default is 0.4. command would be something like (running from within subject's mri dir): mri_gcut -T 0.5 T1.mgz brainmask.gcuts.T-0.5.mgz Carefully inspect the output, overlaid as a heatmap on the T1 and/or previous brainmask.mgz. You might have to clone back in some brain voxels. -Louis On Fri, 11 Apr 2014, Markus Gschwind wrote: Dear Louis (and Bruce), So I have run recon-all -skullstrip -clean-bm -gcut -subjid subjid on my subjects where remaining pieces of dura after a normal recon-all got included into pial surface. I am having a look at the result before continuing with autorecon2 etc. Results are not yet satisfactory as there is still several centimeters of dura included in the brainmask, mostly on the convex part of central regions Is there a possibility to make graph-cut slightly more agressive? Thank you for help! Markus 2014-04-07 22:40 GMT+02:00 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu: Hi Markus, It will only skullstrip the T1 and generate a new brainmask.mgz. So you'll need to run autorecon2 and 3 afterwards. -Louis On Mon, 7 Apr 2014, Markus Gschwind wrote: Dear Louis! Thank you for the link. It says I should use recon-all -skullstrip -clean-bm -gcut -subjid subjid My question is if this command only skullstrips and then stops and I would have to resume with autorecon2 etc. or if it continues until the end and overwrites the whole processing (I'd like to know before I mess up with te subject and have a further 16 hours processing for nothing... ;-) Thanks! Markus 2014-04-07 20:01 GMT+02:00 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu: Hi Markus, Instructions for using gcut within recon-all can be found on this wiki page, near the bottom. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview -Louis On Mon, 7 Apr 2014, Bruce Fischl wrote: Hi Markus that looks pretty blurry and low contrast, although it's hard to tell without windowing it. Does the intensity normalization remove the contrast? If so, you can try making it less aggressive with the -gentle flag or playing with individual parameters (like -b). I can't remember the graph cuts stuff. Hopefully Nick or Zeke or someone will point you in the right direction Bruce On Mon, 7 Apr 2014, Markus Gschwind wrote: Dear Bruce, Thanks for your detailed answer! it's tough to tell for sure on just a single slice, particularly if it is the intensity normalized one that removes a lot of the contrast if it is (as you suspect) doing the wrong thing. What does the orig look like? We try pretty hard to avoid including deep, highly myelinated gray matter inside the white matter surface, but of course if the contrast is low enough we can fail. If you scroll backwards and forward a few slices does or look in a different orientation does it look different/better? Sometimes the surface is curving sharply and this kind of thing will show up on a single slice, but actually isn't a significant inaccuracy. Yes, when scrolling throug the slides it really appears
Re: [Freesurfer] wm and pial edits - what to correct and what not?
Good to hear. That was just a naming convention to keep track of how each version was generated. To continue, all you need to do is rename the good brainmask (generated with the modified gcuts command) to brainmask.mgz. -Louis On Fri, 11 Apr 2014, Markus Gschwind wrote: Thanks Louis! Great. It seems I need -T 0.65. That looks fine. Is it necessary - to name the modified brainmask.gcuts.T065.mgz? - and keep both brainmask.mgz and brainmask.gcuts.mgz in the mri folder? And then continue with recon-all autorecon2 autorecon3 -s subjectid Is that correct? Thank you so much! Markus 2014-04-11 17:23 GMT+02:00 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu: Hi Markus, You can try running mri_gcut with a slightly higher T value, default is 0.4. command would be something like (running from within subject's mri dir): mri_gcut -T 0.5 T1.mgz brainmask.gcuts.T-0.5.mgz Carefully inspect the output, overlaid as a heatmap on the T1 and/or previous brainmask.mgz. You might have to clone back in some brain voxels. -Louis On Fri, 11 Apr 2014, Markus Gschwind wrote: Dear Louis (and Bruce), So I have run recon-all -skullstrip -clean-bm -gcut -subjid subjid on my subjects where remaining pieces of dura after a normal recon-all got included into pial surface. I am having a look at the result before continuing with autorecon2 etc. Results are not yet satisfactory as there is still several centimeters of dura included in the brainmask, mostly on the convex part of central regions Is there a possibility to make graph-cut slightly more agressive? Thank you for help! Markus 2014-04-07 22:40 GMT+02:00 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu: Hi Markus, It will only skullstrip the T1 and generate a new brainmask.mgz. So you'll need to run autorecon2 and 3 afterwards. -Louis On Mon, 7 Apr 2014, Markus Gschwind wrote: Dear Louis! Thank you for the link. It says I should use recon-all -skullstrip -clean-bm -gcut -subjid subjid My question is if this command only skullstrips and then stops and I would have to resume with autorecon2 etc. or if it continues until the end and overwrites the whole processing (I'd like to know before I mess up with te subject and have a further 16 hours processing for nothing... ;-) Thanks! Markus 2014-04-07 20:01 GMT+02:00 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu: Hi Markus, Instructions for using gcut within recon-all can be found on this wiki page, near the bottom. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freevie w -Louis On Mon, 7 Apr 2014, Bruce Fischl wrote: Hi Markus that looks pretty blurry and low contrast, although it's hard to tell without windowing it. Does the intensity normalization remove the contrast? If so, you can try making it less aggressive with the -gentle flag or playing with individual parameters (like -b). I can't remember the graph cuts stuff. Hopefully Nick or Zeke or someone
Re: [Freesurfer] Large areas of white matter ignored, even with control points
Hi Andrea, Take a look at the ?h.orig.nofix surfaces. Does it look like the wm edits were picked up in those initial surfaces? Also, just check that the edits to the wm.mgz were 255 and that there are no major disconnects anywhere. -Louis On Fri, 4 Apr 2014, Andrea Grant wrote: I was able to quickly edit my WM.mgz file using the contour edit that Louis suggested. However, when I then re-run the recon-all with -autorecon2-wm and -autorecon3, it doesn't correct the problem. I'm attaching two figures (with and without the edited WM.mgz overlay). What are my next steps to correct the segmentation? Thanks, Andrea On Fri, Mar 7, 2014 at 3:25 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Andrea, You can use the contour tool in the voxel edit mode to quickly and roughly fill in wm. Use the tool with the wm.mgz selected in the volume layer list but set the brainmask (or T1) as the reference. Set brush value to 255, and then do crtl+alt+leftbutton while dragging the mouse to adjust the contour, and then crtl+leftclick to fill in selected regions. Note that the cerebellar white matter may be outlined by the contour as well, but if it doesn't connect with the cortical wm then it won't be filled in. -Louis ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Freesurfer QDEC Buckner Data
Hi Saurabh, Did the wget command fail for you? I just tried it and the download started without any issues. You can also just paste the ftp address into your browser and download it that way as well. -Louis On Mon, 7 Apr 2014, Saurabh Thakur wrote: Hello Freesurfer Expert, I am working on QDEC and looking forward to download buckner_data from link mentioned below: wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz Needing data asap. Please share alternative mirror link to download the buckner_data. cheers Saurabh Thakur, ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] wm and pial edits - what to correct and what not?
Hi Markus, Instructions for using gcut within recon-all can be found on this wiki page, near the bottom. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview -Louis On Mon, 7 Apr 2014, Bruce Fischl wrote: Hi Markus that looks pretty blurry and low contrast, although it's hard to tell without windowing it. Does the intensity normalization remove the contrast? If so, you can try making it less aggressive with the -gentle flag or playing with individual parameters (like -b). I can't remember the graph cuts stuff. Hopefully Nick or Zeke or someone will point you in the right direction Bruce On Mon, 7 Apr 2014, Markus Gschwind wrote: Dear Bruce, Thanks for your detailed answer! it's tough to tell for sure on just a single slice, particularly if it is the intensity normalized one that removes a lot of the contrast if it is (as you suspect) doing the wrong thing. What does the orig look like? We try pretty hard to avoid including deep, highly myelinated gray matter inside the white matter surface, but of course if the contrast is low enough we can fail. If you scroll backwards and forward a few slices does or look in a different orientation does it look different/better? Sometimes the surface is curving sharply and this kind of thing will show up on a single slice, but actually isn't a significant inaccuracy. Yes, when scrolling throug the slides it really appears consistent across several slides (actually the attached screenshots showed Freeview in coronal, sagittal and axial perspective of the same region). Here is the orig attached together with the wm, pial and white. So how should I treat it? As for the dura, that certainly looks like a problem for thickness estimates. Have you tried using the graph cuts skull stripping? That is more aggressive than mri_watershed. You can also play with the watershed parameters to try to get more dura removed. Finally, if you have a T2-space FLAIR scan we can use that to properly reposition the surfaces (or less ideally, a T2-space scan without a FLAIR inversion). No, unfortunately there are no other images at disposition. How would one go with the graph cuts ? I found mri_gcut [-110| -mult filename |-T value] in_filename out_filename, but how is it run within recon-all in order to repair (FS version 5.3)? Thank you so much! Markus 2014-04-07 14:47 GMT+02:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Markus it's tough to tell for sure on just a single slice, particularly if it is the intensity normalized one that removes a lot of the contrast if it is (as you suspect) doing the wrong thing. What does the orig look like? We try pretty hard to avoid including deep, highly myelinated gray matter inside the white matter surface, but of course if the contrast is low enough we can fail. If you scroll backwards and forward a few slices does or look in a different orientation does it look different/better? Sometimes the surface is curving sharply and this kind of thing will show up on a single slice, but actually isn't a significant inaccuracy. As for the dura, that certainly looks like a problem for thickness estimates. Have you tried using the graph cuts skull stripping? That is more aggressive than mri_watershed. You can also play with the watershed parameters to try to get more dura removed. Finally, if you have a T2-space FLAIR scan we can use that to properly reposition the surfaces (or less ideally, a T2-space scan without a FLAIR inversion). cheers Bruce On Mon, 7 Apr 2014, Markus Gschwind wrote: Dear all, I would like to show some very frequent and typical cases of segmentation problems in my bunch of data of normal subjects (after recon-all), of which I couldn't find a description in the wiki(http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWith Data/FreeviewEditingaRecon). I am therefore not sure if these types of error are serious and will affect later results like thickness, curvature, GWR, etc. Here are the examples (c.f. attached screenshots from Freeview) 1) In the primary sensory-motor cortex it frequently happens that the ?h.white line lies several mm within the wm border (c.f. yellow arrow), I did not observe this behavior in other places. Would I need to edit that? 2) Sometimes the ?h.pial line includes also dura or parts of the skull (green arrow). Is it necessary to edit that as well? 3) Another question concerns the yellow parts of the wm which sometimes are much larger than the ventricles and also include both caudate nuclei (not shown). Is this a
Re: [Freesurfer] QDEC tutorial data- problem in downloading
Hi Saurabh, Are you receiving any type of error messages? The Buckner tutorial data tar file is 11GB so it might be the case that the network you are on has some file size limits imposed. Try downloading this for instance, which is only 17.3MB but located in the same ftp directory as the Buckner data. If that works then you will need to contact your system administrator. ftp://surfer.nmr.mgh.harvard.edu/pub/data/bert.raw.tar.gz On Mon, 7 Apr 2014, Saurabh Thakur wrote: Hello Freesurfer , I am looking forward for alternative mirror link to download the QDEC data. i.e Buckner_data_tutorial_subj Since link provided is not working. I have tried many times. Thanks in advance, cheers Saurabh Thakur, ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] wm and pial edits - what to correct and what not?
