Re: [Freesurfer] freesurfer
Hi HweeLing, I think something like: mri_vol2vol -mov input -targ template -o output -interp nearest should work. As Doug says, you should use the aparc+aseg.mgz as your input. Use your MNI template as your target, and call your output whatever you want. Be sure to use the nearest neighbor interpolation method. This will put your whole aparc+aseg into MNI space, and then the label for STS is 1030 and 2030. Hope that works. Jenni On Tue, Sep 16, 2008 at 9:05 AM, Hwee Ling Lee [EMAIL PROTECTED] wrote: Hi, I'm re-posting a question. Pardon my ignorance. How do I use this mri_vol2vol command? I tried to follow the notes, however, I'm not quite sure, hence I was not able to write a ROI mask. Cheers, HL -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Doug Greve Sent: 12 September 2008 18:10 To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu; Hwee Ling Lee Subject: Re: [Freesurfer] freesurfer You can also skip the 1st two steps and just convert aparc+aseg.mgz to MNI with mri_vol2vol (make sure to use the --interp nearest flag). Then look for voxels with values 1030 (left STG) or 2030 (right STG). doug Bruce Fischl wrote: Hi HweeLing, I think the aparc.a2005s has the STS labeled in it, so you should already have what you need in individual space. You could use mri_annot2label, mri_label2vol and mri_vol2vol to transform this into MNI if you need to. cheers, Bruce On Fri, 12 Sep 2008, Hwee Ling Lee wrote: Hi All, I was looking for methods to create a superior temporal sulcus mask (upper and lower boundary). From my understanding, Freesurfer does a pretty good job in labeling the sulcus, hence I was wondering if there are possible ways to write the particular ROI as a mask image for each individual subject, and preferably to be in the MNI space or if not, at least in the native space. Thank you. Best wishes, HweeLing --- Hwee Ling, Lee Max-Planck Institute for Biological Cybernetics Cognitive Neuroimaging Spemannstrasse 41 72076 Tuebingen Germany Tel: +49-70701-601-1785 Fax: +49-7071-601-616 [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.kyb.mpg.de/~hweeling --- ___ 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ 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 -- Jenni Pacheco, MA Learning and Memory Lab The University of Texas at Austin Department of Psychology 1 University Station A8000 Austin, TX 78712 phone: (512) 471-2727 fax: (512) 471-5935 email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] segmentation errors
Hi Nicola, Its hard to tell from this one slice. My experience is that if you look on the wm.mgz volume up and back a few slices you'll notice a slice where there are edits to be made! Jenni On Tue, Aug 5, 2008 at 9:07 AM, Nicola Hobbs [EMAIL PROTECTED]wrote: Hello all, We've noticed some errors in the wm and pial segmentations (see t1.png) even though the wm.mgz seems to be correct (see wm.png). Could you advise us on the best way to correct these errors? Many thanks, Nicola -- Nicola Hobbs Dementia Research Centre National Hospital for Neurology and Neurosurgery Queen Square London WC1N 3BG +44 (0)845 155 5000 x723839 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Jenni Pacheco, MA Learning and Memory Lab The University of Texas at Austin Department of Psychology 1 University Station A8000 Austin, TX 78712 phone: (512) 471-2727 fax: (512) 471-5935 email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] set up of initial data directories
Hi Stephen, To follow up, your command line should work just fine, and will set up the directories you need. Jenni On Wed, Jul 30, 2008 at 6:56 AM, Bruce Fischl [EMAIL PROTECTED]wrote: HI Stephen, not quite raw image space, but mostly. Definitely not tal coords. We resample into a 256^3 volume aligned with the native scanner coords. cheers, Bruce On Wed, 30 Jul 2008, Stephen Rose wrote: Hi I am a new freesurfer user so I apologize in advance for the basic questions. If I already have my MPRAGE images in mgz format (i.e I don't need to convert the raw dicom data with mri_convert), what changes to the command line (below) do I need so that the all the correct data directories are initially set up (and not call mri_convert)? recon-all -i path-to-structural -s subjid When viewing the results of autorecon1 and 2 are all the surfaces and segmentation results shown in raw image space and not Talairach space? Thanks for your help Stephen A/Prof. Stephen Rose Principal Research Fellow Centre for Magnetic Resonance Centre for Clinical Research University of Queensland Brisbane, QLD, 4072 Australia Telephone: +61 7 33466101 Mobile: 0412023958 Fax: +61 7 33653833 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Jenni Pacheco, MA Learning and Memory Lab The University of Texas at Austin Department of Psychology 1 University Station A8000 Austin, TX 78712 phone: (512) 471-2727 fax: (512) 471-5935 email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all crash on talairach_afd
Hi Rudolph, This step is the talairach failure detection, and it's telling you that the talairach transformation has failed. I don't really know why it failed, but you should take a look at the transform and see if you can fix it. If it's happening systematically on your subjects, check the quality of the volumes generated before this step to make sure they look ok. Here's a page that might be helpful: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Good luck! Jenni On Fri, Jul 25, 2008 at 3:53 PM, Rudolph Pienaar [EMAIL PROTECTED] wrote: Hi - I'm a non-power freesurfer user in as much as I usually just run recon-all and rarely deal with individual steps. This usually addresses 90% of my FS needs. :-) I've been running some recons lately that fail very early on with talairach_afd... If anyone has some advice, I'd be really happy. I've appended the recon-all.log file to this email, but in a nutshell the error report is: Fri Jul 25 16:43:30 EDT 2008 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm # [EMAIL PROTECTED] Talairach Failure Detection Fri Jul 25 16:43:31 EDT 2008 /autofs/space/kaos_005/users/dicom/postproc/2680228390711/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0083, pval=0. threshold=0.0050) Linux node0352 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:28:26 CDT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Jul 25 16:43:32 EDT 2008 -- Rudolph Pienaar, M.Eng, D.Eng / email: [EMAIL PROTECTED] MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Jenni Pacheco, MA Learning and Memory Lab The University of Texas at Austin Department of Psychology 1 University Station A8000 Austin, TX 78712 phone: (512) 471-2727 fax: (512) 471-5935 email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon difficulties
Hi Nils, I'm unable to see your pictures from here, but the things you are describing are generally fixable. I think the following two wiki pages should help you get started! https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits Jenni On Wed, Jul 9, 2008 at 2:42 PM, nils rettby [EMAIL PROTECTED] wrote: There seems to be two problems with the recon. First the pia seems to be intruding into the white matter Then in the other hemisphere there seems to be a hole in the white matter Is there a way to fix this? Please see attached pictures Thanks for your help ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Jenni Pacheco, MA Learning and Memory Lab The University of Texas at Austin Department of Psychology 1 University Station A8000 Austin, TX 78712 phone: (512) 471-2727 fax: (512) 471-5935 email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] White Matter Regional Volumes
Hi Jen, In Doug's absence, let me try and give you the best answer I can! The wmparc.mgz uses the cortical parcellation and grows each label down through the white matter - giving a label of the white matter underneath each cortical unit. Because of this there will be both cortical (ctx) and white matter (wm) measures in the wmparc.stats - the ctx regions being taken directly from the cortical parcellation, and the wm regions resulting from growing those inward. Depending on what version you are using, you can use asegstats2table to tabulate these results, as you would the subcortical segmentation. Check the help on this file, there may be an option to do it directly, or you may have to use a flag to specify a new stats table (i.e., wmparc.stats instead of aseg.stats). Hope this is helpful, Jenni On Wed, Apr 30, 2008 at 8:17 AM, Jenni Pacheco [EMAIL PROTECTED] wrote: Hi Jen, In Doug's absence, let me try and give you the best answer I can! The wmparc.mgz uses the cortical parcellation and grows each label down through the white matter - giving a label of the white matter underneath each cortical unit. Because of this there will be both cortical (ctx) and white matter (wm) measures in the wmparc.stats - the ctx regions being taken directly from the cortical parcellation, and the wm regions resulting from growing those inward. Depending on what version you are using, you can use asegstats2table to tabulate these results, as you would the subcortical segmentation. Check the help on this file, there may be an option to do it directly, or you may have to use a flag to specify a new stats table (i.e., wmparc.stats instead of aseg.stats). Hope this is helpful, Jenni On Wed, Apr 30, 2008 at 7:04 AM, Bruce Fischl [EMAIL PROTECTED] wrote: Hi Jen, Doug is out of town at the fBIRN meeting, and he's the one that will answer this so you might have to wait a bit. cheers, Bruce On Tue, 29 Apr 2008, Jennifer Bramen wrote: I posted the below question regarding white matter volumes to the list last Friday. I think it fell through the cracks because I sent it out in the late afternoon, and was hoping someone could help me understand 1) the outputs of indicvidual wmparc.stats files and 2) how to tabulate these data like we can with gray matter volumes. Thanks again. Jen Hi Freesurfer Users, This may be a newbie question. I am trying to evaluate regional volumes. I have been able to tabulate the gray matter volumes, but cannot figure out how to tabulate all the white matter volumes. I see that in individual folders, there is a file called wmparc.stats. Do any of the tools query this file, or will I need to pull the data manually? Inside this file, I see some of the regions listed as wm-?h-regionname. Next to these are sometimes a lot of zeros and sometimes a bunch of values. I am wondering why so many of these do not have values associated with them. I am also wondering why only some of the regions listed in this file are labeled wm, when the file suggests it contains white matter stats... If there is somewhere on the site that explains white matter volumetric analyses, could someone please send me the link? Thank you Jennifer Bramen -- IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer
Re: [Freesurfer] Restart FreeSurfer
Hi Joel, recon-all -make all -s subjid should work if you are using the latest version. Otherwise you can check which steps were run in the /scripts/recon-all-status.log and rerun them with their individual flags, as listed here: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable Jenni On Tue, Apr 8, 2008 at 5:04 PM, joel bruss [EMAIL PROTECTED] wrote: Hello- I was running recon-all when my machine croaked. I was on the latter-half of day two and I think (hope) that the process was nearing completion. Is there a command to give to FreeSurfer to start back in the pipeline where the process left off or do I have to do each command separately? Specifically, this was the command I used: recon-all -subjid sub1 -all Is there a flag or comment to check/pick up where I left off or am I out of luck? Thanks for your help. -Joel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Jenni Pacheco, MA Learning and Memory Lab The University of Texas at Austin Department of Psychology 1 University Station A8000 Austin, TX 78712 phone: (512) 471-2727 fax: (512) 471-5935 email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] QA tools--Permission denied??
Hi, We had never really finalized the QA Tools to feel comfortable distributing them, and so the permissions on these files are still set so that only the group of us working with them can use it. In fact, I had thought that the wiki page associated with it was likewise only available to those same people (to avoid this exact confusion). Our goal had been to incorporate these scripts into the FS distribution, but that hasn't happened yet. I'm no longer at the center, but I'm sure someone else can give you access to these - if you copy it to your own directory (i.e., don't use our only copy of the scripts). Thanks, Jenni On 10/9/07, Pratap Kunwar [EMAIL PROTECTED] wrote: hi all I tried to use QA tools on the wiki (writen by jpacheco) at https://surfer.nmr.mgh.harvard.edu/fswiki/QATools?action=highlightvalue=qa+tools . I got the following error saying permission denied. I could not even copy the QATOOLS to my folder. thanks pratap [galen:S4_HR_LR18_recon] (nmr-std-env) setenv QA_SCRIPTS /space/tensor/17/users/jpacheco/QAtools [galen:S4_HR_LR18_recon] (nmr-std-env) $QA_SCRIPTS/data_checker/recon_checker -nocheckasegoutliers -s rfa1410 -o QAsnap.html /space/tensor/17/users/jpacheco/QAtools/data_checker/recon_checker: Permission denied. -- FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20071006 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: galen SUBJECTS_DIR: /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18_recon/ PWD: /space/galen/2/users/carl/S4_HR_LR18/S4_HR_LR18_recon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Jenni Pacheco, MA Learning and Memory Lab The University of Texas at Austin Department of Psychology 1 University Station A8000 Austin, TX 78712 phone: (512) 471-2727 fax: (512) 471-5935 email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Switch hemispheres
Hi, If your subject was simply left-right reversed there are directions here on how to fix it: https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal It might be a good idea to make a copy and flip that one, no need to mess up your subject by mistake. Be careful with Left/Right reversal, you really only want to do it if you are really sure it's backwards! Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bruce Fischl Sent: Sunday, September 09, 2007 11:46 AM To: Inês Souta Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Switch hemispheres sorry, I can't remember exactly. You'll have to play with switches like -iid, -ijd, -ikd and -oid, -ojd, -okd, unless someone else remembers explicitly On Sun, 9 Sep 2007, Inês Souta wrote: And how exactly do I use mri_convert to change switch left/right? 2007/9/8, Bruce Fischl [EMAIL PROTECTED]: I think think that will quite work. You can use mri_convert to left/right swap all the volumes then rerun the surface generation I guess (autorecon2-wm and autorecon3 I think would do it) On Thu, 6 Sep 2007, Pedro Paulo Oliveira Jr wrote: I think you can: rename the lh.* files to xx.* rename the rh.* files to lh.* rename the xx.* files to rh.* From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Inês Souta Sent: quinta-feira, 6 de setembro de 2007 12:22 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Switch hemispheres Hi, After processing the hole image I realized that the orientation of the original .mgz file was wrong and I've ended up with switched hemispheres. The right hemisphere is where the left should be, and vice-versa. Otherwise the orientation is right. Since I've already made manual edits, is the anyway of switching hemispheres without having to re-process the hole image again? Thanks, Ines ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Skull Stripping Corrections
Hi Jim, You really only need to be concerned about these issues you've shown if they begin to affect your surfaces - that is, if the pial or white surface includes these regions that it shouldn't. If your surfaces are fine, you can leave this alone! Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of James N. Porter Sent: Friday, July 20, 2007 2:55 PM To: freesurfer Subject: [Freesurfer] Skull Stripping Corrections Hello- I've been working through the Skull Stripping checking/corrections tutorial and have a question. So far, I have found no problems akin to the tutorial, where skull is left behind or brain parts are missing. However, I do see remnants of eyeballs/eye sockets, arteries, and dura/pia/meninges. They don't seem too bad: http://www.tc.umn.edu/~norb0062/skull_strip_leftovers.bmp But I'm wondering how much trouble such remnants can cause down the pipeline. That is to say, when performing these checks should I only be concerned with making sure that all skull has been stripped away without taking away any brain, or should I also be concerned with making sure that all non-brain bits have been stripped away? -- Jim Porter TRiCAM Lab Coordinator Elliott Hall N437 612.624.3892 www.psych.umn.edu/research/tricam ___ 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] Talairach
Hi Sharon, Because the talairach is the second step, when you fix it you really do have to run everything else to have it applied. In terms of how long it is taking - it is a long process, the speed of which is dependent on your computer speed and also on the quality of your data. What type of computer are you running this on? What type of data is it? Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Sharon Ruso Sent: Tuesday, July 10, 2007 5:57 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Talairach Dear FreeSurfers I am pretty new to Freesurfer, and I'm using the workflows which are provided in your website; however, I was wondering If every time, I have to check my Talairach (i.e. and to fix it) Do I have to run the recon-all -autorecon1 ... Which takes hrs, or I have another short option which I can apply after correcting the Talairach transform? P.S following the workflow takes me almost 3-4 days for a subject (looking carefully and fixing everything,, am I on the right track? Help, Please Thank You Sharon ___ 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] missing transforms/talairach.xfm
Hi Rich, recon-all -talairach -s subjid should work just fine! Jenni On Fri, 6 Jul 2007, Richard Frye wrote: For some reason my mris do not have a transforms/talairach.xfm file (created in old version of freesurfer) Is there any way of creating this file without going through the entire freesurfer workflow? Thanks Rich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] glmfit question
Hi Rob, Yes you can run as many iterations as you want to in parallel. The monte carlo does take a long time to run, how many subjects are in your study? Jenni On Thu, 5 Jul 2007, Robert Levy wrote: Hello, This is probably a quick question. It seems to take a long time to generate monte carlo simulation data in mri_glmfit. Is it a bad idea to break the iterations into however many available seychelles nodes I can use? Is that equivalent to running the total number of iterations serially? Thanks, Rob [EMAIL PROTECTED] wrote: hi rob, see below for the answers to some of your questions. Hi Dara and Frida, The analysis is running. There is one part of Frida's example that I will need to emulate once this is done, but if what I have is correct, then the part that takes the most time will be done when I come in to work on Thursday 7/5. Frida, sometime when you have a moment free, could you look over the commands I'm running and tell me if there is anything glaringly (or subtly) wrong? I have tried my best to run it in a way that is consistent with how you did it, but I think there could be things wrong, because I dont 100% understand everything about what these commands are doing, but getting there. There's nothing in these commands that looks like nonsense to me, but for example, I don't know if the smoothing value of 13.488420 is the same in our case. to find this parameter, you want to open a file that's called mri_glmfit_log or something like that. it is created in the third step. however, it usually gives you a value b/w 12.5 and 14.5 and using one vs.the other does not create a huge diffrence. however, try to find the file i'm talking about, open it up, and you'll see. I'm using a threshold of .01, and I don't know if that would cause any parameters other than the threshold to need to change. you should use whatever parameter you want your data displayed at. no that doesn't change anything else. I also don't know why simulation data is generated twice and then both input into the contrast, only b/c it takes a long time to generate 10K simulations, so we broke it up into 2 x 5K. you can also use 1 x 10 k. but I'm following that aspect of your example verbatim at least for now, in the commands that are now running. Also a default glmfit setting is to use dods (diff order diff slope). dods is DEF. the one you want to use. it stands for different offset different slope - you don't want to assume that both groups have the same slope to their data. Is that what we should be using? There is also a doss (same slope) option. Ally, she is one of the RAs who I talked with yesterday about this, mentioned that dods is more unpredictable than doss. Thanks for your help, Rob good luck, f #!/usr/local/bin/bash ## # levy 7/3/07 # ## # Katy ran intergroupavg-sess on 9/20/05 # Last week we used FDR to correct for multiple comparisons on the results of the above contrast between groups, # but the resulting threshold was too conservative. # So now I am running the analysis with a cluster-based threshold using a Monte Carlo simulation # (simulate a null hypothesis with randomnes, and use it to generate a meaningful threshold to judge the results with) # In terms of the freesurfer implementation, this is a different process and does not build on the results of previous commands. # so we start from the beginning # note: rerunning these 2 lines probably unnecessary, but mris_preproc was having problems I thought were due to faulty stxgrinder output # This problem led Doug to discover bugs in mris_preproc and also mkcontrast-sess, which he then fixed # As a result, I re-ran the following 2 commands, which didn't take very long anyhow. mkcontrast-sess -analysis EMerror -contrast ASvfix_6 -a 2 -c 0 -setwdelay -sumdelays stxgrinder-sess -a EMerror -c ASvfix_6 -sf Subject_Lists/bw-group-error-5 # resample onto average7 # ( use version from doug's home directory with bugs corrected... ) /space/greve/1/users/greve/freesurfer/bin/mris_preproc --fsgd fsgd_and_contrast_files/BwGroupError5.fsgd --target average7 --hemi lh --sf Subject_Lists/bw-group-error-5 --a EMerror --c ASvfix_6 --out lh.ASvfix_8s_BwGroupError5.fsfast.mgh | tee -a logs/mris_preproc_BwGroupError5_ASvfix_8s_lh.log /space/greve/1/users/greve/freesurfer/bin/mris_preproc --fsgd fsgd_and_contrast_files/BwGroupError5.fsgd --target average7 --hemi rh --sf Subject_Lists/bw-group-error-5 --a EMerror --c ASvfix_6 --out rh.ASvfix_8s_BwGroupError5.fsfast.mgh | tee -a logs/mris_preproc_BwGroupError5_ASvfix_8s_rh.log mkdir lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/ mkdir rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/ # lh mri_glmfit --really-use-average7 --y lh.ASvfix_8s_BwGroupError5.fsfast.mgh --fsgd fsgd_and_contrast_files/BwGroupError5.fsgd --glmdir lh.ASvfix_8s_BwGroupError5.fsfast.glmdir --surf average7 lh --C fsgd_and_contrast_files/BwGroupError5.mat --sim mc-full 5000 2
RE: [Freesurfer] problems with -clean-bm flag
Hi Antonio, What is the complete command you are using the -clean-bm flag with? Jenni _ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Gallo, Antonio (NIH/NINDS) [F] Sent: Monday, June 25, 2007 7:30 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] problems with -clean-bm flag Hi All, I'm trying to see how much my thickness measures are affected by my manual edits. When I tried to use the -clean-bm flag with autorecon2 I always got this message: -1): read error mri_em_register: could not open mask volume brainmask.mgz. It seems to me that this flag delete the brainmask.mgz file but doesn't generate a new copy of this file from the brainmask.auto.mgz file. Could you help me with that? Thank you in advance, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 *** ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] (no subject)
Hi, The version with the –qcache options is not yet publicly available. We’ll be making a release of that version soon. Jenni _ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Sunday, June 17, 2007 9:07 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] (no subject) hi, when I run the recon-all -s wangrong -qcache command, It goes wrong, show like that: freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.5 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast SUBJECTS_DIR/usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni GSL_DIR /usr/local/freesurfer/lib/gsl FSL_DIR /usr/local/freesurfer/fsl [EMAIL PROTECTED]:~ recon-all -s wangrong -qcache ERROR: Flag -qcache unrecognized. -s wangrong -qcache [EMAIL PROTECTED]:~ qdec [1] 13325 bash: qdec: command not found [1]+ Exit 127 nbsp; qdec [EMAIL PROTECTED]:~ Do I need to install some plug-in software to do Qdec? or what's wrong with my procedure? Thank you! _ http://goto.mail.sohu.com/goto.php3?code=mailadt-ta1 我积分，我得奖，天天乐透！ http://goto.mail.sohu.com/goto.php3?code=mailadt-ta *用搜狗拼音写邮件，体验更流畅的中文输入 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: 回复:RE: [Freesurfer] (no subject)
Hi, The instructions for this are on the wiki page you indicated previously, https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis When you run mris_preproc you specify thickness as the measure you are looking at. We have a new group analysis tool, with a GUI interface, that is now available. Tutorials on that are available here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis The new tool, Qdec, performs the same analyses - but it is hopefully more user friendly. Jenni On Wed, 13 Jun 2007 [EMAIL PROTECTED] wrote: Which command to specify the thickness, can you tell me how to use? Thank you very much! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Question about volume measurements in aseg.stats
Hi Mehul,
Freesurfer uses a partial volume calculation to determine the volumes of
structures from the aseg. Matlab is not doing this, and I'm not sure
about slicer but if it matches matlab than I doubt it has a partial volume
correction either. I would say that the values that are corrected for
partial volumes are more accurate.
