[Freesurfer] preproc-sess and option -mni305-1mm results in an error
Hi, if I apply the following command: preproc-sess -s sessID -fsd bold -nostc -surface fsaverage lhrh -mni305-1mm -fwhm 0 -per-run -nosmooth -force The preprocessing runs into trouble at the following point mri_vol2vol done mri_mask /...path.../bold/001/masks/brain.mni305.1mm.nii /usr/local/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz /...path.../bold/001/masks/brain.mni305.1mm.nii freadFloat: fread failed ERROR: dimension mismatch between source and mask As far as I can see freesurfer uses a 2mm mask for a 1mm brain, which results in the dimension mismatch. How can I get rid of this problem? Cheers Joerg ___ 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] Distance between ROIs on inflated brain
Hi, Is there a way to create and save multiple ROIs given there RAS coordinates in tkmedit and then plot them and measure the distance between them onto an inflated brain surface? Thanks! ~Rayna~ ___ 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] spline_smooth (please reply, no answer from email-list)
Hi Negar, sorry about the delay. The first thing to do is to look at the orig.mgz to see if there is anything funny going on, maybe most of the image is dark with one very bright spot or some other distortion. If that looks ok, please tar up the subject and drop it to me at our file drop (url at thenend of this email). doug On 11/26/2012 09:10 PM, Negar Memarian wrote: Hello Dr. Greve, I'm not sure if my questions actually get posted on the FreeSurfer email list or not, as I have never received a reply. I really need help with the following issue and would appreciate if you or your colleagues please advise: **I've checked similar posts on the email-list and still could not find an answer to my question. I'd really appreciate your attention and feedback: recon-all -autorecon1 crashes for me in one of the steps before skull stripping with an error like this: Done spline_smooth: posixio.c:210: px_pgin: Assertion `*posp== ((off_t)(-1)) || *posp== lseek(nciop-fd, 0, 1)' failed. nu_estimate_np_and_em: crashed while running spline_smooth(termination status=6) nu_correct: crashed while running nu_estimate_np_and_em(termination status=65280) ERROR: nu_correct Linux FreeSurfer2.6.28-11-generic #42-UbuntuSMPFri Apr 17 01:57:59 UTC2009 i686GNU/Linux recon-all -s BT501_FSexited with ERRORS at Mon Nov 26 15:26:10 EST2012 I made sure that I have the newest version of FreeSurfer, the environment variables MNI_DATAPATH and MNI_PERL5LIB and PERL5LIB exist and I ran $FREESURFER_HOME/bin/fixup_mni_paths as well. But unfortunately I still face the same problem. I also tried the process for a different subject, but the same error. Does anyone have any idea how I can fix this? I have attached the recon-all.log file. I'd really appreciate your help. Negar Negar Memarian, MASc, PhD NSERC Postdoctoral Fellow Department of Neurology David Geffen School of Medicine at UCLA -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Regarding freesurfer segmentations for longitudinal data
Hi, I work in the area of longitudinal shape analysis, and have used the longitudinal OASIS data in the past. I was trying to find freesurfer segmentations of structures for the OASIS data, but could only find them for cross-sectional ones. I write to you to ask if you're aware of segmentations made available for the longitudinal OASIS data, specifically the hippocampus regions? If not, could you point me to the best way possible to segment these for the longitudinal OASIS data? Thanks, Prasanna -- -- Let there be peace on earth... And let it begin with me. ___ 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] preproc-sess and option -mni305-1mm results in an error
Yep, that's a bug. I've fixed it in my version. To fix it in yours, do the following two steps: Step 1: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/subcort.mask.1mm.mgz cp subcort.mask.1mm.mgz $SUBJECTS_DIR/fsaverage/mri Step 2: In rawfunc2tal-sess, change: set subcortmask = $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz To if($res == 2) then set subcortmask = $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz else set subcortmask = $FREESURFER_HOME/subjects/fsaverage/mri/subcort.mask.1mm.mgz endif doug On 11/27/2012 04:48 AM, Jörg Pfannmöller wrote: Hi, if I apply the following command: preproc-sess -s sessID -fsd bold -nostc -surface fsaverage lhrh -mni305-1mm -fwhm 0 -per-run -nosmooth -force The preprocessing runs into trouble at the following point mri_vol2vol done mri_mask /...path.../bold/001/masks/brain.mni305.1mm.nii /usr/local/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz /...path.../bold/001/masks/brain.mni305.1mm.nii freadFloat: fread failed ERROR: dimension mismatch between source and mask As far as I can see freesurfer uses a 2mm mask for a 1mm brain, which results in the dimension mismatch. How can I get rid of this problem? Cheers Joerg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] preproc-sess and option -mni305-1mm results in an error