Hi Markus, It will only skullstrip the T1 and generate a new brainmask.mgz. So you'll need to run autorecon2 and 3 afterwards. -Louis On Mon, 7 Apr 2014, Markus Gschwind wrote: Dear Louis! Thank you for the link. It says I should use recon-all -skullstrip -clean-bm -gcut -subjid subjid My question is if this command only skullstrips and then stops and I would have to resume with autorecon2 etc. or if it continues until the end and overwrites the whole processing (I'd like to know before I mess up with te subject and have a further 16 hours processing for nothing... ;-) Thanks! Markus 2014-04-07 20:01 GMT+02:00 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu: Hi Markus, Instructions for using gcut within recon-all can be found on this wiki page, near the bottom. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview -Louis On Mon, 7 Apr 2014, Bruce Fischl wrote: Hi Markus that looks pretty blurry and low contrast, although it's hard to tell without windowing it. Does the intensity normalization remove the contrast? If so, you can try making it less aggressive with the -gentle flag or playing with individual parameters (like -b). I can't remember the graph cuts stuff. Hopefully Nick or Zeke or someone will point you in the right direction Bruce On Mon, 7 Apr 2014, Markus Gschwind wrote: Dear Bruce, Thanks for your detailed answer! it's tough to tell for sure on just a single slice, particularly if it is the intensity normalized one that removes a lot of the contrast if it is (as you suspect) doing the wrong thing. What does the orig look like? We try pretty hard to avoid including deep, highly myelinated gray matter inside the white matter surface, but of course if the contrast is low enough we can fail. If you scroll backwards and forward a few slices does or look in a different orientation does it look different/better? Sometimes the surface is curving sharply and this kind of thing will show up on a single slice, but actually isn't a significant inaccuracy. Yes, when scrolling throug the slides it really appears consistent across several slides (actually the attached screenshots showed Freeview in coronal, sagittal and axial perspective of the same region). Here is the orig attached together with the wm, pial and white. So how should I treat it? As for the dura, that certainly looks like a problem for thickness estimates. Have you tried using the graph cuts skull stripping? That is more aggressive than mri_watershed. You can also play with the watershed parameters to try to get more dura removed. Finally, if you have a T2-space FLAIR scan we can use that to properly reposition the surfaces (or less ideally, a T2-space scan without a FLAIR inversion). No, unfortunately there are no other images at disposition. How would one go with the graph cuts ? I found mri_gcut [-110| -mult filename |-T value] in_filename out_filename, but how is it run within recon-all in order to repair (FS version 5.3)? Thank you so much! Markus 2014-04-07 14:47 GMT+02:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Markus it's tough to tell for sure on just a single slice, particularly if it is the intensity normalized one that removes a lot of the contrast if it is (as you suspect) doing the wrong thing. What does the orig look like? We try pretty hard to avoid including deep, highly myelinated gray matter inside the white matter surface, but of course if the contrast is low enough we can fail. If you scroll backwards and forward a few slices does or look in a different orientation does it look different/better? Sometimes the surface is curving sharply and this kind of thing will show up on a single slice, but actually isn't a significant inaccuracy
Re: [Freesurfer] missing Freesurfer wiki pages
Hi Gabor, Thanks, should be fixed now. Any of the links with the _tktools suffix can be replaced with _freeview to view an alternate version of the wiki page using freeview commands. -Louis On Tue, 1 Apr 2014, Gabor Perlaki wrote: Dear all, Most of the links on https://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction page do not work. If I clik for example on FsTutorial/SkullStripFix the following message will popup: This page does not exist yet. You can create a new empty page, or use one of the page templates. Is there a new page for the recommended workflow which works fine? Thanks, Gabor ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] mris_anatomical_stats aparc pial and aparcstats2table
Hi Andreia, If you remove the underscore from aparc_pial for the --parc flag in the aparcstats2table command, that should do the trick. -Louis On Wed, 26 Mar 2014, _andre...@sapo.pt wrote: Hello list, I'm trying to get aparc surface area from the pial surface in a table using aparcstats2table but I'm not being able to... I've already created the file aparc_pial.stats inside the stats dir running the following command line from the subjects's label dir: mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a ./rh.aparc.annot -c ./aparc.ctab subjectname rh pial And if I open the aparc_pial.stats file the surfaces are bigger then in aparc (white matter). But when I try to get the table using: aparcstats2table --hemi rh --subjects subjectname --parc aparc_pial --meas area -t rh_aparc_surface_pial.txt I get the message: Number of subjects : 1 Building the table.. ERROR: cannot find /home/user/visao/Freesurfer/subjectname/stats/rh.aparc_pial.stats Use --skip flag if you want to continue in such cases What's wrong? Thank you, Andreia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] thickness for subcortical structures
Hi Francesco, This wiki page has pretty good definitions for the morphometry stats. Let us know if you want to clarify anything though. https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats -Louis On Tue, 25 Mar 2014, Francesco Puccettone wrote: Hello, I've read that cortical thickness analyses are limited to the cortex and cannot be used to examine subcortical grey matter. But does subcortical grey matter refer to deep gray matter structures such as the hippocampus, the basal ganglia or the nucleus accumbens - all of which are still technically part of the cerebral cortex - or does it in fact refer to gray matter nuclei surrounded by white matter, for which it would not be possible to model a white a pial surface? Thank you! Francesco ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] bvals and bvecs for dt_recon
Attached are examples of the bvals.dat and bvecs.dat files extracted from siemens dicoms by dt_recon. This was for a 60 dir DTI scan w/ 10 b0s. On Thu, 13 Mar 2014, Chris Watson wrote: dcm2nii should give you bvecs and bvals If you just want to transpose the file, I wrote a script to do it (attached). On 03/13/2014 04:50 PM, Gennan Chen wrote: Anastasia, The thing not clear from me is the format for those files. I did not see an example anywhere in t he wiki or in the distribution. And I am downing tutorial data now. Hope it is there. BTW, do yo u have an example? I know how to get those from private dicom tags. Gen -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Thursday, March 13, 2014 1:37 PM To: Gennan Chen Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bvals and bvecs for dt_recon How is the format different? Is it in 3 rows instead of 3 columns? If so, it should be straightfo rward to convert it yourself from 3 rows to 3 columns. On Thu, 13 Mar 2014, Gennan Chen wrote: Hi! All, Is there an utility to extract bvals and bvecs from GE’s DTI dicom files into the format dt_recon can use? I try to run dt_recon as it is but it did not pick up those values. Those files are from ADNI. Gen __ __ This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator The information in this e-mail is intended only for the person to whom it is addressed. If you be lieve this e-mail was sent to you in error and the e-mail contains patient information, please co ntact 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. This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibite d. If you are not the intended recipient, please contact the sender by reply email and destroy al l copies of the original message. If you are the intended recipient, please be advised that the c ontent of this message is subject to access, review and disclosure by the sender's Email System A dministrator ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.586792 -0.376583 -0.716841 0.894195 0.022917 0.447091 0.729281 -0.410970 0.547041 -0.154251 0.964369 -0.214941 0.117136 0.773539 -0.622830 -0.407575 -0.414994 -0.813427 0.211330 0.753738 0.622269 0.095375 -0.969517 0.225700 -0.135450 -0.033490 -0.990218 -0.142125 -0.750521 -0.645383 -0.637009 0.746109 -0.193757 0.080563 0.971669 0.222192 0.106871 -0.021213 0.994047 0.298747 0.387214 0.872247 -0.207492 -0.803432 0.558072 0.331125 -0.040337 -0.942724 -0.805294 -0.589494 -0.063231 0.337278 -0.749774 -0.569282 0.592396 -0.761390 0.263348 -0.088979 -0.465650 0.880485 -0.527982 -0.430927 0.731803 -0.369111 -0.927082 0.065397 0.311914 0.926381 -0.211018 -0.684511 0.439336 -0.581746 -0.030114 -0.966623 -0.254425 -0.337568 0.744654 -0.575794 -0.574804 0.024806 -0.817915 0.271135 -0.747834 0.605996 -0.935185 0.185421 0.301743 0.889083 0.309665 -0.337104 -0.884343 0.033574 -0.465629 0.545045 0.586317 -0.599298 -0.350774 -0.016274 0.936319 0.416158 -0.900528 -0.125943
Re: [Freesurfer] Brain Segmentation blurred at the interhemisphere surface
Hi Kaiming, I can't say for certain looking at that one slice, but I'm pretty sure it's fine. What you can do is make the surfaces for one hemi a different color than the other hemi, then pan through in the sagittal view and you should see one set of surfaces go out as the other comes in. Also, we always recommend looking at suspected errors in multiple views. -Louis On Tue, 11 Mar 2014, Kaiming Yin wrote: Hi Louis, Thanks, so should this be amended or can be simply left there which may not influence the stats results and further comparison? Great thanks, Kaiming On Mon, Mar 10, 2014 at 8:01 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Kaiming, I'm almost certain you are right at the medial line and what you are seeing is the transition from one hemi to the other. Most likely the brain is slightly oblique and so the sagittal slice does not perfectly bisect the two hemispheres. -Louis On Mon, 10 Mar 2014, Kaiming Yin wrote: Hi FreeSurfer guys, Just want to ask a quick question. So I have been using freesurfer on the analyses on my brain- however I have noticed in certain parts, there hasn't been any segmentations. I have attached a picture, to show what I mean. Is there a reason for this? The blurry part kind of sweeps across the whole brain. Is there anything then, that I can do in freesurfer to still allow it to calculate the segmentation? Many thanks, Kaiming 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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Brain Segmentation blurred at the interhemisphere surface
Hi Kaiming, I'm almost certain you are right at the medial line and what you are seeing is the transition from one hemi to the other. Most likely the brain is slightly oblique and so the sagittal slice does not perfectly bisect the two hemispheres. -Louis On Mon, 10 Mar 2014, Kaiming Yin wrote: Hi FreeSurfer guys, Just want to ask a quick question. So I have been using freesurfer on the analyses on my brain- however I have noticed in certain parts, there hasn't been any segmentations. I have attached a picture, to show what I mean. Is there a reason for this? The blurry part kind of sweeps across the whole brain. Is there anything then, that I can do in freesurfer to still allow it to calculate the segmentation? Many thanks, Kaiming ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Large areas of white matter ignored, even with control points
Hi Andrea, You can use the contour tool in the voxel edit mode to quickly and roughly fill in wm. Use the tool with the wm.mgz selected in the volume layer list but set the brainmask (or T1) as the reference. Set brush value to 255, and then do crtl+alt+leftbutton while dragging the mouse to adjust the contour, and then crtl+leftclick to fill in selected regions. Note that the cerebellar white matter may be outlined by the contour as well, but if it doesn't connect with the cortical wm then it won't be filled in. -Louis On Thu, 6 Mar 2014, Andrea Grant wrote: Hello, I'm working with T1 weighted scans obtained at 7T and have a problem with a subject. I preprocess the images to deal with the B1 inhomogeneity (normalize to PD and mask noisy pixels), and have successfully segmented about 20 scans. I often need to use control points, but they normally work just as I expect. However, I have one subject where large areas of the brain are completely excluded from the segmentation (basically the entire occipital lobe). I added control points and re-ran, to no effect. I'm attaching a screenshot of the brainmask with surfaces, my control points, and the white matter mask. Clearly, the skull stripping wasn't very successful (I adjusted the watershed threshold manually, but at one value I got the current result and at a single integer lower I lost half the brain). I have successfully segmented other subjects with equally poor skull strips, though, so I don't believe this has any bearing on the current issue. Is editing the white matter mask the only way to fix this? If so, do I need to carefully fill in on every slice, or can I just brush in here and there to sort of goose the white matter into that region? I can do the slice by slice fix, but if there's a way to avoid the several hours it will take me, I would love to know! Thanks, Andrea - Andrea Grant Visual Neuroimaging Technologist Center for Magnetic Resonance Research, University of Minnesota 2021 6th St. SE, Minneapolis, MN 55455, 612-626-4948 gran0...@umn.edu umn.edu/~gran0260 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] tkmedit edit voxel tcl script
Hi Pfannmoe, I don't believe it is possible to edit a voxel via tcl scripts. If so the command would be listed on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditReference/TkMeditScripting -Louis On Wed, 5 Mar 2014, Joerg Pfannmoeller wrote: Hello, if I have selected a voxel in a volume with tkmedit with a tcl script, how can I set the voxel value to 0. Sincerely yours pfannmoe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] cannot sign white matter area by control point and white matter edit
Hi Rujing, You might try drawing in the wm thicker than it is already. Also, check there are no disconnects between the wm voxels in the wm.mgz. -Louis On Tue, 4 Mar 2014, charujing123 wrote: Hi all. In troubleshooting, I want to sign some area as white matter by control point and wm edit. However neither of them can work. Thanks. the picture can be got in the attachment. All the best. Rujing Zha 2014-03-04 ___ charujing123 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] How to clone from T1 to brainmask in freeview to amend a bad skull strip
Hi Emad, Which version of FS are you using? The freeview in the 5.3 release has the clone tool within the voxel edit mode, but it's not in 5.1 or earlier. It's represented by an icon with a blue and gray rectangle. Take a look at the 5th section on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewTools/VoxelEdit -Louis On Fri, 28 Feb 2014, Emad Ahmadi wrote: Hi! I want to know how to clone from T1.mgz to brainmask.mgz in freeview (to amend a skullstript that has removed too much). I couldn’t find the tool in freeview. Thank you very much, Emad Emad Ahmadi, MD --- Postdoc Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] {Filename?} Re: Re: recon-all CTABreadASCII error
It should be posted momentarily, sorry for the delay.
