Re: [Freesurfer] recon-all with FLAIR error no FSL installed
Dear all, How fatal is the FSL environment not being initialized for FreeSurfer 5.3 with FLAIR refinement? I do get results (which look good). Should I rerun them with FSL installed? Thank you very much in advance! Sincerely, Veronica -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: maandag 27 mei 2013 14:19 To: Popescu, Veronica Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] recon-all with FLAIR error no FSL installed Hi Veronica thanks for the offer, but I don't need to see them. Glad it seems to be working. As for BBR, I'll leave that for Doug Bruce On Mon, 27 May 2013, Popescu, Veronica wrote: Dear Bruce, They look good to me. Should I upload a couple of them, so you can have a look? They're about 230MB each. My question is: how serious is the BBR not initializing? Should I run everything again with FSL installed? Best wishes, Veronica -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: vrijdag 24 mei 2013 15:59 To: Popescu, Veronica Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] recon-all with FLAIR error no FSL installed Hi Veronica BBR can use FSL or SPM to initialize, although we'll probably add an option in the future to use some things that Martin Reuter and Christian Wachinger are working on. How did the refinement work? We've only run it on a handful of cases, so it's pretty bleeding edge and I'm interested in feedback. cheers Bruce On Fri, 24 May 2013, Popescu, Veronica wrote: Dear all, I am running FreeSurfer 5.3 with FLAIR refinement. I do not have FSL installed. I do get results but there's an error message in the log file (attached) about the FSL installation missing. How bad is it? Do I have to rerun everything with FSL installed? And if so, is there any version that is preferable? Thank you very much in advance! Best wishes, Veronica 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] recon-all with FLAIR error no FSL installed
If the FLAIR was acquired in the same session you might be ok, as bbregister inititialized from the headers will be close enough unless there is large-scale movement between scans. Bruce On Tue, 28 May 2013, Popescu, Veronica wrote: Dear all, How fatal is the FSL environment not being initialized for FreeSurfer 5.3 with FLAIR refinement? I do get results (which look good). Should I rerun them with FSL installed? Thank you very much in advance! Sincerely, Veronica -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: maandag 27 mei 2013 14:19 To: Popescu, Veronica Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] recon-all with FLAIR error no FSL installed Hi Veronica thanks for the offer, but I don't need to see them. Glad it seems to be working. As for BBR, I'll leave that for Doug Bruce On Mon, 27 May 2013, Popescu, Veronica wrote: Dear Bruce, They look good to me. Should I upload a couple of them, so you can have a look? They're about 230MB each. My question is: how serious is the BBR not initializing? Should I run everything again with FSL installed? Best wishes, Veronica -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: vrijdag 24 mei 2013 15:59 To: Popescu, Veronica Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] recon-all with FLAIR error no FSL installed Hi Veronica BBR can use FSL or SPM to initialize, although we'll probably add an option in the future to use some things that Martin Reuter and Christian Wachinger are working on. How did the refinement work? We've only run it on a handful of cases, so it's pretty bleeding edge and I'm interested in feedback. cheers Bruce On Fri, 24 May 2013, Popescu, Veronica wrote: Dear all, I am running FreeSurfer 5.3 with FLAIR refinement. I do not have FSL installed. I do get results but there's an error message in the log file (attached) about the FSL installation missing. How bad is it? Do I have to rerun everything with FSL installed? And if so, is there any version that is preferable? Thank you very much in advance! Best wishes, Veronica The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] rerun interrupted processes
Hi Valeria can you address this type of question to the list so that others can answer and learn from the answers? Yes, you can run recon-all -make all -s subject id and it should pick up from where it left off Bruce On Tue, 28 May 2013, Valeria Contarino wrote: Dear Bruce, I have a new question for you. I was running 30 subjects when processes were interrupted because of no more space left on device. Do I have the chance for starting again the processes from where they stopped? Thank you. Regards, Valeria ___ 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] fix talairach transform