Note that each of those set commands should be a single line. The file to change is $FREESURFER_HOME/fsfast/bin/rawfunc2tal-sess doug On 11/27/2012 01:23 PM, Douglas N Greve wrote: Yep, that's a bug. I've fixed it in my version. To fix it in yours, do the following two steps: Step 1: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/subcort.mask.1mm.mgz cp subcort.mask.1mm.mgz $SUBJECTS_DIR/fsaverage/mri Step 2: In rawfunc2tal-sess, change: set subcortmask = $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz To if($res == 2) then set subcortmask = $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz else set subcortmask = $FREESURFER_HOME/subjects/fsaverage/mri/subcort.mask.1mm.mgz endif doug On 11/27/2012 04:48 AM, Jörg Pfannmöller wrote: Hi, if I apply the following command: preproc-sess -s sessID -fsd bold -nostc -surface fsaverage lhrh -mni305-1mm -fwhm 0 -per-run -nosmooth -force The preprocessing runs into trouble at the following point mri_vol2vol done mri_mask /...path.../bold/001/masks/brain.mni305.1mm.nii /usr/local/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz /...path.../bold/001/masks/brain.mni305.1mm.nii freadFloat: fread failed ERROR: dimension mismatch between source and mask As far as I can see freesurfer uses a 2mm mask for a 1mm brain, which results in the dimension mismatch. How can I get rid of this problem? Cheers Joerg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Subgroup analysis
Hi, Thanks for the reference and explanation of the subtle statistical inferences. It was very useful. You are right in what i am trying to show (c- controls, p1 to p4 patients with varying levels of endogenous factor) which is that when patients are subdivided into levels of endogenous factor there is correlation with the changes seen in dependent variables compared to controls. So far, C v whole P gp - differences seen in plausible areas. C v P1 (greatest endo factor) subgp - no differences C v P4 subgp (lowest endo factor) - differences seen in plausible areas. Given that it is not valid to compare c v p1 and c v p4 (and p1 v p4 shows nothing) is the following valid - perhaps it is similar to what you proposed: Consider c and p1 to p4 as one group of subjects (theoretically the only difference between subjects being level of endogenous factor) but assign each subject a variable which represents level of endoenous factor (c - 1 p1 - 2 p3 - 4 p4 - 5) - then run glm looking for correlation between endogenous factor and dependent variable. Is this very different to what you suggested and any less valid ? Thanks. M ___ 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] Subgroup analysis
Hi Mahinda, make sure to include previous correspondence so that we know what previous the previous suggestions are. Your analysis sounds technically correct if you can justify the 1, 2, and 5 values for the covariate. This design will give you a little more power. doug On 11/27/2012 01:28 PM, Mahinda Yogarajah wrote: Hi, Thanks for the reference and explanation of the subtle statistical inferences. It was very useful. You are right in what i am trying to show (c- controls, p1 to p4 patients with varying levels of endogenous factor) which is that when patients are subdivided into levels of endogenous factor there is correlation with the changes seen in dependent variables compared to controls. So far, C v whole P gp - differences seen in plausible areas. C v P1 (greatest endo factor) subgp - no differences C v P4 subgp (lowest endo factor) - differences seen in plausible areas. Given that it is not valid to compare c v p1 and c v p4 (and p1 v p4 shows nothing) is the following valid - perhaps it is similar to what you proposed: Consider c and p1 to p4 as one group of subjects (theoretically the only difference between subjects being level of endogenous factor) but assign each subject a variable which represents level of endoenous factor (c - 1 p1 - 2 p3 - 4 p4 - 5) - then run glm looking for correlation between endogenous factor and dependent variable. Is this very different to what you suggested and any less valid ? Thanks. M ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Regarding freesurfer segmentations for longitudinal data