-Louis
On Thu, 13 Feb 2014, charujing123 wrote:
Hi Bruce,
I did try, but I am so sorry that size of the attachment is too big to send in
the
mail list.
All the best.
Rujing Zha
2014-02-13
___
charujing123
___
发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu
发送时间：2014-02-13 22:00
主题：Re: {Filename?} Re: Re: [Freesurfer] recon-all CTABreadASCII error
收件人：charujing123charujing...@163.com
抄送：
Hi Rujing
can you cc the list so that others can help?
thanks
Bruce
On Thu, 13 Feb 2014,
charujing123 wrote:
Warning: This message has had one or more attachments removed
(recon-all.cmd). Please read the NMR-MGH-Attachment-Warning.txt
attachment(s) for more information.
Hi Bruce,
Some output of recon-all can be got in the attachment.
Thanks Bruce.
Rujing Zha
2014-02-13
charujing123
发件人：charujing123charujing...@163.com
发送时间：2014-02-13 21:48
主题：Re: [Freesurfer] recon-all CTABreadASCII error
收件人：Bruce Fischlfis...@nmr.mgh.harvard.edu
抄送：freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu
Hi Bruce,
I ran this code succefully last year. But I cannot completely this command
in recent days as errors just above. There is nothing change in the server
during this time. According this ERROR information, I asked administrator to
delete some files in the /tmp folder and change the write access. But it was
still report similar error. And I ran this command as root, then it
terminated as a similar situation.
Thanks Bruce.
All the best.
Rujing Zha
2014-02-13
charujing123
发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu
发送时间：2014-02-13 21:33
主题：Re: [Freesurfer] recon-all CTABreadASCII error
收件人：charujing123charujing...@163.com
抄送：freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu
Hi Rujing
do you have write access to /tmp? Or is it full maybe?
Bruce
On Thu, 13 Feb 2014,
charujing123 wrote:
Dear FS experts,
It represents this message in the command window after ran recon-all
-autorecon-pial -s CON_EIU01 -no-isrunning:
Reading annotation reading colortable from annotation file...
colortable with 36 entries read originally/autofs/space/terrier_001/users
/nicks/freesurfer/average/colortable_desikan
_killiany.txt)
CTABwriteFileASCII(/tmp/mri_segstats.tmp.CON_EIU04.lh.64.ctab): could not
open for writing
Seg base 1000 Permission denied
CTABreadASCII(/tmp/mri_segstats.tmp.CON_EIU04.lh.64.ctab): could not open
file
No such file or directory
ERROR: reading /tmp/mri_segstats.tmp.CON_EIU04.lh.64.ctab
Linux centos2 2.6.18-308.20.1.el5xen #1 SMP Tue Nov 13 11:03:56 EST 2012
?? ? x86_64 x86_64 x86_64 GNU/Linux
recon-all -s CON_EIU04 exited with ERRORS at Thu Feb 13 14:01:12 CST 2014
Thanks.
All the best.
Rujing Zha
2014-02-13
_
___
charujing123
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il
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Re: [Freesurfer] reconstruction error
Hi Osei, Check out this wiki page for how to check the talairach transform and fix it if necessary. If everything looks decent then you can use the -notal-check flag to bypass this step in recon-all. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview -Louis On Thu, 13 Feb 2014, Boadu, Osei B wrote: Hello all, I am trying to do a reconstruction but I keep getting the following error (taken from recon-all.log): ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. Any help would be greatly appreciated and I attached the entire error log. Thank you! Osei The command line executed was: recon-all -all -subjid LCS13 Here is more pertinent information: FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 RedHat release: CentOS release 6.5 (Final) Kernel info: Linux 2.6.32-431.1.2.0.1.el6.x86_64 x86_64 NMR Center info (/space/freesurfer exists): machine: huygens SUBJECTS_DIR: /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI PWD: /homes/1/oboadu ssh huygens setenv SUBJECTS_DIR /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI cd /homes/1/oboadu ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Erasing, adding voxels in Freeview
Hi Alexander, If you are editing FS recons, then you should keep the eraser value set to 1 so that the edits can be detected by recon-all. -Louis On Mon, 10 Feb 2014, Ruopeng Wang wrote: Hi Alexander, Eraser value is used for erasing. Brush value is used for drawing. To erase, just hold shift key and press left mouse button. Best, Ruopeng On 02/10/2014 10:23 AM, Denker, Alexander (NIH/NIMH) [F] wrote: Hi all, This is probably a very elementary error in my use of Freeview, but I have been having trouble adding voxels to scans. I set the eraser value to 0, but when I draw, the voxel still shows up as a black box instead of grey. Am I not setting the right values or am I just in the wrong viewing mode? Thanks! Alexander ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] possible to render hippocampal subfield segmentations as 3D structures?
Hi Salil, You should be able to apply an isosurface to each subfield label in freeview. You can set the color for each isosurface as well, since the default is gray. You need to be in the 3D view in order to display isosurfaces. -Louis On Thu, 6 Feb 2014, Salil Soman wrote: Hi, I generated hippocampal subfield segmentations, can generate statistics, but was wondering if there was a way to visualized the subfield segmentations as a 3D structure? (e.g. like the figure in this paper: http://niacal.northwestern.edu/projects/17) Thank you for your consideration. Best wishes, -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] 3D thickness scale
Hi Jon, If it's the colorbar you are looking for then right-click on the viewing window, then Show Color Bar - inflated_thickness. There are some additional options under Configure Overlay located on the left sidebar. -Louis On Wed, 5 Feb 2014, Jonathan Holt wrote: Hi all, I’ve pulled up a 3D inflated thickness figure by loading the following into freeview lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 I’m wondering how the colors correspond to thickness and whether or not I can generate a scale to help interpret the figure. best, Jon ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Viewing color-map in freesurfer
Hi Rotem, Check out the -dti flag in freeview, pass it a vector and FA volume. You can display the colormap as vectors as well once everything is loaded up. Example command: freeview -dti V1.nii.gz FA.nii.gz -Louis On Mon, 27 Jan 2014, Rotem Saar wrote: Hi, We followed the instructions on this link: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion#Masking to perform diffusion analysis and wanted to ask if there is an option to view the color-map in addition to the FA and ADC maps ? We want to make sure that left-right tracts are red, anterior-posterior are green ect... is this possible ? Thanks Rotem Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev Beer-Sheva 84105 Israel ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] unable to download free surfer
Hi Peter, I think this is due to some maintenance the IT folks are doing on some of the ftp servers. Should be back up by late afternoon (EST). -Louis On Mon, 27 Jan 2014, Davis, Peter wrote: Hi, I am unable to download freesurfer. Is there a problem at the ftp? Thank you, Peter ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] FreeSurfer installation
Hi Neda, Have you read over the linux install directions in the link below? You will need to register and get a license file. After that you should look over the setup and config instructions. https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration -Louis On Wed, 22 Jan 2014, Neda Mohammadi wrote: Hi dear all, I want to use freesurfer for tractography by FSL. I downloaded freesurfer-linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz and I want to install it but I don't know how. Please help me. Thanks in advance, Neda ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] FreeSurfer installation
Hi Neda, Your terminal is probably setup to use the bash environment by default. If you type tcsh, then you'll be using C shell and that command should then work. I see that this is not on the install page, but on the setup/config page there is a note about it. There are also alternate commands to use for bash if you want on that page as well. -Louis On Wed, 22 Jan 2014, Neda Mohammadi wrote: Hi dear Louis, yes I read this link https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall but when I write this command setenv FREESURFER_HOME /usr/local/freesurfer I see this message: bash: setenv: command not found best, Neda On Wed, Jan 22, 2014 at 9:06 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Neda, Have you read over the linux install directions in the link below? You will need to register and get a license file. After that you should look over the setup and config instructions. https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration -Louis On Wed, 22 Jan 2014, Neda Mohammadi wrote: Hi dear all, I want to use freesurfer for tractography by FSL. I downloaded freesurfer-linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz and I want to install it but I don't know how. Please help me. Thanks in advance, Neda 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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Standalone Freeview?
Hi Jeni, Yes it's possible. You could download the most recent version of FS and then just source that version for when you want to use freeview, or copy the freeview.bin over to your current version. If you tell me the OS version you are running I'll send you the proper freeview.bin file. Just send me the output from this command (after sourcing FS): cat $FREESURFER_HOME/build-stamp.txt -Louis On Thu, 16 Jan 2014, Jeni Chen wrote: Hi! I'm wondering if the latest version of Freeview is available in standalone version. I'm currently using FreeSurfer v5.1's tktools for correcting the recon-all outputs, but would like to switch to Freeview. However the version that I have doesn't seem to have the Recon tools, and if I install the latest FS, I will have to rerun the preprocessing... So is it possible to install the latest Freeview separately? Thanks. Jeni Chen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Freeview question
Hi Alan, You can use mri_binarize to pull it out of the aseg.mgz. FYI: Once loaded into freeview you can also generate an isosurface for the hippocampus label in the 3D view. -Louis On Thu, 5 Dec 2013, Alan Francis wrote: Hi Bruce et al, Is it possible to load just the Hippocampal mask/ROI from the ASEG onto a brain in Freeview? thanks, Alan ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] R: Re: R: Re: Linear regression
If you don't have MATLAB you could try using Octave instead. On Wed, 4 Dec 2013, Douglas N Greve wrote: If you don't have matlab, then I don't know of one. The design matrix is in the glmdir folder (Xg.dat), so if SPSS or some other software can read that in, then the analysis will be the same. You can also run mri_glmfit on the mean thicknesses from your ROI. This will not produce a PCC, but you can at least check the p-values against a program that does produce a PCC doug On 12/04/2013 01:06 PM, std...@virgilio.it wrote: Dear Douglas, thank you very much for you kind reply. In the paper I have 3 groups (2 diseases and 1 controls). I have performed cortical thickness analysis among groups, individuating relevant difference in the posterior regions. Next, for one group, I have used qdec to individuate statistically significant regions where NPS test scores and thickness were correlated. 3 nuisance factors was also added to regressor. All results were corrected for multiple comparisons by using a pre-cached cluster-wise Monte-Carlo Simulation. qdec analysis results have individuated a composite region (superior parietal cortex and precuneus) where NPS correlated with thinning. Now, if I understand, I should extract the mean thickness from superior parietal cortex and precuneus and I should perform a linear regression (and partial correlation) with an other statistical program (SPSS for example). Is there a better way to perform a regression the most possible similar to qdec computation? Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 4-dic-2013 17.35 A: std...@virgilio.it, freesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] Linear regression On 12/02/2013 03:14 PM, std...@virgilio.it wrote: Tank you very much. A-Do you mean the partial correlation coeff (PCC) at each voxel averaged over region? Finally a linear regression is done between cortical thickness of a composite region and NPS. However the authors discuss every individual region as related to disease. So a table with partials correlations of individuals ROIs with NPS seems useful to support the discussion. What did you do in the paper? The reviewer mentions a composite region. Did you average the thickness over that region and then do the regression with NPS? B- I'd like to obtain the covariance matrix of the regression made between cortical thickness, group and covariates. How can I do it? I'm not sure what you mean. Would this be a different matrix for each vertex? I cite the referee: The authors must provide the covariance matrix of the regression made between cortical thickness, group and covariates as supplementary information in order to increase the value of the results. Sorry, I don't understand what the reviewer is asking for. doug I don't have Matlab for mri_glmfit_pcc matlab. Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 2-dic-2013 20.47 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Linear regression On 12/02/2013 02:22 PM, std...@virgilio.it wrote: Hi list, I have some questions, please. I performed linear regression by qdec to find the regions where the cortical thinning correlates with neuropsychological test (NPS), taking in account 3 nuisance factors. A- I individuated some posterior regions and now I'd like to build a table with partials correlations of individuals ROIs with NPS. How can I obtain the values for each region? Do you mean the partial correlation coeff (PCC) at each voxel averaged over region? You can get PCC maps using the mri_glmfit_pcc matlab command. You can then do the averaging over region using mri_segstats. B- I'd like to obtain the covariance matrix of the regression made between cortical thickness,group and covariates. How can I do it? I'm not sure what you mean. Would this be a different matrix for each vertex? C- Is there a specific reference for qdec? No, it is just a GLM so any GLM reference will do. Thank you very much, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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