Jenni
On Wed, 13 Jun 2007, Mehul Sampat wrote:
Hi all,
We have a mismatch in the volumes given in the aseg.stats by freesurfer0 and
the volumes computed from the aseg.mgz with other programs like Slicer and
Matlab
I will use the data of subject bert that is already segmented in freesurfer.
In the aseg.stats file (for the subject bert) the volume of the Brain Stem
is 24490 mm^3 ( 24490 voxels ; segmentation id = 16)
If I measure the volume of the brain-stem in matlab i get 25075 voxels the
code used for this is :
[data,m] = load_mgh('/Applications/freesurfer/subjects/bert/mri/aseg.mgh');
temp = (data ==16);
sum(sum(sum(temp)))
---
When I measure the brain stem volume with Slicer 2.6, it gives 25.075 mL
which matches exactly with the Matlab result. (A colleague also tried it
using Analyze and the result matches those of Matlab and Slicer)
Similar trends is seen for other structures also: (for example for the left
Amygdala aseg.stats reports 1723 while with matlab we get 1728).
Question is: Which measurement is more accurate ? I can see that the Matlab
measurement is an approximation (for example the structure may only cover
half the voxel but with matlab we assume it covers the entire voxel).
Does freesurfer use a sophisticated method for measuring the volumes ? If
this is true then it implies that the volume measurements in Slicer and
Analyze are sub-optimal...
Thanks
Mehul
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RE: [Freesurfer] changing subject's name
Hi, Did the process actually stop running? The old location, with the old name is hard coded into some of the volumes. By default freesurfer will first look in the hard coded location, but then it will look in the location based on the current SUBJECTS_DIR and subject name. The last line of output you pasted says: Loading tal xfm file /usr/local/freesurfer/subjects/001/mri/transforms/talairach.xfm This is the correct location - but only if your SUBJECTS_DIR is set to /usr/local/freesurfer/subjects I'm willing to bet that your SUBJECTS_DIR is set wrong - try resetting it and try the command again. You may see the same messages about the talairach, but they are not necessarily errors. Jenni ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] (no subject)
Hi, You don’t need to input the individual subject’s cortical thickness values. When you run the command you will specify a measure – specify thickness – Freesurfer will then gather the thickness information for each subject entered into the FSGD file. You should be able to construct on FSGD file in the same way that it is described on the wiki page. Jenni _ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Monday, June 11, 2007 7:38 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] (no subject) Thank you for previous help. Now I want to compare the cortical thickness of the two groups. Mr Pacheco tells me to use the group analysis to compare. When I read the manual of the group analysis ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis), I meet some problem. When writing the FSGD file, I don't how to input another group thickness (eg, control group) in to the FSGD. If not use method, how to compare the cortical thickness between the two group? _ http://goto.mail.sohu.com/goto.php3?code=mailadt-ta1 我积分，我得奖，天天乐透！ http://goto.mail.sohu.com/goto.php3?code=mailadt-ta *用搜狗拼音写邮件，体验更流畅的中文输入 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Manually editing brainmask.mgz
Hi Jared, What happens when you try and edit? What type of editing are you trying to do? Do you have the right tools selected? I'm going to need a little bit more information on what you are doing and what is going wrong. Thanks, Jenni On Mon, 11 Jun 2007, Jared Conley wrote: FreeSurfer community, I am attempting to manually edit brainmask.mgz in TkMedit and cannot figured out how to do so based on the info in the Wiki. I load the file in X11 with the command tkmedit subjid brainmask.mgz and see the images just fine, but I cannot seem to manually edit them like I can in the segmentation file. Any ideas? Thanks, Jared ___ 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] Manually editing brainmask.mgz
Hi Jared, Mechanically, yes - you would use the edit voxels tool and then use the right button to remove the voxels you do not want. I'm not sure I understand exactly what you are trying to do - and if you eventually want to use Freesurfer to obtain surfaces etc, this will not work. I'd suggest saving your brainmask as something else, and edit that - this way you still have a viable brainmask.mgz to obtain results with. Jenni On Mon, 11 Jun 2007, Jared Conley wrote: Hi Jenni, I am trying to edit the greyscale images of the brainmask.mgz. We are trying to generate an ICC map with only grey/white matter and we need to exclude a few structures that are not removed in the skull-stripping step (i.e. some of the cranial nerves, pituitary, etc.). I assume that I begin by using the Edit Voxels tool (a), but I do not know where to go from there. Thanks, Jared Jenni Pacheco wrote: Hi Jared, What happens when you try and edit? What type of editing are you trying to do? Do you have the right tools selected? I'm going to need a little bit more information on what you are doing and what is going wrong. Thanks, Jenni On Mon, 11 Jun 2007, Jared Conley wrote: FreeSurfer community, I am attempting to manually edit brainmask.mgz in TkMedit and cannot figured out how to do so based on the info in the Wiki. I load the file in X11 with the command tkmedit subjid brainmask.mgz and see the images just fine, but I cannot seem to manually edit them like I can in the segmentation file. Any ideas? Thanks, Jared ___ 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] Manually editing brainmask.mgz
Hi Jared, It's still not completely clear to me what you are trying to do. By segmentation values do you just mean the volumes that will come out of the aseg.mgz? If thats what you mean you should make these edits to the aseg.mgz itself. I'm not certain what will happen if you make these edits to the brainmask - but I'd guess the surfaces won't be accurate, some things may not run at all. Jenni On Mon, 11 Jun 2007, Jared Conley wrote: Jenni, Another question for you. What is the consequence of running autorecon2 after editing on the brainmask.mgz file itself. You mentioned something about it not working if we want to obtain surfaces--what did you mean exactly? CSF surfaces? Ideally, we are editing the brainmask.mgz file so that autorecon2 only segments the brain according to our protocol (which eliminates pituitary, cranial nerves). In the end, we only need segmentation results of basal ganglia and the grey/white matter/lat. ventricles. If we could get the intracranial volume measurements that would be ideal, but I don't think this is possible. Thanks, Jared Jenni Pacheco wrote: Hi Jared, Mechanically, yes - you would use the edit voxels tool and then use the right button to remove the voxels you do not want. I'm not sure I understand exactly what you are trying to do - and if you eventually want to use Freesurfer to obtain surfaces etc, this will not work. I'd suggest saving your brainmask as something else, and edit that - this way you still have a viable brainmask.mgz to obtain results with. Jenni On Mon, 11 Jun 2007, Jared Conley wrote: Hi Jenni, I am trying to edit the greyscale images of the brainmask.mgz. We are trying to generate an ICC map with only grey/white matter and we need to exclude a few structures that are not removed in the skull-stripping step (i.e. some of the cranial nerves, pituitary, etc.). I assume that I begin by using the Edit Voxels tool (a), but I do not know where to go from there. Thanks, Jared Jenni Pacheco wrote: Hi Jared, What happens when you try and edit? What type of editing are you trying to do? Do you have the right tools selected? I'm going to need a little bit more information on what you are doing and what is going wrong. Thanks, Jenni On Mon, 11 Jun 2007, Jared Conley wrote: FreeSurfer community, I am attempting to manually edit brainmask.mgz in TkMedit and cannot figured out how to do so based on the info in the Wiki. I load the file in X11 with the command tkmedit subjid brainmask.mgz and see the images just fine, but I cannot seem to manually edit them like I can in the segmentation file. Any ideas? Thanks, Jared ___ 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] aparc2aseg error
Hi Derin, It's probably that you have done something out of order. The easiest way for me to check this is to see the latest set of processing as dictated by the subject's scripts/recon-all-status.log. If you paste that into an email I can see what happened. Oh, also, were you running this on just the LH - have you processed the RH yet? Jenni On Mon, 11 Jun 2007, Derin Cobia wrote: I'm getting the following error on several of my subjects during the aparc2aseg stage: _ [EMAIL PROTECTED] AParc-to-ASeg Sat Jun 9 12:19:58 EDT 2007 /disk/eli/freesurfer/conte_flash/5111 mri_aparc2aseg --s 5111 --ribbon SUBJECTS_DIR /disk/eli/freesurfer/conte_flash subject 5111 outvol /disk/eli/freesurfer/conte_flash/5111/mri/aparc+aseg.mgz useribbon 1 baseoffset 0 Reading lh white surface /disk/eli/freesurfer/conte_flash/5111/surf/lh.white Building hash of lh white Reading lh pial surface /disk/eli/freesurfer/conte_flash/5111/surf/lh.pial Building hash of lh pial ERROR: lh white and pial have a different number of vertices (190233,189041) Linux eli 2.6.9-34.0.1.ELsmp #1 SMP Wed May 17 16:59:36 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Sat Jun 9 12:20:07 EDT 2007 ___ Do I need to reprocess from a certain stage on, or redo the whole thing? What would have caused this (it didn't happen with some other subjects during the same process batch). I couldn't find any info on this in the archive or wiki, I'm running 3.0.4. Thanks, Derin ___ 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] question re: low contrast images
Hi Jess, I think there is a way to fix the aseg, you can use the control points with the mri_ca_normalize flag as part of the aseg. I've not used the command much, but you should be able to add the flag '-f tmp/control.dat' to the normal mri_ca_normalize command to run this step. We are working on adding this to recon-all, but currently it's not there. You would have to run mri_ca_normalize seperately. Jenni On Thu, 7 Jun 2007, Turner, Jessica wrote: Hi Jenni--Ok, I'm running a couple with control points and I'll see how they come out. Yes, the aseg is not any better--do I need to fix that separately or will the control points work on that?? Thanks, Jess -Original Message- From: Jenni Pacheco [mailto:[EMAIL PROTECTED] Sent: Thursday, June 07, 2007 11:00 AM To: Turner, Jessica Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] question re: low contrast images Hi Jess, It certainly is a problem, from the snapshots though it looks like there is some visible contrast there, so control points should help. be sure to only place them in true WM regions, and avoid partial volumed voxels. A few spread out on each slice should do the trick - no need to overload them. Then you can run recon-all -autorecon2-cp, and see if it fixes your surfaces. How does the aseg look? I'd imagine it's pretty bad as well. Jenni On Thu, 7 Jun 2007, Turner, Jessica wrote: Hi experts-I have some very low-contrast images from an older dataset and the Freesurfer segmentation completely misses the lower and posterior bits of the occipital lobe on many of the subjects (see attached images from an example subject). What is the recommendation in this case? Can I fix this with control points? It's a much more extensive failure than I'm used to seeing fixed with control points. Thanks, Jess Jessica Turner, Ph.D. Project Scientist, FBIRN (www.nbirn.net) Department of Psychiatry and Human Behavior University of California, Irvine Phone: (949) 824-3331 Fax: (949) 824-3324 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] question re: low contrast images
Hi Jess, It certainly is a problem, from the snapshots though it looks like there is some visible contrast there, so control points should help. be sure to only place them in true WM regions, and avoid partial volumed voxels. A few spread out on each slice should do the trick - no need to overload them. Then you can run recon-all -autorecon2-cp, and see if it fixes your surfaces. How does the aseg look? I'd imagine it's pretty bad as well. Jenni On Thu, 7 Jun 2007, Turner, Jessica wrote: Hi experts-I have some very low-contrast images from an older dataset and the Freesurfer segmentation completely misses the lower and posterior bits of the occipital lobe on many of the subjects (see attached images from an example subject). What is the recommendation in this case? Can I fix this with control points? It's a much more extensive failure than I'm used to seeing fixed with control points. Thanks, Jess Jessica Turner, Ph.D. Project Scientist, FBIRN (www.nbirn.net) Department of Psychiatry and Human Behavior University of California, Irvine Phone: (949) 824-3331 Fax: (949) 824-3324 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] subcortical segmentation
Hi Mishkin, Are all the fields blank in the aseg.stats table, or just for some things? It shouldn't be like this. It may be that there are some structures listed in that file that are not labeled in the aseg and then reported as a zero, but it shouldn't be all of them. Were there any error messages at the end of this particular subject's scripts/recon-all.log? Jenni On Tue, 5 Jun 2007, Mishkin Derakhshan wrote: Hi, After running the -subcortseg option, i see the output volumes of certain structures on the screen. Are they stored anywhere in a text file? I checked stats/aseg.stats, and while the column headers indicate that there should be values for NVoxels and Volume_mm3, in the table those two fields are blank for all labels. Is this a bug, or is there another option I need to set to get those fields filled in? thanks, mishkin On 6/1/07, Doug Greve [EMAIL PROTECTED] wrote: unfortunately, you have to go thru the segmentation as that is part of the surface-based stream. doug David Perlman wrote: On this topic, if I *don't* want subcortical segmentation, but rather only surface generation and thickness maps, what's the best option to use for that? It seems like it might be -noaseg, but I couldn't find any references to this flag being used with human data, only with non- human primates, so I thought I'd ask before I assumed I'd figured it out. On Jun 1, 2007, at 1:49 PM, Bruce Fischl wrote: yes, sorry. The subcortical segmentation is early in the processing stream, and pretty much the slowest step. -- -dave Science arose from poetry... when times change the two can meet again on a higher level as friends. -Göthe ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ 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] tkmedit
Hi Lars, Typically the optic nerve is not a problem - it's likely included in all our subjects. If you feel you need to edit it you will want to remove it from the brainmask.mgz volume, to affect where your pial surface is. Jenni -Original Message- From: Lars Tjelta Westlye [mailto:[EMAIL PROTECTED] Sent: Monday, May 21, 2007 5:26 AM To: Jenni Pacheco Cc: 'Freesurfer Mailing List' Subject: RE: [Freesurfer] tkmedit Hi, I have a related question. Should the optic nerve included in the pial surface be considered a problem for the surfaces? The nerve also does create a small bump on the inflated surface as viewed in tksurfer. If so, from which volume should the optic nerve be erased? Thanks for your time. Lars T. Westlye University of Oslo Hi Martin, You should be fine not editing these regions routinely - only, of course, if they pose a problem for your surfaces. For the most part, also, you should be fine to run the entire stream and do any edits that may be needed after the fact - instead of running stepwise and checking each output along the way. Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Martin Chang Sent: Thursday, May 17, 2007 12:34 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] tkmedit Hi, I have a question about using tkmedit. Up until now, our group has been editing out the eye muscles after autorecon-1 and editing out the optic nerve after autorecon-2. I know on earlier versions of freesurfer it was highly recommended to do so because the program would sometimes crash otherwise. However, using the newer version, the program seems to know to not include eye muscles in the pial matter boundary, and the optic nerve does create a region of high curvature at that point, but it doesn't crash the program. I was wondering, in your own analyses, did you do editing at each step (excluding situations that are obviously out of the norm), and would it be a bad thing not to edit those regions in the majority of cases? Thanks, Martin Chang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all exited with ERRORS
Hi Annie, The aparc+aseg has the aseg subcortical labels in the wm regions, and has the parcellation labels along the cortex. This is overlaid on volumes in tkmedit. A description and a snapshot is shown at the bottom of this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData Jenni On Fri, 18 May 2007, Annie Chiu wrote: Hi Jenni, Thanks very much for your speedy reply. Before understanding whether I need aparc+aseg, could you let me know what the file entails? Thanks again, Annie On 5/17/07 5:48 PM, Jenni Pacheco [EMAIL PROTECTED] wrote: Hi Annie, I think what's happening is that it's failing in the aparc+aseg step, but you can verify this by looking at the status log in your subjects scripts/recon-all-status.log This step uses some previously generated input to make a new segmentation. The lh.ribbon.mgz is a newer addition to the recon-all stream, currently run in autorecon2. If your data is old it may not have this, and so the aparc+aseg can not be generated. You can either survive without the aparc+aseg if you don't want it, or you can generate the ?h.ribbon.mgz by running recon-all -cortribbon -s subjid and then trying recon-all -aparc2aseg -s subjid But first, do verify with the status log that this is the step thats failing! Jenni On Thu, 17 May 2007, Chiu, Annie (NIH/NINDS) [F] wrote: Hello all, Using the most updated version of freesurfer, I ran autorecon3 on a set of data obtained with an old version of the software (the first version) and I obtained the following error message: Loading rh annotations from /home/chiuan/freesurfer/subjects/becker2ANNIE/label/rh.aparc.annot Have color table for lh white annotation Have color table for rh white annotation Loading lh ribbon mask from /home/chiuan/freesurfer/subjects/becker2ANNIE/mri/lh.ribbon.mgz ERROR: loading aseg /home/chiuan/freesurfer/subjects/becker2ANNIE/mri/lh.ribbon.mgz Linux mushrat.ninds.nih.gov 2.6.9-42.0.2.ELsmp #1 SMP Thu Aug 17 18:00:32 EDT 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed May 16 22:24:13 EDT 2007 Could someone please clarify? Thanks in advance, Annie ___ 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] Changing the color in Edit Segmentation tool