Hi Parsanna, I am not aware of any publicly available segmentation of the longitudinal oasis data using the longitudinal freesurfer stream. I have done some of that for my longitudinal paper but did not use all time points for that. I may have run all somewhere else, but need to double check. Anyway, you can of course run the longitudinal freesurfer pipeline on the oasis data yourself and get the segmentations from it. Best, Martin On Tue, 2012-11-27 at 11:14 -0700, Prasanna M wrote: Hi, I work in the area of longitudinal shape analysis, and have used the longitudinal OASIS data in the past. I was trying to find freesurfer segmentations of structures for the OASIS data, but could only find them for cross-sectional ones. I write to you to ask if you're aware of segmentations made available for the longitudinal OASIS data, specifically the hippocampus regions? If not, could you point me to the best way possible to segment these for the longitudinal OASIS data? Thanks, Prasanna -- -- Let there be peace on earth... And let it begin with me. ___ 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] Subgroup analysis
On Tue, Nov 27, 2012 at 1:28 PM, Mahinda Yogarajah y.mahi...@gmail.com wrote: Hi, Thanks for the reference and explanation of the subtle statistical inferences. It was very useful. You are right in what i am trying to show (c- controls, p1 to p4 patients with varying levels of endogenous factor) which is that when patients are subdivided into levels of endogenous factor there is correlation with the changes seen in dependent variables compared to controls. So far, C v whole P gp - differences seen in plausible areas. C v P1 (greatest endo factor) subgp - no differences C v P4 subgp (lowest endo factor) - differences seen in plausible areas. Given that it is not valid to compare c v p1 and c v p4 (and p1 v p4 shows nothing) is the following valid - perhaps it is similar to what you proposed: compare c v p1 and c v p4 (and p1 v p4 shows nothing) These are all valid tests on their own. The issue waas that you were making qualitative interpretations of the results. Consider c and p1 to p4 as one group of subjects (theoretically the only difference between subjects being level of endogenous factor) but assign each subject a variable which represents level of endoenous factor (c - 1 p1 - 2 p3 - 4 p4 - 5) - then run glm looking for correlation between endogenous factor and dependent variable. Is this very different to what you suggested and any less valid ? If you have you have entered 5 groups and want to test the linear change over the groups. You can use [2 1 0 -1 2] as the contrast. If you want the linear change over the patients, then you can use [0 1.5 .5 -.5 -1.5]. If you want to detect any difference in the patients, you could try an F-test of [0 1 -1 0 0; 0 0 1 -1 0; 0 0 0 1 -1]. Thanks. M ___ 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] Subgroup analysis
Hi Doug, Sorry the previous suggestion referred to a suggestion from Donald earlier in the thread as follows: You might consider the contrast [0 1.5 .5 -.5 -1.5] across all 5 groups showing a linear effect of disease severity. The first column being controls. I will try that suggestion out, but I have also grouped all the patients and controls together in 1 group (as opposed to 5 different groups), and given that controls contains no endogenous factor giving them a covariate of 1, and then P1 a value of 2, P2 a value of 3, P3 a values of 4 and P4 a value of 5. There are good biological grounds to suspect that that the endogenous factor will increase linearly from P1 to P5, though the values 1 to 5 I have chosen are arbitrary. When I then run the GLM looking for correlation between dependent measure and this covariate, I see significant results in a similar (though more widespread) location compared to when I simply look for a difference between all controls and all patients (C v combined P1 to P4). Thus, I think (hope) the model has shown that Hopefully this is one valid way in which to show that it is the changes in the level of the endogenous factor contribute to the overall group differences (C v combined P1 to P4). Do you agree ? I will however try Donald's method as I also want to show that the interaction between age-thickness (that I see in C v combined P1 to P4) shows a linear effect across P1 to P4. Any suggestions for how I do that ? Thanks, M___ 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] mergecontrasts-sess group map