Hi Laouchedi these alignments look fine. I am a bit concerned at how dark your images are near the top of the head. What coil are you using? This is probably why you are having trouble. cheers Bruce On Tue, 28 May 2013, LAOUCHEDI MAKHLOUF wrote: Hi i have a problem when running recon-all -all, so i decided to split the process into three staps : recon-all -autorecon1, recon-all -autorecon2 and recon-all -autorecon3. i have just finished with the first step (recon-all -autorecon1) and looked for misalignment in talairach transform for all subjects using tkregister2 --mgz --s ctr1 --fstal (i can't use --surf orig because i haven't the surfaces yet). so i used the small red cross in the coronal, sagittal and axial views to align as much as possible. my goal is to extract the cortical labels (cortical parcellation). is it necessary to have a precise talairach transform just for this purpose ? Thank you ___ 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] BBR Register failing
and bbregister? On 05/28/2013 02:03 AM, Salil Soman wrote: It was attached to my earlier email (included again here). The only chnages I made are at lines 129 (set fsvol = brainmask) and 132 (echo FSVOL $fsvol). -S On Mon, May 27, 2013 at 9:14 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Can you send me your original version of fslregister and bregister? On 5/27/13 10:53 PM, Salil Soman wrote: I have been using 5.3 of freesurfer for centos 6. As far as I can tell, the problem was with fslregister, which was getting called by bbregister. I've downloaded the link you just sent, remarked out the line I added to fslregister (see the file I sent in response to your email), and I get the same error. Restoring my modification makes the code work again. Thank you, Sal On Mon, May 27, 2013 at 7:43 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: which version of FS are you using? This was a problem with 5.2 but it should be fixed with 5.3. If you have 5.2 or earlier, you can use this version of bbregister ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister doug On 5/27/13 10:32 PM, Salil Soman wrote: Thank you Doug, fsvol was defined, which was why I was confused. I put in a command to echo the fsvol value in the line before where the error was getting generated, and it echoed ERROR. Adding a line specifically defining fsvol using set in the section fixed the problem (as far as I can tell). -Sal On Mon, May 27, 2013 at 7:16 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Sal, fsvol should be defined. Can you send me your fslregister? doug On 5/26/13 12:58 AM, Salil Soman wrote: Dear Freesurfer experts, WIth the combination of FS 5.3 and FSL 5.0.2.1, It looks like I am having some problems with the fslregister script. From what I have been able to investigate. It looks like there is an issue that fsvol may not get named if you are not dealing .cor files. Code in question from fslregister script: # Use the rawavg as input (for testing only) if($fsvol == rawavg.cor) then set refvol = $SUBJECTS_DIR/$subjid/mri/$fsvol.mgz if(! -e $refvol) then # Does not exist, create set orig = $SUBJECTS_DIR/$subjid/mri/orig.mgz set rawavg = $SUBJECTS_DIR/$subjid/mri/rawavg.mgz set cmd = (mri_vol2vol --mov $rawavg --targ $orig --o $refvol \ --no-save-reg --regheader) echo $cmd | tee -a $LF $cmd | tee -a $LF if($status) exit 1; # Now mask it set brain = $SUBJECTS_DIR/$subjid/mri/brainmask.mgz set cmd = (mri_mask $refvol $brain $refvol) echo $cmd | tee -a $LF $cmd | tee -a $LF I think this lack of fsvol being named results in the errors I am getting: -- /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.756/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.756/fslregister/refvol.fslregister.nii mri_convert: extra arguments (not and following) Any suggestions would be a huge help. -Sal On Sat, May 25, 2013 at 8:35 PM, Salil Soman salso...@stanford.edu mailto:salso...@stanford.edu wrote: Done. Thank you for your consideration. The best I can figure so far is 1) the script's attempt to make the tmp.bbregister.7392 directory fails and 2) (after I manually make this directory), there seems to be something going wrong at the level of fslregister I have fsl 5.0.2.1 and freesurfer 5.3 running, and am regularly able to run freesurfer and tracula (using only the flirt method, the bbr method was giving me trouble as well). The code is all running on a sun grid engine, with individual ubuntu 12.04.1 LTS machines. Your help on this
Re: [Freesurfer] minor bug report
This is an annoying mismatch between linux and osx. On 05/25/2013 11:09 PM, Joseph Dien wrote: when I run: isxconcat-sess -sf sessidlist.dat -analysis CPA.sm05.lh -all-contrasts -o secondLevel I get the error messages: secondLevel/CPA.sm05.mni305/log/isxconcat.log stat: illegal option -- c usage: stat [-FlLnqrsx] [-f format] [-t timefmt] [file ...] stat: illegal option -- c usage: stat [-FlLnqrsx] [-f format] [-t timefmt] [file ...] stat: illegal option -- c usage: stat [-FlLnqrsx] [-f format] [-t timefmt] [file …] ... I'm assuming this isn't a serious problem as it just seems to affect what goes into the log file but thought you might want to know. This is on OS X 10.8.2 with Freesurfer 5.2.0. Cheers! Joe Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com mailto:jdie...@mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] area measurements FS5.1