Re: [Freesurfer] recon-all strip skull and neck by brain volume mask
Hi Rujing, If portions of gray matter have been removed, then that will need to be corrected. You can definitely remove skull/dura manually from the brainmask.mgz volume (see link below), but that can be time-consuming and may not be necessary. It's hard to know for sure if a brainmask.mgz is bad until you have generated the surfaces or have some experience with similar cases processed with Freesurfer. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview -Louis On Tue, 3 Dec 2013, Rujing Zha wrote: Dear Louis, Thanks for your helpful prompt in advance. I see. In my case, there is a not properly stripping, there is a not properly gray matter(there are a some skull considered as gray matter). Did you mean I can draw the segmentation without considering the skull stripping? And a bad brainmask.mgz will not influence the GM thickness analysis? Thanks in advance. All the best. 2013-12-03 Rujing Zha 发件人：Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu 发送时间：2013-12-03 03:58 主题：Re: [Freesurfer] recon-all strip skull and neck by brain volume mask 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing, Even if there is some skull/dura left after the skullstrip step in recon-all, it still may not negatively impact the surfaces. It might be worth running the remaining recon-all steps to see how the surfaces turn out. If you want to swap-in a better skullstripped volume into the recon-all stream then you just need to replace the brainmask.mgz and continue with autorecon2 and autorecon3. Keep in mind that the new brainmask.mgz volume still needs to be in the conformed anatomical space, so use the T1.mgz or brainmask.mgz to create the improved skullstrip volume which will replace the existing brainmask.mgz. -Louis On Mon, 2 Dec 2013, Rujing Zha wrote: Dear all, Part of subjects 3d images cannot be stripped skull and neck properly in ?? ? recon-all default. I have got the brain volume mask, how I can using the ?? ? existing proper mask to help strip skull in recon-all and next workflow? ?? ? Thanks.Any reply will be appreciated. All the best. 2013-12-02 _ ___ Rujing Zha ___ Freesurfer mailing list Freesurfer@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 i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] viewing slices dynamically by tkmedit
Hi Rujing, You can hold down the up and down keys to scroll through a volume in tkmedit, no need to keep clicking the slice buttons. -Louis On Tue, 3 Dec 2013, Rujing Zha wrote: Hi Louis, Thanks for your helpful suggestion. Maybe I just click the slice -/+ module if I want to view all the slices of one subject's volume in tkmedit. But I do not want to click the button continuously to view all the slices. I want to press a button/key once, then I can see all the slices one by one in a volume automatically; the automatically view will halt if I press a button/key again or other button/key. Thanks in advance. All the best. 2013-12-03 Rujing Zha 发件人：Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu 发送时间：2013-12-03 03:50 主题：Re: [Freesurfer] viewing slices dynamically by tkmedit 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing, You can use a tcl script to take several snapshots in tkmedit, then you could use the convert command (part of ImageMagick distro) or something similar to create an animated gif. With the convert command you ?? ? would use the -adjoin and -delay flags. You could use one of the tcl scripts from the QA tools scripts as a good start (e.g. snap_tkmedit.tcl). ?? ? You could also get multiple snapshots with freeview using command line flags and a shell script. -Louis On Sat, 30 Nov 2013, Rujing Zha wrote: Dear all, I want to see the slices as a shape of movie in tkmedit. Do anyone can te ll me how to do it? Thanks. All the best. 2013-11-30 _ ___ Rujing Zha The information in this e-mail is intended only for the person to whom it i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] talairach_mixed_with_skull.gca file missing in average directory of local version stable5_3_0
Hi Koene, It looks like Nick copied that volume over on 11/27. Thanks for pointing that out. -Louis On Tue, 26 Nov 2013, Koene Van Dijk wrote: Hi there, We've been using this local version of Freesurfer: /cluster/freesurfer/centos6_x86_64/stable5 And this file was relevant: /cluster/freesurfer/centos6_x86_64/stable5/average/talairach_mixed_with_skull.gca We want to switch to the newest version of Freesurfer at the beginning of a new study but we can't find that talairach_mixed_with_skull.gca file in the /cluster/freesurfer/centos6_x86_64/stable5_3_0 directory. Is it possible to also include the talairach_mixed_with_skull.gca file in: /cluster/freesurfer/centos6_x86_64/stable5_3_0/average/? Thanks, Koene ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] viewing slices dynamically by tkmedit
Hi Rujing, You can use a tcl script to take several snapshots in tkmedit, then you could use the convert command (part of ImageMagick distro) or something similar to create an animated gif. With the convert command you would use the -adjoin and -delay flags. You could use one of the tcl scripts from the QA tools scripts as a good start (e.g. snap_tkmedit.tcl). You could also get multiple snapshots with freeview using command line flags and a shell script. -Louis On Sat, 30 Nov 2013, Rujing Zha wrote: Dear all, I want to see the slices as a shape of movie in tkmedit. Do anyone can tell me how to do it? Thanks. All the best. 2013-11-30 Rujing Zha ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] recon-all strip skull and neck by brain volume mask
Hi Rujing, Even if there is some skull/dura left after the skullstrip step in recon-all, it still may not negatively impact the surfaces. It might be worth running the remaining recon-all steps to see how the surfaces turn out. If you want to swap-in a better skullstripped volume into the recon-all stream then you just need to replace the brainmask.mgz and continue with autorecon2 and autorecon3. Keep in mind that the new brainmask.mgz volume still needs to be in the conformed anatomical space, so use the T1.mgz or brainmask.mgz to create the improved skullstrip volume which will replace the existing brainmask.mgz. -Louis On Mon, 2 Dec 2013, Rujing Zha wrote: Dear all, Part of subjects 3d images cannot be stripped skull and neck properly in recon-all default. I have got the brain volume mask, how I can using the existing proper mask to help strip skull in recon-all and next workflow? Thanks.Any reply will be appreciated. All the best. 2013-12-02 Rujing Zha ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Freesurfer course troubleshooting presentation slides
Hi Janosch, The link on the course schedule page should point to the correct version now. http://surfer.nmr.mgh.harvard.edu/pub/docs/Nov2013/freesurfer.failure_modes.ppt -Louis On Wed, 27 Nov 2013, Janosch Linkersdörfer wrote: Hi, thank you very much for providing the lectures of the last Freesurfer course as videos! I am just watching them, and it seem that the .ppt file provided for the troubleshooting lecture does not match the slides used in the video. It would be great if you could provide the slides used in the video! Thanks, J ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] your mail
Hi Pietro, I think you should try redoing the control points from scratch, but with fewer control points and sparser placement. Currently you have 198 control points tightly packed in only a couple regions. Furthermore, there is one control point at 128, 128, 128 which is right in the thalamus which should not be there, maybe an accidental click? Take a look at the placement of the control points in the snapshots on this tutorial page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints_freeview If you compare the norm.mgz volumes before/after editing, you will notice the extreme hyper-intense wm (130+) in the temporal lobes after adding control points and rerunning. The norm.mgz is passed to mri_pretess to create the wm.mgz. You can see there is overlap between the hyper-intense voxels on the norm and the voxels not being included in the wm mask, which leads to major errors in the wm surface. -Louis On Fri, 15 Nov 2013, pietro de rossi wrote: Good morning Dr Vinke, did you have the chance to take a look at the subject I uploaded a few days ago? thanks again. Kind regards, Pietro -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 90280774 web: http://www.neuropsichiatrialab.com ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Re Freesurfer type
Hi Anna, Yes, search for 'build-stamp' in the recon-all.log. There's also the build-stamp.txt in the scripts dir, but the recon-all.log will tell you if different versions were run by looking at the build-stamp for each invocation in the log. -Louis On Fri, 15 Nov 2013, Anna Jonsson wrote: Dear list members, I was wondering where in the Freesurfer output the information on which freesurfer version has been used to process scans is located? eg recon-all.log? Thank you, Kind Wishes, Anna ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] request
Hi Pietro, Yes, the filedrop would be fine or you can upload using ftp. https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange -Louis On Mon, 11 Nov 2013, pietro de rossi wrote: Dear Freesurfers, I am working on the segmentation of mdeft structural images (Siemens Allegra 3T-acquired) of schizophrenia patients. I had troubles editing temporal regions (especially superior temporal gyrus) by adding control points. After re-running the image in the pipeline (autorecon2-cp) the problem on the STG was solved but the pial and white matter boundaries in the lower temporal regions were completely messed up. Could anyone take a look and tell me if the image is editable? I would like to upload the pre and post editing folders so that an expert can give me an opinion. Is this the correct link to upload files and folders? https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Sorry to bother you all but this would be extremely helpful given that I experienced a similar problem in several subjects of this sample. Thanks in advance, Pietro -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 90280774 web: http://www.neuropsichiatrialab.com ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] request
Yes, just tar/zip it up first. On Mon, 11 Nov 2013, pietro de rossi wrote: ok. is it possible to upload the whole subject folder? 2013/11/11 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu Hi Pietro, Yes, the filedrop would be fine or you can upload using ftp. https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange -Louis On Mon, 11 Nov 2013, pietro de rossi wrote: Dear Freesurfers, I am working on the segmentation of mdeft structural images (Siemens Allegra 3T-acquired) of schizophrenia patients. I had troubles editing temporal regions (especially superior temporal gyrus) by adding control points. After re-running the image in the pipeline (autorecon2-cp) the problem on the STG was solved but the pial and white matter boundaries in the lower temporal regions were completely messed up. Could anyone take a look and tell me if the image is editable? I would like to upload the pre and post editing folders so that an expert can give me an opinion. Is this the correct link to upload files and folders? https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Sorry to bother you all but this would be extremely helpful given that I experienced a similar problem in several subjects of this sample. Thanks in advance, Pietro -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 90280774 web: http://www.neuropsichiatrialab.com 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. -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 90280774 web: http://www.neuropsichiatrialab.com ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] saving in GIFTI .func.gii format
Hi Shahin, You can use mri_convert to convert the mri_glmfit output to GIFTI (.gii). -Louis On Fri, 8 Nov 2013, SHAHIN NASR wrote: Hi Surfers I have done a surface-based group-averaged mapping and now I need to save the results of the mri_glmfit (sig.nii) command in GIFTI .func.gii format. Does mri_glmfit support this output format? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Segmentation question
Hi Rashmi, This page has the definition you are looking for (FS v5.3). https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats -Louis On Thu, 7 Nov 2013, Rashmi Singh wrote: FreeSurfer experts, May you please educate me how the supra tentorial volume (STV) measured by FreeSurfer and which date does it take as input file to calculate this variable. Thanks, Rashmi ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Segmentation question