Hi Jared, How are you selecting the segmentation that you wish to be changing it to? Have you opened the Segmentation Bruch Info dialog window and selected from the list in there? jenni On Fri, 18 May 2007, Jared Conley wrote: In response to the questions, I do see the segmentation properly in colors (as a translucent color overlay on the anatomical), and I am sure I am using the Edit Segmentation tool. Clicking and dragging with the tool does change the segmentation volume, it just does not change it to the Sgmtn label (in the tools window) that I want. It doesn't matter what value I choose in the Segmentation Brush Info, the Sgmtn label line says Right-accumbens-intens and the paint is grey or white depending on the background color of the segmentation label map. Any further ideas? Thanks. Kevin Teich wrote: Sorry, I was thinking you were talking about Scuba. Do you see the segmentation properly, in colors? If not, there was probably an error in loading the segmentation; do you see any errors in the shell window? If you do see the segmentation volume displayed properly as a translucent color overlay on the anatomical, are you sure you are using the Edit Segmentation tool? It's a paintbrush over a volume divided into quarters. Does clicking and dragging with the tool actually change the segmentation volume, that is, can you mouse over the edited voxels and verify that the values in the Sgmtn label line in the tools window matches the value you selected in the Segmentation Brush Info dialog? On Thu, May 17, 2007 at 02:56:57PM -0400, Jared Conley wrote: Yes, I believe so. The layer's color map is set to FreeSurferColorLUT.txt when loading the segmentation. The Segmentation Brush source is set at Segmentation (under Configure Segmentation Brush)--I imagine that's what you are referring to when you say target layer. Kevin Teich wrote: Are you sure the Target Layer is set to the segmentation volume layer? And that that layer's color map type is set to LUT? On Thu, May 17, 2007 at 11:23:49AM -0400, Jared Conley wrote: I am attempting to edit the segmentation results in TkMedit, according to the following Wiki directions ( TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations): A segmentation can be edited with the Edit Segmentation tool, which can be activated by pushing the icon_copy.gif button on the Main Toolbar, by choosing *Tools-Edit Segmentation*, or by pressing the 'g' key. By clicking with button 2 with this tool, you can 'paint' a label in the segmentation. The color used can be set in the dialog box brought up by choosing *Tools-Configure Segmentation Brush* However, I am not able to change the color to match the structure I am wanting to edit (I have tried selecting three different structures at random and the color of the editing remains grey). Any ideas? ___ 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] Changing the color in Edit Segmentation tool
When you are editing the segmentation, are you using the middle button to change the label? jenni On Fri, 18 May 2007, Jared Conley wrote: Jenni Pacheco wrote: Hi Jared, How are you selecting the segmentation that you wish to be changing it to? Have you opened the Segmentation Bruch Info dialog window and selected from the list in there? jenni On Fri, 18 May 2007, Jared Conley wrote: In response to the questions, I do see the segmentation properly in colors (as a translucent color overlay on the anatomical), and I am sure I am using the Edit Segmentation tool. Clicking and dragging with the tool does change the segmentation volume, it just does not change it to the Sgmtn label (in the tools window) that I want. It doesn't matter what value I choose in the Segmentation Brush Info, the Sgmtn label line says Right-accumbens-intens and the paint is grey or white depending on the background color of the segmentation label map. Any further ideas? Thanks. Kevin Teich wrote: Sorry, I was thinking you were talking about Scuba. Do you see the segmentation properly, in colors? If not, there was probably an error in loading the segmentation; do you see any errors in the shell window? If you do see the segmentation volume displayed properly as a translucent color overlay on the anatomical, are you sure you are using the Edit Segmentation tool? It's a paintbrush over a volume divided into quarters. Does clicking and dragging with the tool actually change the segmentation volume, that is, can you mouse over the edited voxels and verify that the values in the Sgmtn label line in the tools window matches the value you selected in the Segmentation Brush Info dialog? On Thu, May 17, 2007 at 02:56:57PM -0400, Jared Conley wrote: Yes, I believe so. The layer's color map is set to FreeSurferColorLUT.txt when loading the segmentation. The Segmentation Brush source is set at Segmentation (under Configure Segmentation Brush)--I imagine that's what you are referring to when you say target layer. Kevin Teich wrote: Are you sure the Target Layer is set to the segmentation volume layer? And that that layer's color map type is set to LUT? On Thu, May 17, 2007 at 11:23:49AM -0400, Jared Conley wrote: I am attempting to edit the segmentation results in TkMedit, according to the following Wiki directions ( TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations): A segmentation can be edited with the Edit Segmentation tool, which can be activated by pushing the icon_copy.gif button on the Main Toolbar, by choosing *Tools-Edit Segmentation*, or by pressing the 'g' key. By clicking with button 2 with this tool, you can 'paint' a label in the segmentation. The color used can be set in the dialog box brought up by choosing *Tools-Configure Segmentation Brush* However, I am not able to change the color to match the structure I am wanting to edit (I have tried selecting three different structures at random and the color of the editing remains grey). Any ideas? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Thanks, Jenni for the assistance. Yes, I have gone to Tools/Configure Segmentation Brush.../Segmentation Brush Info in the TkMedit Tools window. In the Segmentation Brush Info window, I have selected my desired structure color (with the Main Anatomical used as source) and still no change in the Sgmnt label when I attempt to edit the segmentation. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Changing the color in Edit Segmentation tool
It's a MAC thing. With a standard three-button mouse it's the middle button that adds the label. If you use a MAC mouse or other non 3-button mouse there are other keystrokes which you may have to do in order to have the middle button option. sorry, Jenni On Fri, 18 May 2007, Jared Conley wrote: Jenni Pacheco wrote: When you are editing the segmentation, are you using the middle button to change the label? jenni On Fri, 18 May 2007, Jared Conley wrote: Jenni Pacheco wrote: Hi Jared, How are you selecting the segmentation that you wish to be changing it to? Have you opened the Segmentation Bruch Info dialog window and selected from the list in there? jenni On Fri, 18 May 2007, Jared Conley wrote: In response to the questions, I do see the segmentation properly in colors (as a translucent color overlay on the anatomical), and I am sure I am using the Edit Segmentation tool. Clicking and dragging with the tool does change the segmentation volume, it just does not change it to the Sgmtn label (in the tools window) that I want. It doesn't matter what value I choose in the Segmentation Brush Info, the Sgmtn label line says Right-accumbens-intens and the paint is grey or white depending on the background color of the segmentation label map. Any further ideas? Thanks. Kevin Teich wrote: Sorry, I was thinking you were talking about Scuba. Do you see the segmentation properly, in colors? If not, there was probably an error in loading the segmentation; do you see any errors in the shell window? If you do see the segmentation volume displayed properly as a translucent color overlay on the anatomical, are you sure you are using the Edit Segmentation tool? It's a paintbrush over a volume divided into quarters. Does clicking and dragging with the tool actually change the segmentation volume, that is, can you mouse over the edited voxels and verify that the values in the Sgmtn label line in the tools window matches the value you selected in the Segmentation Brush Info dialog? On Thu, May 17, 2007 at 02:56:57PM -0400, Jared Conley wrote: Yes, I believe so. The layer's color map is set to FreeSurferColorLUT.txt when loading the segmentation. The Segmentation Brush source is set at Segmentation (under Configure Segmentation Brush)--I imagine that's what you are referring to when you say target layer. Kevin Teich wrote: Are you sure the Target Layer is set to the segmentation volume layer? And that that layer's color map type is set to LUT? On Thu, May 17, 2007 at 11:23:49AM -0400, Jared Conley wrote: I am attempting to edit the segmentation results in TkMedit, according to the following Wiki directions ( TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations): A segmentation can be edited with the Edit Segmentation tool, which can be activated by pushing the icon_copy.gif button on the Main Toolbar, by choosing *Tools-Edit Segmentation*, or by pressing the 'g' key. By clicking with button 2 with this tool, you can 'paint' a label in the segmentation. The color used can be set in the dialog box brought up by choosing *Tools-Configure Segmentation Brush* However, I am not able to change the color to match the structure I am wanting to edit (I have tried selecting three different structures at random and the color of the editing remains grey). Any ideas? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Thanks, Jenni for the assistance. Yes, I have gone to Tools/Configure Segmentation Brush.../Segmentation Brush Info in the TkMedit Tools window. In the Segmentation Brush Info window, I have selected my desired structure color (with the Main Anatomical used as source) and still no change in the Sgmnt label when I attempt to edit the segmentation. Jenni, Thanks--it was a button issue. It is working now! I was confused because I was following the Wiki directions (http://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide_2fTkMeditWorkingWithData_2fTkMeditSegmentations?action=highlightvalue=TkMedit) and on my Mac, it is Button 3 (according to System Preferences) that paints a label in the segmentation, not Button 2 as indicated. I didn't know what you meant by the middle button, but I started to experiment and discovered it was Button 3 that paints the label. Thanks again for your help. Should I change this Wiki page to indicate that it is Button 3 or is this just an issue for those who use Macs with the new standard Mac mouse? Best, Jared ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] tkmedit
Hi Martin, You should be fine not editing these regions routinely - only, of course, if they pose a problem for your surfaces. For the most part, also, you should be fine to run the entire stream and do any edits that may be needed after the fact - instead of running stepwise and checking each output along the way. Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Martin Chang Sent: Thursday, May 17, 2007 12:34 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] tkmedit Hi, I have a question about using tkmedit. Up until now, our group has been editing out the eye muscles after autorecon-1 and editing out the optic nerve after autorecon-2. I know on earlier versions of freesurfer it was highly recommended to do so because the program would sometimes crash otherwise. However, using the newer version, the program seems to know to not include eye muscles in the pial matter boundary, and the optic nerve does create a region of high curvature at that point, but it doesn't crash the program. I was wondering, in your own analyses, did you do editing at each step (excluding situations that are obviously out of the norm), and would it be a bad thing not to edit those regions in the majority of cases? Thanks, Martin Chang _ PC Magazine's 2007 editors' choice for best Web mail-award-winning Windows Live Hotmail. http://imagine-windowslive.com/hotmail/?locale=en-usocid=TXT_TAGHM_migratio n_HM_mini_pcmag_0507 ___ 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] recon-all exited with ERRORS
Hi Annie, I think what's happening is that it's failing in the aparc+aseg step, but you can verify this by looking at the status log in your subjects scripts/recon-all-status.log This step uses some previously generated input to make a new segmentation. The lh.ribbon.mgz is a newer addition to the recon-all stream, currently run in autorecon2. If your data is old it may not have this, and so the aparc+aseg can not be generated. You can either survive without the aparc+aseg if you don't want it, or you can generate the ?h.ribbon.mgz by running recon-all -cortribbon -s subjid and then trying recon-all -aparc2aseg -s subjid But first, do verify with the status log that this is the step thats failing! Jenni On Thu, 17 May 2007, Chiu, Annie (NIH/NINDS) [F] wrote: Hello all, Using the most updated version of freesurfer, I ran autorecon3 on a set of data obtained with an old version of the software (the first version) and I obtained the following error message: Loading rh annotations from /home/chiuan/freesurfer/subjects/becker2ANNIE/label/rh.aparc.annot Have color table for lh white annotation Have color table for rh white annotation Loading lh ribbon mask from /home/chiuan/freesurfer/subjects/becker2ANNIE/mri/lh.ribbon.mgz ERROR: loading aseg /home/chiuan/freesurfer/subjects/becker2ANNIE/mri/lh.ribbon.mgz Linux mushrat.ninds.nih.gov 2.6.9-42.0.2.ELsmp #1 SMP Thu Aug 17 18:00:32 EDT 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed May 16 22:24:13 EDT 2007 Could someone please clarify? Thanks in advance, Annie ___ 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] mris_anatomical_stats
Hi Cate, I think you have to use the -f flag to specify an output file, otherwise it just prints to the screen. mris_anatomical_stats usage: mris_anatomical_stats [options] subject name hemi [surface name] This program measures a variety of anatomical properties valid options are: -i low thresh hi thresh - only consider thicknesses in the specified range. -l label file - limit calculations to specified label -t thickness file - use specified file for computing thickness statistics -a annotation file - compute properties for each label in the annotation file separately -b - tabular output -f tablefile - table output to a file (different format than -b) -log log- will write the stats into a file named log -nsmooth # - will smooth the thicknessmap # of iterations before using it Jenni On Fri, 11 May 2007, Catherine Hartley wrote: Hi, I'm trying to get the anatomical statistics for a new parcellation, ? h.aparc.splitcingulate.annot, I've created using mris_divide_parcellation. I've tried using mris_anatomical_stats with various argument structures (specifying output filenames, not specifiying output filenames) and can't seem to get it to write a ?h.aparc.splitcingulate.stats file. It generates and outputs summary statistics, but it does not write a .stats file to the stats directory: [catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats mm103184 lh inflated -a mm103184/label/lh.aparc.splitcingulate.annot reading volume /Applications/freesurfer/subjects/reruns/mm103184/mri/ wm.mgz... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.inflated... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.pial... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.white... done. computing second fundamental form... ... done. total white matter volume = 516178 mm^3 total surface area = 81462 mm^2 total gray matter volume= 230187 mm^3 average cortical thickness = 2.175 mm +- 0.836 mm average integrated rectified mean curvature = 0.025 average integrated rectified Gaussian curvature = 0.096 folding index = 9766.477 intrinsic curvature index = 937.896 [catemac:freesurfer/subjects/reruns] cate% Thanks for your help! -Cate ___ 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] Does 'color scale bar' show the cortical thicknessor[-log10(p)]?
Ruiwang, The first figure on the FsTutorial/Visualization page was made using a contrast of: (2) [0 0 1] for DOSS 'If you wanted to make a direct comparison between thickness and age, regardless of gender, you could use the contrast vector [0 0 1]' Therefore, the regions of red and blue are showing results for the direct comparison of thickness and age regardless of gender. There is no figure showing the interaction between thickness and the two groups - we did not run that in this tutorial. If you have your own copy of the tutorial data you could certainly run this comparison, but as it is there is no figure on the wiki that shows this because that contrast was not run. The only figures are showing the interaction between thickness and age regardless of gender. Jenni -Original Message- From: Ruiwang Huang [mailto:[EMAIL PROTECTED] Sent: Thursday, May 10, 2007 5:30 AM To: Freesurfer Mailing List Cc: Jenni Pacheco; Nick Schmansky Subject: Re: [Freesurfer] Does 'color scale bar' show the cortical thicknessor[-log10(p)]? Hi, Jenni Hi, Nick Many thanks for your explanations. I agree with you that the inflated surface figure, the first figure of FsTutorial/Visualization, (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) constains information of the two groups' thickness But the descriptions in Session_1a (FreeSurfer Tutorial: Group Analysis) show that the FSGD file is # ABC # subject Age Gender ... and the contrast vector can be selected (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/CreateContrastVectors) (1) [1 -1 0] for DOSS 'If you wanted to compare the thickness differences between Males and Females, while regressing out age you could use a contrast vector [1 -1 0]'. (2) [0 0 1] for DOSS 'If you wanted to make a direct comparison between thickness and age, regardless of gender, you could use the contrast vector [0 0 1]' I would like to know the thickness differences between Males and Females. If the contrast vector is [1 -1 0], does the blue/red area in the first figure of FsTutorial/Visualization show the interaction between the thickness and the two gender groups (M, F)? Which group has got thinner thickness at the red/blue area? Maybe the red/blue area relate to the intercept of average thickness of Male/Female at that area? I really appreciate your further explanation. Rhuang On Wednesday 09 May 2007 20:48, you wrote: Hi, So the contrast used to perform this statistical test kept the two groups (male and female) constant and only looked for an interaction between thickness and age. So in this case the blue is where thickness and age are negatively correlated (as the age goes up the cortex gets thinner) and the red regions show areas where thickness and age are positively correlated (as the age goes up the cortex gets thicker). This is based on the contrast used to create the sig.mgh, shown in session 1a under day 2. Does this help? Jenni On Wed, 9 May 2007, Ruiwang Huang wrote: Hi Jenni, Many thanks for message. I tried to go through the Freesurfer Tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial) There are three sessions in Day-2, including Session_1a and Session_1b. In Session_1a (FreeSurfer Tutorial: Group Analysis), the FSGD file was presented as a table. Several columns corresponds to # A BC # subject Age Gender Session_1b follows Session_1a. In Session_1b (just below the first figure), the sentence ' Next, load FSGD file lh.gender_age.glmdir/y.fsgd in the same directory by selecting File - Load Group Descriptor File. ' implies the blue/red areas relating to the two groups (M, F), I think. I would like to know which group (gender: M, F) has got thin thickness at the blue/red area in the first figure? Any further suggestions please? Rhuang On Wednesday 09 May 2007 19:16, Jenni Pacheco wrote: Hi, I'm not sure where you are getting the descriptions below. This statistical map on the surface is actually looking at the correlations of thickness and age, not gender. Can you be more specific as to what you are refering to with the following descriptions: the 'color scale bar' indicates area coded in blue == cortical thickness of Female that of Male (eg. 1mm 2mm), area coded in red == cortical thickness of Female that of Male (eg. 3mm of Female 2mm of Male). Jenni On Wed, 9 May 2007, Ruiwang Huang wrote: Hi Jenni Thanks a lot for your reply. Following the descriptions on FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) the 'color scale bar' indicates area coded in blue == cortical thickness of Female that of Male (eg. 1mm 2mm), area coded in red == cortical thickness of Female
RE: [Freesurfer] Does 'color scale bar' show the cortical thickness or[-log10(p)]?