Hi, I have processed a sample with FS 5.1 and would like to do a group analysis of surface-based area. According to the release notes ( ** ) there is an issue with the conversion into standard space. I found a former post pointing to a version of preproc-sess that to my understanding should fix that, but the file is not there any more. Is there any quick fix for this problem without having to move to 5.3 / could I get that file? Thanks, Benjamin ** There is a bug in the way that FS converts surface-based area (eg, lh.area) and volume (eg, lh.volume) into standard space. The files themselves are fine, it is the way they are transfered to standard space that is the problem. You will not need to re-analyze any of your individual subject data. The volumes of the subcortical structures are unaffected by this problem. Global measures of cortical volume are also unaffected. -- Benjamín Garzón, Ph.D. Karolinska Institutet Department of Neuroscience Retzius Väg 8 17177 Stockholm (SWEDEN) ___ 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] area measurements FS5.1
try that link again doug On 05/28/2013 10:16 AM, Benjamín Garzón wrote: Hi, I have processed a sample with FS 5.1 and would like to do a group analysis of surface-based area. According to the release notes ( ** ) there is an issue with the conversion into standard space. I found a former post pointing to a version of preproc-sess that to my understanding should fix that, but the file is not there any more. Is there any quick fix for this problem without having to move to 5.3 / could I get that file? Thanks, Benjamin ** There is a bug in the way that FS converts surface-based area (eg, lh.area) and volume (eg, lh.volume) into standard space. The files themselves are fine, it is the way they are transfered to standard space that is the problem. You will not need to re-analyze any of your individual subject data. The volumes of the subcortical structures are unaffected by this problem. Global measures of cortical volume are also unaffected. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] nuintensitycor and skullstrip problems
can you send me the whole .mgz volume? And your recon-all command line that fails? On Tue, 28 May 2013, LAOUCHEDI MAKHLOUF wrote: hi i send you the rawavg.mgz of the subject with the massive artefact. i inform you that i proceeded differently by splitting the recon-all -all into three steps (as in freesurfer wiki) : (1) recon-all -autorecon1, (2) recon-all -autorecon2 (3) recon-all -autorecon3. i just finished with the first step which still didn't work for some subjects so i deleted then in my SUBJECTS_DIR then i run recon-all -i to regenerate them. after that i re-run recon-all -autorecon1 and it worked even for the subject with the artefacted rawavg.mgz i am sending you. i noticed also that some extra cerebral structures like dura is not fully removed after the skullstripping step, and i reviewed some of my previous datasets i processed with freesurfer and i noticed that the cortical ribbon (containing the cortical parcellation) fits well the gray matter. so is a wise idea to not bother a lot about these some extra cerebral structures left and just go forward with the rest of the recon-all pipeline (but of course i'll take a look a posteriori). Thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_anatomical_stats segmentation fault
Rob, can you send me your label? doug On 05/27/2013 01:00 PM, Rob Tennyson wrote: Hi All, I'm running mris_anatomical_stats with a few manually defined labels. For a few of my subjects, I am getting the error: Segmentation fault on one of the labels. However, the other manually defined labels process without any errors on these same subjects. For example, I am running mri_anatomical_stats on subject 33_bay6 with a manually defined ERC label, a manually defined PHC label, and a manually defined medial frontal gyrus label. The only label that runs an error for this subject is the PHC label. This PHC label runs without any errors on the rest of my subjects. Here is what is displayed when running a label that fails: mris_anatomical_stats -f PHC.stats.04.txt -l lh.PHC_1.label -b 33_bay6 lh limiting computations to label lh.PHC_1.label. reading volume /Volumes/BigRaid/Rob/subjects/33_bay6/mri/wm.mgz... reading input surface /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... reading input pial surface /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.pial... reading input white surface /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... Segmentation fault Does anyone know what may be causing the Segmentation fault and what steps I should take to fix it? Thank you for your help! Rob ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mris_resample: Command not found.