Hi Rashmi, Several of the morphometry stats were changed between 5.1 and 5.3. I don't remember the specifics, but Doug or someone else on the list may know. Alternatively, you could use the mri_segstats from 5.3 to calculate the morphometry stats for your 5.1 data. -Louis On Thu, 7 Nov 2013, Rashmi Singh wrote: I am using version V5.1.0 is it different for that or the information is the same irrespective of the version I use. Rashmi On 11/7/13 1:57 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Rashmi, This page has the definition you are looking for (FS v5.3). https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats -Louis On Thu, 7 Nov 2013, Rashmi Singh wrote: FreeSurfer experts, May you please educate me how the supra tentorial volume (STV) measured by FreeSurfer and which date does it take as input file to calculate this variable. Thanks, Rashmi 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Segmentation question
Here is the recon-all table for 5.1, see the segstats step. You can also search for that flag in the recon-all script and see what input/flags are passed to mri_segstats. https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.1 On Thu, 7 Nov 2013, Rashmi Singh wrote: Can you tell me what is the input file that free surfer used to calculate STV. I am not sure the webpage below gives that information. Thanks, Rashmi On 11/7/13 1:57 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Rashmi, This page has the definition you are looking for (FS v5.3). https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats -Louis On Thu, 7 Nov 2013, Rashmi Singh wrote: FreeSurfer experts, May you please educate me how the supra tentorial volume (STV) measured by FreeSurfer and which date does it take as input file to calculate this variable. Thanks, Rashmi 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] MRISread error
Hi Anita, I don't believe you have the complete path set to your SUBJECTS_DIR environmental variable, unless Desktop is in your root dir which I doubt is the case. Easy way to set the variable: cd /path/to/tutorial/data/ setenv SUBJECTS_DIR $PWD Also, check you have fsaverage symlinked to the SUBJECTS_DIR cd $SUBJECTS_DIR ln -s /usr/local/freesurfer/subjects/fsaverage . That should do the trick. -Louis On Tue, 5 Nov 2013, Anita van Loenhoud wrote: Hi everyone, I run into an error when I try to do the tutorial on ROI group analysis. I downloaded the tutorial set, but did not put it into FREESURFER_HOME/subjects, because my computer doesn't allow it. I made my own folder and copied everything in there. The error arises when I try to map a label from the fsaverage subject to a target subject: mri_label2label \ --srcsubject fsaverage \ --srclabel fsaverage/label/lh.BA45.label \ --trgsubject 004 \ --trglabel 004/label/lh.BA45.label \ --hemi lh \ --regmethod surface srclabel = fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = 004 trglabel = 004/label/lh.BA45.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR Desktop/anita-vumc/anitapddatabase-freesurfer/buckner_data/tutorial_subjs/ group_analysis_tutorial FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration Desktop/anita-vumc/anitapddatabase-freesurfer/buckner_data/tutorial_subjs/ group_analysis_tutorial/fsaverage/surf/lh.sphere.reg MRISread(Desktop/anita-vumc/anitapddatabase-freesurfer/buckner_data/tutoria l_subjs/group_analysis_tutorial/fsaverage/surf/lh.sphere.reg): could not open file No such file or directory ERROR: could not readDesktop/anita-vumc/anitapddatabase-freesurfer/buckner_data/tutorial_subjs/g roup_analysis_tutorial/fsaverage/surf/lh.sphere.reg In related posts I read that it might have to do with the creation of symbolic links. I made sure that in my SUBJECTS_DIR, fsaverage is a symbolic link to my FREESURFER_HOME/subjects directory, in which surf/lh.sphere.reg etc are stored. What am I doing wrong? Does it still have to do with the fact that I put the tutorial data in another folder? Hope you can help me, Thanks in advance, Anita ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] mri_segment WM/GM limits
Hi Jon, You can use the -clean flag, or you can just delete all the directories in the subject's recon directory except the mri folder, and then delete everything in the mri folder leaving the orig folder which contains the 001.mgz which is equivalent to the nifiti volume(s) initially passed to recon-all. -Louis On Tue, 5 Nov 2013, Jonathan Holt wrote: Also, quick question . . . How exactly do you run a recon from scratch without nifti images? I’d always delete the directory and restart with mri_convert -i … Jon On Nov 5, 2013, at 10:40 AM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Jon, I see the area you are talking about. I'm rerunning the recon from scratch to start with a clean copy since the case you sent has been rerun multiple times and there are a bunch of control points. The fact that the rh.orig.nofix looks good makes me optimistic that this can be fixed. I'll get back to you soon. -Louis On Mon, 4 Nov 2013, Louis Nicholas Vinke wrote: Got it, I'll take a look. On Mon, 4 Nov 2013, Jonathan Holt wrote: OK, been uploaded as JONbrain.tar Please let me know! On Nov 4, 2013, at 1:15 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jon maybe you should upload your data and we'll take a look cheers Bruce On Mon, 4 Nov 2013, Jonathan Holt wrote: Bruce, If I understand you correctly, you?re saying I should tweak my expert options? Should I further change the limits, how so? You previously advised that I not adjust the -p threshold, is this still the case? Basically, I?m still confused after your response. Sorry to bother, Jon On Nov 4, 2013, at 12:52 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jon this is almost certainly due to a topological defect. Improving the segmentation quality can frequently reduce the # of defects and get rid of big ones, so if you find that the wm segmentation isn't as visually accurate as is usually the case, using expert opts to improve its quality may also get rid of the problem you are seeing cheers Bruce On Mon, 4 Nov 2013, Jonathan Holt wrote: Hey Louis, thanks for your response. It?s actually a bit different, in my case an entire sulcus, including the empty space within it has been segmented and surfaced as white matter. I?m trying to reduce the WM surface such that the empty space is not included. I?ve tried removing segmentation manually and running recon-all -autorecon2-noaseg -subjid SUBJID that doesn?t work, the empty space is simply resegmented and the surface doesn?t change.. I should note that this has worked for me in the past on some brains. Since there are no WM voxels to remove I didn?t bother with removing any of them. I ran recon-all -autorecon2 -autorecon3 -expert expert.opts -s subjID with mri_segment -wlo/-ghi/-whi all reduced by 10 and that hasn?t worked? I?m open for ideas. I should also note that this problem is not an issue in rh.orig.nofix (sorry about duplicate email, Louis) On Nov 4, 2013, at 11:30 AM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Jon, The limit numbers correspond to voxel intensities in the brainmask.mgz. I believe you will want a lower number for the -wlo/-wm_low flag to make the wm surf extend further out, assuming that the wm voxels that are not being captured by the surface is hypo-intense ( 110). -Louis On Thu, 31 Oct 2013, Jonathan Holt wrote: HI experts, I?m wondering how these limits work, and whether the limit numbers indicate voxel intensity. If I wanted WM to be segmented more aggressively would I plug in a higher number or a lower number? Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https
Re: [Freesurfer] mri_segment WM/GM limits
Hi Jon, The limit numbers correspond to voxel intensities in the brainmask.mgz. I believe you will want a lower number for the -wlo/-wm_low flag to make the wm surf extend further out, assuming that the wm voxels that are not being captured by the surface is hypo-intense ( 110). -Louis On Thu, 31 Oct 2013, Jonathan Holt wrote: HI experts, I’m wondering how these limits work, and whether the limit numbers indicate voxel intensity. If I wanted WM to be segmented more aggressively would I plug in a higher number or a lower number? Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] mri_segment WM/GM limits
Got it, I'll take a look. On Mon, 4 Nov 2013, Jonathan Holt wrote: OK, been uploaded as JONbrain.tar Please let me know! On Nov 4, 2013, at 1:15 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jon maybe you should upload your data and we'll take a look cheers Bruce On Mon, 4 Nov 2013, Jonathan Holt wrote: Bruce, If I understand you correctly, you?re saying I should tweak my expert options? Should I further change the limits, how so? You previously advised that I not adjust the -p threshold, is this still the case? Basically, I?m still confused after your response. Sorry to bother, Jon On Nov 4, 2013, at 12:52 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jon this is almost certainly due to a topological defect. Improving the segmentation quality can frequently reduce the # of defects and get rid of big ones, so if you find that the wm segmentation isn't as visually accurate as is usually the case, using expert opts to improve its quality may also get rid of the problem you are seeing cheers Bruce On Mon, 4 Nov 2013, Jonathan Holt wrote: Hey Louis, thanks for your response. It?s actually a bit different, in my case an entire sulcus, including the empty space within it has been segmented and surfaced as white matter. I?m trying to reduce the WM surface such that the empty space is not included. I?ve tried removing segmentation manually and running recon-all -autorecon2-noaseg -subjid SUBJID that doesn?t work, the empty space is simply resegmented and the surface doesn?t change.. I should note that this has worked for me in the past on some brains. Since there are no WM voxels to remove I didn?t bother with removing any of them. I ran recon-all -autorecon2 -autorecon3 -expert expert.opts -s subjID with mri_segment -wlo/-ghi/-whi all reduced by 10 and that hasn?t worked? I?m open for ideas. I should also note that this problem is not an issue in rh.orig.nofix (sorry about duplicate email, Louis) On Nov 4, 2013, at 11:30 AM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Jon, The limit numbers correspond to voxel intensities in the brainmask.mgz. I believe you will want a lower number for the -wlo/-wm_low flag to make the wm surf extend further out, assuming that the wm voxels that are not being captured by the surface is hypo-intense ( 110). -Louis On Thu, 31 Oct 2013, Jonathan Holt wrote: HI experts, I?m wondering how these limits work, and whether the limit numbers indicate voxel intensity. If I wanted WM to be segmented more aggressively would I plug in a higher number or a lower number? Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] problem with freesurfer installation/tkmedit
Hi Elissa, The invalid drawable terminal output you can ignore when running Freeview. Presumably bert is not located in /Applications/freesurfer/elissa_thesis/, so that's why the bert commands are failing. Not the same subjects directory that ABU is in. To fix the tkmedit library error it looks like you just need to install xquartz on your mac. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26311.html The recon-all.log for the 8.5hr recon looks fine. Was it processed locally and does your mac have a solid-state drive by chance? -Louis On Tue, 22 Oct 2013, Elissa McIntosh wrote: Hi, I think there is a problem with my freesurfer installation (newest version 5.3). First, when trying this freeview command (see below) I found on the “Testing your freesurfer installation” page using my own data, freesurfer opened, but I am concerned about the “invalid drawable” lines. The message happened when I ran this command on the bert data. [CoS-Psychology-Murphy-iMac-QAD:/Applications/freesurfer] cmurphy% freeview -v $SUBJECTS_DIR/ABU/mri/norm.mgz -v $SUBJECTS_DIR/ABU/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/ABU/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/ABU/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/ABU/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red 2013-10-22 12:47:02.811 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.812 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.826 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.826 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.839 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.840 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.853 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.853 Freeview[4214:703] invalid drawable reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) MRISread(/Applications/freesurfer/elissa_thesis/bert/surf/rh.pial): could not open file No such file or directory MRISread failed MRISread(/Applications/freesurfer/elissa_thesis/bert/surf/rh.pial): could not open file rfer/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) CTABisEntryValid: index -1 was OOB No such file or directory CTABisEntryValid: index -1 was OOB No such file or directory CTABisEntryValid: index -1 was OOB iginally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) CTABisEntryValid: index -1 was OOB No such file or directory CTABisEntryValid: index -1 was OOB No such file or directory CTABisEntryValid: index -1 was OOB No such file or directory CTABisEntryValid: index -1 was OOB No such file or directory CTABisEntryValid: index -1 was OOB iginally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Second, my next issue is that I am unable to use tkmedit to view my data. See command below and error message. [CoS-Psychology-Murphy-iMac-QAD:/Applications/freesurfer] cmurphy% tkmedit ABU orig.mgz dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer/tktools/tkmedit.bin Reason: image not found Trace/BPT trap I've tried other tkmedit commands and have gotten same error messages. I tried commands on bert data but got same errors. Third, I'd like to know if it is normal that a recon all could only take between 8-9 hours. I have attached the recon-all.log for the subject I am trying to view. Here is some additional information about my mac incase you see any glaring system inadequacies. Processor 2.5 GHz Intel Core i5 Memory 4 GB 1333 MHz DDR3 Graphics AMD Radeon HD 6750M 512 MB Software Mac OS X Lion 10.7.5 (11G63) Thank you, Elissa ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Tcsh-error with Freesurfer