Hi Doug and Freesurfers, I recently used mergecontrasts-sess to merge two contrasts of an analysis in 50 different subjects. The command ran on each subject individually and created a sig.nii and sig.ovpl file within a merged contrast folder for each subject. I'd now like to look at an average map of the merged contrasts across all 50 subjects. Does anyone know how to go about getting this average map for my group of 50 subjects? Command I ran to get the sig.nii/sig.ovpl file for each subject: mergecontrasts-sess -mergedcontrast Merge_7vFix_1vFix -conjunction andor -analysis SIRP_Stable5 -contrast Cond7vFix 3 pos 0 -contrast Cond1vFix 3 pos 0 -map sig -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/50_MTH_Subjects -df /cluster/roffman/users/Stable5_PerRun Any help would be greatly appreciated! Thanks, Alex ___ 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] Subgroup analysis
sorry, what I meant to request is that you keep everything in a single email. If they are spread out over multiple emails, then we have to go back and find the relevant ones. As you know, we answer many emails, and it is burdensome to have to keep track of particular emails. thanks! doug On 11/27/2012 04:00 PM, MAHINDA YOGARAJAH wrote: Hi Doug, Sorry the previous suggestion referred to a suggestion from Donald earlier in the thread as follows: You might consider the contrast [0 1.5 .5 -.5 -1.5] across all 5 groups showing a linear effect of disease severity. The first column being controls. I will try that suggestion out, but I have also grouped all the patients and controls together in 1 group (as opposed to 5 different groups), and given that controls contains no endogenous factor giving them a covariate of 1, and then P1 a value of 2, P2 a value of 3, P3 a values of 4 and P4 a value of 5. There are good biological grounds to suspect that that the endogenous factor will increase linearly from P1 to P5, though the values 1 to 5 I have chosen are arbitrary. When I then run the GLM looking for correlation between dependent measure and this covariate, I see significant results in a similar (though more widespread) location compared to when I simply look for a difference between all controls and all patients (C v combined P1 to P4). Thus, I think (hope) the model has shown that Hopefully this is one valid way in which to show that it is the changes in the level of the endogenous factor contribute to the overall group differences (C v combined P1 to P4). Do you agree ? I will however try Donald's method as I also want to show that the interaction between age-thickness (that I see in C v combined P1 to P4) shows a linear effect across P1 to P4. Any suggestions for how I do that ? Thanks, M -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Problem Visualizing Hippocampal Subfield Segmentation in FreeView
Hi FS community, I was trying to view the results of the hippocampal subfield segmentation but had trouble overlaying the subfields on the nu.mgz file. I tried letting it run for a while but it still does not work. Below I have included the commands I used in Terminal: [dyn-128-59-230-112:subjects/bert/mri] learninglab2% freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz -p-labels posterior_right_* posterior_Right-Hippocampus.mgz -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt 2012-11-27 19:18:38.964 freeview.bin[20154:607] invalid drawable 2012-11-27 19:18:38.969 freeview.bin[20154:607] invalid drawable 2012-11-27 19:18:38.987 freeview.bin[20154:607] invalid drawable 2012-11-27 19:18:38.989 freeview.bin[20154:607] invalid drawable 2012-11-27 19:18:39.006 freeview.bin[20154:607] invalid drawable 2012-11-27 19:18:39.008 freeview.bin[20154:607] invalid drawable 2012-11-27 19:18:39.025 freeview.bin[20154:607] invalid drawable 2012-11-27 19:18:39.027 freeview.bin[20154:607] invalid drawable QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB Can not find index for color name left_CA2-3 CTABrgbAtIndexi: index -1 was OOB QThread: Destroyed while thread is still running I looked over the mailing list and saw that someone had a similar problem in the past and tried to follow that solution. It did not seem to work for me: [dyn-128-59-230-112:/Applications] learninglab2% cd $FREESURFER_HOME/ [dyn-128-59-230-112:/Applications/freesurfer] learninglab2% sed -i s/CA2_3/CA2\/3/g FreeSurferColorLUT.txt sed: 1: FreeSurferColorLUT.txt: invalid command code F [dyn-128-59-230-112:/Applications/freesurfer] learninglab2% sed -i s/CA4_DG/CA4\/DG/g FreeSurferColorLUT.txt sed: 1: FreeSurferColorLUT.txt: invalid command code F Does anybody know what's going on? Thanks for your help, Juan ___ 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] p-value too small?
