[Freesurfer] Gray matter
Dear FS experts, I have a double question about the gray matter calculations in FS: - Revising the aseg.stats, I noticed that there is a Total Gray Volume calculation. Is there a mgz volume with the gray matter? I cannot find it on the output mri folder... - How this total Gray Volume is calculated? Which structures are taken into account? Is there any file with this information Kind Regards, -- Jordi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Whole Brain definition
Hello Freesurfer experts, I am currently doing some TBM analysis and to compute whole brain atrophy I consider all the structures except ventricles and CSF from aseg.mgz in my definition. Should I also include the cortex definition from aparc+aseg? If yes, should I then use aparc+aseg or aparc.a2009s+aseg segmentation file? Any help will be greatly appreciated. Akshay Univ. of Copenhagen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Xhemi stat questions
Dear Doug,I've seen that you restore the files to download, for the Xhemi registration. While I'm checking for the statistical process, I've seen that the one I have is: Date: 2012/12/06 16:06:52, Revision: 1.59.2.4, and the one that is on your ftp server is Date: 2012/12/06 16:06:17, Revision: 1.66, So mine is a lower version but recent hour, and the actual is newer version but seems that was created before the one I have. My question is, Which one should I keep? If I change the mris_precproc version. Shall I re-run this step before statistical analyses, to create a new lh.lh-rh.thickness.sm00.mgh?On the other hand I have some doubts about the statistical procedure. It's supposed that if I apply the Xhemi registration, as result the left and right hemispheres are equals to each other on every subject, so:A) Where can I get the CT values after the Xhemi registration to FSaverage_sym for the left and right hemispheres?B) Given that I have two groups, Patients and Control, with two levels each, i.e male-female (Gp1male Gp1female Gp2male Gp2female Gp1maleVar1 Gp1femaleVar1 Grp2maleVar1 Grp2femaleVar1), and that I can set the contrasts and fsgd files as with a normal CT analisis, but only on my lh.lh-rh.thickness.smXX.mgh, wich is suppose to contain the left-right differences across subjects, right? Wich would be the right interpretation? of: 1) 5 .5 -.5 -.5 0 0 0 02) 5 -.5 .5 -.5 0 0 0 03) 0 0 0 0 .5 .5 -.5 -.54) 0 0 0 0 5 -.5 .5 -.5Many thanks in advanced.Gabriel. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] cortical recontruction error
Dear Freesurfers, I'm new and I'm starting using Freesurfer. I'm having a problem with one subject, during the cortical reconstruction (recon-all) the process stops at this stage: mri_cc http://surfer.nmr.mgh.harvard.edu/fswiki/mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz subjid at this point: final transformation (x=128.0, yr=0.978, zr=0.153): 1.000 -0.003 0.017 -1.456; 0.003 1.000 0.000 8.654; -0.017 0.000 1.000 25.201; 0.000 0.000 0.000 1.000; without giving me any error message, it just stops. Do you have some ideas for why it happens? thanks to everyone, Claudia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] offset in qdec GUI
Hi list, I have a question, probably trivial, on onset in qdec GUI. What's this? And what I can do using it? Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] correction on question: offset in qdec GUI
Hi list, I have a question, probably trivial, on OFFSET in qdec GUI. What's this? And what I can do using it? Stefano ---BeginMessage--- Hi list, I have a question, probably trivial, on onset in qdec GUI. What's this? And what I can do using it? Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ---End Message--- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Brodmann area thickness, surface area and volume
Hi Andreia the issue is that the BA labels contain every point that has any non-zero probability (no matter how small!) of being in that label. So the total label area is almost certainly always bigger than the actual BA. Anastasia has some scripts for automatically computing the correct threshold, and I believe she and Nick integrated them into 5.2 so that the stats are computed both thresholded and unthresholded, hopefully they can comment. Bruce On Fri, 22 Mar 2013, _andre...@sapo.pt wrote: Hi all, I'm using FS 5.0 and some time ago I was told by Bruce that I had to threshold the BA in order to have an approximate area when overlaying in the inflated surface. To get surface area values I also need to use the label_area and put a threshold having the possibility to choose the surface that I want, either white or pial. But I can also get the BA stats in a table for all subjects and areas using either mris_anatomical_stats (on each label) or usinga script by Jamaan to get the table (since I already have the ?.BA.stats files), right? My question is, which is the better/correct way to get the thickness and surface area values of the BA to export for statistical analysis since there are the thresolds issue. I want to study mainly cortical thickness and surface area but also look also at the volume (which is surface-based, thus thickness*surface are will not be = volume since they are an average from each label, right?). I' not sure of which approach to follow now... Does it depend on the measure I'll be using? Thank you! Andreia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Whole Brain definition
Hi Ashkay, if you are doing voxel-wise TBM it probably doesn't matter. The definition of gray matter should be consistent between the two, just the labels of what bit of cortex they are will change. cheers Bruce On Fri, 22 Mar 2013, Akshay wrote: Hello Freesurfer experts, I am currently doing some TBM analysis and to compute whole brain atrophy I consider all the structures except ventricles and CSF from aseg.mgz in my definition. Should I also include the cortex definition from aparc+aseg? If yes, should I then use aparc+aseg or aparc.a2009s+aseg segmentation file? Any help will be greatly appreciated. Akshay Univ. of Copenhagen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] correction on question: offset in qdec GUI
Hi Stefano I believe it's the offset of the center of the color scale. So for example in the red/positive blue/negative one, the cross-over doesn't have to be at 0 cheers Bruce On Fri, 22 Mar 2013, std...@virgilio.it wrote: Hi list, I have a question, probably trivial, on OFFSET in qdec GUI. What's this? And what I can do using it? Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] R: Re: correction on question: offset in qdec GUI
Hi Bruce, I'm referring to offset in qdec/Display threshold line, near Min/Mid/Max. For example, I'm noting that if set +1 as offset the red statistical area is more larger. Stefano Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 22-mar-2013 13.48 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] correction on question: offset in qdec GUI Hi Stefano I believe it's the offset of the center of the color scale. So for example in the red/positive blue/negative one, the cross-over doesn't have to be at 0 cheers Bruce On Fri, 22 Mar 2013, std...@virgilio.it wrote: Hi list, I have a question, probably trivial, on OFFSET in qdec GUI. What's this? And what I can do using it? Stefano The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Error with .license after upgrading to 5.2
Hi list, after upgrading to 5.2 (from 5.1), I am consistently getting a license error (see below). The strange thing is that my .license is the same file I was using on 5.1 and worked fine. I have also tried multiple modifications of file permission/owners (its a local install so I can be root) but no luck. Thanks in advance, Nicola ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] FreeSurfer 5.2 Segmentation Talairach Registration Issues
Dear All, We have been running the recon-all pipeline in 5.2 and have been encountering some difficulties with segmentations. We have isolated these issues to problems with Talairach registrations, and have been re-running recon-all with the Talairach registrations manually corrected in tkregister2; however, doing so appears to worsen our segmentation problems. In particular, the orig surface appears substantially shrunk away from the filled and white matter volumes. Has anyone encountered such difficulties with manually corrected Talairach registrations placed in the processing stream, or indeed, seen the surface shrink to such an extent? We initially provided recon-all with synthesised volumes obtained using MRI-synthesise from the developer version (our raw scans are high-resolution PDw and T1w volumes). Any insights would be greatly appreciated. Many thanks, Dan --- Daniel Carey, M.Sc., Marie Curie PhD Fellow, Centre for Brain and Cognitive Development, Birkbeck College, 32 Torrington Sq., London, WC1E 7JL UK ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FreeSurfer 5.2 Segmentation Talairach Registration Issues
Hi Dan that sounds worrisome. I don't think we've seen this problem in our test cases. Can you upload an example so we can take a look? thanks Bruce On Fri, 22 Mar 2013, Daniel Carey wrote: Dear All, We have been running the recon-all pipeline in 5.2 and have been encountering some difficulties with segmentations. We have isolated these issues to problems with Talairach registrations, and have been re-running recon-all with the Talairach registrations manually corrected in tkregister2; however, doing so appears to worsen our segmentation problems. In particular, the orig surface appears substantially shrunk away from the filled and white matter volumes. Has anyone encountered such difficulties with manually corrected Talairach registrations placed in the processing stream, or indeed, seen the surface shrink to such an extent? We initially provided recon-all with synthesised volumes obtained using MRI-synthesise from the developer version (our raw scans are high-resolution PDw and T1w volumes). Any insights would be greatly appreciated. Many thanks, Dan --- Daniel Carey, M.Sc., Marie Curie PhD Fellow, Centre for Brain and Cognitive Development, Birkbeck College, 32 Torrington Sq., London, WC1E 7JL UK ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Brodmann area thickness, surface area and volume