Hi Philippe, See link below regarding the error you are getting, although recon-all is probably failing because you need to pass not only the path but one dicom file which is part of the T1-weighted scan. If you run the command below in the directory where you copied the dicom files, you will get an unpack.log as output listing each run and the first dicom in each series. Pick out the run you want to process in Freesurfer and include the associated dicom file at the end of the argument passed with the -i flag. unpacksdcmdir -scanonly scan.log -src . -targ . http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28978.html On Mon, 21 Oct 2013, Philippe Blaes wrote: Dear Sir / madam, I'm a last year student of Medical Imaging (from Hoge school Universiteit Brussel, HUB). In January i'm defending my thesis. My subject is MRI and Alzheimer's disease. With volumetry I want to show that the Hippocampi have a smaller volume then normal patients. I used the program: SPM, VBM and IBASPM previous year, but I got weird results from those software. My supervisors said that it's probably the best to use a new software, so i'm trying to use Freesurfer. I'm not used to programming with Linux (Xbuntu), so it's a bit difficult for me personally. Also the physicist (who i colaborate with) isn't used to programming. This is my problem: When i open Virtualbox (installed with freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full) I go to file-system - usr - local - freesurfer - subjects (the map where also the subjectBert is in it). In the subject-folder is paste a folder with only T1-Dicom images. After i copied pasted the DICOM-files in the subjects folder, i go to the terminal. There I type: tcsh to setup freesurfer (I read it on the Freesurfer wiki site). After that I type: recon-all -s new folder where the new made files are putted in \ -i $SUBJECTS_DIR/name of the folder where my DICOM-files are in (here i made an archive of the DICOM-files, extented with .mgz) \ -autorecon1 When i hit Enter, i get a message that says: tcsh v6.17.06 has an exit code bug! Please update tcsh! There is also a new folder created, with some subfolders (BEM, label, scripts , MRI ,etc.). But there is nothing to see in those folders. My question is how can I update tcsh so I can do the recon-all procedure? Hopefully you can help me, Thank you in advance, Kind regards, Philippe Blaes (3rd year Medical Imaging) ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Viewing auxiliary and main volumes simultaneously
Hi Jon, You can do this with using the -c flag followed by the path to the control.dat file, presumably in the tmp folder of the subject's recon folder. FYI: under the help menu in Freeview is a quick reference guide for shortcut keys and common actions. Also, type 'freeview -help' in a terminal to see more commandline options for freeview. -Louis On Tue, 24 Sep 2013, Douglas N Greve wrote: I don't know. Maybe one of our RAs could chime in. Ruopeng is away today, but he might be able to answer when he gets back. doug On 09/24/2013 03:49 PM, Jon Holt wrote: Doug, I sent another mail but I never saw it pop up. Can I load Control points in freeview from the command line? On Sep 24, 2013, at 3:40 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: not from within tkmedit, but you can open two instances of it doug On 09/24/2013 11:58 AM, Jonathan Holt wrote: Is there any way to accomplish this? Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Editing WM
Hi Francesco, Could you maybe send a snapshot of the brainmask and wm volumes where you are seeing this? If you deleted any voxels on the wm mask then they should be a value of 1. You might want to look at the ?h.orig.nofix surfaces to see if that area in question looks better (or at least different). Ultimately the position of the wm surface is what is important, not the presence or absence of wm voxels (in the wm.mgz) which basically just initialize the wm surfaces. -Louis On Mon, 9 Sep 2013, Francesco Siciliano wrote: Hi, I've noticed that occasionally when I manually edit recons, the white matter surface will be drawn to include a portion of the volume where no white matter pixels are present. Therefore, when I go to correct the incorrectly drawn surface, there are no pixels to delete under the white matter mask. It is almost as if I have deleted the pixels already yet I have not and the white matter surface is still drawn to include an area where there are no white matter pixels. Why could this be happening? Does it matter as long as there are no pixels in the incorrect area? Thank you, Francesco Francesco Siciliano, B.A. Research Assistant Department of Child and Adolescent Psychiatry The New York State Psychiatric Institute Columbia University 1051 Riverside Drive, Unit 74 New York, NY 10032 (212) 543-6155 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Recon checker - actual file order disagrees with common file order
Hi Sinead, In short, it is most likely a bug. I think the current version of the QA tools scripts expects a 5.1 recon-all stream, so the output order of files being slightly different in 5.2/5.3 causes this error/warning to appear. In the future you should just run QA tools with the -snaps-only flag. -Louis On Wed, 4 Sep 2013, Sinead Kelly wrote: Dear all, I have preprocessed my data using Freesurfer v5.2. I have checked the the recon-all.log for each subject to make sure that the process completed without error and that all the appropriate files were created. I have also visually inspected each image. However, when I run recon checker (from freesurfer QA tools) I receive the following error for all of my subjects: 'actual file order disagrees with common file order'. Is this a bug or do I need to re-run the preprocessing again from scratch? If I need to re-run, is there a way to ensure that this won't happen again? Kind regards, Sinead -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Mask from cortical parcellation
Hi Stefano, Take a look at the lobe mapping section on this wiki page. Example commands near the end. https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation -Louis On Wed, 4 Sep 2013, std...@virgilio.it wrote: Hi list, I need to create a mask of frontal, parietal, temporal and occipital lobes in a subject by using cortical parcellation output. Is it possible? Eventually, how can I transform these masks file to mii.gz (to import them in FSL analysis). Thank you very much. Regards, Stefano ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] pial surface editing
Hi, We figured out was the problem was. Just so others on the list are aware, when deleting voxels from the brainmask.mgz or brainmask.finalsurfs.manedit.mgz volumes in Freeview, you should verify that the deleted voxels have a value of 1, not 0. The 5.3 version of Freeview has a Recon Editing checkbox in the voxel edit window which makes the erasing function (shift + click) set voxels to 1 instead of 0 by default. Alternatively, you can set the brush value to 1 and just paint in the deleted voxels. You will have to do this if you are using an older version of Freeview. -Louis On Wed, 28 Aug 2013, Harms, Michael wrote: If you're following the instructions of the tutorial, then I don't know why your edits to brain.finalsurfs.manedit.mgz wouldn't be reflected in the pial surface. Perhaps one of the FS developers will have a thought as to what is going wrong. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Francesco Siciliano sici...@nyspi.columbia.edu Date: Wednesday, August 28, 2013 12:36 PM To: Harms, Michael mha...@wustl.edu Subject: RE: [Freesurfer] pial surface editing My main issue is that the edits I make to brain.finalsurfs.manedit.mgz are not being incorporated into the reconfiguration of the pial surface. What I mean to say is that when I load the pial surface onto the brainmask, the changes that I made to brain.finalsurfs.manedit.mgz, where the pial surface incorrectly extended into the cerebellum, have not been taken into account. The countour of the pial surface that borders that cerebellum has not been altered. Do you have any idea why this may be occurring? -Francesco Francesco Siciliano, B.A. Research Assistant Department of Child and Adolescent Psychiatry The New York State Psychiatric Institute Columbia University 1051 Riverside Drive, Unit 74 New York, NY 10032 (212) 543-6155 From: Harms, Michael [mha...@wustl.edu] Sent: Wednesday, August 28, 2013 12:19 PM To: Francesco Siciliano; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial surface editing Are you saying that edits to brainmask.mgz and brain.finalsurfs.manedit.mgz are not showing up as affecting the actual pial surfaces themselves? I would focus on whether the pial surfaces are fixed, not whether edits to brain.finalsurfs.manedit.mgz are back-propagated to brainmask.mgz. (I suspect they are not). cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Francesco Siciliano sici...@nyspi.columbia.edu Date: Wednesday, August 28, 2013 11:01 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] pial surface editing Hello, I am having a few issues with editing the pial surface in freeview. It appears as though the edits I make to the brainmask are not being taken into account when I re-run recon-all. I work on a MacBook Pro and have been using shift+click to delete voxels at a brush value of 1 and then saving the brainmask.mgz back into the mri folder. When making edits to the brainmask I have the brainmask highlighted. Upon clicking save, the mri folder contains both brainmask.mgz and brainmask.mgz~ (The version with a ~ seems to indicate the older version of the file based on modification time). Additionally, the edits that I make to brain.finalsurfs.manedit.mgz for pial surface that has extended into the cerebellum seems to not be taken into account when I re-run recon-all. I have been making a copy of brain.finalsurfs.mgz, pasting it into the mri folder, and renaming it brain.finalsurfs.manedit.mgz. I then load this volume and make edits to it according to the same specifications as the brainmask.mgz. Shouldn't I be able to see changes made to the pial surface in the brainmask.mgz from edits I make to the brain.finalsurfs.manedit.mgz after running recon-all? Neither the brainmask.mgz nor the brain.finalsurfs.mgz take into account the edits I've made on brain.finalsurfs.manedit.mgz. I'm not sure if I'm deleting voxels incorrectly or saving incorrectly. I've tried to troubleshoot several times and keep encountering similar issues. The version of FreeSurfer that I am working from is: freesurfer-i686-apple-darwin9.8.0-stable5-20110525 My editing interface looks slightly different from the current version explained on the freesurfer wiki. I do not have an option to select recon-editing. Adding control points, however, has
Re: [Freesurfer] make the annotation more transparent in freeview?
Hi Daniel, With the volume highlighted in the side bar you should have an opacity slide bar which you can move to adjust the transparency of the volume. -Louis On Fri, 2 Aug 2013, Yang, Daniel wrote: Hi FreeSurer Expert, I am wondering if there is a way that the annotation can be made somewhat transparent in freeview so that I can still see the functional activation on top of the annotation? Thanks, Daniel ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Using gcut multiple times
Hi Chris, I believe if you do not include the -clean-bm flag then it should have an effect when run multiple times. You should make a copy of the brainmask.mgz and brainmask.gcuts.mgz to compare before/after to verify if there are any differences. -Louis On Tue, 30 Jul 2013, Chris Watson wrote: Hello, Is there any value in running recon-all with -gcut multiple times? e.g. in a case where skull/dura continues to be left on brainmask.mgz? Thanks, Chris ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] recon-all stopped with error
Hi Pom, Does the following path exist? /home/pom/Software/freesurfer/subjects/fsaverage/label/ if so, do it contain lh.BA1.label? It probably has something do with the fsaverage symbolic link. A few lines up in your error log it prints Too many levels of symbolic links. -Louis On Mon, 29 Jul 2013, Pom Sailasuta wrote: Hi, I am wondering the errors I got from recon-all is from my FreeSurfer installation, please comments. Here is my error: Reporting on 70 segmentations /home/pom/Software/freesurfer/subjects/S009002A/label # #@# BA Labels lh Mon Jul 29 07:24:35 PDT 2013 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /home/pom/Software/freesurfer/subjects; ln -s /home/pom/Software/freesurfer/subjects/fsaverage; cd - mri_label2label --srcsubject fsaverage --srclabel /home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject S009002A --trglabel ./lh.BA1.label --hemi lh --regmethod surface Too many levels of symbolic links mri_label2label: could not open label file /home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label srclabel = /home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = S009002A trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/pom/Software/freesurfer/subjects FREESURFER_HOME /home/pom/Software/freesurfer Loading source label. Invalid argument ERROR reading /home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label Linux PomLinux 2.6.32-45-generic-pae #104-Ubuntu SMP Tue Feb 19 21:36:53 UTC 2013 i686 GNU/Linux recon-all -s S009002A exited with ERRORS at Mon Jul 29 07:24:35 PDT 2013 For more details, see the log file /home/pom/Software/freesurfer/subjects/S009002A/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting // thanks Pom ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] recon-all stopped with error