Hi Rhuang, On that particular page the color bar is showing the sigificance (-log10(p)) for the group difference in that example. However, if you were displaying a cortical thickness map for an individual subject the color bar would then be showing the cortical thickness values (in mm). It is showing the negative values to indicate the direction of the effect. Because of the way this analysis was set up the blue regions show areas where older subjects are significantly thinner than younger subjects and the red regions show areas where younger subjects are significantly thinner than older subjects. Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ruiwang Huang Sent: Wednesday, May 09, 2007 4:20 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Does 'color scale bar' show the cortical thickness or[-log10(p)]? Dear All, I am puzzled by the meaning of 'color scale bar', which appears in the first figure of the FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) Could you please let me know the meaning of colorbar? Does the 'color scale bar' show the cortical thickness or [-log10(p)]? Why the colorbar indicates the positive and negative value in the first figure? Many thanks in advance Rhuang ___ 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] Does 'color scale bar' show the cortical thicknessor[-log10(p)]?
Hi, I'm not sure where you are getting the descriptions below. This statistical map on the surface is actually looking at the correlations of thickness and age, not gender. Can you be more specific as to what you are refering to with the following descriptions: the 'color scale bar' indicates area coded in blue == cortical thickness of Female that of Male (eg. 1mm 2mm), area coded in red == cortical thickness of Female that of Male (eg. 3mm of Female 2mm of Male). Jenni On Wed, 9 May 2007, Ruiwang Huang wrote: Hi Jenni Thanks a lot for your reply. Following the descriptions on FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) the 'color scale bar' indicates area coded in blue == cortical thickness of Female that of Male (eg. 1mm 2mm), area coded in red == cortical thickness of Female that of Male (eg. 3mm of Female 2mm of Male). Could you please tell me whether my understanding is correct or not? Best wishes Rhuang On Wednesday 09 May 2007 13:38, Jenni Pacheco wrote: Hi Rhuang, On that particular page the color bar is showing the sigificance (-log10(p)) for the group difference in that example. However, if you were displaying a cortical thickness map for an individual subject the color bar would then be showing the cortical thickness values (in mm). It is showing the negative values to indicate the direction of the effect. Because of the way this analysis was set up the blue regions show areas where older subjects are significantly thinner than younger subjects and the red regions show areas where younger subjects are significantly thinner than older subjects. Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ruiwang Huang Sent: Wednesday, May 09, 2007 4:20 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Does 'color scale bar' show the cortical thickness or[-log10(p)]? Dear All, I am puzzled by the meaning of 'color scale bar', which appears in the first figure of the FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) Could you please let me know the meaning of colorbar? Does the 'color scale bar' show the cortical thickness or [-log10(p)]? Why the colorbar indicates the positive and negative value in the first figure? Many thanks in advance Rhuang ___ 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] Does 'color scale bar' show the cortical thicknessor[-log10(p)]?
Hi, So the contrast used to perform this statistical test kept the two groups (male and female) constant and only looked for an interaction between thickness and age. So in this case the blue is where thickness and age are negatively correlated (as the age goes up the cortex gets thinner) and the red regions show areas where thickness and age are positively correlated (as the age goes up the cortex gets thicker). This is based on the contrast used to create the sig.mgh, shown in session 1a under day 2. Does this help? Jenni On Wed, 9 May 2007, Ruiwang Huang wrote: Hi Jenni, Many thanks for message. I tried to go through the Freesurfer Tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial) There are three sessions in Day-2, including Session_1a and Session_1b. In Session_1a (FreeSurfer Tutorial: Group Analysis), the FSGD file was presented as a table. Several columns corresponds to # A BC # subject Age Gender Session_1b follows Session_1a. In Session_1b (just below the first figure), the sentence ' Next, load FSGD file lh.gender_age.glmdir/y.fsgd in the same directory by selecting File - Load Group Descriptor File. ' implies the blue/red areas relating to the two groups (M, F), I think. I would like to know which group (gender: M, F) has got thin thickness at the blue/red area in the first figure? Any further suggestions please? Rhuang On Wednesday 09 May 2007 19:16, Jenni Pacheco wrote: Hi, I'm not sure where you are getting the descriptions below. This statistical map on the surface is actually looking at the correlations of thickness and age, not gender. Can you be more specific as to what you are refering to with the following descriptions: the 'color scale bar' indicates area coded in blue == cortical thickness of Female that of Male (eg. 1mm 2mm), area coded in red == cortical thickness of Female that of Male (eg. 3mm of Female 2mm of Male). Jenni On Wed, 9 May 2007, Ruiwang Huang wrote: Hi Jenni Thanks a lot for your reply. Following the descriptions on FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) the 'color scale bar' indicates area coded in blue == cortical thickness of Female that of Male (eg. 1mm 2mm), area coded in red == cortical thickness of Female that of Male (eg. 3mm of Female 2mm of Male). Could you please tell me whether my understanding is correct or not? Best wishes Rhuang On Wednesday 09 May 2007 13:38, Jenni Pacheco wrote: Hi Rhuang, On that particular page the color bar is showing the sigificance (-log10(p)) for the group difference in that example. However, if you were displaying a cortical thickness map for an individual subject the color bar would then be showing the cortical thickness values (in mm). It is showing the negative values to indicate the direction of the effect. Because of the way this analysis was set up the blue regions show areas where older subjects are significantly thinner than younger subjects and the red regions show areas where younger subjects are significantly thinner than older subjects. Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ruiwang Huang Sent: Wednesday, May 09, 2007 4:20 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Does 'color scale bar' show the cortical thickness or[-log10(p)]? Dear All, I am puzzled by the meaning of 'color scale bar', which appears in the first figure of the FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) Could you please let me know the meaning of colorbar? Does the 'color scale bar' show the cortical thickness or [-log10(p)]? Why the colorbar indicates the positive and negative value in the first figure? Many thanks in advance Rhuang ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] problem of group analysis
Hi, What was the exact command you were trying to run? Jenni _ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Wang, Xin Sent: Thursday, May 03, 2007 12:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] problem of group analysis Hello, Group I have a question about mri_glmfit. I can not run this commend on my data. An error MatrixReadTxT: could not scan value [1] [2] file exists ERROR: loading C age.mat appeared. I do not know what is wrong. The only warning I saw is ERROR: cound not find volume $SUBJECTS_DIR/average/surf/../mri/orig. Does it exist? when I ran mri_surf2surf. I am doing group comparison of cortical thickness on 2X2 data. The following is my fsgd.txt and *.mat. GroupDescriptorFile 1 Title thick vs group Class group1 Class group2 Variables age Input APL02R700 group1 48 Input APN02G650 group1 35 Input APN02G700 group2 35 Input APN03L700 group2 30 DefaultVariable age age.mat: -1, 1, 0 If anyone know what is wrong in my analysis, please help. Thank you in advance, Xin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] about the Gray matter volume
This is reported in the ?h.aparc.stats file that is generated when the parcellation is run. Jenni _ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of hankee Sent: Sunday, April 29, 2007 8:43 AM To: freesurfer Subject: [Freesurfer] about the Gray matter volume How to calculate the total gray matter volume of the brain using FreeSurfer software ? hankee， mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] 2007-04-29 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] about the Gray matter volume
Hankee, mris_volume will simply return the volume of the surface you request. You will have to do the subtraction, pial minus white, yourself. Jenni _ From: hankee [mailto:[EMAIL PROTECTED] Sent: Sunday, April 29, 2007 12:24 PM To: Jenni Pacheco Subject: Re: (瑞星提示-此邮件可能是垃圾邮件)RE: [Freesurfer] about the Gray matter volume I can't see the total gray matter volume in the ?h.aparc.stats file.If I run the mris_volume ?h.surface command in the subjid/surf directory, It will produce the new file in this directory? which data will include in this file? After that I use the formula:gm volume = pial volume - white volume to create the total gray matter volume? Am I right? Thank you very much! hankee hankee， mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] 2007-04-30 - Original Message - From: Jenni mailto:[EMAIL PROTECTED] Pacheco To: duhanjian mailto:[EMAIL PROTECTED] Sent: 2007-04-29, 22:39:59 Subject: (瑞星提示-此邮件可能是垃圾邮件)RE: [Freesurfer] about the Gray matter volume Hi Hankee, You can use mris_volume to find this if you can’t get it from the aparc.stats: https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats Jenni _ From: hankee [mailto:[EMAIL PROTECTED] Sent: Sunday, April 29, 2007 10:01 AM To: Jenni Pacheco Subject: Re: (瑞星提示-此邮件可能是垃圾邮件)RE: [Freesurfer] about the Gray matter volume But I only can see the the total white matter volume in the ?h.aparc.stats file,don't have total gray matter volume it the this file. Thank you! hankee [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] 2007-04-29 - Original Message - From: Jenni Pacheco mailto:[EMAIL PROTECTED] To: duhanjian,'freesurfer' mailto:[EMAIL PROTECTED],freesurfer@nmr.mgh.harvard.edu Sent: 2007-04-29, 21:16:25 Subject: (瑞星提示-此邮件可能是垃圾邮件)RE: [Freesurfer] about the Gray matter volume This is reported in the ?h.aparc.stats file that is generated when the parcellation is run. Jenni _ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of hankee Sent: Sunday, April 29, 2007 8:43 AM To: freesurfer Subject: [Freesurfer] about the Gray matter volume How to calculate the total gray matter volume of the brain using FreeSurfer software ? [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] 2007-04-29 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Grainy thickness ribbon
Hi Burak, Your best bet is to keep this question going to the list. I'll leave it for Bruce, or Doug, or Nick to answer. Jenni _ From: Burak Ozkalayci [mailto:[EMAIL PROTECTED] Sent: Thursday, April 19, 2007 7:11 AM To: Jenni Pacheco Subject: Re: [Freesurfer] Grainy thickness ribbon Hi Jenni, In fact no. I need a ribbon whose voxel values are assigned according to the cortical thickness. the mri/?h.ribbon.mgz is just a binary mask for the ribbon (as you can check from the cortical thickness ribbon images I attached to my former mail). I think that the -fillribbon option for the mri_surf2vol function does not work properly when the pial surface is selected like: mri_surf2vol --volreg reg.dat --surfval ../surf/lh.thickness_max --hemi lh --template ./orig/001.mgz --outvol leftThickness_max_filled_pial.nii --fillribbon --surf pial the ribbon is filled in the normal directions of the surface which seem to give correct results for the white surface but for pial surface the direction of the normals should be reversed I think. By comparing the images I attached to the former mail, you can see that the filled ribbon from the pial and the white surface is different. I hope I could make it clear. Thanks again for any response, help. Burak Jenni Pacheco wrote: Hi Burak, I'm not really sure what you are trying to do, but a cortical ribbon is generated as part of the recon process, mri/?h.ribbon.mgz. Perhaps this is what you are looking for? Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of burak ozkalayci Sent: Wednesday, April 18, 2007 6:39 AM To: Freesurfer Mailing List Subject: [Freesurfer] Grainy thickness ribbon Dear surfers, I try to get a thickness map of the cortex by using the mri_surf2vol function. However when I used it like : mri_surf2vol --volreg reg.dat --surfval ../surf/lh.thickness_max --hemi lh --template ./orig/001.mgz --outvol leftThickness_max_filled_pial.nii --fillribbon it generates a very grainy map. I think that those unassigned voxels are not hit by the normals of vertices on the white surface. To compensate it I tried to fill the ribon with the normals originated from the pial surface by : mri_surf2vol --volreg reg.dat --surfval ../surf/lh.thickness_max --hemi lh --template ./orig/001.mgz --outvol leftThickness_max_filled_pial.nii --fillribbon --surf pial however the ribbon I get is shifted to the outer side of the cortex. I think the normals of the pial are oriented to show outer space of the cortex and they hit the voxels at the outerspace. I also attached the thickness maps of the ribbon I get from the white and the pial surfaces and the T1 image. They are the same slice of the volume, and you can see that pial one passes beyond the pial surface in general. In the help of mri_surf2vol for the fillribbon option, it is explained as iterate projfrac from 0 to 1. And when the code is running I saw that iteration has a 0.05 step. I wonder whether is it possible to define the stepsize and the range for example 0 to -1 to reverse the hitting voxels. Thanks in advance. Burak ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Grainy thickness ribbon
Hi Burak, I'm not really sure what you are trying to do, but a cortical ribbon is generated as part of the recon process, mri/?h.ribbon.mgz. Perhaps this is what you are looking for? Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of burak ozkalayci Sent: Wednesday, April 18, 2007 6:39 AM To: Freesurfer Mailing List Subject: [Freesurfer] Grainy thickness ribbon Dear surfers, I try to get a thickness map of the cortex by using the mri_surf2vol function. However when I used it like : mri_surf2vol --volreg reg.dat --surfval ../surf/lh.thickness_max --hemi lh --template ./orig/001.mgz --outvol leftThickness_max_filled_pial.nii --fillribbon it generates a very grainy map. I think that those unassigned voxels are not hit by the normals of vertices on the white surface. To compensate it I tried to fill the ribon with the normals originated from the pial surface by : mri_surf2vol --volreg reg.dat --surfval ../surf/lh.thickness_max --hemi lh --template ./orig/001.mgz --outvol leftThickness_max_filled_pial.nii --fillribbon --surf pial however the ribbon I get is shifted to the outer side of the cortex. I think the normals of the pial are oriented to show outer space of the cortex and they hit the voxels at the outerspace. I also attached the thickness maps of the ribbon I get from the white and the pial surfaces and the T1 image. They are the same slice of the volume, and you can see that pial one passes beyond the pial surface in general. In the help of mri_surf2vol for the fillribbon option, it is explained as iterate projfrac from 0 to 1. And when the code is running I saw that iteration has a 0.05 step. I wonder whether is it possible to define the stepsize and the range for example 0 to -1 to reverse the hitting voxels. Thanks in advance. Burak ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] aseg visualization question
Hi, I just want to clear up some confusion about this topic. There is a difference currently between the dev (and stable) versions within the Martinos Center and versions that have been posted for download. Some versions will require you to specify a color table, and also to use the mri/ designation before the aseg.mgz file name. Other versions will not need (and fail if you use) the mri/ designation before the aseg.mgz filename. These versions do not need a color table, as it will read one in by default. It makes the most sense (to me) to continually update the wiki pages to be current with the newest versions, so there are times when certain commands may not be the same as your version - generally nothing drastic. Sorry for any confusion the current documentation has caused. Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Doug Greve Sent: Monday, April 16, 2007 7:16 PM To: Nick Schmansky Cc: Morgan Hough; Freesurfer Mailing List Subject: Re: [Freesurfer] aseg visualization question Newer (dev) versions will use $FREESURFER_HOME/FreeSurferColorLUT.txt as the default. On Thu, 12 Apr 2007, Nick Schmansky wrote: This should work: tkmedit good_output brainmask.mgz \ lh.white -aux T1.mgz \ -aux-surface rh.white \ -segmentation mri/aseg.mgz \ $FREESURFER_HOME/FreeSurferColorLUT.txt On Thu, 2007-04-12 at 16:54 +0100, Morgan Hough wrote: I have a quick question about an error we are getting with FS 3.0.5 when we are using tkmedit as described in the tutorial to display the segmentations overlaid on the T1. tkmedit good_output brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz The first error seems to regard the new requirement that a color LUT be passed with the segmentation option. If we add tkmedit good_output brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz tkmeditColorsCMA Then the message reduces to a problem of opening the segmentation file which it says is not in the right .cor format. I assume this is a legacy error message but I am not sure if I need to rename the aseg.mgz file or pass in another option with the file type. Thanks in advance for your time. Cheers, -Morgan ___ 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ 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] erroneous 'no space left on device' error
Hi Katie, It's actually writing to /tmp, on 'whatever', which appears to be full. You should clear out some space on that so that selxavg can write it's little temporary files and then everything should be fine! whatever:jpacheco[/homes/3/jpacheco] cd /tmp/ whatever [tmp] df -h . FilesystemSize Used Avail Use% Mounted on /dev/hda2 5.8G 5.5G 0 100% / whatever [tmp] Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Kathryn Devaney Sent: Wednesday, April 04, 2007 10:59 PM To: freesurfer@nmr.mgh.harvard.edu; help Subject: [Freesurfer] erroneous 'no space left on device' error Hi all, I am trying to run an analysis in /space/stego/2/ (on machine 'whatever') and I can run mkanalysis, but when I try to run selxavg, I get the following error, in both std and dev environments: whatever:subj27/mystudy% selxavg-sess -sf sessid -df sesspar -analysis m4_fmc -noomnibus INFO: WhitenFlag = 0 -- selxavg-sess logfile is /autofs/space/stego_002/users/kdevaney/m4/subj27/mystudy/log/selxavg-sess-bo ld-m4_fmc-070404224944.log -- --- /autofs/space/stego_002/users/kdevaney/m4/subj27 Wed Apr 4 22:49:45 EDT 2007 INFO (subj27): RunList = 003 004 005 007 008 009 010 011 012 013 014 015 cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cat: /tmp/countncond.11619: No such file or directory however: whatever:subj27/mystudy% df . -h FilesystemSize Used Avail Use% Mounted on bronto:/local_mount/space/stego/2 63G 5.7G 57G 10% /autofs/space/stego_002 There is clearly plenty of space left. Any help is appreciated, thanks! Katie ___ 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] erroneous 'no space left on device' error
Glad to hear it! -Original Message- From: Kathryn Devaney [mailto:[EMAIL PROTECTED] Sent: Wednesday, April 04, 2007 11:11 PM To: Jenni Pacheco Cc: freesurfer@nmr.mgh.harvard.edu; 'help' Subject: Re: [Freesurfer] erroneous 'no space left on device' error Thank you, Jenni! It's working now. K Jenni Pacheco wrote: Hi Katie, It's actually writing to /tmp, on 'whatever', which appears to be full. You should clear out some space on that so that selxavg can write it's little temporary files and then everything should be fine! whatever:jpacheco[/homes/3/jpacheco] cd /tmp/ whatever [tmp] df -h . FilesystemSize Used Avail Use% Mounted on /dev/hda2 5.8G 5.5G 0 100% / whatever [tmp] Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Kathryn Devaney Sent: Wednesday, April 04, 2007 10:59 PM To: freesurfer@nmr.mgh.harvard.edu; help Subject: [Freesurfer] erroneous 'no space left on device' error Hi all, I am trying to run an analysis in /space/stego/2/ (on machine 'whatever') and I can run mkanalysis, but when I try to run selxavg, I get the following error, in both std and dev environments: whatever:subj27/mystudy% selxavg-sess -sf sessid -df sesspar -analysis m4_fmc -noomnibus INFO: WhitenFlag = 0 -- selxavg-sess logfile is /autofs/space/stego_002/users/kdevaney/m4/subj27/mystudy/log/selxavg-sess-bo ld-m4_fmc-070404224944.log -- --- /autofs/space/stego_002/users/kdevaney/m4/subj27 Wed Apr 4 22:49:45 EDT 2007 INFO (subj27): RunList = 003 004 005 007 008 009 010 011 012 013 014 015 cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cat: /tmp/countncond.11619: No such file or directory however: whatever:subj27/mystudy% df . -h FilesystemSize Used Avail Use% Mounted on bronto:/local_mount/space/stego/2 63G 5.7G 57G 10% /autofs/space/stego_002 There is clearly plenty of space left. Any help is appreciated, thanks! Katie ___ 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] How to edit orig surface?