Hi Bruce, Thank you for the quick response! In the meanwhile, does that also apply to cortical thickness and volume? Thank you! Andreia Quoting Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Andreia the issue is that the BA labels contain every point that has any non-zero probability (no matter how small!) of being in that label. So the total label area is almost certainly always bigger than the actual BA. Anastasia has some scripts for automatically computing the correct threshold, and I believe she and Nick integrated them into 5.2 so that the stats are computed both thresholded and unthresholded, hopefully they can comment. Bruce On Fri, 22 Mar 2013, _andre...@sapo.pt wrote: Hi all, I'm using FS 5.0 and some time ago I was told by Bruce that I had to threshold the BA in order to have an approximate area when overlaying in the inflated surface. To get surface area values I also need to use the label_area and put a threshold having the possibility to choose the surface that I want, either white or pial. But I can also get the BA stats in a table for all subjects and areas using either mris_anatomical_stats (on each label) or usinga script by Jamaan to get the table (since I already have the ?.BA.stats files), right? My question is, which is the better/correct way to get the thickness and surface area values of the BA to export for statistical analysis since there are the thresolds issue. I want to study mainly cortical thickness and surface area but also look also at the volume (which is surface-based, thus thickness*surface are will not be = volume since they are an average from each label, right?). I' not sure of which approach to follow now... Does it depend on the measure I'll be using? Thank you! Andreia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Brodmann area thickness, surface area and volume
yes. Surface area will be the affected much more than thickness (and volume of course scales with area) On Fri, 22 Mar 2013, _andre...@sapo.pt wrote: Hi Bruce, Thank you for the quick response! In the meanwhile, does that also apply to cortical thickness and volume? Thank you! Andreia Quoting Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Andreia the issue is that the BA labels contain every point that has any non-zero probability (no matter how small!) of being in that label. So the total label area is almost certainly always bigger than the actual BA. Anastasia has some scripts for automatically computing the correct threshold, and I believe she and Nick integrated them into 5.2 so that the stats are computed both thresholded and unthresholded, hopefully they can comment. Bruce On Fri, 22 Mar 2013, _andre...@sapo.pt wrote: Hi all, I'm using FS 5.0 and some time ago I was told by Bruce that I had to threshold the BA in order to have an approximate area when overlaying in the inflated surface. To get surface area values I also need to use the label_area and put a threshold having the possibility to choose the surface that I want, either white or pial. But I can also get the BA stats in a table for all subjects and areas using either mris_anatomical_stats (on each label) or usinga script by Jamaan to get the table (since I already have the ?.BA.stats files), right? My question is, which is the better/correct way to get the thickness and surface area values of the BA to export for statistical analysis since there are the thresolds issue. I want to study mainly cortical thickness and surface area but also look also at the volume (which is surface-based, thus thickness*surface are will not be = volume since they are an average from each label, right?). I' not sure of which approach to follow now... Does it depend on the measure I'll be using? Thank you! Andreia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] help with contrasts
On Thu, Mar 21, 2013 at 8:59 PM, Laura M. Tully tully.la...@googlemail.comwrote: oops sorry! (I also miscalculated the # of regressors - there's actually 12 (not 10 as previously noted). Here is the list of column labels: Grp1male Grp1female Grp2male Grp2female Grp1maleVar1 Grp1femaleVar1 Grp1maleVar2 Grp1femaleVar2 Grp2maleVar1 Grp2femaleVar1 Grp2maleVar2 Grp2femaleVar2 And what I think is actually an F test looking for group x var 1 interaction OR group x variable 2 interaction whilst accounting for gender. .5 .5 -.5 -.5 0 0 0 0 0 0 0 0 0 0 0 0 .5 .5 -.5 -.5 The Contrast for group*var1 would be: 0 0 0 0 .5 .5 0 0 -.5 -.5 0 0 The Contrast for group*var2 would be: 0 0 0 0 0 0 .5 .5 0 0 -.5 -.5 But what I actually WANT to test is a multiple regression style model - i.e. if I put var 1 AND 2 into the model together do they explain more variance than either variable alone, AND does this vary by group (is this even a sensible contrast to make?). Which I *think* would look something like this... 0 0 0 0 .125 .125 .125 .125 .125 .125 .125 .125 People generally don't ask that question. The answer is when you add more variables, you will explain more variance. Tests about overall model fits are generally assessed with the AIC, BIC, etc. metrics. I'm not sure if there is anyway in regression to say that the amount of variance explained is different by group unless you run 2 separate models. If you think this might be a valid question, I'd consult a statistician - which I am not. Laura. On Thu, Mar 21, 2013 at 5:51 PM, MCLAREN, Donald mclaren.don...@gmail.com wrote: Please include the list of the column labels. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Thu, Mar 21, 2013 at 6:43 PM, Laura M. Tully tully.la...@googlemail.com wrote: hi Experts, I'm struggling to conceptualize the appropriate contrasts for my cortical thickness analysis. I have four classes [two groups; two levels (patients,controls; male,female) and two behavioral variables. I want to see if together the two variables account significant proportion of the variance in y (thickness) and if this differs by group whilst regressing out gender. - i.e. if I enter both behavioral variables into the model does it account for more variance than either variable on their own (after controlling for gender)? What I have is this: .5 .5 -.5 -.5 0 0 0 0 0 0 0 0 .5 .5 -.5 -.5 Does this look right? Thanks! Laura. -- -- Laura M. Tully, MA Social Neuroscience Psychopathology, Harvard University Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience ltu...@mednet.ucla.edu ltu...@fas.harvard.edu 310-267-0170 -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- -- Laura M. Tully, MA Social Neuroscience Psychopathology, Harvard University Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience ltu...@mednet.ucla.edu ltu...@fas.harvard.edu 310-267-0170 -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] help with contrasts
Thanks Donald for your help. One final question - putting the does the amount of variance explained vary by group? question aside, if I wanted to run a multiple regression style model within one group looking at the contribution of the two behavioral variables together, does it make sense to weight the two variables as part of the same chunk of variance e.g. 0 0 0 0 .125 .125 .125 .125 .125 .125 .125 .125 (which I think will run a model looking at the contribution of variables 1 2 together regardless of group or gender). If so, I'm assuming I could adjust the model and run separate GLMs within each group, as you suggested - I just want to make sure I am understanding the weights correctly first... LT On Fri, Mar 22, 2013 at 8:23 AM, MCLAREN, Donald mclaren.don...@gmail.comwrote: On Thu, Mar 21, 2013 at 8:59 PM, Laura M. Tully tully.la...@googlemail.com wrote: oops sorry! (I also miscalculated the # of regressors - there's actually 12 (not 10 as previously noted). Here is the list of column labels: Grp1male Grp1female Grp2male Grp2female Grp1maleVar1 Grp1femaleVar1 Grp1maleVar2 Grp1femaleVar2 Grp2maleVar1 Grp2femaleVar1 Grp2maleVar2 Grp2femaleVar2 And what I think is actually an F test looking for group x var 1 interaction OR group x variable 2 interaction whilst accounting for gender. .5 .5 -.5 -.5 0 0 0 0 0 0 0 0 0 0 0 0 .5 .5 -.5 -.5 The Contrast for group*var1 would be: 0 0 0 0 .5 .5 0 0 -.5 -.5 0 0 The Contrast for group*var2 would be: 0 0 0 0 0 0 .5 .5 0 0 -.5 -.5 But what I actually WANT to test is a multiple regression style model - i.e. if I put var 1 AND 2 into the model together do they explain more variance than either variable alone, AND does this vary by group (is this even a sensible contrast to make?). Which I *think* would look something like this... 0 0 0 0 .125 .125 .125 .125 .125 .125 .125 .125 People generally don't ask that question. The answer is when you add more variables, you will explain more variance. Tests about overall model fits are generally assessed with the AIC, BIC, etc. metrics. I'm not sure if there is anyway in regression to say that the amount of variance explained is different by group unless you run 2 separate models. If you think this might be a valid question, I'd consult a statistician - which I am not. Laura. On Thu, Mar 21, 2013 at 5:51 PM, MCLAREN, Donald mclaren.don...@gmail.com wrote: Please include the list of the column labels. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Thu, Mar 21, 2013 at 6:43 PM, Laura M. Tully tully.la...@googlemail.com wrote: hi Experts, I'm struggling to conceptualize the appropriate contrasts for my cortical thickness analysis. I have four classes [two groups; two levels (patients,controls; male,female) and two behavioral variables. I want to see if together the two variables account significant proportion of the variance in y (thickness) and if this differs by group whilst regressing out gender. - i.e. if I enter both behavioral variables into the model does it account for more variance than either variable on their own (after controlling for gender)? What I have is this: .5 .5 -.5 -.5 0 0 0 0 0 0 0 0 .5 .5 -.5 -.5 Does this look right? Thanks! Laura. -- -- Laura M. Tully, MA Social Neuroscience Psychopathology, Harvard University Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience ltu...@mednet.ucla.edu ltu...@fas.harvard.edu 310-267-0170 -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the
Re: [Freesurfer] help with contrasts