Hello, I am trying to perform an inter-subject registration using mri_cvs_register on version 5.3. When I ran mri_cvs_check, my feedback was I needed to find mri_cvs_register.settings.txt but I didn't worry about this per Lilla's post: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.html mri_cvs_register kicks off well, but eventually it ends with: mris_resample: Command not found. I go into my $FREESURFER_HOME/bin directory and note that mris_resample is truly not there. Did I not install 5.3 properly? I have attached a log file in case this helps. Cheers, Daniel MLL_to_MNI152_T1_1mm.mri_cvs_register.1305241528.log Description: MLL_to_MNI152_T1_1mm.mri_cvs_register.1305241528.log ___ 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] BBR Register failing
I know, but I want to see what version of bbregister you are using On 05/28/2013 10:29 AM, Salil Soman wrote: I did not make any changes to bbregister. Thank you for all your help. Sal On May 28, 2013 6:57 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: and bbregister? On 05/28/2013 02:03 AM, Salil Soman wrote: It was attached to my earlier email (included again here). The only chnages I made are at lines 129 (set fsvol = brainmask) and 132 (echo FSVOL $fsvol). -S On Mon, May 27, 2013 at 9:14 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Can you send me your original version of fslregister and bregister? On 5/27/13 10:53 PM, Salil Soman wrote: I have been using 5.3 of freesurfer for centos 6. As far as I can tell, the problem was with fslregister, which was getting called by bbregister. I've downloaded the link you just sent, remarked out the line I added to fslregister (see the file I sent in response to your email), and I get the same error. Restoring my modification makes the code work again. Thank you, Sal On Mon, May 27, 2013 at 7:43 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: which version of FS are you using? This was a problem with 5.2 but it should be fixed with 5.3. If you have 5.2 or earlier, you can use this version of bbregister ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister doug On 5/27/13 10:32 PM, Salil Soman wrote: Thank you Doug, fsvol was defined, which was why I was confused. I put in a command to echo the fsvol value in the line before where the error was getting generated, and it echoed ERROR. Adding a line specifically defining fsvol using set in the section fixed the problem (as far as I can tell). -Sal On Mon, May 27, 2013 at 7:16 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Sal, fsvol should be defined. Can you send me your fslregister? doug On 5/26/13 12:58 AM, Salil Soman wrote: Dear Freesurfer experts, WIth the combination of FS 5.3 and FSL 5.0.2.1, It looks like I am having some problems with the fslregister script. From what I have been able to investigate. It looks like there is an issue that fsvol may not get named if you are not dealing .cor files. Code in question from fslregister script: # Use the rawavg as input (for testing only) if($fsvol == rawavg.cor) then set refvol = $SUBJECTS_DIR/$subjid/mri/$fsvol.mgz if(! -e $refvol) then # Does not exist, create set orig = $SUBJECTS_DIR/$subjid/mri/orig.mgz set rawavg = $SUBJECTS_DIR/$subjid/mri/rawavg.mgz set cmd = (mri_vol2vol --mov $rawavg --targ $orig --o $refvol \ --no-save-reg --regheader) echo $cmd | tee -a $LF $cmd | tee -a $LF if($status) exit 1; # Now mask
Re: [Freesurfer] mris_resample: Command not found.
Hi Daniel, What operating system are you using? Lilla On Tue, 28 May 2013, Barron, Daniel S wrote: Hello, I am trying to perform an inter-subject registration using mri_cvs_register on version 5.3. When I ran mri_cvs_check, my feedback was I needed to find mri_cvs_register.settings.txt but I didn't worry about this per Lilla's post: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.html mri_cvs_register kicks off well, but eventually it ends with: mris_resample: Command not found. I go into my $FREESURFER_HOME/bin directory and note that mris_resample is truly not there. Did I not install 5.3 properly? I have attached a log file in case this helps. Cheers, Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_anatomical_stats segmentation fault
Nothing looks like it is wrong with that label. Can you verify that the white surface has not been changed since the label was created? Check how many vertices the white surface has with mris_info. The PHC label references a vertex index as high as 163798. If the white surface does not have that many veritices, then that could cause the problem. doug On 05/28/2013 10:33 AM, Rob Tennyson wrote: Hi Doug, Attached are the three labels I'm having an issue with (each with a different subject). These are built from areas that we found functional differences between a healthy control group and a MDD group. I was going to take a look at the anatomical stats to see if there are thickness or volume differences as well. I am also going to review the white surface soon as Bruce suggested. On Tue, May 28, 2013 at 9:26 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Rob, can you send me your label? doug On 05/27/2013 01:00 PM, Rob Tennyson wrote: Hi All, I'm running mris_anatomical_stats with a few manually defined labels. For a few of my subjects, I am getting the error: Segmentation fault on one of the labels. However, the other manually defined labels process without any errors on these same subjects. For example, I am running mri_anatomical_stats on subject 33_bay6 with a manually defined ERC label, a manually defined PHC label, and a manually defined medial frontal gyrus label. The only label that runs an error for this subject is the PHC label. This PHC label runs without any errors on the rest of my subjects. Here is what is displayed when running a label that fails: mris_anatomical_stats -f PHC.stats.04.txt -l lh.PHC_1.label -b 33_bay6 lh limiting computations to label lh.PHC_1.label. reading volume /Volumes/BigRaid/Rob/subjects/33_bay6/mri/wm.mgz... reading input surface /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... reading input pial surface /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.pial... reading input white surface /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... Segmentation fault Does anyone know what may be causing the Segmentation fault and what steps I should take to fix it? Thank you for your help! Rob ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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 mailto: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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] area measurements FS5.1
Thanks, Doug. I guess it's the mris_preproc file there what I need, not preproc-sess... Does this version do the areal interpolation as described in Winkler 2012 'Measuring and comparing brain cortical surface area and other areal quantities http://www.academia.edu/1604228/Measuring_and_comparing_brain_cortical_surface_area_and_other_areal_quantities'? Best regards, Benjamin On 05/28/2013 04:16 PM, Benjamín Garzón wrote: Hi, I have processed a sample with FS 5.1 and would like to do a group analysis of surface-based area. According to the release notes ( ** ) there is an issue with the conversion into standard space. I found a former post pointing to a version of preproc-sess that to my understanding should fix that, but the file is not there any more. Is there any quick fix for this problem without having to move to 5.3 / could I get that file? Thanks, Benjamin ** There is a bug in the way that FS converts surface-based area (eg, lh.area) and volume (eg, lh.volume) into standard space. The files themselves are fine, it is the way they are transfered to standard space that is the problem. You will not need to re-analyze any of your individual subject data. The volumes of the subcortical structures are unaffected by this problem. Global measures of cortical volume are also unaffected. -- Benjamín Garzón, Ph.D. Karolinska Institutet Department of Neuroscience Retzius Väg 8 17177 Stockholm (SWEDEN) ___ 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] resampling surfaces to native space, mri_surf2surf not scaling properly?