what is fsavg in that same directory? Maybe fsaverage was renamed to fsavg? You would just need to copy the fsaverage recon folder back into /home/pom/Software/freesurfer/subjects, no need to reinstall. -Louis On Mon, 29 Jul 2013, Pom Sailasuta wrote: hi, yes, but it is a link, not sure how is this happen. /// [pom@PomLinux /home/pom]% pwd /home/pom/Software/freesurfer/subjects [pom@PomLinux /home/pom]% ls -al total 10981644 drwxr-xr-x 9 pom pom 4096 2013-07-29 07:24 . drwxr-xr-x 17 pom pom 4096 2013-07-28 20:07 .. drwxr-xr-x 12 pom pom 4096 2012-04-21 11:46 bert drwxr-xr-x 3 pom pom 4096 2012-04-22 06:37 buckner_data -rw-r--r-- 1 pom pom 11245151143 2012-04-21 23:33 buckner_data-tutorial_subjs.tar.gz lrwxrwxrwx 1 pom pom 48 2013-07-29 07:24 fsaverage - /home/pom/Software/freesurfer/subjects/fsaverage drwxr-xr-x 10 pom pom 4096 2012-04-21 15:32 fsavg drwxr-xr-x 12 pom pom 4096 2011-08-16 11:27 harris drwxr-xr-x 13 pom pom 4096 2012-04-21 15:13 LarryR -rw-r--r-- 1 pom pom 1512 2011-05-22 08:12 README drwxr-xr-x 13 pom pom 4096 2013-07-28 20:09 S009002A drwxr-xr-x 2 pom pom 4096 2012-04-21 15:33 sample -rw-rw-rw- 1 pom pom 492 2012-04-21 18:43 .xdebug_tkmedit / I think it linked to itself, should I re-install freesurfer. thanks Pom On Mon, Jul 29, 2013 at 1:09 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Pom, Does the following path exist? /home/pom/Software/freesurfer/subjects/fsaverage/label/ if so, do it contain lh.BA1.label? It probably has something do with the fsaverage symbolic link. A few lines up in your error log it prints Too many levels of symbolic links. -Louis On Mon, 29 Jul 2013, Pom Sailasuta wrote: Hi, I am wondering the errors I got from recon-all is from my FreeSurfer installation, please comments. Here is my error: Reporting on 70 segmentations /home/pom/Software/freesurfer/subjects/S009002A/label # #@# BA Labels lh Mon Jul 29 07:24:35 PDT 2013 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /home/pom/Software/freesurfer/subjects; ln -s /home/pom/Software/freesurfer/subjects/fsaverage; cd - mri_label2label --srcsubject fsaverage --srclabel /home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject S009002A --trglabel ./lh.BA1.label --hemi lh --regmethod surface Too many levels of symbolic links mri_label2label: could not open label file /home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label srclabel = /home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = S009002A trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/pom/Software/freesurfer/subjects FREESURFER_HOME /home/pom/Software/freesurfer Loading source label. Invalid argument ERROR reading /home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label Linux PomLinux 2.6.32-45-generic-pae #104-Ubuntu SMP Tue Feb 19 21:36:53 UTC 2013 i686 GNU/Linux recon-all -s S009002A exited with ERRORS at Mon Jul 29 07:24:35 PDT 2013 For more details, see the log file /home/pom/Software/freesurfer/subjects/S009002A/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting // thanks Pom 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. -- Pom ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended
Re: [Freesurfer] recon-all stopped with error
ok, that's good. Just make a symlink to the fsaverage dir from your subjects dir (/home/pom/Software/freesurfer/subjects) i.e. cd /home/pom/Software/freesurfer/subjects ln -s ./fsavg/fsaverage . -Louis On Mon, 29 Jul 2013, Pom Sailasuta wrote: fsavg dir contains several directories. [pom@PomLinux /home/pom]% cd fsavg [pom@PomLinux /home/pom]% ls fsaverage fsaverage3 fsaverage4 fsaverage5 fsaverage6 lh.EC_average rh.EC_average V1_average thanks again. On Mon, Jul 29, 2013 at 1:23 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: what is fsavg in that same directory? Maybe fsaverage was renamed to fsavg? You would just need to copy the fsaverage recon folder back into /home/pom/Software/freesurfer/subjects, no need to reinstall. -Louis On Mon, 29 Jul 2013, Pom Sailasuta wrote: hi, yes, but it is a link, not sure how is this happen. /// [pom@PomLinux /home/pom]% pwd /home/pom/Software/freesurfer/subjects [pom@PomLinux /home/pom]% ls -al total 10981644 drwxr-xr-x 9 pom pom 4096 2013-07-29 07:24 . drwxr-xr-x 17 pom pom 4096 2013-07-28 20:07 .. drwxr-xr-x 12 pom pom 4096 2012-04-21 11:46 bert drwxr-xr-x 3 pom pom 4096 2012-04-22 06:37 buckner_data -rw-r--r-- 1 pom pom 11245151143 2012-04-21 23:33 buckner_data-tutorial_subjs.tar.gz lrwxrwxrwx 1 pom pom 48 2013-07-29 07:24 fsaverage - /home/pom/Software/freesurfer/subjects/fsaverage drwxr-xr-x 10 pom pom 4096 2012-04-21 15:32 fsavg drwxr-xr-x 12 pom pom 4096 2011-08-16 11:27 harris drwxr-xr-x 13 pom pom 4096 2012-04-21 15:13 LarryR -rw-r--r-- 1 pom pom 1512 2011-05-22 08:12 README drwxr-xr-x 13 pom pom 4096 2013-07-28 20:09 S009002A drwxr-xr-x 2 pom pom 4096 2012-04-21 15:33 sample -rw-rw-rw- 1 pom pom 492 2012-04-21 18:43 .xdebug_tkmedit / I think it linked to itself, should I re-install freesurfer. thanks Pom On Mon, Jul 29, 2013 at 1:09 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Pom, Does the following path exist? /home/pom/Software/freesurfer/subjects/fsaverage/label/ if so, do it contain lh.BA1.label? It probably has something do with the fsaverage symbolic link. A few lines up in your error log it prints Too many levels of symbolic links. -Louis On Mon, 29 Jul 2013, Pom Sailasuta wrote: Hi, I am wondering the errors I got from recon-all is from my FreeSurfer installation, please comments. Here is my error: Reporting on 70 segmentations /home/pom/Software/freesurfer/subjects/S009002A/label # #@# BA Labels lh Mon Jul 29 07:24:35 PDT 2013 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /home/pom/Software/freesurfer/subjects; ln -s /home/pom/Software/freesurfer/subjects/fsaverage; cd - mri_label2label --srcsubject fsaverage --srclabel /home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject S009002A --trglabel ./lh.BA1.label --hemi lh --regmethod surface Too many levels of symbolic links mri_label2label: could not open label file /home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label srclabel = /home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = S009002A trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0
Re: [Freesurfer] recon-all stopped with error
You are getting the same error as before? Could you send the log/terminal output? Are the folders in fsavg symlinks also? On Mon, 29 Jul 2013, Pom Sailasuta wrote: So now I got the following in /home/pom/Software/freesurfer/subjects dir and still no lh.BA1.label per your first email. [pom@PomLinux /home/pom/Software/freesurfer/subjects]% ls -al total 10981644 drwxr-xr-x 9 pom pom 4096 2013-07-29 10:39 . drwxr-xr-x 17 pom pom 4096 2013-07-28 20:07 .. drwxr-xr-x 12 pom pom 4096 2012-04-21 11:46 bert drwxr-xr-x 3 pom pom 4096 2012-04-22 06:37 buckner_data -rw-r--r-- 1 pom pom 11245151143 2012-04-21 23:33 buckner_data-tutorial_subjs.tar.gz lrwxrwxrwx 1 pom pom 17 2013-07-29 10:39 fsaverage - ./fsavg/fsaverage drwxr-xr-x 10 pom pom 4096 2012-04-21 15:32 fsavg drwxr-xr-x 12 pom pom 4096 2011-08-16 11:27 harris drwxr-xr-x 13 pom pom 4096 2012-04-21 15:13 LarryR -rw-r--r-- 1 pom pom 1512 2011-05-22 08:12 README drwxr-xr-x 13 pom pom 4096 2013-07-28 20:09 S009002A drwxr-xr-x 2 pom pom 4096 2012-04-21 15:33 sample -rw-rw-rw- 1 pom pom 492 2012-04-21 18:43 .xdebug_tkmedit On Mon, Jul 29, 2013 at 1:37 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: ok, that's good. Just make a symlink to the fsaverage dir from your subjects dir (/home/pom/Software/freesurfer/subjects) i.e. cd /home/pom/Software/freesurfer/subjects ln -s ./fsavg/fsaverage . -Louis On Mon, 29 Jul 2013, Pom Sailasuta wrote: fsavg dir contains several directories. [pom@PomLinux /home/pom]% cd fsavg [pom@PomLinux /home/pom]% ls fsaverage fsaverage3 fsaverage4 fsaverage5 fsaverage6 lh.EC_average rh.EC_average V1_average thanks again. On Mon, Jul 29, 2013 at 1:23 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: what is fsavg in that same directory? Maybe fsaverage was renamed to fsavg? You would just need to copy the fsaverage recon folder back into /home/pom/Software/freesurfer/subjects, no need to reinstall. -Louis On Mon, 29 Jul 2013, Pom Sailasuta wrote: hi, yes, but it is a link, not sure how is this happen. /// [pom@PomLinux /home/pom]% pwd /home/pom/Software/freesurfer/subjects [pom@PomLinux /home/pom]% ls -al total 10981644 drwxr-xr-x 9 pom pom 4096 2013-07-29 07:24 . drwxr-xr-x 17 pom pom 4096 2013-07-28 20:07 .. drwxr-xr-x 12 pom pom 4096 2012-04-21 11:46 bert drwxr-xr-x 3 pom pom 4096 2012-04-22 06:37 buckner_data -rw-r--r-- 1 pom pom 11245151143 2012-04-21 23:33 buckner_data-tutorial_subjs.tar.gz lrwxrwxrwx 1 pom pom 48 2013-07-29 07:24 fsaverage - /home/pom/Software/freesurfer/subjects/fsaverage drwxr-xr-x 10 pom pom 4096 2012-04-21 15:32 fsavg drwxr-xr-x 12 pom pom 4096 2011-08-16 11:27 harris drwxr-xr-x 13 pom pom 4096 2012-04-21 15:13 LarryR -rw-r--r-- 1 pom pom 1512 2011-05-22 08:12 README drwxr-xr-x 13 pom pom 4096 2013-07-28 20:09 S009002A drwxr-xr-x 2 pom pom 4096 2012-04-21 15:33 sample -rw-rw-rw- 1 pom pom 492 2012-04-21 18:43 .xdebug_tkmedit / I think it linked to itself, should I re-install freesurfer. thanks Pom On Mon, Jul 29, 2013 at 1:09 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Pom, Does the following path exist? /home/pom/Software/freesurfer/subjects/fsaverage/label/ if so, do it contain lh.BA1.label? It probably has something do with the fsaverage symbolic link. A few lines up in your error log it prints Too many levels of symbolic links. -Louis On Mon, 29 Jul 2013, Pom Sailasuta wrote: Hi
Re: [Freesurfer] break up time course nifti
Hi Aaron, You can use the -f or -nth flags with mri_convert. -Louis On Mon, 29 Jul 2013, Aaron Tanenbaum wrote: hola freesurfers, I have a time course surface nii files. I would like to break up the time course into many nii files for each time frame. Is there an easy way of doing this. Thank you Aaron Tanenbaum ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] break up time course nifti (fwd)
Forwarding to the list so others can chime in. -- Forwarded message -- Date: Mon, 29 Jul 2013 18:19:38 -0400 From: Subhabrata Chaudhury su...@scientist.com To: Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu, Aaron Tanenbaum aaron.b.tanenb...@gmail.com Subject: Re: [Freesurfer] break up time course nifti Greetings Dr. Vinke and Dr. Tanenbaum, I saw your recent freesurfer posts. I have piped BOLD volumeetric nii files for each TR onto the subject's freesurfer surface using bbregister. The resulting surface files (1 for each TR) are in mgh format. Now I want to do a first level glm analysis on the surface files. I havent come across any tool that will allow me to conduct a first level glm analysis using the mgh files. So I was thinking if there is a way to convert these mgh files to nii files and then be able to read in these 'surface' nii files into fsl or spm or afni. Do you have some experience in this regard that you can share ? I will be highly obliged if you can help me with this and share your thoughts. Thank you for your help, Subha - Original Message - From: Louis Nicholas Vinke Sent: 07/29/13 05:46 PM To: Aaron Tanenbaum Subject: Re: [Freesurfer] break up time course nifti Hi Aaron, You can use the -f or -nth flags with mri_convert. -Louis On Mon, 29 Jul 2013, Aaron Tanenbaum wrote: hola freesurfers, I have a time course surface nii files. I would like to break up the time course into many nii files for each time frame. Is there an easy way of doing this. Thank you Aaron Tanenbaum ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] WM and pial surfaces problem
Hi Laouchedi, You'll have to run autorecon3 as well to regenerate the pial surfaces. FYI: aseg.mgz, brain.finalsurfs.mgz, wm.mgz and filled.mgz are all volumes, not surfaces. All play a part in generating the surfaces though. -Louis On Fri, 19 Jul 2013, LAOUCHEDI MAKHLOUF wrote: Hi in fact, the wm intensities are mostly below 110 so i seeded control points in the wm (across many slices) and then i run recon-all with only autorecon2. at the end i notices that the problem still not fixed. according to ReconAllDevTable section, the final surfaces (aseg.mgz, brain.finalsurfs.mgz, wm.mgz, filled.mgz) are done at the autorecon2 step; Or should i run autorecon3 to fix the problem ? Thanks _ De : Bruce Fischl fis...@nmr.mgh.harvard.edu À : LAOUCHEDI MAKHLOUF laouma...@yahoo.fr Cc : freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Envoyé le : Jeudi 18 juillet 2013 15h31 Objet : Re: [Freesurfer] WM and pial surfaces problem Hi Laouchedi what are the intensities in the white matter in that region in the brain.mgz? If significantly below 110, try sprinkling a few control points there cheers BruceOn Thu, 18 Jul 2013, LAOUCHEDI MAKHLOUF wrote: Hi i run recon-all on a subject and when checking the surfaces, i noticed that a big part of the temporal part is badly segmented; this concerned WM as well as the grey matter. on the RecommendedReconstruction page, it is explained how to remove parts of non-pial structures considered as so, but not how to move the red surface to include missed wm and grey matter. thank you for help 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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] freeview surface vertex point save?