Hi, What does your aseg.mgz look like? Jenni _ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of deepa preeti Sent: Monday, April 02, 2007 9:31 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] How to edit orig surface? Hi, I am trying to do cortical segmentation. But unfortunately during autorecon2 stage, in some of the scans the orig surface did not include some of the wm, even though these regions are included in wm.mgz and so, the pial surface failed to include them as well. How to edit in this case? ( because this region is already there in wm.mgz ). I have attached the brainmask wm.mgz. Any suggestions greatly appreciated. Thanks, Preeti Ramasamy. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Quality control
Hi Paul, I would have said you'll need to edit the wm, but you say you've tried. Could you send along a shot of that same exact slice but on the wm.mgz volume? thanks, Jenni On Mon, 26 Mar 2007, Doug Greve wrote: I'll leave the first question for Bruce or Jenni. The 2nd depends on what you are going to do with the talairach. If you are not going to be reporting talairach coords, then you can be quite sloppy as they are only used to create seed points for more-or-less finding the CC, pons, etc. If you are going to report talairach coords, then you only need to align the outside of the brain to the mni305. There is no perfect talairach reg, and in the best case it's going to be pretty awful:). If you get it within a centimeter, you're probably ok. doug Paul Greenberg wrote: Hello, I've got a question about cortical surfaces in the ventral regions below the basal ganglia and about tkregister output quality control. I'm using the latest version of freesurfer: freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.5 1) In the majority of my data sets, white matter surfaces near the basal ganglia rise dorsally to include large volumes of the basal ganglia (putamen, nucleus accumbens, both hemispheres) - attached image. This results in inaccurate cortical volumes and thickness estimates from the surface based data for these regions. How can I compensate for these surface problems in order to get the best possible estimate of total cortical volume? I've tried editing the white matter manually and this has little effect on the locations of white matter surfaces in the basal ganglia. 2) I'm having a difficult time knowing how to determine if the talairach registration is good enough for each data set, and judging the quality of my manual edits using tkregister. Could you post an additional series of tiff or jpg images (multiple parasagittal, coronal, horizontal) showing how cortical surfaces and movable volumes are supposed to align in each plane? It would help to see examples of registrations that are perfect, good enough not to edit, and bad enough to require adjustment. Thanks very much!, Paul ___ 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] aseg.stats
Hi Joan, The aseg.mgz file is the actual segmentation volume. FreeSurferColorLUT.txt is simply a text look up table with label numbers, colors, and identifying tags. In the most recent versions of Freesurfer you do not need to include this in your command line, it will open with this automatically, but if you wanted to specify the look up table you would do so after the segmentation volume: -segmentation volume lookup table As for the aseg.stats, not sure why it's empty. This is a simple text file (more or cat will open it) - but there is nothing there? Have you tried to just run: recon-all -segstats -s subjid Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Joan Fisher Sent: Sunday, March 25, 2007 10:09 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] aseg.stats It turns out that the segmentation is fine in aseg.mgz (although for some reason I am unable to view the segmentation with FreeSurferColorLUT.txt as it says it wasn't valid or wasn't found even though it is in my directory) and yet the aseg.stats table was not generated. (Doug?) How does one generate a table if the aseg.mgz file is accurate but the aseg.stats file is not? Many thanks, Joan ___ 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] Two problems
Hi Juergen, The error you are getting here: ERROR: Flag -Patient03_2001 unrecognized. -Patient03_2001 -all ERROR: Flag -Patient03_2002 unrecognized. -Patient03_2002 -all Is because you are using '-Patient03_2001' as a flag in your command, which is not a valid flag. What is it that you are trying to run? I am making a guess that you might be trying to run the entire recon process on your subject, if that is the case you want to use the command: recon-all -all -s Patient03_2001 Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Juergen Haenggi Sent: Tuesday, March 20, 2007 7:35 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Two problems Dear Freesurfer users I have two problems: I upgraded Freesurfer (from Linux CentOS4 v3.0.3 to v3.0.5) and recognized that the foreach command do not work any longer. The following error occured: ERROR: Flag -Patient03_2001 unrecognized. -Patient03_2001 -all ERROR: Flag -Patient03_2002 unrecognized. -Patient03_2002 -all The other problem concerns the selection of the tcsh shell on Mac OS X. I can change from a bash to a tcsh shell. Thanks for help in advance Best regards Juergen --- Juergen Haenggi, Ph.D. student Department of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) [EMAIL PROTECTED] (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) --- ___ 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] missing cerebellum
Hi Derin, I guess it depends on your surfaces. Sometimes, with the cerebellum missing, they aren't accurate especially in some posterior and inferior regions. If they are fine then you probably only need to rerun the aseg (recon-all -subcortseg -s subjid). If the surfaces need to be fixed then you will have to do all of autorecon2 and autorecon3. Jenni On Wed, 7 Mar 2007, Derin Cobia wrote: I noticed that one of our subjects made it through the processing stream (successfully) with the cerebellum missing, thus creating a bad aseg.mgz. I filled it back in, and was wondering if I needed to reprocess it completely under autorecon2 and 3 again, or just run -aseg and whatever else it needed. Thanks. -Derin ___ 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] Reprocessing the data with new FS release
Hi Antonio, Your edits will be preserved whenever you run recon-all (any part of it) unless you specifically indicate that they shouldn't by using one of the -clean... flags. I would recommend re-running the entire thing recon-all -all to be sure that all of your subjects are processed with the same version. Jenni On Wed, 21 Feb 2007, Gallo, Antonio (NIH/NINDS) [F] wrote: Hi all, Since we have updated Freesurfer with the last (3.0.5) release, we were wondering at which point we should reprocess (i.e autorecon1, autorecon2, etc) our data in order to retain the edits we have made using the previous version. Thank you, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 *** ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Legacy flag
Hi Alex, The legacy flag needs to be used with old data (pre version 3) in order to update it to version three compatible data. You want to specifically keep pre version 3 data separate from version 3 data, as folding patterns and atlases are intrinsically different. Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Fornito, Alexander Sent: Sunday, February 11, 2007 10:45 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Legacy flag Hi, I was just seeking some clarification re: the legacy flag in recon-all. Can I use it on subjects procssed with older versions of Freesurfer to reconstruct surfaces that will be consistent with those generated with older versions (i.e., I can collapse data from the two versions), or is the legacy flag intended to allow new versions of recon-all to be used on old data, effectively 'updating' the surfaces (meaning they should not be analyzed together with data generated using older versions). Thanks, Alex Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] ___ 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] converting from siemens IMA to mgz
Hi Binyam, I think you need to give it the IMA file name, so something like: mri_convert -it siemens -ot mgz 001/file.IMA 001.mgz If that doesn't work there are other options we can try. Jenni On Fri, 2 Feb 2007, Binyam Nardos wrote: Hi all, I just loaded raw structural scans into one of my subject directories. They are of siemens IMA format and I used the following command: mri_convert -it siemens -ot mgz 001/ 001.mgz I then got the following error: reading from 001/... ERROR: could not parse 001/ ERROR: siemensRead(): 001/ I tried finding similar problems in the threads but nothing yet. Appreciate any help, Binyam Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601 The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] 1) annot files on T1 and 2) seed points
Hi Joan, 1) When I call up aparc+aseg on the T1 image, I get the cortex that has been parcellated, but I do not get the parcellation -- that information is in the .annot files that seem to be viewable only using tksurfer and not tkmedit. Is there a way to see the full parcellation on T1.mgz? The .annot files can only be loaded on top of a surface in tksurfer. As you saw, the aparc+aseg.mgz is a segmentation that can be viewed in tkmedit, over the T1.mgx volume. What information were you hoping to get from the .annot file loaded on the T1.mgz? 2) Trying to run freesurfer on only the Right hemisphere on a child who has no left hemisphere, I've run into the problem where freesurfer wants to divide the intact hemisphere into half. When I try to use the seed points, it hasn't fixed the problem. Is this a problem of syntax or something else? These are the commands I used that I thought would work: mri_fill -C -93 -18 89 -P -35 -22 28 -rh -59 -23 105 subjects/005/mri.mgz subjects/005/mri/filled.mgz That part seemed to work, then: recon-all -hemi rh -s 005 -autorecon2-wm -autorecon2-wm starts with the mri_fill step, effectively re-doing what you had done in your own command, but without the extra options. Try running your mri_fill command again, and if the resulting filled.mgz volume looks ok, then run: recon-all -hemi rh -s 005 -autorecon2-wm -nofill which will use your filled.mgz volume from the mri_fill step and run tessellate onward. If you are using a very recent dev release there is a flag to start at this point: recon-all -hemi rh -s 005 -autorecon2-perhemi Jenni ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] surf2surf
Hi Chacko, Can you copy the exact command line straight from your terminal along with the error output and paste it here. Thanks, Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Chacko Cherian Sent: Monday, January 29, 2007 7:34 PM To: Freesurfer Subject: [Freesurfer] surf2surf Hello users, I wanted to use mri_surf2surf for surface smoothing but it gives me an error saying --s is not an option. mri_surf2surf --hemi lh \ --s average \ --sval lh.gender_age.thickness.mgh \ --fwhm 10 \ --tval lh.gender_age.thickness.10.mgh it didnt work with srcsubject either.The average subject is in the $SUBJECTS_DIR. THAnks in advance Chacko. Don't get soaked. Take a quick peak at the forecast with the Yahoo! Search weather shortcut. http://tools.search.yahoo.com/shortcuts/#loc_weather ___ 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] the dorsolateral prefrontal cortex
Hi Li, This page here has instructions on how you can make a label on your surface, with tksurfer. https://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide_2fTkSurferWorkingWithData_2fTkSurferLabel once you have made and saved a label you can use mris_anatomical stats to get the information you are looking for from this label. https://surfer.nmr.mgh.harvard.edu/fswiki/mris_5fanatomical_5fstats Hope this helps. Jenni On Tue, 23 Jan 2007 [EMAIL PROTECTED] wrote: Hello All, We want to get the information about the dorsolateral prefrontal cortex. However, two parcellation maps (?h.aparc.annot and ?h.aparc.a2005s.annot)didn't show this structure directly. Can you please tell me how to draw the ROI for the dorsolateral prefrontal cortex in the Final Surface of the brain? and how to get values for thickness and volume for this structure? Thanks, Li ___ 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] Coloring problem after autorecon2
Hi Niels, This looks like what would happen to the aseg if it was run on a subject who was missing a cerebellum. Did you run the aseg before you manually fixed the cerebellum and not re-run it? If so, the aseg needs to be rerun (in fact, all of -autorecon2 does). Another thought is, how did you manually edit to fix the missing cerebellum? Did you use command line procedures, like increasing the preflooding height or using the option -wsatlas? Or did you do it by hand with the edit voxels tool in tkmedit? If you've done it by hand, were you on the appropriate volume (brainmask.mgz) and did you do it for every slice that there was missing cerebellum? My recommendation for fixing a completely missing cerebellum is always to use the command line. Increasing the preflooding height (or using the atlas flag) should work everytime: recon-all -skullstrip -wsthresh 35 -clean-bm -s subject recon-all -skullstrip -wsatlas -clean-bm -s subject Jenni On Fri, 5 Jan 2007, Niels Bergsland wrote: Hi list, After completing autorecon1, I found the cerebellum missing and I manually editted for this case. But I found after autorecon2, the cerebellum were not filled with appropriate color at all. I have uploaded a picture to my webspace. Please see: http://www.lucidthoughts.org/download/color_failure.png I can also upload the dicoms to the drop box if this would help. Thanks! Niels Bergsland ___ 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] control points and white matter edits
Hi Paul, The inferior temporal regions are the trickiest, especially in low quality scans - without seeing any images, you may have achieved as close as you are going to get. Be careful with control points, more is not always better, quality over quantity, you want to be sure you have put them in correct locations, not on partial volumed voxels, and only in regions that are supposed to be wm. While adding voxels to the wm volume will have some impact on where the final surface lays, it is also dependant on finding the best intensity gradient. If your scans are lower quality with intensity troubles that will likely trump any edits you've made. If you'd like to upload one of your subjects I am happy to take a look at it - although I will be out of town all next week so it might take me a while to get to it. Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Paul Greenberg Sent: Friday, January 05, 2007 7:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] control points and white matter edits Hi all, I'm having trouble getting accurate white and pial surfaces in inferior temporal regions on a few lower quality scans with significant intensity variation. I've added hundreds of control points and drawn in white matter in these regions when control points failed to recover unlabeled cortex, but when re-running the scripts with either -autorecon2-wm, or -autorecon2-cp, followed by -autorecon3 the surfaces are still not accurate. Are there other interventions I can to to get more accurate surfaces? If you manually add white matter why will the regenerated white matter surfaces not always extend around the hand drawn parts? Thanks, Paul ___ 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] Talairach problem
Hi Akram, Can you copy one of these subjects to: /space/tensor/14/users/jenni/testdir and I will play with it and see what I can do - I have some scripts that might do something. Jenni On Fri, 1 Dec 2006, Akram Bakkour wrote: Hi, I'm running everything on thigpen. setenv SUBJECTS_DIR /space/thigpen/8/users/akram/ADNI_processing I'm having trouble fixing the talairach of these 4 subjects: 005_S_0572 023_S_0030 116_S_0382 126_S_0405 I've tried: mri_convert brainmask.mgz brainmask.mnc mritotal -protocol icbm brainmask.mnc brainmask.xfm cp brainmask.xfm transforms/talairach.xfm This worked for a few other subjects which had similar talairach problems, but didn't work for these four. I tried loading them in tkregister2: tkregister2 --mgz --s $subject --fstal but the volume won't load. Any suggestions how to fix these talairachs? Thanks! Akram. ___ 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] command for aseg stats to export to spreadsheet(excel)
You can use asegstats2table. Jenni Pacheco, M.A. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Bldg. 149, 13th Street, CNY 2301 Charlestown, MA 02129 [EMAIL PROTECTED] -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Chacko Cherian Sent: Wednesday, November 22, 2006 5:02 PM To: Freesurfer Subject: [Freesurfer] command for aseg stats to export to spreadsheet(excel) Hello Users, I wanted to know if there is a command to directly export the aseg-stats table to a spreadsheet rather than cuttting and pasting. And wishing all of you a very happy Thanksgiving and a great weekend!! Regards Chacko. Yahoo! Music Unlimited Access over 1 million songs. http://music.yahoo.com/unlimited ___ 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] command for aseg stats to export to spreadsheet(excel)
There should be some help associated with it, try simplying typibg asegstats2table or maybe asegstats2table --help Jenni Pacheco, M.A. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Bldg. 149, 13th Street, CNY 2301 Charlestown, MA 02129 [EMAIL PROTECTED] -Original Message- From: Chacko Cherian [mailto:[EMAIL PROTECTED] Sent: Wednesday, November 22, 2006 5:16 PM To: Jenni Pacheco Cc: Freesurfer Subject: Re: [Freesurfer] command for aseg stats to export to spreadsheet(excel) Thank you Jenni. How do i use asegstats2table?What is the command?Is it a tcl script file?If so,could you also mention where it is located. Regards Chacko. - Original Message From: Jenni Pacheco [EMAIL PROTECTED] To: Chacko Cherian [EMAIL PROTECTED]; Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, November 22, 2006 3:04:28 PM Subject: RE: [Freesurfer] command for aseg stats to export to spreadsheet(excel) You can use asegstats2table. Jenni Pacheco, M.A. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Bldg. 149, 13th Street, CNY 2301 Charlestown, MA 02129 [EMAIL PROTECTED] -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Chacko Cherian Sent: Wednesday, November 22, 2006 5:02 PM To: Freesurfer Subject: [Freesurfer] command for aseg stats to export to spreadsheet(excel) Hello Users, I wanted to know if there is a command to directly export the aseg-stats table to a spreadsheet rather than cuttting and pasting. And wishing all of you a very happy Thanksgiving and a great weekend!! Regards Chacko. Yahoo! Music Unlimited Access over 1 million songs. http://music.yahoo.com/unlimited ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Cheap talk? Check out Yahoo! Messenger's low PC-to-Phone call rates. http://voice.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] white matter segmentation
Hi Jenny, It would depend on what the real cause of the problem is, whether you would edit the wm.mgz or something else. It seems, from your emails, that you think the wm.mgz looks ok, but the ?h.white surface (which appears as a yellow line when displayed in tkmedit) does not follow it. When you load the ?h.orig or the ?h.orig.nofix into tkmedit, does this line follow the white matter boundary better, worse, or the same as your ?h.white surface. I might have an easier time helping you figure this out if I could take a look at this particular subject. Could you upload the entire subject (with all outputs and sub dirs) on our file drop. https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Thanks, Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jenny Kirchner Sent: Thursday, November 09, 2006 1:52 PM To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] white matter segmentation Hi Bruce, I am running the latest version of Freesurfer. I am sorry but I am still not really sure as to how to fix the wrong segmentation. Even if I see that there was an error before the topology correction (which basically means that the correction made it worse?), how and where do I correct it. As I said, the wm.mgz looks fine, it's just that the ?h.white segmentation does not correspond to the wm.mgz. So the basic question is, if I do the edits in the brainmask or in the wm.mgz. Thanks again! Jenny On 11/9/06, Bruce Fischl [EMAIL PROTECTED] wrote: Hi Jenny, it's probably the topology correction that is causing your problem. What version are you running? Look for a topological error in that region (i.e. a hole or a handle). You can usually see the defects on the ?h.inflated.nofix surface. Load it with: tksurfer -orig orig.nofix $subject $hemi inflated.nofix this will let you use save point in tksurfer and goto point in tkmedit to find and fix the location of the defect (in the wm.mgz volume) cheers, Bruce On Thu, 9 Nov 2006, Jenny Kirchner wrote: Hi Bruce, thanks for the quick response. I am still not quite sure though where to do the edits. On the brainmask? I originally thought that I have to do the edits of the white matter segmentation on the wm.mgz. However, on the wm.mgz the white matter segmentation looks fine (i.e., the superior temporal gyrus is correctly classified as tissue). Thanks for your help. Best, Jenny On 11/9/06, Bruce Fischl [EMAIL PROTECTED] wrote: Hi Jenny, the ?h.white is pretty much our final say one where the gray/white boundary is, and is usually substantially more accurate than the wm.mgz. Your dataset has a lot of motion artifact, but mostly looks okay except for the superior temporal gyrus, which has been chopped. You'll need to edit this back in. What version are you running? As for editing, an incorrect white surface can lead to an incorrect pial one, so you're probably better off rerunning things before trying to edit the pial. Also, the rerunning after pial editing is fast relative to the whole process, just a couple of hours I think. cheers, Bruce On Wed, 8 Nov 2006, Jenny Kirchner wrote: Hi, I am working on a case for which I have run autorecon 2. Edits seem necessary on both the pial surface and the white matter segmentation. I am now wondering if it is better to first do the white matter edits and then run autorecon 2 again to see if the pial surface errors improved or if it is more economic to do the pial surface edits in the same step. I also have a question concerning the differences in segmentation between the wm.mgz and the ?h.white. I am attaching two screenshots for you to be able to see it. The wm.mgz is showing white matter, which in the lh.white (loaded on top of the brainmask.mgz) is not defined as white matter as shown by the yellow line. (See temporal pole of the left hemisphere). I am wondering which of the both segmentations is correct, the wm.mgz version or the lh.white version and where exactely I have to do the edits. Thanks a lot for your help! Best, Jenny ___ 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] is this ok?