Hi Doug, I am afraid the p values are still too small in Free Surfer Linux-centos4_x86_64-stable-pub-v5.1.0-full. I redid mkanalysis-sess mkcontrast-sess selxavg3-sess in 5.1., it looks verz similar as in 4.5., including a whole of 0.0 in the center of the cluster. Any further advice? Thanks, Caspar 2012/11/26 Douglas Greve gr...@nmr.mgh.harvard.edu: No, it does not. With version 5 I went to a simple AR1 model instead. doug On 11/26/12 10:34 PM, Caspar M. Schwiedrzik wrote: Hi Doug, thanks for the input. What I meant is that in version 5.1, mkanalysis-sess does not seem to recognize the -taumax flag to set the maximum delay for the autocorrelation function. Caspar 2012/11/26 Douglas N Greve gr...@nmr.mgh.harvard.edu: On 11/26/2012 02:12 PM, Caspar M. Schwiedrzik wrote: Hi Doug, I'll do that. Two quick follow-up questions regarding 5.1: - it seems that I cannot specify taumax anymore in mkanalysis-sess. Is there another argument that would allow me to set the autocorrelation? What do you mean by set the autocorrelation? You can turn it off with -no-whiten. - in a block design, would refeventduration be the block length or the length of the individual events within a block? The block length. This will not change the p-values, only percent signal change values (often not even looked at). doug Thanks, Caspar 2012/11/26 Douglas N Grevegr...@nmr.mgh.harvard.edu: Hi Caspar, I think I fixed this in later versions. If you upgrade, you can run the stats from 5.1 with recons from 4.5 (just don't mix recons from different versions). doug On 11/26/2012 01:15 PM, Caspar M. Schwiedrzik wrote: Hi! I ran into a funny problem when calculating contrasts in Freesurfer 4.5.0. Namely, the center of my cluster of significant voxels has a p-value of -0.0, resulting in a funny whole where you would otherwise expect to find the most significant voxel(s). It seems that the p-value is too small. Is there a workaround available? Thank you very much, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fwd: (no subject)
Hi Hugh how far is the closest visible white matter? Do you have any other image types (e.g. a FLAIR)? Bruce On Wed, 28 Nov 2012, Hugh Pemberton wrote: Hi freesurfers, Just want to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples.. Cheers, Hugh On 21 November 2012 11:29, Hugh Pemberton hughpembert...@gmail.com wrote: Hi Bruce, Just to let you know the new mris_topo_fixer worked and there was no error with the recon. I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples.. Cheers, Hugh On 16 November 2012 14:44, Hugh Pemberton hughpembert...@gmail.com wrote: Hi Bruce, I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a few screen shots as examples.. Cheers, Hugh On 16 November 2012 11:14, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: this is a bug in the topology fixer. Maybe Zeke or Nick can post a new version of it? Was it mris_topo_fixer that was runing or mris_fix_topology? On Fri, 16 Nov 2012, Hugh Pemberton wrote: Hi Bruce, Thanks for getting back to me. In terminal window it says freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 but recon-all -version give me $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ Hugh On 16 November 2012 11:05, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Hugh This is fixed in the newest version. What version are you running? Bruce On Nov 15, 2012, at 6:48 PM, Hugh Pemberton hughpembert...@gmail.com wrote: Hi, I have just received this error after a recon-all subjid- ___ all : ERROR: _FindFacePath: could not find path! /home/hughp/freesurfer/subjects/B__/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated cp ../surf/lh.orig_corrected ../surf/lh.orig Linux naoshi-WS 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B__ exited with ERRORS at Thu Nov 15 11:40:44 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Many thanks in advance, Best, Hugh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] (no subject)