Thanks for your response, Douglas. I tried your suggestion, it doesn't appear to have changed the transformation at all though. There is still no scaling being applied to the surface. Is there anything else I can try to fix this problem? Thanks, Geoff From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, May 24, 2013 5:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] resampling surfaces to native space, mri_surf2surf not scaling properly? Try mri_surf2surf --sval-xyz pial --reg resamp_brain.mgz.reg rawavg.mgz --tval resamp_lh_pial --tval-xyz --hemi lh --s 1158119_3_6 On 05/24/2013 04:42 PM, Gunter, Geoffrey wrote: Hello, I'm trying to resample Freesurfer output volumes and surfaces back into their native anatomical space using mri_vol2vol and mri_surf2surf. The volumes appear to be resampled correctly, their resolution and orientation match the original images'. However, the resampled surfaces do not appear to have been transformed correctly by mri_surf2surf. When I visually compare them to the Freesurfer-space surfaces overlaid on the brain images in FreeView, TKMEdit, Paraview-CAWorks, etc., they seem to be identical to the un-transformed, Freesurfer-space surfaces. In addition, when I check the list of vertices for transformed and untransformed surfaces, the coordinates of each vertex are unchanged. These are the commands that I'm using: mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o resamp_brain.mgz mri_surf2surf --sval-xyz pial --reg resamp_brain.mgz.reg --tval resamp_lh_pial --tval-xyz --hemi lh --s 1158119_3_6 The registration file, resamp_brain.mgz.reg looks like this: subject-unknown 0.937500 0.937500 1.00 1.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 1.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 1.000e+00 0.000e+00 0 0 0 1 round My Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Could it be that mri_surf2surf is not applying scaling transformations correctly? Thanks for your help, Geoff ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] area measurements FS5.1
We don't have an implementation of Anderson's code that we are releasing. mris_preproc (not preproc-sess) has a mechanism to perform areal interpolation that is not as good as Anderson's, but it is what we have. doug On 05/28/2013 11:19 AM, Benjamín Garzón wrote: Thanks, Doug. I guess it's the mris_preproc file there what I need, not preproc-sess... Does this version do the areal interpolation as described in Winkler 2012 'Measuring and comparing brain cortical surface area and other areal quantities http://www.academia.edu/1604228/Measuring_and_comparing_brain_cortical_surface_area_and_other_areal_quantities'? Best regards, Benjamin On 05/28/2013 04:16 PM, Benjamín Garzón wrote: Hi, I have processed a sample with FS 5.1 and would like to do a group analysis of surface-based area. According to the release notes ( ** ) there is an issue with the conversion into standard space. I found a former post pointing to a version of preproc-sess that to my understanding should fix that, but the file is not there any more. Is there any quick fix for this problem without having to move to 5.3 / could I get that file? Thanks, Benjamin ** There is a bug in the way that FS converts surface-based area (eg, lh.area) and volume (eg, lh.volume) into standard space. The files themselves are fine, it is the way they are transfered to standard space that is the problem. You will not need to re-analyze any of your individual subject data. The volumes of the subcortical structures are unaffected by this problem. Global measures of cortical volume are also unaffected. -- Benjamín Garzón, Ph.D. Karolinska Institutet Department of Neuroscience Retzius Väg 8 17177 Stockholm (SWEDEN) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] resampling surfaces to native space, mri_surf2surf not scaling properly?