Hi Chacko, Can you upload one subject to our filedrop so that I can have a look. https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Thanks, Jenni On Mon, 6 Nov 2006, Chacko Cherian wrote: Thanks Bruce. I Am using version 3.0.3,..wat can i do to to get better pial surface images? IS it something to do with the skull stripping stage or is it the motion artifacts which cause a reduction in the overall resoution of the image? Chacko. - Original Message From: Bruce Fischl [EMAIL PROTECTED] To: Chacko Cherian [EMAIL PROTECTED] Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Monday, November 6, 2006 4:25:05 PM Subject: Re: [Freesurfer] is this ok? Hi Chako, I wouldn't worry too much about the inflated - it looks okay. Probably a result of the large motion artifact in your data. The pial surface is more worrisome - what version are you running? They are usually *much* better than this. Bruce On Mon, 6 Nov 2006, Chacko Cherian wrote: Hello freesurer users, Is it ok to have such edges on the inflated surface?Is there something I can do to rectify this? THe second image is the brainmask and wm volume as seen using tkmedit. (tkmedit subj1 brainmask.mgz lh.white -aux wm.mgz -aux-surface rh.white) THanks in advance Best, Chacko Cherian ___ 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] Aseg inforrmation
Hi Aju, The BrainMaskVOl in the aseg.stats file uses all of the voxels that are in the brainmask.mgz volume. the BrainSegVol uses all of the voxels that are labeled in the aseg.mgz segmentation. Jenni On Fri, 27 Oct 2006, Ajith Kumar U wrote: Hi Freesurfers, I have some questions about the aseg.stats file. What do the brainmask and brain segmentation volumes refer to? Is there a helpfile that defines these. Thanks Aju. ** Mr.Ajith Kumar U Junior Research Fellow, Department of Audiology, All India Institute of Speech and Hearing, Naimisham Camppus, Manasagangothri, Mysore,570006 INDIA. ** ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Freesurfer crash
Title: Freesurfer crash Hi Ingo, Sometimes when you click to open the file menu you can actually click really quickly on quit, which can open up right under your mouse depending on where all the windows are on the screen. Try clicking and holding your mouse button down while the mean opens and then move away from the quit button. Jenni From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Wolf, Ingo Sent: Sunday, October 22, 2006 5:48 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer crash Hi everyone. I habe a rather obscure problem. After loading a volume with tkmedit, I tried to open the file menu via the file button in the menu bar and instanly freesurfer crashes. The software is installed on a Apple PowerMac OSX 10.4.6, Dual G5 2.5 GHz, Memory 2.5 GB. I wonder if this is a hardware problem? Thanks Ingo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] recon-all error
It appears that you are still having a problem because there are spaces in the name of your dicom file: mri_convert /root/Cath/ADULT /usr/local/freesurfer/subjects/Cath01/mri/orig/001.mgz unknown file type for file /root/Cath/ADULT Its looking to convert the file /root/Cath/ADULT which it cant identify as a dicom because its actually named ADULT 14-0005-0001-0001.dcm There may be some more fixes you could introduce to your recon-all script, but you could also try renaming your dicoms to something without a space and use those that might be easier. Jenni From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Anil Roy Sent: Monday, October 09, 2006 5:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all error Thanks a lot. recon-all runs after applying the fix. However, I seem to have run into a different error. Here is the output after running recon-all on the same dcm file: # recon-all -i /root/Cath/ADULT\ 14-0005-0001-0001.dcm -subjid Cath01 -sd /usr/local/freesurfer/subjects INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux dhcp-129-105-146-165.speech.northwestern.edu 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 i686 i686 i386 GNU/Linux WM removal version /usr/local/freesurfer/subjects/Cath01 mri_convert /root/Cath/ADULT /usr/local/freesurfer/subjects/Cath01/mri/orig/001.mgz mri_convert /root/Cath/ADULT /usr/local/freesurfer/subjects/Cath01/mri/orig/001.mgz unknown file type for file /root/Cath/ADULT Linux dhcp-129-105-146-165.speech.northwestern.edu 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Mon Oct 9 16:01:02 CDT 2006 The files I'm using are the T1 weighted anatomical images from a 3T Seimens scanner. The only operation done on the files prior to the recon-all procedure is to rename them. Thanks, Anil. On 10/6/06, Nick Schmansky [EMAIL PROTECTED] wrote: Anil, It does seem that the recon-all script does not handle input files containing spaces.However, you can fix your recon-all script by editing it and replacing the 'case -i' section with this: case -i if( $#argv 1) goto arg1err; set InputVol = $argv[1]; shift; if(! -e $InputVol) then echo ERROR: cannot find $InputVol exit 1; endif if(! -r $InputVol) then echo ERROR: $InputVol exists but is not readable exit 1; endif set InVolDir= `dirname$InputVol`; set InVolBase = `basename $InputVol`; pushd $InVolDir /dev/null set InVolDir = `pwd`; popd /dev/null set InputVol = $InVolDir/$InVolBase; set InputList = ($InputList $InputVol); set DoConvertInput = 1; breaksw The change is the inclusion of double-quotes on certain variables. This fix will appear in the next stable release. Nick On Fri, 2006-10-06 at 16:25 -0500, Anil Roy wrote: Hello all, I get the following error when I feed in a dicom file into recon-all. The dicom file is in a directory with 159 other dcm files. Can you please tell me how to rectify this or what the source of the error is. [EMAIL PROTECTED] freesurfer]# recon-all -i /root/Cath/ADULT\ 14-0005-0001-0001.dcm -subjid E001 -sd /usr/local/freesurfer/subjects -all set: Variable name must begin with a letter. Thanks, Anil. ___ 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] Odd brainmask.auto and brainmask data and behavior
Hi Graham, I'd appreciate if someone could explain the brainmask.auto.mgz, and brainmask.mgz logic? This is a feature that we use to track the edits that you make to the brainmask.mgz volume and allow recon-all to run while maintaining your edits by default. There are a few different scenarios - I'll try and outline them here: *When you run recon-all for the first time on a new set of data: the '-skullstrip' step will generate a brainmask.auto.mgz, and since there is no brainmask.mgz created yet it will copy the brainmask.auto.mgz to brainmask.mgz - they should be the same at this point. *If you run recon-all again on this set of data: the '-skullstrip' step will generate a new brainmask.auto.mgz, overwriting the old one. Then, because there is a brainmask.mgz present it will compare this file to the brainmask.auto.mgz and if there is a difference it will use the brainmask.mgz in subsequent steps. (the difference being something that you edited and wanted to be in there that wasn't done automatically in the '-skullstrip' step.) *If you are running the latest version of recon-all on OLD legacy data (using the '-legacy' flag): your old brain.mgz volume will be copied to brainmask.mgz. the '-skullstrip' step will generate a new brainmask.auto.mgz, overwriting the old one. Then, because there is a brainmask.mgz present it will compare this file to the brainmask.auto.mgz and if there is a difference it will use the brainmask.mgz in subsequent steps. (the difference being edits you made toyour legacy data that you wanted to be in there). Somewhat alarming is that in a brainmask volume, I'm seeing some full-brightness (255) values on the edge of the mask (border of brain and nothing), which are certainly not in the input volume T1.mgz volume. Question 0: Is the detailed image data in brainmask.mgz ever used, or is it simply a zero/not-zero mask? Ie: is the meaning masked brain, or mask using non-zero values to show where brain is. I'll leave this one for someone else. If no one else answers it (because I've left an unanswered question in the middle of my reply and they didnt notice) then please post it again!!! Question 1: Is there a rationale for 255 values? I'm not sure where these are coming from in your volume - I assume you havent done any editting on this one. If they are also not in the brainmask.auto.mgz you could try running: recon-all -skullstrip -clean-bm And hopefully they'll go away. The '-clean-bm' flag will tell it to trash any edits you've done to the brainmask.mgz volume, making brainmask.auto.mgz and brainmask.mgz the same. But, as I said, I'm not sure where these extra voxels came from. That led me to look at the brainmask.auto volume, and the bad values are not there either. The recon-all script is a bit puzzling and convoluted in this area -- Question 2: It appears that the Skull Stripping section of the script uses a -keep flag on mri_watershed. This isn't explained on the wiki doc page -- what does it do? (And why does mri_watershed get BMA and two BM's?) I got this from the mri_watershed help message: -keep PreEditVol PostEditVol NewWithEditsVol : keep edits as indicated by the differences between pre and post volumes.Note: this does not change output, just create NewW ithEditsVol Question 3: In the normal case, does brainmask.auto.mgz just get copied to brainmask.mgz? If so it's a puzzle to me how these wind up different (in the cases I looked at the mgz files are not the same size). Hopefully my description above has answered this one. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Odd brainmask.auto and brainmask data and behavior
Hi Graham, If the voxels that were added are of a value 255 and in a location where gray matter was intended to be extended I don't think the edits were done in the right way. It sounds like voxels have been added to that volume when really you want them to be cloned into to it. This puts them in directly from some other volume (i.e., the T1) and keeps the intensities etc consistent. It's basically just using a different feature of the Edit Voxels tool. You can see a description here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix (at the bottom under manual editting the Cloning tool is described!) Jenni On Wed, 13 Sep 2006, Graham Wideman wrote: Jenni: Thanks for your reply and explanation of the brainmask logic and rationale. As for this: Question 1: Is there a rationale for 255 values? (in the brainmask volume) I'm not sure where these are coming from in your volume - I assume you havent done any editting on this one. These subjects' data may well have been edited (not by me, hence my not knowing exactly what's what here). And I suppose it's the brainmask.mgz volume that would have been edited, and the act of editing it sets voxels to 255 perhaps? (The 255's are in the appropriate locations to add additional grey matter to the edges.) That leads me to believe that the answer to this: Question 0: Is the detailed image data in brainmask.mgz ever used, or is it simply a zero/not-zero mask? Ie: is the meaning masked brain, or mask using non-zero values to show where brain is. ... is that brainmask.mgz is used by subsequent steps as a mask in combination with some other image volume providing the actual image. In that case the actual intensities of brainmask.mgz are ignored. And I now see in the script that mri_ca_normalize does indeed use brainmask.mgz with the mask flag, so I guess I'm probably right that the actual intensities are unimportant. (And nu.mgz provides the actual image). Phew, I think I now have that straight... for this week :-) Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Converting .dcm to COR files
Hi Camilo, You need to give it the path and filename for the first dicom in the series, I think 003DCM is the directory, so you'll need to include the file name for one of the dicoms. Also, you should consider converting to a .mgz file - as that is the input for most everything that Freesurfer is doing these days, and not COR. To do this you can simply specify the output filename: mri_convert /path/to/dicom/file.dcm /path/where/you/want/003.mgz Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Friday, August 18, 2006 5:33 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Converting .dcm to COR files Hi Freesurfer help, I am trying to convert my .dcm files to COR format. I use: mri_convert -ot cor 003DCM 003 I get the following error: mri_convert -ot cor 003DCM 003 reading from 003DCM... corRead(): can't open file /autofs/space/rao_001/users/patrickp/eeg_propofol/control_01... /bourget/control_01/mri/orig/003DCM/COR-.info I am running the standar enviroment in the nmr, and the location of my files is: /autofs/space/rao_001/users/patrickp/eeg_propofol/control_01/... bourget/control_01/mri/orig Can someone give me some advise in this issue? Thanks, Camilo ___ 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] Skull marrow and skull stripping
Bo, It looks like control points will do the trick - in the wm. Your white surfaces are missing some regions too. Control points will fix this and subsequently fix your pial surfaces as well. Give them a try, but be sure to get the control points in wm voxels, not too close to the wm/gm boundary. Jenni On Wed, 16 Aug 2006, Bo Shi wrote: Sorry, message cut off mid-write; We're having some trouble with the pial surface for the temporal lobes. All four datasets we've processed so far have temporal lobe pial surfaces that are significantly smaller than they should be (attached) I know there are control points for white matter - is there an equivalent for gray matter? On Wed, 2006-08-16 at 14:44 -0400, Bruce Fischl wrote: no - we don't really use the cortex labels from the aseg for this reason (and others). Instead we use the surfaces (?h.white and ?h.pial) for computing cortical properties, so you should be all set. cheers, Bruce On Wed, 16 Aug 2006, Bo Shi wrote: Hi Bruce, The pial surface for the top regions of the brain do fairly well in ignoring the marrow, however, the unwanted regions still get classified as gray matter (image attached). This will adversely affect the reported cortex volume no? Thanks, Bo On Wed, 2006-08-16 at 14:14 -0400, Bruce Fischl wrote: Hi Bo, does it affect your pial surface? You may be fine with just leaving it in. cheers, Bruce On Wed, 16 Aug 2006, Bo Shi wrote: Howdy - It seems that the skullstripping step is having some trouble removing bone marrow (see attached image). Adjusting watershed values (I've tried as low as 5) does not make any significant improvement. Does anyone else have this issue? Can anyone provide any hints as to how I might get a better automated skull-strip? I've been manually removing the marrow but it's getting real old. Any thoughts would be much appreciated. Bo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] no brain.tri and brain.mgz
You should have brainmask.mgz after -autorecon1 though. Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Nick Schmansky Sent: Thursday, August 10, 2006 6:55 PM To: Jiansong Xu Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] no brain.tri and brain.mgz The brain.mgz file won't appear until after the -autorecon2 stage. Refer to this page for files output at each recon-all stage: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable On Thu, 2006-08-10 at 15:16 -0700, Jiansong Xu wrote: Dear Friends: I'm playing with the tutorial. I didn't get the brain.tri and brain.mgz files after the first step, see below for the command: recon-all -subjid bert -autorecon1 Best Jiansong ___ 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] Feature request for tkmedit
Hi, tkmedit does ask for you to save your edits if you've made them and try to close - but I think this only happens when you exit out of tkmedit by doing File -- Quit (which in some cases is a better way of closing tkmedit anyway). Jenni On Tue, 8 Aug 2006 [EMAIL PROTECTED] wrote: Hi, It would be great if tkmedit would ask if you have saved your edits before closing. Any chance of getting this added? As it currently stands, it is easy to just press the little x in the corner of the tkmedit window and close it, without recording any of your work. Of course no-one does this when they are fresh, but after hours of editing one sometimes is in a state of rapturous bliss and forgets these little details. ___ 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] Recon all finished with errors, How do I see what errors?