You'd want an F test with 2 rows. One for the F-test of var 1 and one for the F-test of var2. A significant F-test won't tell you if your significantly better though than the F-test of var 1 only in the model. However, this sounds more like a model fitting question, which would be best addressed using AIC, BIC, etc. metrics of the overall model fit. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Fri, Mar 22, 2013 at 11:38 AM, Laura M. Tully tully.la...@googlemail.com wrote: Thanks Donald for your help. One final question - putting the does the amount of variance explained vary by group? question aside, if I wanted to run a multiple regression style model within one group looking at the contribution of the two behavioral variables together, does it make sense to weight the two variables as part of the same chunk of variance e.g. 0 0 0 0 .125 .125 .125 .125 .125 .125 .125 .125 (which I think will run a model looking at the contribution of variables 1 2 together regardless of group or gender). If so, I'm assuming I could adjust the model and run separate GLMs within each group, as you suggested - I just want to make sure I am understanding the weights correctly first... LT On Fri, Mar 22, 2013 at 8:23 AM, MCLAREN, Donald mclaren.don...@gmail.com wrote: On Thu, Mar 21, 2013 at 8:59 PM, Laura M. Tully tully.la...@googlemail.com wrote: oops sorry! (I also miscalculated the # of regressors - there's actually 12 (not 10 as previously noted). Here is the list of column labels: Grp1male Grp1female Grp2male Grp2female Grp1maleVar1 Grp1femaleVar1 Grp1maleVar2 Grp1femaleVar2 Grp2maleVar1 Grp2femaleVar1 Grp2maleVar2 Grp2femaleVar2 And what I think is actually an F test looking for group x var 1 interaction OR group x variable 2 interaction whilst accounting for gender. .5 .5 -.5 -.5 0 0 0 0 0 0 0 0 0 0 0 0 .5 .5 -.5 -.5 The Contrast for group*var1 would be: 0 0 0 0 .5 .5 0 0 -.5 -.5 0 0 The Contrast for group*var2 would be: 0 0 0 0 0 0 .5 .5 0 0 -.5 -.5 But what I actually WANT to test is a multiple regression style model - i.e. if I put var 1 AND 2 into the model together do they explain more variance than either variable alone, AND does this vary by group (is this even a sensible contrast to make?). Which I *think* would look something like this... 0 0 0 0 .125 .125 .125 .125 .125 .125 .125 .125 People generally don't ask that question. The answer is when you add more variables, you will explain more variance. Tests about overall model fits are generally assessed with the AIC, BIC, etc. metrics. I'm not sure if there is anyway in regression to say that the amount of variance explained is different by group unless you run 2 separate models. If you think this might be a valid question, I'd consult a statistician - which I am not. Laura. On Thu, Mar 21, 2013 at 5:51 PM, MCLAREN, Donald mclaren.don...@gmail.com wrote: Please include the list of the column labels. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the
[Freesurfer] Talairach manual correction
Hello! After completing the talairach correction in tkregister2 (saving the changes with the SAVEREG button), I am running recon-all -all -s subj. But now I'm wondering if by doing it this way the changes will be incorporated or the process will start from the beggining leaving everything as before the manual corrections... Is there any flag needed? Thank you, Andreia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Error with .license after upgrading to 5.2
Hi - no luck unfortunately (I had already tried changing permissions) On 03/22/2013 04:09 PM, Varghese Chikku wrote: Hi Nicola, Can you try this command,and echo the license.It may ask for password.I have similar issues with 5.2 and this how i sorted. sudo chmod -R a+rwX /Applications/freesurfer then echo each line of the licence. Let me know In thanks chikku ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Gray matter
Hi Jordi,I think you are looking for the information contained on the wiki:http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStatsTotalGray - total gray matter volume. This is simply the sum of SubCortGray + lhCortex + rhCortex + CerebellumGM. As such, it includes both surface-based volume calculations and voxel counts. To get a volume.mgz for the GM, you can use matlab and the aseg.mgz, or mri_extract_label, both with the number-IDs of the corresponding labels, as found in FreeSurferColorLUT.txtCheers,Gabriel. El 22/03/13, Jordi Delgado jordi...@pic.es escribió:Dear FS experts,I have a double question about the gray matter calculations in FS:- Revising the aseg.stats, I noticed that there is a Total Gray Volume calculation. Is there a mgz volume with the gray matter? I cannot find it on the output mri folder... - How this total Gray Volume is calculated? Which structures are taken into account? Is there any file with this informationKind Regards, -- Jordi -- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] hippo subfield
I'm running: recon-all -s Diff02 -hippo-subfields with the following error. Thanks. Stefano Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova/Diff02Actual FREESURFER_HOME /Applications/freesurfer-rw-rw-r-- 1 Stefano wheel 49 Mar 22 16:53 /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.logDarwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64##@# Hippocampal Subfields processing Fri Mar 22 16:56:31 CET 2013\n mkdir -p /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults\n kvlSegmentHippocampalSubfields.sh Diff02 left /Applications/freesurfer/subjects/subject_prova/Diff02 /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults \nDoing left sidemeshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gzcompressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txtboundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgzsubjectName: Diff02side: leftinputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02outputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResultsdirectory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02 already existsdirectory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left already existscd /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/leftcp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/nu.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/aseg.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/transforms/talairach.xfm .cp /Applications/freesurfer/data/GEMS/imageDump.mgz .kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939dyld: Library not loaded: libITKCommon.3.16.dylib Referenced from: /Applications/freesurfer/bin/kvlApplyTransform Reason: image not found/Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 77530 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.03280.0258 144.0010 -0.0330 0.9994 -0.00862.65600.02550.0094 0.9996 -3.1939Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s Diff02 exited with ERRORS at Fri Mar 22 16:56:31 CET 2013 For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.logTo report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Error with .license after upgrading to 5.2
Just use the license file from your previous version (or you can apply for a new license for free, but this is redundant). cp $OLD_FREESURFER_HOME/.license $NEW_FREESURFER_HOME/.license where the $OLD and $NEW are directories freesurfer 5.1 and 5.2 sit, respectively. Lingqiang Hi - no luck unfortunately (I had already tried changing permissions) On 03/22/2013 04:09 PM, Varghese Chikku wrote: Hi Nicola, Can you try this command,and echo the license.It may ask for password.I have similar issues with 5.2 and this how i sorted. sudo chmod -R a+rwX /Applications/freesurfer then echo each line of the licence. Let me know In thanks chikku ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Lingqiang Kong Ph.D candidate Auditory Neuroscience Laboratory Perceptual Neuroimaging Laboratory Boston University 677 Beacon St. Boston, MA 02215 http://www.cns.bu.edu/~shinn/ANL/index.html http://people.bu.edu/fmri/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] R: R: Re: correction on question: offset in qdec GUI
If I'd like to show a contrast map between two group, which is the correct form? If I set offset=1 the red area will be more larger, with more results than offset=0, the the blue (negative) will be stable. If I apply the Montecarlo Sim the results will seem to be in accord to offset=0. Which is the true map? Thanks, Stefano Messaggio originale Da: std...@virgilio.it Data: 22-mar-2013 14.59 A: fis...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: correction on question: offset in qdec GUI Hi Bruce, I'm referring to offset in qdec/Display threshold line, near Min/Mid/Max. For example, I'm noting that if set +1 as offset the red statistical area is more larger. Stefano Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 22-mar-2013 13.48 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] correction on question: offset in qdec GUI Hi Stefano I believe it's the offset of the center of the color scale. So for example in the red/positive blue/negative one, the cross-over doesn't have to be at 0 cheers Bruce On Fri, 22 Mar 2013, std...@virgilio.it wrote: Hi list, I have a question, probably trivial, on OFFSET in qdec GUI. What's this? And what I can do using it? Stefano The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Gray matter
Hi Gabriel, I will try it! Thank you! 2013/3/22 Gabriel Gonzalez Escamilla ggon...@upo.es Hi Jordi, I think you are looking for the information contained on the wiki: http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats *TotalGray* - total gray matter volume. This is simply the sum of SubCortGray + lhCortex + rhCortex + CerebellumGM. As such, it includes both surface-based volume calculations and voxel counts. To get a volume.mgz for the GM, you can use matlab and the aseg.mgz, or mri_extract_label, both with the number-IDs of the corresponding labels, as found in FreeSurferColorLUT.txt Cheers, Gabriel. El 22/03/13, *Jordi Delgado * jordi...@pic.es escribió: Dear FS experts, I have a double question about the gray matter calculations in FS: - Revising the aseg.stats, I noticed that there is a Total Gray Volume calculation. Is there a mgz volume with the gray matter? I cannot find it on the output mri folder... - How this total Gray Volume is calculated? Which structures are taken into account? Is there any file with this information Kind Regards, -- Jordi -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Error with .license after upgrading to 5.2
Hi, that is exactly what I did (see my first message) - that's why I'm so puzzled! Nicola On 03/22/2013 05:05 PM, Lingqiang Kong wrote: Just use the license file from your previous version (or you can apply for a new license for free, but this is redundant). cp $OLD_FREESURFER_HOME/.license $NEW_FREESURFER_HOME/.license where the $OLD and $NEW are directories freesurfer 5.1 and 5.2 sit, respectively. Lingqiang Hi - no luck unfortunately (I had already tried changing permissions) On 03/22/2013 04:09 PM, Varghese Chikku wrote: Hi Nicola, Can you try this command,and echo the license.It may ask for password.I have similar issues with 5.2 and this how i sorted. sudo chmod -R a+rwX /Applications/freesurfer then echo each line of the licence. Let me know In thanks chikku ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] trac-all -prep exited with errors