The problem is with the way you are creating the registration matrix, use this instead tkregister2 --mov rawavg.mgz --targ orig.mgz --regheader --noedit --reg resamp_brain.mgz.reg doug On 05/28/2013 11:19 AM, Gunter, Geoffrey wrote: Thanks for your response, Douglas. I tried your suggestion, it doesn't appear to have changed the transformation at all though. There is still no scaling being applied to the surface. Is there anything else I can try to fix this problem? Thanks, Geoff From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, May 24, 2013 5:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] resampling surfaces to native space, mri_surf2surf not scaling properly? Try mri_surf2surf --sval-xyz pial --reg resamp_brain.mgz.reg rawavg.mgz --tval resamp_lh_pial --tval-xyz --hemi lh --s 1158119_3_6 On 05/24/2013 04:42 PM, Gunter, Geoffrey wrote: Hello, I'm trying to resample Freesurfer output volumes and surfaces back into their native anatomical space using mri_vol2vol and mri_surf2surf. The volumes appear to be resampled correctly, their resolution and orientation match the original images'. However, the resampled surfaces do not appear to have been transformed correctly by mri_surf2surf. When I visually compare them to the Freesurfer-space surfaces overlaid on the brain images in FreeView, TKMEdit, Paraview-CAWorks, etc., they seem to be identical to the un-transformed, Freesurfer-space surfaces. In addition, when I check the list of vertices for transformed and untransformed surfaces, the coordinates of each vertex are unchanged. These are the commands that I'm using: mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o resamp_brain.mgz mri_surf2surf --sval-xyz pial --reg resamp_brain.mgz.reg --tval resamp_lh_pial --tval-xyz --hemi lh --s 1158119_3_6 The registration file, resamp_brain.mgz.reg looks like this: subject-unknown 0.937500 0.937500 1.00 1.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 1.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 1.000e+00 0.000e+00 0 0 0 1 round My Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Could it be that mri_surf2surf is not applying scaling transformations correctly? Thanks for your help, Geoff ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_resample: Command not found.
Hi Lilla, I'm using OSX 10.8.3 Thanks, Daniel From: Lilla Zollei [lzol...@nmr.mgh.harvard.edu] Sent: Tuesday, May 28, 2013 10:04 AM To: Barron, Daniel S Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: mris_resample: Command not found. Hi Daniel, What operating system are you using? Lilla On Tue, 28 May 2013, Barron, Daniel S wrote: Hello, I am trying to perform an inter-subject registration using mri_cvs_register on version 5.3. When I ran mri_cvs_check, my feedback was I needed to find mri_cvs_register.settings.txt but I didn't worry about this per Lilla's post: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.html mri_cvs_register kicks off well, but eventually it ends with: mris_resample: Command not found. I go into my $FREESURFER_HOME/bin directory and note that mris_resample is truly not there. Did I not install 5.3 properly? I have attached a log file in case this helps. Cheers, Daniel 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] mris_resample: Command not found.
Hello Daniel, This is a confirmed issue with the 64bit Mac build. A patch to fix the issue will be available shortly (~hours). I will email the list and you personally once it is available. Sorry for the inconvenience. -Zeke On 05/28/2013 11:36 AM, Barron, Daniel S wrote: Hi Lilla, I'm using OSX 10.8.3 Thanks, Daniel From: Lilla Zollei [lzol...@nmr.mgh.harvard.edu] Sent: Tuesday, May 28, 2013 10:04 AM To: Barron, Daniel S Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: mris_resample: Command not found. Hi Daniel, What operating system are you using? Lilla On Tue, 28 May 2013, Barron, Daniel S wrote: Hello, I am trying to perform an inter-subject registration using mri_cvs_register on version 5.3. When I ran mri_cvs_check, my feedback was I needed to find mri_cvs_register.settings.txt but I didn't worry about this per Lilla's post: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.html mri_cvs_register kicks off well, but eventually it ends with: mris_resample: Command not found. I go into my $FREESURFER_HOME/bin directory and note that mris_resample is truly not there. Did I not install 5.3 properly? I have attached a log file in case this helps. Cheers, Daniel The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_anatomical_stats on custom 'thickness' file
I would use mri_segstats and specify the --annot option doug On 05/28/2013 01:28 PM, Martijn Steenwijk wrote: Dear all, I've created a custom '.mgh' file containing values on the cortical surface using mri_vol2surf. I would like to compute some statistics on this surface in the aparc-areas computed by freesurfer. Can I then just use mri_anatomical_stats with option -t specifying the custom mgh file as 'thickness' input? Or does mri_anatomical_stats something more complex than just averaging the values inside each region? Best, Martijn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] white matter volume per lobe...