Hi Jake, Did it write out the wm.seg.mgz file (would be in the subjects mri directory)? Is it possible that you either don't have write permissions in that directory or that you are out of disk space? Jenni On Mon, 7 Aug 2006, Jake Freimer wrote: I was running autorecon2-cp and it said it finished with errors, below are the recon-all.log and recon-all-status.log, I couldn't figure out what the error is. Mon Aug 7 10:37:16 PDT 2006 [EMAIL PROTECTED] Intensity Normalization2 Mon Aug 7 10:37:16 PDT 2006 [EMAIL PROTECTED] Mask BFS Mon Aug 7 11:01:39 PDT 2006 [EMAIL PROTECTED] WM Segmentation Mon Aug 7 11:01:59 PDT 2006 Darwin lion.bmap.ucla.edu 8.7.0 Darwin Kernel Version 8.7.0: Fri May 26 15:20:53 PDT 2006; root:xnu-792.6.76.obj~1/RELEASE_PPC Power Macintosh powerpc recon-all exited with ERRORS at Mon Aug 7 11:12:31 PDT 2006 .. [EMAIL PROTECTED] Mask BFS Mon Aug 7 11:01:39 PDT 2006 /private/Network/Servers/dns2.bmap.ucla.edu/Volumes/BMC3/BMCUsers3/ascott/Documents/freesurfer/subjects/td21new/mri \n mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz \n threshold mask volume at 5 Talairach transform /usr/local/freesurfer/subjects/td21new/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /private/Network/Servers/dns2.bmap.ucla.edu/Volumes/BMC3/BMCUsers3/ascott/Documents/freesurfer/subjects/td21new/mri/transforms/talairach.xfm writing masked volume to brain.finalsurfs.mgz... # [EMAIL PROTECTED] WM Segmentation Mon Aug 7 11:01:59 PDT 2006 \n cp wm.mgz wm.seg.mgz \n \n mri_segment -keep brain.mgz wm.seg.mgz \n preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM: 105.9 +- 5.5 [80.0 -- 125.0] GM: 70.1 +- 9.7 [30.0 -- 96.0] setting bottom of white matter range to 79.7 setting top of gray matter range to 89.4 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 4126 sparsely connected voxels removed... thickening thin strands 20 segments, 2519 filled 2784 bright non-wm voxels segmented. 2121 diagonally connected voxels added... white matter segmentation took 10.4 minutes writing output to wm.seg.mgz... Darwin lion.bmap.ucla.edu 8.7.0 Darwin Kernel Version 8.7.0: Fri May 26 15:20:53 PDT 2006; root:xnu-792.6.76.obj~1/RELEASE_PPC Power Macintosh powerpc recon-all exited with ERRORS at Mon Aug 7 11:12:31 PDT 2006 Thanks -Jake ___ 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] Total Brain Volume
Hi Anil, There are two values in the aseg.stats file - BrainMaskVOl and BrainSegVol. BrainMaskVol is the volume of all the voxels that are included in the brainmask.mgz volume. BrainSegVol is the volume of all the voxels that are labeled in the aseg.mgz segmentation. -- Jenni Pacheco, M.A. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Bldg. 149, 13th Street, CNY 2301 Charlestown, MA 02129 [EMAIL PROTECTED] On Fri, 28 Jul 2006, Anil Roy wrote: Hello All, Does freesurfer generate a file with total brain volume after the recon-all procedure? Where can this be accessed? Thanks, AR. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] caudate/putamen values for mri_segstats
Hi Thang, The Caudate and the Putamen are labeled. They should be in your aseg.stats file as Left-Putamen Right-Putamen Left-Caudate and Right-Caudate. If they are not there then there is likely something wrong with your aseg. the label that is specifically called Left-Caudate/Putamen and Right-Caudate/Putamen is not something that corresponds to a label in our aseg, and there are no plans to change the current labels. You should be using the values from Left-Putamen Right-Putamen Left-Caudate and Right-Caudate. -- Jenni Pacheco, M.A. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Bldg. 149, 13th Street, CNY 2301 Charlestown, MA 02129 [EMAIL PROTECTED] On Fri, 28 Jul 2006, Nguyen, Thang Q wrote: Thank you Jenni, those were the regions to which I was referring. Are there any plans for those zero-value regions to be labeled? We're interested in investigating the insula, Left-Caudate/Putamen, and Right-Caudate/Putamen and would like to know if there are any plans for these regions to be labeled. Thank you for your time, -Thang -Original Message- From: Jenni Pacheco [mailto:[EMAIL PROTECTED] Sent: Thursday, July 27, 2006 6:13 PM To: 'Bruce Fischl'; Nguyen, Thang Q Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] caudate/putamen values for mri_segstats Thang, As Bruce said, there should be something called Left-Putamen Right-Putamen Left-Caudate Right-Caudate that should NOT have zero values. There is something in that file called Left-Caudate/Putamen and Right-Caudate/Putamen that will have a zero value has there is nothing in the aseg that is labeled as that. Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bruce Fischl Sent: Thursday, July 27, 2006 9:05 PM To: Nguyen, Thang Q Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] caudate/putamen values for mri_segstats Hi Thang, putamen and caudate should definitely *not* be 0. Did you look at the aseg volume in tkmedit? How does it look? Bruce On Thu, 27 Jul 2006, Nguyen, Thang Q wrote: Hello all, I used mri_segstats to get subcortical volumes my subjects. However, for some of the regions like the putamen and caudate, I get values of zero. I have been told that these values are either no longer in use or have not been in use yet. Is there a way of manually getting values for these regions? Thank you for all the help, -Thang ___ 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] Edit label
I think that mri_mergelabels will do all the steps that Rahul describes below for you. You can input as many labels as you want (i think) and specify an output name. USAGE: mri_mergelabels -i label1 -i label2 ... -o outputlabel good luck, Jenni On Thu, 27 Jul 2006, Rahul Desikan wrote: Hi Dhruman, To the best of my knowldge, the wiki page does not contain any information on using tksurfer to add labels together. My suggestion would be the following: 1) Load the subject in using tksurfer (tksurfer subjectname hemi inflated) 2) Load in the parcellation you want to edit (e.g. rh.aparc.annot) 3) Click on a label of interest to you (e.g. caudalmiddlefrontal) 4) Then, click the 'Custom Fill' button in the Tksurfer Tools window. This button looks like a paint can and can be found in the second row of the Tksurfer Tools window. Keep this 'Custom Fill' window open for later (see steps 5-8 below). 5) Choose only the 'Up to other labels' option in the 'Custom Fill' options bar 6) In the tksurfer window where you can see the rh.aparc.annot file loaded and the inflated surface, click on a label you would like to add (e.g. rostralmiddlefrontal). 7) Then go to the 'Action' portion of the 'Custom Fill' options bar and choose 'Add to existing label'. If you look at the label bar below, it should show you which label you are adding to. 8) Repeat steps 6 and 7 for all labels you would like to add to the original one you have already selected (e.g. add rostralmiddlefrontal, superiorfrontal, precentral, parsopercularis, etc.--to caudalmiddlefrontal, the label you had already selected). 9) Once you have selected all the labels you would like to have added together, click the new label, make sure it is highlighted and save it as a new label (e.g. rh.frontal.label) I am including an image that shows what the final result might look like for the frontal lobe (lateral view) once you have added together all of your frontal subregions together. best, Rahul On Thu, 27 Jul 2006, Goradia, Dhruman D wrote: Hello Rahul, Thank you for your reply. I tried to combine the different regions to create one label for each lobe but could not figure it out. Can you suggest how I can combine different regions using tksurfer? Is there a wiki page where the steps are explained? Thank you -Dhruman -Original Message- From: Rahul Desikan [mailto:[EMAIL PROTECTED] Sent: Thursday 27 July 2006 15:15 To: Goradia, Dhruman D Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edit label Hi Dhruman, If you are interested in lobe-wise comparisons, you can indeed add up the individual regions of a specific lobe, create one massive label for that lobe, and get statistics on those. For example, if you were interested in the temporal lobe, you could combine: lateral occipital cuneus lingual pericalcarine and generate an *h.occiptal.label (you can use tksurfer to combine the regions). You could do the same for the other labels and thus create a 'lobe based' parcellation. Once you are done, you can use mris_anatomical_stats to generate stats on the new labels you have generated. best, Rahul On Thu, 27 Jul 2006, Goradia, Dhruman D wrote: Hi all, I am interested in lobe wise surface measurement. I read Desikan et al. paper to understand that their atlas divides the lobes into different region and freesurfer uses that atlas to gets measurement for each region. Is it possible to load the Desikan label and edit it to fuse all the region belonging to each lobe and create a new label, which I could use to get surface measurement? Thanks in advance. Dhruman ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_em_register args, ICV, etc
The ICV is calculated during the -segstats step with all of the other volume measures that use the aseg. They are all found within the aseg.stats file in the stats subdir. Jenni On Mon, 24 Jul 2006, Graham Wideman wrote: Folks: A couple of weeks ago, Bruce noted that: EM Registration with Skull is for generating ICV measures ... so I just got around to investigating where the ICV measures might be getting saved. Bottom line is I don't see what file that ICV measure is getting saved into. Details: I tried to figure out which program/script does this step, and what files it produces which might capture ICV. 1. Which commands correspond to the EM Registration with Skull step? Clue: wiki recon-all shows this step employs the noskull-lta step. Looking in recon-all script, this corresponds to the DoSkullLTA variable, and that in turn leads us to mri_em_register as the pertinent command. 2. Looking at docs for mri_em_register in the wiki shows 4 arguments, only one of which is flagged. Looking at actual help output from mri_em_register shows about 50 flagged arguments, none described. 3. The pertinent bit of script looks like this: set xopts = `fsr-getxopts mri_em_register $XOptsFile`; set cmd = (mri_em_register -skull -t transforms/talairach.lta \ $xopts nu_noneck.mgz $FREESURFER_HOME/average/$GCASkull \ transforms/talairach_with_skull.lta) 4. From all this, I don't see what output file mri_em_register might be placing the ICV into. Clues? Thanks, Graham ___ 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] recon-all malloc error
Hi Rutvik, Have you looked at your surfaces, is there a problem with the rh that you may need to fix manually before trying the topology fixer again? Jenni On Fri, 21 Jul 2006, Rutvik Desai wrote: recon-all exited with the following error. Running on a Powermac G5 with 1G ram. Any ideas? thanks, Rutvik - Fix Topology rh Thu Jul 20 13:29:52 CDT 2006 /usr/local/freesurfer/subjects/2628/scripts mris_fix_topology 2628 rh reading input surface /usr/local/freesurfer/subjects/2628/surf/rh.qsphere... before topology correction, eno=-510 (nv=191807, nf=384696, ne=577013, g=256) using quasi-homeomorphic spherical map to tessellate cortical surface... mris_fix_topology(124) malloc: *** vm_allocate(size=2075615232) failed (error code=3) mris_fix_topology(124) malloc: *** error: can't allocate region mris_fix_topology(124) malloc: *** set a breakpoint in szone_error to debug could not allocate 16108 edges for retessellation Cannot allocate memory reading T1 volume from T1... reading wm segmentation from wm... 136542 ambiguous faces found in tessellation 246 of 4410 overlapping edges discarded 1 of 299 overlapping edges discarded 175 of 1655 overlapping edges discarded retessellating defect 3 with 4269 vertices (convex hull=26247). 661414 of 8448632 overlapping edges discarded 7 of 59 overlapping edges discarded 0 of 45 overlapping edges discarded retessellating defect 6 with 16108 vertices (convex hull=7747). ERROR: mris_fix_topology exited with non-zero status ___ 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] Exporting Anatomical Stats
In the latest version there is asegstats2table and aparcstats2table which will do what you want. Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Thursday, June 15, 2006 9:42 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Exporting Anatomical Stats I ran all three -autorecons and also was able to get my volumetric statistics. I was wondering if there is a way (make my life easier) to export all the information given in the anatomical stats directly to a spreadsheet format without having to copy and paste eveything. I have OpenOffice.org Calc on this computer, although I've never used it before. ___ 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] error message
Hi Sarah, Why are you using this script what are you trying to do? I wrote this for Rahul with one purpose in mind, it might be that there is a better way for you to do what you want. Jenni From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Sarah J Greene Sent: Monday, June 12, 2006 12:14 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] error message I was running the subcortical labelling script (aseg_rerun.csh) using the old version of freesurfer, and have received this error message: mri_read(): couldn't determine type of file mri_ca_register: could not open input volume -T I am not sure how to fix this error. I would appreciate any input!! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mghWrite failure in mri_remove_neck
Hi Graham, In regards to #2, below, there shouldn't be anything extra you have to do when re-running things. It will write over the old files that are there with no problem. Jenni On Tue, 30 May 2006, Graham Wideman wrote: Doug: There's over 200 gig space on that drive, and I have since test copied over 100 Meg to the mri directory (as the same user, so permissions seem OK). Questions: 1. Is mghWrite failure salient, or is this just mri_remove_neck checking for an existing file in order to delete it (ie: it's not really an error). 2. In general, does recon-all happily restart at wherever stage you tell it, and overwrite existing files, or is some special action necessary to deal with existing files? Thanks, Graham At 5/30/2006 10:10 AM, Doug Greve wrote: Can you verify that the disk was not full? doug Graham Wideman wrote: Folks: In our first attempt at a complete run of recon-all, we hit this odd failure: recon-all stopped after the mri_remove_neck stage, claiming that: 1. mri_remove_neck couldn't mghWrite to nu_noneck.mgz 2. But then appeared to perform the neck removal anyway and write the output 3. But then the subsequent step: mri_em_register failed saying that it can't read nu_noneck.mgz ... and sure enough, there is no such file there. The recon-all.log for these steps is copied below. This doesn't appear to be a permissions problem, as the script happily wrote other files to the same mri directory. I do wonder whether mri_remove_neck was actually using the correct directory (we are not using the default SUBJECTS_DIR), but the logic for that is in an executable that I don't think we have source for? But the primary troubleshooting question is why the mghWrite failed, but processing continued anyway, with the subsequent writing output message suggesting success of this step (but no file to show for it). Clues? Thanks, Graham ___ 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] troubleshooting
Hi Amanda, What are the intensity values of the regions that are being left out? If they aren't near 110 then you should definitely use some control points. Where are the rh surfaces including some of the left hemisphere? Is it along the medial wall? Jenni On Wed, 24 May 2006, Amanda Dow wrote: I ran one of my brains through recon-all and the skull strip and talairach were normal. When I checked the white matter edits with tkmedit, the right hemisphere wm and pial surface lines are including some of the left hemisphere, and the right temporal lobes are not included as white matter or in the pial surface. I thought it may be a tailarach problem, but it looks normal. Any suggestion on what could be wrong. I may try using control points and re-running it with recon-all -autorecon2-cp... Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] which script creates the design matrix?