What version are you running? On Nov 27, 2012, at 8:51 PM, Hugh Pemberton hughpembert...@gmail.com wrote: Generally about 4 or 5 slices away, no other images unfortunately! Any ideas or is the atrophy just too great? Also meant to ask about another control point based issue I've had - occasionally, if I've added a few to the temporal lobes because only a small amount has been left out and then run autorecon2 and autorecon3 the result is just a load more of the temporal lobe being left out, I've attached another couple of screen shots, in this example there's about 20 slices of left out matter. Cheers, Hugh On 28 November 2012 12:34, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Hugh how far is the closest visible white matter? Do you have any other image types (e.g. a FLAIR)? Bruce On Wed, 28 Nov 2012, Hugh Pemberton wrote: Hi freesurfers, Just want to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples.. Cheers, Hugh On 21 November 2012 11:29, Hugh Pemberton hughpembert...@gmail.com wrote: Hi Bruce, Just to let you know the new mris_topo_fixer worked and there was no error with the recon. I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples.. Cheers, Hugh On 16 November 2012 14:44, Hugh Pemberton hughpembert...@gmail.com wrote: Hi Bruce, I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a few screen shots as examples.. Cheers, Hugh On 16 November 2012 11:14, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: this is a bug in the topology fixer. Maybe Zeke or Nick can post a new version of it? Was it mris_topo_fixer that was runing or mris_fix_topology? On Fri, 16 Nov 2012, Hugh Pemberton wrote: Hi Bruce, Thanks for getting back to me. In terminal window it says freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 but recon-all -version give me $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ Hugh On 16 November 2012 11:05, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Hugh This is fixed in the newest version. What version are you running? Bruce On Nov 15, 2012, at 6:48 PM, Hugh Pemberton hughpembert...@gmail.com wrote: Hi, I have just received this error after a recon-all subjid- ___ all : ERROR: _FindFacePath: could not find path! /home/hughp/freesurfer/subjects/B__/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated cp ../surf/lh.orig_corrected ../surf/lh.orig Linux naoshi-WS 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B__ exited with ERRORS at Thu Nov 15 11:40:44 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Many thanks in advance, Best, Hugh ___ 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
Re: [Freesurfer] (no subject)
5.1.0 On 28 November 2012 13:59, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: What version are you running? On Nov 27, 2012, at 8:51 PM, Hugh Pemberton hughpembert...@gmail.com wrote: Generally about 4 or 5 slices away, no other images unfortunately! Any ideas or is the atrophy just too great? Also meant to ask about another control point based issue I've had - occasionally, if I've added a few to the temporal lobes because only a small amount has been left out and then run autorecon2 and autorecon3 the result is just a load more of the temporal lobe being left out, I've attached another couple of screen shots, in this example there's about 20 slices of left out matter. Cheers, Hugh On 28 November 2012 12:34, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Hugh how far is the closest visible white matter? Do you have any other image types (e.g. a FLAIR)? Bruce On Wed, 28 Nov 2012, Hugh Pemberton wrote: Hi freesurfers, Just want to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples.. Cheers, Hugh On 21 November 2012 11:29, Hugh Pemberton hughpembert...@gmail.com wrote: Hi Bruce, Just to let you know the new mris_topo_fixer worked and there was no error with the recon. I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples.. Cheers, Hugh On 16 November 2012 14:44, Hugh Pemberton hughpembert...