what is is labled? On 05/28/2013 01:42 PM, Gonzalo Rojas Costa wrote: Hi Doug: I use the instructions that you told me... But, why I get the gray colored region (red arrow) ?... Sincerely, Gonzalo Rojas Costa Message: 15 Date: Mon, 27 May 2013 22:41:41 -0400 From: Douglas Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] white matter volume per lobe... To: freesurfer@nmr.mgh.harvard.edu Message-ID: 51a41965.6050...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed you will need to run mri_annotation2label and specify the output to be an annotation file instead of a segmentation. Then you will have to run mri_aparc2aseg, specifying your lobes annotation as well as --labelwm (look in the recon-all.log file for an example of how wmparc.mgz is created). Then run mri_segstats (you can also get an example from the recon-all.log file). doug -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] white matter volume per lobe...
Hi Doug: It is labeled as wm-rh-fusiform and wm-lh-fusiform Sincerely, Gonzalo Rojas Costa On Tue, May 28, 2013 at 1:47 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what is is labled? On 05/28/2013 01:42 PM, Gonzalo Rojas Costa wrote: Hi Doug: I use the instructions that you told me... But, why I get the gray colored region (red arrow) ?... Sincerely, Gonzalo Rojas Costa Message: 15 Date: Mon, 27 May 2013 22:41:41 -0400 From: Douglas Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] white matter volume per lobe... To: freesurfer@nmr.mgh.harvard.edu Message-ID: 51a41965.6050...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed you will need to run mri_annotation2label and specify the output to be an annotation file instead of a segmentation. Then you will have to run mri_aparc2aseg, specifying your lobes annotation as well as --labelwm (look in the recon-all.log file for an example of how wmparc.mgz is created). Then run mri_segstats (you can also get an example from the recon-all.log file). doug -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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. -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] white matter volume per lobe...
You will need to create a new color table. It is currently referencing FreeSurferColorLUT.txt. If you load the segmentation as both a segmentation and the aux volume, you can see the number associated with the color. You will need to create a table similar to FreeSurferColorLUT.txt doug On 05/28/2013 01:51 PM, Gonzalo Rojas Costa wrote: Hi Doug: It is labeled as wm-rh-fusiform and wm-lh-fusiform Sincerely, Gonzalo Rojas Costa On Tue, May 28, 2013 at 1:47 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what is is labled? On 05/28/2013 01:42 PM, Gonzalo Rojas Costa wrote: Hi Doug: I use the instructions that you told me... But, why I get the gray colored region (red arrow) ?... Sincerely, Gonzalo Rojas Costa Message: 15 Date: Mon, 27 May 2013 22:41:41 -0400 From: Douglas Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] white matter volume per lobe... To: freesurfer@nmr.mgh.harvard.edu Message-ID: 51a41965.6050...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed you will need to run mri_annotation2label and specify the output to be an annotation file instead of a segmentation. Then you will have to run mri_aparc2aseg, specifying your lobes annotation as well as --labelwm (look in the recon-all.log file for an example of how wmparc.mgz is created). Then run mri_segstats (you can also get an example from the recon-all.log file). doug -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_anatomical_stats on custom 'thickness' file
Thanks Doug for your quick reply. But mri_segstats computes the average value inside the cortical region in the volume, right? That's not wat I want to have, I want to know the average value of the data in the volume on the wm/gm surface (i sampled with projfrac = 0). Any thoughts? On Tue, May 28, 2013 at 7:46 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: I would use mri_segstats and specify the --annot option doug On 05/28/2013 01:28 PM, Martijn Steenwijk wrote: Dear all, I've created a custom '.mgh' file containing values on the cortical surface using mri_vol2surf. I would like to compute some statistics on this surface in the aparc-areas computed by freesurfer. Can I then just use mri_anatomical_stats with option -t specifying the custom mgh file as 'thickness' input? Or does mri_anatomical_stats something more complex than just averaging the values inside each region? Best, Martijn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_anatomical_stats on custom 'thickness' file
It can do both. When you spec --annot, then it does it on the surface and you have to pass it surface data (which you already have since you ran vol2surf). doug On 05/28/2013 02:03 PM, Martijn Steenwijk wrote: Thanks Doug for your quick reply. But mri_segstats computes the average value inside the cortical region in the volume, right? That's not wat I want to have, I want to know the average value of the data in the volume on the wm/gm surface (i sampled with projfrac = 0). Any thoughts? On Tue, May 28, 2013 at 7:46 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I would use mri_segstats and specify the --annot option doug On 05/28/2013 01:28 PM, Martijn Steenwijk wrote: Dear all, I've created a custom '.mgh' file containing values on the cortical surface using mri_vol2surf. I would like to compute some statistics on this surface in the aparc-areas computed by freesurfer. Can I then just use mri_anatomical_stats with option -t specifying the custom mgh file as 'thickness' input? Or does mri_anatomical_stats something more complex than just averaging the values inside each region? Best, Martijn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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 mailto: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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_anatomical_stats on custom 'thickness' file