Hi Lars, Can you point me at the wiki page you are looking at - may just be a typo. I'll see if I can fix it. Jenni On Wed, 17 May 2006, Lars M. Rimol wrote: Hi, I am using FS v3.02. I am using the tutorial to figure out how to do group analysis with the new FS version but there is one step that is confusing. The tutorial says that I should first create a FSGDF (and run make_average-subject), and then it says that running mris_glm will create the design matrix. But further down on the page it says that that mri_glmfit is replacing mris_glm. So, does that mean that I no longer have to use mris_glm to create the design matrix, and that mri_glmfit will create it? So I should run 1) make_average_subject, 2) mri_preproc and mri_surf2surf, and 3) mri_glmfit? Or does it mean that I should run 1) make_average_subject, 2) glms_mri , 3) mri_preproc and mri_surf2surf, and 4) mri_glmfit? Thank you! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] aseg.stats question
Hi Sasha, Besides the Right-Thalamus-Proper, as Bruce pointed out, none of those are typically labeled during the normal aseg run by recon-all. In the aseg.stats file you will likely find a bunch of zeros listed for these, and other things that are not labeled (i.e., Spinal-Cord, Soft-Tissue, Nerve, Bone, Air, Orbital-Fat, Tongue etc.) Jenni On Mon, 15 May 2006, Sasha Wolosin wrote: Dear all, I would like to know what some of the abbreviations of areas in the aseg.stats file stand for, in particular: Left-F3orb Left-lOg Left-aOg Left-mOg Left-pOg Left-Stellate Left-Porg Left-Aorg and Right-Thalamus vs Right-Thalamus-Proper Where may I find documentation on these names? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return 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] segmentation
Hi Valentina, Yes - as long as the surface (yellow line) is ok there is no need to edit anything. Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Durastanti, Valentina (NIH/NINDS) [F] Sent: Thursday, May 04, 2006 9:19 PM To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] segmentation Hi Bruce, thanks! so if the yellow line is ok I don't need to remove the voxel exceeding or add the voxel missing right? thanks valentina From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thu 5/4/2006 7:15 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] segmentation Hi Velentina, the segmentation is just a preliminary estimate of the gray/white boundary. The ?h.white surface (usually displayed in yellow) is the official and final estimate and the one you should be worried about. Bruce On Thu, 4 May 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote: Hi, I have a question: at the end of the segmentation (before the manual editing) I found that there are some voxel exceeding the yellow line and I can't figure out if they will be included in the WM count or if they will be included in the GM count. Have I to remove them even if they go over the line? Thanks Valentina ___ 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] recon-all - skip motion correction
If you have only one acquisition and it is in mri/orig.mgz you can use the -nomotioncor flag to skip the motion correction step and carry on from there. Jenni On Wed, 3 May 2006, Darren Weber wrote: --[PinePGP]--[begin]-- --[PinePGP]--- -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi, we have only 1 orig.mgz file, so motion correction is not required. In this case, it would be ideal if recon-all auto-detected or at least had an option to skip motion correction. As it is, it fails entirely when no 001.mgz file exists. I have a file called orig.mgz, should it be renamed to 001.mgz even though there is no 002.mgz? endorphin.32 ls -l ucsf_disc01/mri/orig/ total 5784 - -rw-rw-rw-1 dweber dnl 5907576 May 3 13:52 orig.mgz endorphin.31 recon-all -subjid ucsf_disc01 -all INFO: SUBJECTS_DIR is /data/dnl-raid2/freesurfer/subjects Actual FREESURFER_HOME /data/dnl-raid1/freesurfer - -rw-rw1 dweber dnl 56553 May 3 13:55 /data/dnl-raid2/freesurfer/subjects/ucsf_disc01/scripts/recon-all.log Linux endorphin.ucsfmedicalcenter.org 2.4.21-20.ELsmp #1 SMP Wed Aug 18 20:46:40 EDT 2004 i686 i686 i386 GNU/Linux WM removal version # [EMAIL PROTECTED] MotionCor Wed May 3 13:55:54 PDT 2006 ERROR: no run data found in /data/dnl-raid2/freesurfer/subjects/ucsf_disc01/mri. Make sure to have a volume called 001.mgz in /data/dnl-raid2/freesurfer/subjects/ucsf_disc01/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux endorphin.ucsfmedicalcenter.org 2.4.21-20.ELsmp #1 SMP Wed Aug 18 20:46:40 EDT 2004 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed May 3 13:55:54 PDT 2006 Thanks, Darren - -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself. Thomas Willis (The Anatomy of the Brain and Nerves, 1664) -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://enigmail.mozdev.org iD8DBQFEWRnuxaCYN7qs0v4RAo91AKCisc5QNJhVDGySLbhZivaA/TBwjACeNuLs i71i+loDc67uAvWeHV37NzA= =eoyz -END PGP SIGNATURE- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer PinePGP: Encryption backend encountered error. --[PinePGP][end]-- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Results files
Hi Francesca, Freesurfer now runs two parcellations, by default. One (?h.aparc.annot) uses the Desikan-Killiany atlas and the other (?h.aparc.a2005s.annot) uses Christophe's atlas. The two stat files are the different statistical outputs that come from each of the different atlases. Jenni On Tue, 2 May 2006, Bagnato, Francesca (NIH/NINDS) [E] wrote: Dear All: I am using the last relaease of freesurefr and I am uncertain about the '.aparc.stats' file. Precisly: differences between this file and the '.aparc.a2005s.stats' and '.aparc.stats' are not clear. Does the latter selecet dome of the cortical regions form the first one? If so, avg thick of similar regions does not look to coincide according to the numbers I got. Just wondering... Thanks for your 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
RE: [Freesurfer] Skullstripping
Which version of Freesurfer are you using? The newest versions write a file called brainmask.mgz, but the subsequent steps do recognize and use this. Can you elaborate more on the specific problems/error messages you are encountering? Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Joao Pereira Sent: Friday, April 28, 2006 6:51 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Skullstripping Can someone explain me why my the recon-all skull stripping option is writting a file named brainmask.mgz instead of brain.mgz? This is a problem because the subsequent procedures do not recognize the file. Thank you! JP ___ 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] FW: FW: Recon-all longitudinal script
Hi Thang, I'm not sure if you've tried this, but try adding -mgz to the command line when running recon-all-nmr-long. Jenni On Wed, 12 Apr 2006, Nguyen, Thang Q wrote: -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tuesday, April 11, 2006 5:42 PM To: Nguyen, Thang Q Subject: Re: FW: Recon-all longitudinal script Hi Thang, please post this to the list Bruce On Tue, 11 Apr 2006, Nguyen, Thang Q wrote: Hello Bruce Fischl, I was wondering if you could help me with this Freesurfer issue. I am trying to run the longituduinal script (recon-all-nmr-long) that Xiao sent me. We have installed the latest 2006 version of Freesurfer which works in mgz format. I have tried running recon-all on one subject and running the longitudinal script on the second subject. Unfortunately, it errors out saying that the script can't find the mgz format. I have added the mgz extension and it also gives me the same problem. I have tried recon-all on the second subject as well and then running the longitudinal script but it gives me this error: * Sphere rh Mon Apr 10 18:04:19 PDT 2006 /raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S zetoR2/scripts cp /raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S zetoR/surf/rh.sphere /raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S zetoR2/surf/rh.sphere - Surf Reg rh Mon Apr 10 18:04:19 PDT 2006 /raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S zetoR2/scripts Too many )'s. * Since Xiao left, I no longer have a contact for this problem. I have contacted Karl Helmer and he hasn't responded. I was wondering if you could help me. Thank you, Thang Nguyen From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Friday, April 07, 2006 3:36 PM To: Nguyen, Thang Q Subject: Re: Recon-all longitudinal script I think you run recon-all on the first time point, then -long on the subsequent ones. But I've never actually run it myself :). doug Nguyen, Thang Q wrote: Hello Doug Greve, I am trying to run a longitudinal analysis using the recon-all-nmr-long binary from Xiao. I was wondering if you could answer some questions I have. Do I need to process each longitudinal scan using recon-all first and then apply the longitudinal analysis to the first scan or can I simply run the recon-all-nmr-long for the subsequent subjects without running recon-all on those datasets? Thank you for your time, -Thang ___ 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 - autorecon1 will not write to established directory
Hi Adam, you shouldn't need to use -i orig.mgz when running -autorecon1, this will already use orig.mgz when re-running this step. You should be able to simply use: recon-all -autorecon1 -s 13667 If you are trying to do something different, and you wish to specify a different input and re-run a subject that is already there you will need to add the flag -force to the command. (and the -i flag requires a full path to the file) So, like this: recon-all -i /full/path/to/file -autorecon1 -force -s 13667 Jenni On Tue, 11 Apr 2006, adam walczak wrote: Hi, I have been having some basic problems with regard to paths. Freesurfer doesn't seem to want to write to directories that already exist. I was wondering if there is something different I need to do (I am running the reconstruction tutorial) to make this work. freesurfer-Linux-rh9-stable-pub-v3.0.1 SUBJECTS_DIR is /cajal/public/programs/freesurfer/subjects which: recon-all / autorecon1 pwd - /cajal/public/programs/freesurfer/subjects/13667/mri command line - recon-all -i orig.mgz -autorecon1 -s 13667 error- INFO: SUBJECTS_DIR is /cajal/public/programs/freesurfer/subjects ERROR: /cajal/public/programs/freesurfer/subjects/13667 exists I am at a loss as to why this happens. Any help would be appreciated. Adam Walczak - Love cheap thrills? Enjoy PC-to-Phone calls to 30+ countries for just 2¢/min with Yahoo! Messenger with Voice.___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Translate label file from average subject to allsubjects
Hi Jon, You should use mri_label2label. mri_label2label --help will give you usage and examples. Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jonathan Wisco Sent: Wednesday, March 15, 2006 5:50 PM To: Freesurfer Subject: [Freesurfer] Translate label file from average subject to allsubjects Hi, I would like to translate a label created from an average subject inflated surface to all the subjects. How would I do that? Should I first use mri_surf2surf to resample the average subject inflated surface to all the other subjects? Would a label that was created on the average subject then automatically be translatable to the subjects? Thanks, Jon -- Jonathan J. Wisco, Ph.D. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Building 149, 13th St. Charlestown, MA 02129 E-mail: [EMAIL PROTECTED] Tel: 617-851-8492 Fax: 617-726-7422 ___ 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] talairach
Hi Valentina, Your tkregister2 command does not specify any surfaces to load, so you should not expect to see any. This is good, because you have not generated any surfaces if you've only run -autorecon1. The surfaces are generated during -autorecon2. you are seeing things as would be expected up to the point you are at. Jenni On Mon, 13 Mar 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote: I tried to check the talairach transformation after the autorecon1 typing: tkregister2 --mgz --s sunject name --fstal But I haven't a surface at this step and I can't see the green line Can you tell me what's happening? ___ 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] [martinos-tech] New average subject and stable release, v3.0 (fwd)
I am re-sending an email that Doug wrote earlier this week, as it was a thorough description of some pretty important changes to the average subject and talairach subject. There is a new average subject to replace average7 that ALSO replaces the talairach subject. It is called fsaverage and can be found in the distribution itself (no additional downloads needed): $FREESURFER_HOME/subjects/fsaverage as an additional note, fsaverage can only be used with subjects processed the new way (i.e., with automatic filling of the entire ventricle). Another average subject that will be compatible with subjects processed the old way (i.e., manual editting of the wm) will be available soon. Please read Dougs email below if you missed it!! Jenni -- Forwarded message -- Date: Mon, 06 Mar 2006 18:12:55 -0500 From: Doug Greve [EMAIL PROTECTED] Reply-To: [EMAIL PROTECTED] To: [EMAIL PROTECTED], Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Subject: [martinos-tech] New average subject and stable release, v3.0 Sorry in advance for the long email ... We have a new average subject that we are recommending that people use instead of average7. This subject can also replace the talairach subject as well. The name of the fsaverage, and it can be found in the distribution itself: $FREESURFER_HOME/subjects/fsaverage To set up a link in your SUBJECTS_DIR, do the following: cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage fsaverage There is a README file in $FREESURFER_HOME/subjects/fsaverage that describes how this subject was created. IMPORTANT: Differences between average7 and fsaverage, and FIX_VERTEX_AREA with impacts on mri_surfcluster and mri_glmfit. As some people have noted, the total surface area of average7 was much less than that of a typical subject (by about 40%). This caused the areas of clusters as reported by mri_surfcluster to be too small. HOWEVER, a bug in the routine that computed the vertex area caused the clusters to be 50% too large. So, the net effect was that the clusters were about the right size :). Stay with me. The surface area of the new average subject (fsaverage) is that of a typical subject, SO, it is IMPORTANT that it be used in conjunction with the fixed vertex area. This affects only two programs: mri_surfcluster and mri_glmfit. After today (March 6, 2006), if you use average7 with mri_surfcluster or mri_glmfit, they will give the following error: ERROR: you have selected subject average7. It is recommended that you use the fsaverage subject in $FREESURFER_HOME/subjects. If you really want to use average7, re-run this program with --really-use-average7 as the first argument. If you chose to do so, then it will print out: INFO: you have selected subject average7 (and REALLY want to use it) instead of fsaverage. So I'm going to turn off fixing of vertex area to maintain compatibility with the pre-stable3 release. The results should be the same as when you ran it prior to the stable3 release. If you have used average7 along with Monte Carlo or Permutation simulation, inferences based on those simulations should still be correct. The only problem will be that the cluster area might be a little different. If you have used a non-average subject as your common surface space or an average subject that you created prior to March 1, 2006, then the cluster sizes will appear to drop by a third the next time your run mri_glmfit or mri_surfcluster. Again, any mri_glmfit simulation results will still be valid. For backwards compatibility, you can add --no-fix-vertex area to either mri_surfcluster or mri_glmfit. The new versions of mri_surfcluster or mri_glmfit will include the following line in their summary/logfile output: # FixVertexAreaFlag 1 The value will either be 1 or 0 depending upon whether it was fixed or not fixed. Again, sorry for the long-winded email. I know this is pretty confusing, so don't hesitate to write with questions as we get this sorted out. PLEASE send questions to the group to help in this process. thanks doug Nick Schmansky wrote: Freesurfer community, A new stable release, v3.0, is now available. The Release Notes page describing what's new, and a link to the download page, is here: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes All users, including those using prior 'dev' releases, are encouraged to upgrade to this release. Updates to the stable release will be issued if major bugs are found (and fixed), and as new features which do not affect existing functionality become available. The Freesurfer development team ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in:
Re: [Freesurfer] dev-version/new version question.
As a note for everyone since this question has come up a lot, one of the many cool new features of recon-all is that it saves all of your edits, every time, by default. You have to specify with certain flags when you want it to ignore your edits (see https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags for a list of flags). This applies to edits to manual talairach registrations, seed points for cutting planes, control points for normalization, edits to the brainmask.mgz volume, edits to the wm.mgz volume, and edits to the aseg.mgz subcortical segmentation. Every time you re-run anything that you have changed in these will be saved and used in subsequent steps. This should make re-running your subjects with a new version relatively painless. Martin, in terms of your compatibility question, my recommendation is to always use the exact same version for a group study, its the only way you can be sure everything has been done consistently. During the time between Feb 10 (your current version) and the release there were many changes made to the code, although off the top of my head I can't make any guesses as to how this may affect your group study. Jenni On Thu, 9 Mar 2006, Martin Ystad wrote: Hi, I'm currently using the freesurfer-Linux-centos4-dev20060210-full release, and I'm thinking of upgrading to the new stable release. However, I've done a lot of processing with the 20060210-release, and I'm not very keen on starting all over again with the new release. Do you recommend that I reprocess my subjects on the new stable release before doing a group study, or are they similar enough in terms of results, so that I don't need to? In case I do need to run everything over, which steps do I need to rerun (certainly not all?), and can I keep my manual edits to the brainmask- or wm-volume? Thanks, Martin Ystad University of Bergen, Norway. ___ 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 tutorial
Hi Gabe, What version of freesurfer are you using? The -autorecon-all, -autorecon1, and -i flags should work with a current version - but are relatively new. If you are using an older version these flags will not work. Could you also send the specific command line and error message you are receiving. When reporting bugs it's really helpful if you included some pertinent information so we can better help you: https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thanks, Jenni On Mon, 27 Feb 2006, Gabe Castillo wrote: Hello, I am new to using freesurfer. I have installed it successfully and am attempting to go through the tutorial. The tutorial seems to be out of date. I am at the Data Conversion step of the tutorial with the tutorial_subjs directory from the gzipped buckner_data tarball. If I try to run recon-all -i 014-anon/001.dcm -i 015-anon/001.dcm -s anon it complains about the -i flag. It also complained about the -autorecon-all and -autrecon1 flags. Looking through the usage output, I'm guessing that these have been replaced by -all and -stage1 respectively. What has the -i flag been changed too. Forgive my ignorance, if anybody has a changelog or can point me to one, I'd be happy to dig around for this info. Thanks, Gabe Castillo ___ 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] mris
Francesca, Can you provide some more information. Please refer to https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting thanks, Jenni On Wed, 21 Dec 2005, Bagnato, Francesca (NIH/NINDS) [F] wrote: Dear All: I am having an error saying: couldn't determine type of file /mri/wm when I lunch the mris_anatomical_stats. I am not sure how to deal with that. THANKS! -francesca Francesca Bagnato, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Jenni Pacheco, M.A. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Bldg. 149, 13th Street, CNY 2301 Charlestown, MA 02129 [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] talairach transform with brain.mgz
Hi Lars, You should be able to just move on with -autorecon2 as normal. The only need to re-do anything would be if your poor talairach caused some other step to be wrong (i.e., the skull strip failed or the normalization failed because the talairach was wrong). If those are fine, then continue with -autorecon2. If you ever need to re-run -autorecon1 for these subjects just be sure to use the flag -notalairach so that your manually corrected talairach won't be overwritten. Jenni On Fri, 9 Dec 2005, Lars M. Rimol wrote: Hi, We have 15 out of 16 data sets with Final Objective Function value 0.1. We also find some deviations from the talairach (or MNI) volume when we visually inspect the images (fixed vs. movable) in tkregister2. But we are unsure how large the deviations must be for it to be a problem, so we rely on the Final Objective Function value. When it comes to the intensity normalization, that's even harder to inspect visually, so we don't really know how to check that (unless there are really huge effects). But when we use the brain.mgz image as input for the talairach, the Final Objective Value improves, that's why we've started using that. So we need to know how to proceed from there. (We use the recommended reconstruction, so we check the talairach and skullstrip after autorecon1.) Thanks! -- yours, Lars M. Rimol depends why you needed to improve the talairach. If it's just for reporting purposes and the filling/intensity normalization all worked fine then you don't need to. cheers, Bruce Hi, After having redone mri_convert with an edited brain.mgz as input file, in order to improve the talairach transform, and after having changed the file names (brain.xfm - talairach.xfm), should we then go to autorecon2? (or do we need to re-run some more scripts from autorecon1?) -- yours, Lars M. Rimol -- Jenni Pacheco, M.A. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Bldg. 149, 13th Street, CNY 2301 Charlestown, MA 02129 [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] T1 volume problem
Hi Michele, For now the best work-around is to just re-run recon-all -normalization -subjid subjid this will regenerate a T1 that has the skull and you can use this to fix your skull strip. I might suggest you rename your current T1.mgz volume before running this, otherwise you will write over it. Jenni On Tue, 15 Nov 2005, Bruce Fischl wrote: Hi Michele, this is the way that the dev version currently works - the T1 gets recreated in a 2nd pass that rerun the intensity normalization. We're going to change this in the upcoming official release because it's too confusing. Bruce On Tue, 15 Nov 2005, Michele Perry wrote: Hi, I am having problems with the dev version of Freesurfer. I realized after viewing the aseg that there was a skullstrip problem that I hadn't noticed when I checked the brain volume between -autorecon1 and -autorecon2. When I open brain.mgz and T1.mgz in tkmedit, they look identical (i.e. I can't see skull in the T1). Any idea what went wrong? Michele ___ 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 -- Jenni Pacheco, M.A. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Bldg. 149, 13th Street, CNY 2301 Charlestown, MA 02129 [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Keeping edits
Hi Alex, I've looked into your problem and I do see what you mean. Here's a brief run-down on the different flags. -autorecon2-cp begins with -normalization2, using your control points. Problem is it WILL write over the brain volume, creating a new one. It then finishes the stream from here, using -keepwmedits when running the -segmentation step to preserve any editing you've done to the wm volume. -autorecon2-wm begins with a newly edited wm volume and first runs -fill generating a new filled.mgz volume and then completes the stream from here. -autorecon2-pial simply reruns -makefinalsurfs and -cortribbon to remake the final surfaces, reflecting any editing that was done to the brain volume. We are currently working on a new flag to combat this problem, but until then - here are my suggestions for you now. 1. If your brain editing is necessary for achieving an accurate wm volume: a. set your control points and run recon-all -normalization2 -usecontrolpoints to fix the intensity. b. make your edits to the brain.mgz volume c. run recon-all -segmentation -keepwmedits to generate a new wm, reflecting your changes to the brain volume and keeping any previous wm edits. d. you will then still need to complete the rest of the stream. You can do this using this command: recon-all -autorecon2 -nosubcortseg -nonormalization2 -nosegmentation. 2. If your brain editing is only necessary for obtaining an accurate pial surface: a. set your control points and run recon-all -autorecon2-cp (you can add in -nofinalsurfs and -nocortribbon if you are sure that your control points won't fix your pial surfaces without edits. This will save a little processing time, but those steps don't take a tremendous amount of time) b. make your brain volume edits (if the problem wasn't fixed with the control points) c. run recon-all -autorecon2-pial to regenerate your final surfaces. hope this helps! Jenni On Tue, 18 Oct 2005, Fornito, Alexander wrote: Hi, Is there any way to run autorecon2-cp with an edited brain volume so that it concurrently adjusts the pial surface. Everytime I try to run it, it seems to erase my edits to the brain volume. Howeever, running autorecon2-wm or -pial, uses the brain edits. Some help on this would be much appreciated as it would save me a lot of re-processing time! Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Jenni Pacheco, M.A. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Bldg. 149, 13th Street, CNY 2301 Charlestown, MA 02129 [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