Hi I ran trac-all -prep -c dmrirc_single_subject and got the following error: here's the end of the output from trac-all: RegMat --- 1.000 -0.016 -0.000 4.210; 0.000 -0.005 1.000 2.417; -0.016 -1.000 -0.005 0.018; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -64, ref det = -1 Cleaning up Started at Fri Mar 22 11:35:44 CDT 2013 Ended at Fri Mar 22 11:38:10 CDT 2013 BBR-Run-Time-Sec 146 bbregister Done To check results, run: tkregister2 --mov /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/dwi.nii.gz --reg /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.dat --surf convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anatorig.bbr.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2diff.bbr.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2anatorig.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.bbr.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2diff.bbr.mat #- #@# Inter-subject registration Fri Mar 22 11:38:10 CDT 2013 flirt -in /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/brain_anat.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/brain_anat_mni.nii.gz -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat -cost mutualinfo convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2anat.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.flt.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.flt.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2diff.flt.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.flt.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.bbr.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.bbr.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2diff.bbr.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.bbr.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2mni.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2anat.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2anatorig.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2mni.mat #- #@# Masks Fri Mar 22 11:41:27 CDT 2013 flirt -in /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/mni/lowb_brain_mask.flt.nii.gz -applyxfm -init /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.flt.mat -interp nearestneighbour flirt -in /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/diff/lowb_brain_mask.nii.gz -ref /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/brain_anat_orig.nii.gz -out /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/anatorig/lowb_brain_mask.flt.nii.gz -applyxfm -init /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anatorig.flt.mat -interp nearestneighbour Error: failed to open file /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/anatorig/lowb_brain_mask.flt.nii.gz ERROR: Could not open image
Re: [Freesurfer] trac-all -prep exited with errors
Hi Jon - Can you please send all of trac-all.log? Sometimes there are hints earlier than where the error actually occurs. Thanks, a.y On Fri, 22 Mar 2013, Jon Wieser wrote: Hi I ran trac-all -prep -c dmrirc_single_subject and got the following error: here's the end of the output from trac-all: RegMat --- 1.000 -0.016 -0.000 4.210; 0.000 -0.005 1.000 2.417; -0.016 -1.000 -0.005 0.018; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -64, ref det = -1 Cleaning up Started at Fri Mar 22 11:35:44 CDT 2013 Ended at Fri Mar 22 11:38:10 CDT 2013 BBR-Run-Time-Sec 146 bbregister Done To check results, run: tkregister2 --mov /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/dwi.nii.gz --reg /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.dat --surf convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anatorig.bbr.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2diff.bbr.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2anatorig.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.bbr.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2diff.bbr.mat #- #@# Inter-subject registration Fri Mar 22 11:38:10 CDT 2013 flirt -in /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/brain_anat.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/brain_anat_mni.nii.gz -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat -cost mutualinfo convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2anat.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.flt.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.flt.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2diff.flt.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.flt.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.bbr.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.bbr.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2diff.bbr.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.bbr.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2mni.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2anat.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2anatorig.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2mni.mat #- #@# Masks Fri Mar 22 11:41:27 CDT 2013 flirt -in /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/mni/lowb_brain_mask.flt.nii.gz -applyxfm -init /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.flt.mat -interp nearestneighbour flirt -in /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/diff/lowb_brain_mask.nii.gz -ref /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/brain_anat_orig.nii.gz -out /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/anatorig/lowb_brain_mask.flt.nii.gz -applyxfm -init
Re: [Freesurfer] hippo subfield
Hi Stefano, Can you do ldd kvlApplyTransform and send us the result? Koen On 3/22/13, std...@virgilio.it std...@virgilio.it Hippocampal Subfields processing Fri Mar 22 16:56:31 CET 2013\n mkdir -p /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults\n kvlSegmentHippocampalSubfields.sh Diff02 left /Applications/freesurfer/subjects/subject_prova/Diff02 /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults \nDoing left sidemeshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gzcompressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txtboundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgzsubjectName: Diff02side: leftinputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02outputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResultsdirectory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02 already existsdirectory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left already existscd /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/leftcp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/nu.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/aseg.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/transforms/talairach.xfm .cp /Applications/freesurfer/data/GEMS/imageDump.mgz .kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939dyld: Library not loaded: libITKCommon.3.16.dylib Referenced from: /Applications/freesurfer/bin/kvlApplyTransform Reason: image not found/Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 77530 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.03280.0258 144.0010 -0.03300.9994 -0.00862.65600.0255 0.00940.9996 -3.1939Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s Diff02 exited with ERRORS at Fri Mar 22 16:56:31 CET 2013 For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.logTo report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] R: Re: hippo subfield
I'm sorry but, what's meaning ldd kvlApplyTransform? What's I should do more simply? Stefano Messaggio originale Da: k...@nmr.mgh.harvard.edu Data: 22-mar-2013 18.22 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] hippo subfield Hi Stefano, Can you do ldd kvlApplyTransform and send us the result? Koen On 3/22/13, std...@virgilio.it std...@virgilio.it Hippocampal Subfields processing Fri Mar 22 16:56:31 CET 2013\n mkdir -p /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults\n kvlSegmentHippocampalSubfields.sh Diff02 left /Applications/freesurfer/subjects/subject_prova/Diff02 /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults \nDoing left sidemeshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gzcompressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txtboundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgzsubjectName: Diff02side: leftinputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02outputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResultsdirectory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02 already existsdirectory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left already existscd /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/leftcp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/nu.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/aseg.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/transforms/talairach.xfm .cp /Applications/freesurfer/data/GEMS/imageDump.mgz .kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939dyld: Library not loaded: libITKCommon.3.16.dylib Referenced from: /Applications/freesurfer/bin/kvlApplyTransform Reason: image not found/Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 77530 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.03280.0258 144.0010 -0.03300.9994 -0.00862.65600.0255 0.00940.9996 -3.1939Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s Diff02 exited with ERRORS at Fri Mar 22 16:56:31 CET 2013 For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.logTo report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] R: Re: R: Re: R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts
Thank you Anastasia. I'm checking bvecs/bvals. I obtain it by DTI table creator (http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html) bvecs/bvals should be done. Gradients can be the unique responsable? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 22-mar-2013 17.07 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts Your gradient table is wrong. See where I've marked the corpus callosum in your screenshot. The eigenvectors are not pointing along the corpus callosum, but perpendicular to it. So they're off by 90 degrees, which means the same is true about the vectors in your gradient table. On Fri, 22 Mar 2013, std...@virgilio.it wrote: Hi Anastasia - I attacked the screenshots. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 22-mar-2013 1.39 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts Hi Stefano - There's nothing in these screenshots that tells you that the eigenvectors are correct. These are vectors, so the way to check them is to display them as lines. You display dtifit_V1 as lines, overlaid on dtifit_FA. Then you see if the lines point in the right direction. a.y On Fri, 22 Mar 2013, std...@virgilio.it wrote: Here they are attacked. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 21-mar-2013 21.50 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or lacking tracts Can you send a screenshot that shows dtifit_V1 and dtifit_FA? On Thu, 21 Mar 2013, std...@virgilio.it wrote: I have checked the gradient directions. How can I resolve the brain mask problem. Can I send you my files of this subject? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 20-mar-2013 22.46 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or lacking tracts There are chunks of the brain missing from the brain mask. This may cause some tracts to be incomplete or missing. But you should still check that the gradient directions are correct, so you know if you have multiple problems or just one. The FA map can't tell you if the gradient table was correct, you have to check the eigenvectors in dtifit_V1 for that. On Wed, 20 Mar 2013, std...@virgilio.it wrote: File attacked Messaggio originale Da: std...@virgilio.it Data: 20-mar-2013 22.34 A: ayend...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: Problem with tracula: incomplete or lacking tracts Thank you Anastasia. I'm checking gradient table but I would like underline that I'm noting some holes in dti_FA.nii.gz and not in dwi.nii.gz (I have attacked the relative images). Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 20-mar-2013 16.40 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Problem with tracula: incomplete or lacking tracts Hi Stefano - Have you checked that your gradient table is correct by looking at the output of the tensor fit? a.y On Wed, 20 Mar 2013, std...@virgilio.it wrote: Hi list and Anastasia, if you remember the last week I had same problems with tracula output: the final tract are lacking or incomplete for same subjects. Some of these are less wrong (only forceps major), other have more evident error (you can see this in picture that I have attacked). To resolve this issue I have: 1-checked the correct overlap of dwi and dwi_mask 2-rerun data with new version 5.2 3-rerun new registration using bbregister (fsl/spm option): for example, in the subject of the picture attacked, the .mincost file now contains as first value 0.87 (previous it was 1.1) Please, give me an advise Thanks Stefano Messaggio originale Da: std...@virgilio.it Data: 12-mar-2013 17.47 A: ayend...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: R: Re: Question on tracula and dwi-T1 overlap I got it from mri directory but I'm understanding that this directory isn't ok.I'm attacking the image from dlabel/diff/aparc+aseg.bbr.nii Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 12-mar-2013 17.19 A: std...@virgilio.it
Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts
Yes, the unique one. On Fri, 22 Mar 2013, std...@virgilio.it wrote: Thank you Anastasia. I'm checking bvecs/bvals. I obtain it by DTI table creator (http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html) bvecs/bvals should be done. Gradients can be the unique responsable? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 22-mar-2013 17.07 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts Your gradient table is wrong. See where I've marked the corpus callosum in your screenshot. The eigenvectors are not pointing along the corpus callosum, but perpendicular to it. So they're off by 90 degrees, which means the same is true about the vectors in your gradient table. On Fri, 22 Mar 2013, std...@virgilio.it wrote: Hi Anastasia - I attacked the screenshots. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 22-mar-2013 1.39 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts Hi Stefano - There's nothing in these screenshots that tells you that the eigenvectors are correct. These are vectors, so the way to check them is to display them as lines. You display dtifit_V1 as lines, overlaid on dtifit_FA. Then you see if the lines point in the right direction. a.y On Fri, 22 Mar 2013, std...@virgilio.it wrote: Here they are attacked. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 21-mar-2013 21.50 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or lacking tracts Can you send a screenshot that shows dtifit_V1 and dtifit_FA? On Thu, 21 Mar 2013, std...@virgilio.it wrote: I have checked the gradient directions. How can I resolve the brain mask problem. Can I send you my files of this subject? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 20-mar-2013 22.46 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or lacking tracts There are chunks of the brain missing from the brain mask. This may cause some tracts to be incomplete or missing. But you should still check that the gradient directions are correct, so you know if you have multiple problems or just one. The FA map can't tell you if the gradient table was correct, you have to check the eigenvectors in dtifit_V1 for that. On Wed, 20 Mar 2013, std...@virgilio.it wrote: File attacked Messaggio originale Da: std...@virgilio.it Data: 20-mar-2013 22.34 A: ayend...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: Problem with tracula: incomplete or lacking tracts Thank you Anastasia. I'm checking gradient table but I would like underline that I'm noting some holes in dti_FA.nii.gz and not in dwi.nii.gz (I have attacked the relative images). Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 20-mar-2013 16.40 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Problem with tracula: incomplete or lacking tracts Hi Stefano - Have you checked that your gradient table is correct by looking at the output of the tensor fit? a.y On Wed, 20 Mar 2013, std...@virgilio.it wrote: Hi list and Anastasia, if you remember the last week I had same problems with tracula output: the final tract are lacking or incomplete for same subjects. Some of these are less wrong (only forceps major), other have more evident error (you can see this in picture that I have attacked). To resolve this issue I have: 1-checked the correct overlap of dwi and dwi_mask 2-rerun data with new version 5.2 3-rerun new registration using bbregister (fsl/spm option): for example, in the subject of the picture attacked, the .mincost file now contains as first value 0.87 (previous it was 1.1) Please, give me an advise Thanks Stefano Messaggio originale Da: std...@virgilio.it Data: 12-mar-2013 17.47 A: ayend...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: R: Re: Question on tracula and dwi-T1 overlap I got it from mri directory but I'm understanding that this directory isn't ok.I'm attacking the image from dlabel/diff/aparc+aseg.bbr.nii Stefano Messaggio originale Da:
Re: [Freesurfer] trac-all -prep exited with errors
Hi Jon - The error says that it can't open a file *for writing*. Any chance it's a disk space issue or, if the file already exists, a permission issue? a.y On Fri, 22 Mar 2013, Jon Wieser wrote: HI Ansatasia I have attached the trac-all.log Jon - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, March 22, 2013 11:49:35 AM Subject: Re: [Freesurfer] trac-all -prep exited with errors Hi Jon - Can you please send all of trac-all.log? Sometimes there are hints earlier than where the error actually occurs. Thanks, a.y On Fri, 22 Mar 2013, Jon Wieser wrote: Hi I ran trac-all -prep -c dmrirc_single_subject and got the following error: here's the end of the output from trac-all: RegMat --- 1.000 -0.016 -0.000 4.210; 0.000 -0.005 1.000 2.417; -0.016 -1.000 -0.005 0.018; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -64, ref det = -1 Cleaning up Started at Fri Mar 22 11:35:44 CDT 2013 Ended at Fri Mar 22 11:38:10 CDT 2013 BBR-Run-Time-Sec 146 bbregister Done To check results, run: tkregister2 --mov /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/dwi.nii.gz --reg /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.dat --surf convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anatorig.bbr.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2diff.bbr.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2anatorig.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.bbr.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2diff.bbr.mat #- #@# Inter-subject registration Fri Mar 22 11:38:10 CDT 2013 flirt -in /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/brain_anat.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/brain_anat_mni.nii.gz -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat -cost mutualinfo convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2anat.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.flt.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.flt.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2diff.flt.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.flt.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.bbr.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.bbr.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2diff.bbr.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.bbr.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2mni.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2anat.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2anatorig.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2mni.mat #- #@# Masks Fri Mar 22 11:41:27 CDT 2013 flirt -in /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/mni/lowb_brain_mask.flt.nii.gz -applyxfm -init
[Freesurfer] Two questions regarding mri_fill and mris_fix_topology
Dear FreeSurfers, I amprocessing some T1-weighted images of the human brain with an isotropic resolution of.5 mm using version 5.1. After mri_fill my hemispheres are separated nicely and the cerebellum is completely removed. However, looking at the filled.mgz,posterior and superior of the corpus callosum some residualof white matter can be found in the longitudinal fissure. It does not remain if I look at the conformeddata, altough theseleftovers arefound in the wm.mgz of both datasets.As this does not happen using conformed data I assume that the cutting plane is not broad enough in case of higher resolution data or something related. Is there some way to tweak this? Secondly, I currentlyskip the -fix stage of recon-all completely while processing this data, but I would like to correct at least some of its defects.I already I have seen in the help of mris_fix_topology that it is possible to fix just one defect and Iextracted the defects and their number of vertices using the defect-seg script. Isit possible to save the resulting surface, so I am able to correct the defects I want toconsecutively? Best, Falk ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Two questions regarding mri_fill and mris_fix_topology