@gmail.com wrote: Hi Bruce, I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a few screen shots as examples.. Cheers, Hugh On 16 November 2012 11:14, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: this is a bug in the topology fixer. Maybe Zeke or Nick can post a new version of it? Was it mris_topo_fixer that was runing or mris_fix_topology? On Fri, 16 Nov 2012, Hugh Pemberton wrote: Hi Bruce, Thanks for getting back to me. In terminal window it says freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0 but recon-all -version give me $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ Hugh On 16 November 2012 11:05, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Hugh This is fixed in the newest version. What version are you running? Bruce On Nov 15, 2012, at 6:48 PM, Hugh Pemberton hughpembert...@gmail.com wrote: Hi, I have just received this error after a recon-all subjid- ___ all : ERROR: _FindFacePath: could not find path! /home/hughp/freesurfer/**subjects/B__/**scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated cp ../surf/lh.orig_corrected ../surf/lh.orig Linux naoshi-WS 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B__ exited with ERRORS at Thu Nov 15 11:40:44 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.**edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Many thanks in advance, Best, Hugh __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurferhttps://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/**compliancelinehttp://www.partners.org/complianceline.
Re: [Freesurfer] (no subject)
Try it with nicks control point-fixed recon-all and see if it works better On Nov 27, 2012, at 10:44 PM, Hugh Pemberton hughpembert...@gmail.com wrote: 5.1.0 On 28 November 2012 13:59, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: What version are you running? On Nov 27, 2012, at 8:51 PM, Hugh Pemberton hughpembert...@gmail.com wrote: Generally about 4 or 5 slices away, no other images unfortunately! Any ideas or is the atrophy just too great? Also meant to ask about another control point based issue I've had - occasionally, if I've added a few to the temporal lobes because only a small amount has been left out and then run autorecon2 and autorecon3 the result is just a load more of the temporal lobe being left out, I've attached another couple of screen shots, in this example there's about 20 slices of left out matter. Cheers, Hugh On 28 November 2012 12:34, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Hugh how far is the closest visible white matter? Do you have any other image types (e.g. a FLAIR)? Bruce On Wed, 28 Nov 2012, Hugh Pemberton wrote: Hi freesurfers, Just want to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples.. Cheers, Hugh On 21 November 2012 11:29, Hugh Pemberton hughpembert...@gmail.com wrote: Hi Bruce, Just to let you know the new mris_topo_fixer worked and there was no error with the recon. I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples.. Cheers, Hugh On 16 November 2012 14:44, Hugh Pemberton hughpembert...@gmail.com wrote: Hi Bruce, I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a few screen shots as examples.. Cheers, Hugh On 16 November 2012 11:14, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: this is a bug in the topology fixer. Maybe Zeke or Nick can post a new version of it? Was it mris_topo_fixer that was runing or mris_fix_topology? On Fri, 16 Nov 2012, Hugh Pemberton wrote: Hi Bruce, Thanks for getting back to me. In terminal window it says freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 but recon-all -version give me $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ Hugh On 16 November 2012 11:05, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Hugh This is fixed in the newest version. What version are you running? Bruce On Nov 15, 2012, at 6:48 PM, Hugh Pemberton hughpembert...@gmail.com wrote: Hi, I have just received this error after a recon-all subjid- ___ all : ERROR: _FindFacePath: could not find path! /home/hughp/freesurfer/subjects/B__/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated cp ../surf/lh.orig_corrected ../surf/lh.orig Linux naoshi-WS 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B__ exited with ERRORS at Thu Nov 15 11:40:44 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Many thanks in advance, Best, Hugh ___ 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