Hi Jason, Yes, although I think it's only an option in freeview from the 5.2/5.3 Freesurfer releases. -Louis On Thu, 18 Jul 2013, Jason Tourville wrote: Hi there,The tksurfer/tkmedit combo allowed one to select and save a point on the inflated surface and then go to that point in the volume. Does freeview have a similar capability? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Terminated Recon-all jobs
Hi Jon, Also, delete the IsRunning.lh+rh file in the scripts recon dir, or add the '-no-isrunning' flag to the recon-all command when re-running. -Louis On Thu, 18 Jul 2013, Z K wrote: Jon, The way to solve this problem is to use the nohup command, for example: $nohup recon-all -s testsubject1 -all -Zeke On 07/18/2013 12:41 PM, Jonathan Holt wrote: hey all, I've had a few jobs that were recently terminated due to a broken ssh pipe, is there anything i should do to before re-running those same jobs in order to avoid any issues? jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] pial surface midline fix
Hi Jason, If the hemi masks look peculiar in the filled.mgz then you can try seed points for the corpus callosum. See this page for details, go to section titled seed points, fill and cut. https://surfer.nmr.mgh.harvard.edu/fswiki/Edits -Louis On Thu, 18 Jul 2013, Jason Tourville wrote: Hi,I've encountered a recon-all'ed scan in which the pial surface along the posterior midline jumps on cortex in the opposite hemisphere. Is there a simple fix for this, perhaps using a hemisphere mask? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Motion correction in recon-all
Hi Panos, The motion correction itself is carried out using the mri_robust_template binary. The motion correction step also includes an mri_convert command to conform the volume and mri_add_xform_to_header. example taken from recon-all dev table: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable mri_robust_template --mov 001.mgz 002.mgz --average 1 --template rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout --subsample 200 --lta -Louis On Mon, 15 Jul 2013, Fotiadis, Panagiotis wrote: Hi FS Community, I was wondering which command(s) is(are) being used in the Motion Correction part of the recon-all process, to merge the mri/orig/XXX.mgz files and correct for any motion. Thank you for your time! Best, Panos ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Pial surface missing parts of the brain
Hi Ye, A couple control points should do the trick. -Louis On Thu, 11 Jul 2013, ye tian wrote: Dear Freesurfers, Is it true that a small piece of the brain is missing in the attached (all three views)? How do I correct this problem? Thank you very much! Sincerely, Ye ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Editing multiple sources of error in freesurfer
Hi Ye, Is the dura in question affecting the surfaces? If so you can delete the dura, add control points and then run command 4 below. You don't need to rerun autorecon1. -Louis On Thu, 11 Jul 2013, ye tian wrote: Dear freesurfers, I have a subject for which I need to delete some dura in brainmask.mgz and to add some control points. I wonder whether I can do it the following way (to save time): 1. Manually delete extra dura in brainmask.mgz 2. recon-all autoreon1 3. Add control points 4. recon-all -autoreon2-cp -autorecon3 Thank you very much! Sincerely, Ye ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Order of Edits + Intensity Normalization
Hi Peter, After completing your Talairach and skullstrip edits have you regenerated the brainmask.mgz? I'd recommend running the rest of recon-all (-autorecon2 -autorecon3) to see how the surfaces come out. After that you can go ahead with intensity normalization (with control points), and wm/pial edits if necessary. It is only necessary to add control points and to make edits to the brainmask/wm volumes to correct inaccuracies in the surfaces. Intensity normalization and wm edits will influence both wm and pial surfaces. Pial edits only influence the pial surface. The pial surface grows out from the wm surface so wm edits will affect the pial surface as well intensity normalization - wm surf - pial surf You can perform all 3 types of editing at the same time and then rerun from the second intensity normalization step onwards in the recon-all stream. Freesurfer tries to normalize wm to 110, but inevitably not all wm is normalized exactly to 110. Placing a control point on any voxel with an intensity less than 110 tells freesurfer to boost the intensity of that voxel to 110, as well as adjust the proximal intensities of other voxels nearby to a lesser degree. Voxels with intensities less than 110 can be included in the wm surface. This will be the case if the first steep drop-off in intensity (presumed to be the gm/wm boundary) is detected at a point where voxels are below 110. Freesurfer is looking for relative steep gradients in intensity which should correspond to the gm/wm boundary and the pial/csf boundary. I assume the wm voxels at 70 you see within the wm surface are located in a different area of the brain from the non-wm voxels of the same intensity which are not being included in the wm surface. In other words the relative differences in intensity between the gm and wm differ in those two areas. -Louis On Mon, 1 Jul 2013, Peter Boulos wrote: Resending, would greatly appreciate some input so I can move forward: I have a fairly basic question regarding the order in which I should perform the edits. After running the full recon on all of my subjects I have now completed the Talairach edits and the skull strip edits on my subjects. At this point I am attempting to seek out help in terms of performing the edits on white/grey matter border from a more experienced user but have a couple of days before I can meet with them. Therefore, can I go ahead and do the pial surface edits before or does the intensity normalization and white/grey boundary edits need to be done first before the pial surface? As in will those edits alter what I do in later steps? Also, I am having a hard time understanding what I am doing with intensity normalization. Am I just ensuring that there are sections of an intensity of 110 in the white matter boundaries of each subject? Am I only looking for white matter that appears to be left out in a disastrous way in this step or should I be very meticulous about this? I am confused because I have areas considered white matter in free surfer that appear to be white matter by visual inspection that have intensities as low as 70 but then areas of the same intensity outside of the boundary. I realize that the program is probably using intensity data along with location data but do not understand how I am supposed to ensure that whether something with an intensity lower than 110 is indeed white matter by visual inspection alone. I apologize for the simplicity of my understanding at this point and thank you for your time. Peter ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] re gcareg ?
Additional info on GCA: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GcaFormat On Fri, 28 Jun 2013, Bruce Fischl wrote: GCA = gaussian classifier array (a spatially varying set of Gaussians). I don't see ismri/no. on the page, but maybe you mean the mri directory? On Fri, 28 Jun 2013, Dov Sadan wrote: Hi, Thank you all for the wonderful project! From time to time while reading some of the wiki pages it has the feeling of reading ancient Chinese. https://surfer.nmr.mgh.harvard.edu/fswiki/gcareg I'd be happy if anyone help me understand what GCA ? and ismri/no. are ? Thanks in advance, Dov ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] IOError: [Errno 13] Permission denied: 'aseg_stats.txt'
Hi Chikku, I think this is a permissions issue. Check that you have write permissions to where you are trying to write the stats table. -Louis On Wed, 19 Jun 2013, Varghese Chikku wrote: Dear FS team, I tried to run this command asegstats2table --subjects bert ernie fred margaret --meas volume --tablefile aseg_stats.txt But got this error,permission denied, SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files Building the table.. Writing the table to aseg_stats.txt Traceback (most recent call last): File /usr/local/freesurfer/bin/asegstats2table, line 517, in module write_table(options, rows, columns, table) File /usr/local/freesurfer/bin/asegstats2table, line 462, in write_table tw.write() File /usr/local/freesurfer/bin/datastruct_utils.py, line 58, in write fp = open(self.filename, 'w') IOError: [Errno 13] Permission denied: 'aseg_stats.txt' freesurfer@freesurfer-VirtualBox:/usr/lib$ Many thanks Chikku ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Mapping annotation files from one subject to another
Hi Peter, mri_surf2surf is what you want to use for this. -Louis On Mon, 17 Jun 2013, Peter Savadjiev wrote: Hello, I have an annotation file for fsaverage, which I would like to map it to a particular subject. What would be the best way to do so? I tried a combination of calls to mris_ca_train and mris_ca_label, but the latter gave me an error. First I ran mris_ca_train lh lh.sphere.reg fsaverage/label/file.annot fsaverage /tmp/output.gcs (where file and output are some file names) and that executed without any problems. Then I ran mris_ca_label subject_id lh lh.sphere.reg /tmp/output.gcs ./lh.newfile.annot (here subject_id is some subjects' name, and output and newfile are some names) and I got the error: could not open translation file $FREESURFER_HOME/Simple_surface_labels2002.txt Maybe there is a simpler way to perform this task? Or maybe an easy way to fix this error? Any help will be much appreciated. Thank you, Peter ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] command not found
Hi Clelia, What do you run to source FS and do you get any output in your terminal after doing so? What operating system are you running? You might try using c-shell instead of bash. -Louis On Fri, 24 May 2013, clelia pellicano wrote: Hi Louis, thank you for your answer. I sourced freesurfer again, but I still get 'command not found'. What can I try? Thank you, Clelia On Thu, May 23, 2013 at 7:15 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Clelia, If this is in a new terminal then you'll have to source freesurfer again. See here for details: https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration -Louis On Wed, 22 May 2013, clelia pellicano wrote: Hi, I have run recon-all -s bert -all to try my installation and it worked. Now, when I try to use other command (and also again recon-all -s bert -all) I always get this: dyn1097-8:subjects cpellica$ tkmedit bert orig.mgz -bash: tkmedit: command not found dyn1097-8:subjects cpellica$ tkmedit -s bert orig.mgz -bash: tkmedit: command not found dyn1097-8:subjects cpellica$ tksurfer -s bert rh pial -bash: tksurfer: command not found dyn1097-8:subjects cpellica$ qdec -bash: qdec: command not found dyn1097-8:subjects cpellica$ recon-all help -bash: recon-all: command not found dyn1097-8:subjects cpellica$ recon-all -s bert -all -bash: recon-all: command not found I don't know how to do. Please, could you help me? Thanks Clelia 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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] command not found
Hi Clelia, That mv command is failing presumably because SetUpFreeSurfer.txt does not exist in that directory. What are you trying to do with the mv command? It does look like freesurfer was sourced successfully. Are the FreeSurfer related commands still not found? Don't forget to cc the freesurfer mailing list. -Louis On Fri, 24 May 2013, clelia pellicano wrote: Hi Louise, I'm now using tcsh. Here what I did [dyn1097-8:~] cpellica% setenv FREESURFER_HOME /Applications/freesurfer [dyn1097-8:~] cpellica% source /Applications/freesurfer/SetUpFreesurfer.csh freesurfer-Darwin-lion-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl [dyn1097-8:~] cpellica% mv SetUpFreeSurfer.txt SetUpFreeSurfer.csh mv: rename SetUpFreeSurfer.txt to SetUpFreeSurfer.csh: No such file or directory Do you have any advice? Thanks Clelia On Fri, May 24, 2013 at 3:04 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Clelia, What do you run to source FS and do you get any output in your terminal after doing so? What operating system are you running? You might try using c-shell instead of bash. -Louis On Fri, 24 May 2013, clelia pellicano wrote: Hi Louis, thank you for your answer. I sourced freesurfer again, but I still get 'command not found'. What can I try? Thank you, Clelia On Thu, May 23, 2013 at 7:15 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Clelia, If this is in a new terminal then you'll have to source freesurfer again. See here for details: https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration -Louis On Wed, 22 May 2013, clelia pellicano wrote: Hi, I have run recon-all -s bert -all to try my installation and it worked. Now, when I try to use other command (and also again recon-all -s bert -all) I always get this: dyn1097-8:subjects cpellica$ tkmedit bert orig.mgz -bash: tkmedit: command not found dyn1097-8:subjects cpellica$ tkmedit -s bert orig.mgz -bash: tkmedit: command not found dyn1097-8:subjects cpellica$ tksurfer -s bert rh pial -bash: tksurfer: command not found dyn1097-8:subjects cpellica$ qdec -bash: qdec: command not found dyn1097-8:subjects cpellica$ recon-all help -bash: recon-all: command not found dyn1097-8:subjects cpellica$ recon-all -s bert -all -bash: recon-all: command not found I don't know how to do. Please, could you help me? Thanks Clelia 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. ___ Freesurfer mailing list Freesurfer@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.