Hi Falk I don't think it's possible to fix just one defect, unless Florent included some option that I am not aware of. I also wouldn't worry too much about the filled.mgz. Make sure that the aseg.mgz and the ?h.white and ?h.pial are accurate cheers Bruce On Fri, 22 Mar 2013, Falk Lüsebrink wrote: Dear FreeSurfers, I am processing some T1-weighted images of the human brain with an isotropic resolution of .5 mm using version 5.1. After mri_fill my hemispheres are separated nicely and the cerebellum is completely removed. However, looking at the filled.mgz, posterior and superior of the corpus callosum some residual of white matter can be found in the longitudinal fissure. It does not remain if I look at the conformed data, altough these leftovers are found in the wm.mgz of both datasets. As this does not happen using conformed data I assume that the cutting plane is not broad enough in case of higher resolution data or something related. Is there some way to tweak this? Secondly, I currently skip the -fix stage of recon-all completely while processing this data, but I would like to correct at least some of its defects. I already I have seen in the help of mris_fix_topology that it is possible to fix just one defect and I extracted the defects and their number of vertices using the defect-seg script. Is it possible to save the resulting surface, so I am able to correct the defects I want to consecutively? Best, Falk ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] R: Re: hippo subfield
Hi Stefano, From the command line, type: ldd kvlApplyTransform and send us the output that you get. Cheers, /Eugenio On Fri, 2013-03-22 at 18:44 +0100, std...@virgilio.it wrote: I'm sorry but, what's meaning ldd kvlApplyTransform? What's I should do more simply? Stefano Messaggio originale Da: k...@nmr.mgh.harvard.edu Data: 22-mar-2013 18.22 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] hippo subfield Hi Stefano, Can you do ldd kvlApplyTransform and send us the result? Koen On 3/22/13, std...@virgilio.it std...@virgilio.it Hippocampal Subfields processing Fri Mar 22 16:56:31 CET 2013\n mkdir -p /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults\n kvlSegmentHippocampalSubfields.sh Diff02 left /Applications/freesurfer/subjects/subject_prova/Diff02 /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults \nDoing left sidemeshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gzcompressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txtboundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgzsubjectName: Diff02side: leftinputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02outputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResultsdirectory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02 already existsdirectory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left already existscd /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/leftcp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/nu.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/aseg.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/transforms/talairach.xfm .cp /Applications/freesurfer/data/GEMS/imageDump.mgz .kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939dyld: Library not loaded: libITKCommon.3.16.dylib Referenced from: /Applications/freesurfer/bin/kvlApplyTransform Reason: image not found/Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 77530 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.03280.0258 144.0010 -0.03300.9994 -0.00862.6560 0.0255 0.00940.9996 -3.1939Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s Diff02 exited with ERRORS at Fri Mar 22 16:56:31 CET 2013 For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.logTo report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, MGH, Harvard Medical School 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] R: Re: R: Re: hippo subfield
From command line I obtain: Stefano% ldd kvlApplyTransformldd: Command not found. I do not know is useful, but I have done this analysis with the previous version with any problem. Stefano Messaggio originale Da: igles...@nmr.mgh.harvard.edu Data: 22-mar-2013 19.19 A: std...@virgilio.it Cc: k...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: hippo subfield Hi Stefano, From the command line, type: ldd kvlApplyTransform and send us the output that you get. Cheers, /Eugenio On Fri, 2013-03-22 at 18:44 +0100, std...@virgilio.it wrote: I'm sorry but, what's meaning ldd kvlApplyTransform? What's I should do more simply? Stefano Messaggio originale Da: k...@nmr.mgh.harvard.edu Data: 22-mar-2013 18.22 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] hippo subfield Hi Stefano, Can you do ldd kvlApplyTransform and send us the result? Koen On 3/22/13, std...@virgilio.it std...@virgilio.it Hippocampal Subfields processing Fri Mar 22 16:56:31 CET 2013\n mkdir -p /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults\n kvlSegmentHippocampalSubfields.sh Diff02 left /Applications/freesurfer/subjects/subject_prova/Diff02 /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults \nDoing left sidemeshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gzcompressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txtboundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgzsubjectName: Diff02side: leftinputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02outputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResultsdirectory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02 already existsdirectory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left already existscd /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/leftcp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/nu.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/aseg.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/transforms/talairach.xfm .cp /Applications/freesurfer/data/GEMS/imageDump.mgz .kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939dyld: Library not loaded: libITKCommon.3.16.dylib Referenced from: /Applications/freesurfer/bin/kvlApplyTransform Reason: image not found/Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 77530 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.03280.0258 144.0010 -0.03300.9994 -0.00862.6560 0.0255 0.00940.9996 -3.1939Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s Diff02 exited with ERRORS at Fri Mar 22 16:56:31 CET 2013 For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.logTo report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, MGH, Harvard Medical School 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you
Re: [Freesurfer] R: Re: R: Re: hippo subfield
He's on a Mac, so the command would be: otool -L kvlApplyTransform and the output will be: kvlApplyTransform: libITKCommon.3.16.dylib (compatibility version 3.16.0, current version 3.16.0) libITKIO.3.16.dylib (compatibility version 3.16.0, current version 3.16.0) libITKznz.3.16.dylib (compatibility version 3.16.0, current version 3.16.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.5) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 159.1.0) /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 52.0.0) which is a little odd. Stefano, I will get back to you while I debug the issue. -Zeke On 03/22/2013 02:39 PM, std...@virgilio.it wrote: From command line I obtain: Stefano% ldd kvlApplyTransform ldd: Command not found. I do not know is useful, but I have done this analysis with the previous version with any problem. Stefano Messaggio originale Da: igles...@nmr.mgh.harvard.edu Data: 22-mar-2013 19.19 A: std...@virgilio.it Cc: k...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: hippo subfield Hi Stefano, From the command line, type: ldd kvlApplyTransform and send us the output that you get. Cheers, /Eugenio On Fri, 2013-03-22 at 18:44 +0100, std...@virgilio.it wrote: I'm sorry but, what's meaning ldd kvlApplyTransform? What's I should do more simply? Stefano Messaggio originale Da: k...@nmr.mgh.harvard.edu Data: 22-mar-2013 18.22 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] hippo subfield Hi Stefano, Can you do ldd kvlApplyTransform and send us the result? Koen On 3/22/13, std...@virgilio.it std...@virgilio.it Hippocampal Subfields processing Fri Mar 22 16:56:31 CET 2013\n mkdir -p /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults\n kvlSegmentHippocampalSubfields.sh Diff02 left /Applications/freesurfer/subjects/subject_prova/Diff02 /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults \nDoing left sidemeshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gzcompressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txtboundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgzsubjectName: Diff02side: leftinputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02outputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResultsdirectory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02 already existsdirectory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left already existscd /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/leftcp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/nu.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/aseg.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/transforms/talairach.xfm .cp /Applications/freesurfer/data/GEMS/imageDump.mgz .kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939dyld: Library not loaded: libITKCommon.3.16.dylib Referenced from: /Applications/freesurfer/bin/kvlApplyTransform Reason: image not found/Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 77530 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.03280.0258 144.0010 -0.03300.9994 -0.00862.6560 0.0255 0.00940.9996 -3.1939Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s Diff02 exited with ERRORS at Fri Mar 22 16:56:31 CET 2013 For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.logTo report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at
[Freesurfer] R: Re: R: Re: R: Re: hippo subfield
otool: Command not found. Messaggio originale Da: zkauf...@nmr.mgh.harvard.edu Data: 22-mar-2013 18.43 A: std...@virgilio.it Cc: igles...@nmr.mgh.harvard.edu, k...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: hippo subfield He's on a Mac, so the command would be: otool -L kvlApplyTransform and the output will be: kvlApplyTransform: libITKCommon.3.16.dylib (compatibility version 3.16.0, current version 3.16.0) libITKIO.3.16.dylib (compatibility version 3.16.0, current version 3.16.0) libITKznz.3.16.dylib (compatibility version 3.16.0, current version 3.16.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.5) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 159.1.0) /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 52.0.0) which is a little odd. Stefano, I will get back to you while I debug the issue. -Zeke On 03/22/2013 02:39 PM, std...@virgilio.it wrote: From command line I obtain: Stefano% ldd kvlApplyTransform ldd: Command not found. I do not know is useful, but I have done this analysis with the previous version with any problem. Stefano Messaggio originale Da: igles...@nmr.mgh.harvard.edu Data: 22-mar-2013 19.19 A: std...@virgilio.it Cc: k...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: hippo subfield Hi Stefano, From the command line, type: ldd kvlApplyTransform and send us the output that you get. Cheers, /Eugenio On Fri, 2013-03-22 at 18:44 +0100, std...@virgilio.it wrote: I'm sorry but, what's meaning ldd kvlApplyTransform? What's I should do more simply? Stefano Messaggio originale Da: k...@nmr.mgh.harvard.edu Data: 22-mar-2013 18.22 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] hippo subfield Hi Stefano, Can you do ldd kvlApplyTransform and send us the result? Koen On 3/22/13, std...@virgilio.it std...@virgilio.it Hippocampal Subfields processing Fri Mar 22 16:56:31 CET 2013\n mkdir -p /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults\n kvlSegmentHippocampalSubfields.sh Diff02 left /Applications/freesurfer/subjects/subject_prova/Diff02 /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults \nDoing left sidemeshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gzcompressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txtboundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgzsubjectName: Diff02side: leftinputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02outputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResultsdirectory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02 already existsdirectory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left already existscd /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/leftcp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/nu.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/aseg.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/transforms/talairach.xfm .cp /Applications/freesurfer/data/GEMS/imageDump.mgz .kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939dyld: Library not loaded: libITKCommon.3.16.dylib Referenced from: /Applications/freesurfer/bin/kvlApplyTransform Reason: image not found/Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 77530 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.03280.0258 144.0010 -0.03300.9994 -0.00862.6560 0.0255 0.00940.9996 -3.1939Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s Diff02 exited with ERRORS at Fri Mar 22 16:56:31 CET 2013 For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.logTo report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
[Freesurfer] R: Re: R: Re: R: Re: hippo subfield
[iMac-di-Stefano:freesurfer/subjects] Stefano% otool -L kvlApplyTransformotool: Command not found. Messaggio originale Da: zkauf...@nmr.mgh.harvard.edu Data: 22-mar-2013 18.43 A: std...@virgilio.it Cc: igles...@nmr.mgh.harvard.edu, k...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: hippo subfield He's on a Mac, so the command would be: otool -L kvlApplyTransform and the output will be: kvlApplyTransform: libITKCommon.3.16.dylib (compatibility version 3.16.0, current version 3.16.0) libITKIO.3.16.dylib (compatibility version 3.16.0, current version 3.16.0) libITKznz.3.16.dylib (compatibility version 3.16.0, current version 3.16.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.5) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 159.1.0) /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 52.0.0) which is a little odd. Stefano, I will get back to you while I debug the issue. -Zeke On 03/22/2013 02:39 PM, std...@virgilio.it wrote: From command line I obtain: Stefano% ldd kvlApplyTransform ldd: Command not found. I do not know is useful, but I have done this analysis with the previous version with any problem. Stefano Messaggio originale Da: igles...@nmr.mgh.harvard.edu Data: 22-mar-2013 19.19 A: std...@virgilio.it Cc: k...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: hippo subfield Hi Stefano, From the command line, type: ldd kvlApplyTransform and send us the output that you get. Cheers, /Eugenio On Fri, 2013-03-22 at 18:44 +0100, std...@virgilio.it wrote: I'm sorry but, what's meaning ldd kvlApplyTransform? What's I should do more simply? Stefano Messaggio originale Da: k...@nmr.mgh.harvard.edu Data: 22-mar-2013 18.22 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] hippo subfield Hi Stefano, Can you do ldd kvlApplyTransform and send us the result? Koen On 3/22/13, std...@virgilio.it std...@virgilio.it Hippocampal Subfields processing Fri Mar 22 16:56:31 CET 2013\n mkdir -p /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults\n kvlSegmentHippocampalSubfields.sh Diff02 left /Applications/freesurfer/subjects/subject_prova/Diff02 /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults \nDoing left sidemeshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gzcompressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txtboundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgzsubjectName: Diff02side: leftinputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02outputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResultsdirectory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02 already existsdirectory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left already existscd /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/leftcp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/nu.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/aseg.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/transforms/talairach.xfm .cp /Applications/freesurfer/data/GEMS/imageDump.mgz .kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939dyld: Library not loaded: libITKCommon.3.16.dylib Referenced from: /Applications/freesurfer/bin/kvlApplyTransform Reason: image not found/Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 77530 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.03280.0258 144.0010 -0.03300.9994 -0.00862.6560 0.0255 0.00940.9996 -3.1939Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s Diff02 exited with ERRORS at Fri Mar 22 16:56:31 CET 2013 For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.logTo report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list
[Freesurfer] problem with registration in preprocessing
Hi Doug, I am running fsfast preprocessing on my data and I am getting an error on one of the runs. This is the preprocessing code that I run: preproc-sess -s 130321_xu_Object4catmulti_01 -per-run -sliceorder siemens -fsd bold -fwhm 0 -mni305-2mm -surface self lhrh The error seems to happen during the fsl registration on the last run (out of 12 runs): /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 flirt.fsl -ref bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii -in bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/018/tmp.bbregister.1228/reg.init.dat.fsl.mat -init bold/018/tmp.bbregister.1228/fslregister/fslmat0.trans.mat -schedule /ncf/apps/freesurfer-5.1.0//bin/flirt.newdefault.20080811.sch terminate called after throwing an instance of 'NEWMAT::SingularException' Abort ERROR: flirt bellow is the register-sess log file. I have only included the section for the registration of the last run. I have looked at the raw data of this run and it does not look different from the other runs (all other runs are successfully registered). I am running freesurfer 5.1. Any idea how I can fix the error? Thanks, Maryam $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux ncfws08.rc.fas.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /ncf/apps/freesurfer-5.1.0/ mri_convert bold/018/template.nii.gz bold/018/tmp.bbregister.1228/template.nii mri_convert bold/018/template.nii.gz bold/018/tmp.bbregister.1228/template.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from bold/018/template.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998239, -0.0522464, 0.0280991) j_ras = (0.0500393, -0.995986, -0.0742193) k_ras = (0.031864, -0.0726825, 0.996846) writing to bold/018/tmp.bbregister.1228/template.nii... fslregister --s blue_street_kcb --mov bold/018/tmp.bbregister.1228/template.nii --reg bold/018/tmp.bbregister.1228/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/018/tmp.bbregister.1228/fslregister --dof 6 Log file is bold/018/tmp.bbregister.1228/reg.init.dat.fslregister.log Fri Mar 22 14:42:18 EDT 2013 --s blue_street_kcb --mov bold/018/tmp.bbregister.1228/template.nii --reg bold/018/tmp.bbregister.1228/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/018/tmp.bbregister.1228/fslregister --dof 6 $Id: fslregister,v 1.34.2.1 2011/03/28 20:35:36 greve Exp $ ncfws08.rc.fas.harvard.edu Linux ncfws08.rc.fas.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -- /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 mri_convert /ncf/vcn/Maryam/mri-space/subjects/blue_street_kcb/mri/brainmask.mgz bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii mri_convert /ncf/vcn/Maryam/mri-space/subjects/blue_street_kcb/mri/brainmask.mgz bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /ncf/vcn/Maryam/mri-space/subjects/blue_street_kcb/mri/brainmask.mgz... TR=2530.00, TE=3.45, TI=1100.00, flip angle=7.00 i_ras = (-1, 4.47035e-08, -4.65661e-08) j_ras = (-5.58793e-08, -4.05125e-08, -1) k_ras = (-5.96046e-08, 1, 1.11759e-08) writing to bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii... -- /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 mri_convert bold/018/tmp.bbregister.1228/template.nii bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii --frame 0 mri_convert bold/018/tmp.bbregister.1228/template.nii bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from bold/018/tmp.bbregister.1228/template.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998239, -0.0522464, 0.0280991) j_ras = (0.0500393, -0.995986, -0.0742193) k_ras = (0.031864, -0.0726825, 0.996846) keeping frame 0 writing to bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii... Mov determinant is 35.3062 Swapping dims for pos det WARNING:: Flipping Left/Right orientation (as det 0) tkregister_tcl /ncf/apps/freesurfer-5.1.0//tktools/tkregister2.tcl target volume bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii movable volume bold/018/tmp.bbregister.1228/template.nii reg file bold/018/tmp.bbregister.1228/fslregister/swapreg.dat LoadVol0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii INFO: target does not conform to COR format, so I'm going to reslice to COR.
Re: [Freesurfer] trac-all -prep exited with errors
Can you run the flirt command that gives the error directly on the command line? On Fri, 22 Mar 2013, Jon Wieser wrote: Hi Anastasia, we have plenty of disk space, 386 GB the file does not exist freesurfer/dlabel/anatorig/lowb_brain_mask.flt.nii.gz the entire freesurfer directory has read,write, and executable permission Jon - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, March 22, 2013 1:06:22 PM Subject: Re: [Freesurfer] trac-all -prep exited with errors Hi Jon - The error says that it can't open a file *for writing*. Any chance it's a disk space issue or, if the file already exists, a permission issue? a.y On Fri, 22 Mar 2013, Jon Wieser wrote: HI Ansatasia I have attached the trac-all.log Jon - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, March 22, 2013 11:49:35 AM Subject: Re: [Freesurfer] trac-all -prep exited with errors Hi Jon - Can you please send all of trac-all.log? Sometimes there are hints earlier than where the error actually occurs. Thanks, a.y On Fri, 22 Mar 2013, Jon Wieser wrote: Hi I ran trac-all -prep -c dmrirc_single_subject and got the following error: here's the end of the output from trac-all: RegMat --- 1.000 -0.016 -0.000 4.210; 0.000 -0.005 1.000 2.417; -0.016 -1.000 -0.005 0.018; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -64, ref det = -1 Cleaning up Started at Fri Mar 22 11:35:44 CDT 2013 Ended at Fri Mar 22 11:38:10 CDT 2013 BBR-Run-Time-Sec 146 bbregister Done To check results, run: tkregister2 --mov /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/dwi.nii.gz --reg /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.dat --surf convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anatorig.bbr.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2diff.bbr.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2anatorig.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.bbr.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2diff.bbr.mat #- #@# Inter-subject registration Fri Mar 22 11:38:10 CDT 2013 flirt -in /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/brain_anat.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/brain_anat_mni.nii.gz -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat -cost mutualinfo convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2anat.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.flt.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.flt.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2diff.flt.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.flt.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.bbr.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.bbr.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2diff.bbr.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.bbr.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2mni.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2anat.mat convert_xfm -omat
[Freesurfer] advice in registering a binary mask to Freesurfer space.
Hi All, I wanted to get peoples advice on the best method of registration/interpolation to use on a manually traced segmentation (and its structural) that is not in the same space and orientation as the structurals I started Freesurfer with (although they both originally came from the same image. I want to maintain the integrity of the manual traced binary mask through this registration and reslice. For a number of reasons, I do not want to take Freesurfers output to the space of the manual segmentation. What do people think is a good technique? Flirt nearest neighbor interpolation? Something different from Freesurfer? ANTs? - Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] hippo subfield
Stefano, In order to fix this issue please follow these instruction exactly: 1) Download the file kvl.zip from this link: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/ 2) Overwrite the existing kvl files in /Application/freesurfer/bin with the files in kvl.zip I was able to replicate your issue and solve it using the steps above. If these steps do not solve the issue for you, please respond with a the exact error you receive. Hope this helps. -Zeke On 03/22/2013 12:00 PM, std...@virgilio.it wrote: I'm running: recon-all -s Diff02 -hippo-subfields with the following error. Thanks. Stefano Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova/Diff02 Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 Stefano wheel 49 Mar 22 16:53 /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.log Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 # #@# Hippocampal Subfields processing Fri Mar 22 16:56:31 CET 2013 \n mkdir -p /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults \n kvlSegmentHippocampalSubfields.sh Diff02 left /Applications/freesurfer/subjects/subject_prova/Diff02 /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults \n Doing left side meshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz compressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz subjectName: Diff02 side: left inputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02 outputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults directory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02 already exists directory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left already exists cd /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/nu.mgz . cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/aseg.mgz . cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/transforms/talairach.xfm . cp /Applications/freesurfer/data/GEMS/imageDump.mgz . kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 dyld: Library not loaded: libITKCommon.3.16.dylib Referenced from: /Applications/freesurfer/bin/kvlApplyTransform Reason: image not found /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 77530 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 *failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.03280.0258 144.0010 -0.03300.9994 -0.00862.6560 0.02550.00940.9996 -3.1939* *Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64* * * *recon-all -s Diff02 exited with ERRORS at Fri Mar 22 16:56:31 CET 2013* For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.log To report a problem, see http://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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] trac-all -prep exited with errors
It will, unless it doesn't find the anatomical segmentation of the subject ($SUBJECTS_DIR/$subj/mri/aparc+aseg.mgz). On Fri, 22 Mar 2013, Jon Wieser wrote: I ran the flirt command on command line and got the same error. I noticed that the freesurfer/dlabel directory did not have an anatorig directory in it. I created this anatorig directory in the freesurfer/dlabel directory and ran the flirt command again. it ran ok. it created the /freesurfer/dlabel/anatorig/lowb_brain_mask.flt Is Trac-all supposed to create the freesurfer/dlabel/anatorig directory? I will try running trac-all again Jon - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, March 22, 2013 2:23:10 PM Subject: Re: [Freesurfer] trac-all -prep exited with errors Can you run the flirt command that gives the error directly on the command line? On Fri, 22 Mar 2013, Jon Wieser wrote: Hi Anastasia, we have plenty of disk space, 386 GB the file does not exist freesurfer/dlabel/anatorig/lowb_brain_mask.flt.nii.gz the entire freesurfer directory has read,write, and executable permission Jon - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, March 22, 2013 1:06:22 PM Subject: Re: [Freesurfer] trac-all -prep exited with errors Hi Jon - The error says that it can't open a file *for writing*. Any chance it's a disk space issue or, if the file already exists, a permission issue? a.y On Fri, 22 Mar 2013, Jon Wieser wrote: HI Ansatasia I have attached the trac-all.log Jon - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, March 22, 2013 11:49:35 AM Subject: Re: [Freesurfer] trac-all -prep exited with errors Hi Jon - Can you please send all of trac-all.log? Sometimes there are hints earlier than where the error actually occurs. Thanks, a.y On Fri, 22 Mar 2013, Jon Wieser wrote: Hi I ran trac-all -prep -c dmrirc_single_subject and got the following error: here's the end of the output from trac-all: RegMat --- 1.000 -0.016 -0.000 4.210; 0.000 -0.005 1.000 2.417; -0.016 -1.000 -0.005 0.018; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -64, ref det = -1 Cleaning up Started at Fri Mar 22 11:35:44 CDT 2013 Ended at Fri Mar 22 11:38:10 CDT 2013 BBR-Run-Time-Sec 146 bbregister Done To check results, run: tkregister2 --mov /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/dwi.nii.gz --reg /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.dat --surf convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anatorig.bbr.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2diff.bbr.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2anatorig.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.bbr.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2diff.bbr.mat #- #@# Inter-subject registration Fri Mar 22 11:38:10 CDT 2013 flirt -in /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/brain_anat.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/brain_anat_mni.nii.gz -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat -cost mutualinfo convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2anat.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.flt.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.flt.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2diff.flt.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.flt.mat convert_xfm -omat
[Freesurfer] R: Re: hippo subfield
Hi Zeke, as you explain I have download the kvl.zip and put it in /Application/freesurfer/bin. After rerunning I have: [iMac-di-Stefano:freesurfer/subjects/subject_prova] Stefano% recon-all -s Diff01 -hippo-subfieldsSubject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_provaActual FREESURFER_HOME /Applications/freesurfer-rw-rw-r-- 1 Stefano wheel 697785 Mar 22 23:56 /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.logDarwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64##@# Hippocampal Subfields processing Fri Mar 22 23:56:49 CET 2013\n mkdir -p /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults\n kvlSegmentHippocampalSubfields.sh Diff01 left /Applications/freesurfer/subjects/subject_prova /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults \nDoing left sidemeshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gzcompressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txtboundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgzsubjectName: Diff01side: leftinputDirectory: /Applications/freesurfer/subjects/subject_provaoutputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResultsdirectory /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01 already existsdirectory /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left already existscd /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/leftcp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/nu.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/aseg.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/transforms/talairach.xfm .cp /Applications/freesurfer/data/GEMS/imageDump.mgz .kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939dyld: Library not loaded: libITKCommon.3.16.dylib Referenced from: /Applications/freesurfer/bin/kvlApplyTransform Reason: image not found/Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 5481 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.03280.0258 144.0010 -0.0330 0.9994 -0.00862.65600.02550.0094 0.9996 -3.1939Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s Diff01 exited with ERRORS at Fri Mar 22 23:56:49 CET 2013 For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.logTo report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Messaggio originale Da: zkauf...@nmr.mgh.harvard.edu Data: 22-mar-2013 20.53 A: std...@virgilio.it, freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] hippo subfield Stefano, In order to fix this issue please follow these instruction exactly: 1) Download the file kvl.zip from this link: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/ 2) Overwrite the existing kvl files in /Application/freesurfer/bin with the files in kvl.zip I was able to replicate your issue and solve it using the steps above. If these steps do not solve the issue for you, please respond with a the exact error you receive. Hope this helps. -Zeke On 03/22/2013 12:00 PM, std...@virgilio.it wrote: I'm running: recon-all -s Diff02 -hippo-subfields with the following error. Thanks. Stefano Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova/Diff02 Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 Stefano wheel 49 Mar 22 16:53 /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.log Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 # #@# Hippocampal Subfields processing Fri Mar 22 16:56:31 CET 2013 \n mkdir -p /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults \n kvlSegmentHippocampalSubfields.sh Diff02 left /Applications/freesurfer/subjects/subject_prova/Diff02