Sorry, indeed, my reply was too quick. Seems to work, the results are similar to mri_anatomical_stats. I'm not sure whether this is relevant; but the sampling seems to be not equally dense in the different regions. Does mri_segstats somehow cope with this? Best, Martijn On Tue, May 28, 2013 at 8:03 PM, Martijn Steenwijk martijnsteenw...@gmail.com wrote: Thanks Doug for your quick reply. But mri_segstats computes the average value inside the cortical region in the volume, right? That's not wat I want to have, I want to know the average value of the data in the volume on the wm/gm surface (i sampled with projfrac = 0). Any thoughts? On Tue, May 28, 2013 at 7:46 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I would use mri_segstats and specify the --annot option doug On 05/28/2013 01:28 PM, Martijn Steenwijk wrote: Dear all, I've created a custom '.mgh' file containing values on the cortical surface using mri_vol2surf. I would like to compute some statistics on this surface in the aparc-areas computed by freesurfer. Can I then just use mri_anatomical_stats with option -t specifying the custom mgh file as 'thickness' input? Or does mri_anatomical_stats something more complex than just averaging the values inside each region? Best, Martijn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_anatomical_stats segmentation fault
Hi Doug, It appears that the subject I'm having the PHC issue with has fewer than 163798 vertices - it has 123249 vertices - however, it seems that all of our subjects have fewer vertices and I do not run into an error with any other subjects with this label. Also, I'm able to load the label onto my data in freeview without any issue. I'm having some problems opening my surfaces with tksurfer on my lab desktop, though. Should I upload the subjects in question so you can take a look? Thanks! Rob On Tue, May 28, 2013 at 10:06 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Nothing looks like it is wrong with that label. Can you verify that the white surface has not been changed since the label was created? Check how many vertices the white surface has with mris_info. The PHC label references a vertex index as high as 163798. If the white surface does not have that many veritices, then that could cause the problem. doug On 05/28/2013 10:33 AM, Rob Tennyson wrote: Hi Doug, Attached are the three labels I'm having an issue with (each with a different subject). These are built from areas that we found functional differences between a healthy control group and a MDD group. I was going to take a look at the anatomical stats to see if there are thickness or volume differences as well. I am also going to review the white surface soon as Bruce suggested. On Tue, May 28, 2013 at 9:26 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: Rob, can you send me your label? doug On 05/27/2013 01:00 PM, Rob Tennyson wrote: Hi All, I'm running mris_anatomical_stats with a few manually defined labels. For a few of my subjects, I am getting the error: Segmentation fault on one of the labels. However, the other manually defined labels process without any errors on these same subjects. For example, I am running mri_anatomical_stats on subject 33_bay6 with a manually defined ERC label, a manually defined PHC label, and a manually defined medial frontal gyrus label. The only label that runs an error for this subject is the PHC label. This PHC label runs without any errors on the rest of my subjects. Here is what is displayed when running a label that fails: mris_anatomical_stats -f PHC.stats.04.txt -l lh.PHC_1.label -b 33_bay6 lh limiting computations to label lh.PHC_1.label. reading volume /Volumes/BigRaid/Rob/subjects/** 33_bay6/mri/wm.mgz... reading input surface /Volumes/BigRaid/Rob/subjects/**33_bay6/surf/lh.white... reading input pial surface /Volumes/BigRaid/Rob/subjects/**33_bay6/surf/lh.pial... reading input white surface /Volumes/BigRaid/Rob/subjects/**33_bay6/surf/lh.white... Segmentation fault Does anyone know what may be causing the Segmentation fault and what steps I should take to fix it? Thank you for your help! Rob __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.** harvard.edu 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
Re: [Freesurfer] mri_anatomical_stats on custom 'thickness' file
what do you mean? That the vertices are not uniform? mri_segstats just computes the mean over the parcellation without reference to non-uniformity. doug On 05/28/2013 02:15 PM, Martijn Steenwijk wrote: Sorry, indeed, my reply was too quick. Seems to work, the results are similar to mri_anatomical_stats. I'm not sure whether this is relevant; but the sampling seems to be not equally dense in the different regions. Does mri_segstats somehow cope with this? Best, Martijn On Tue, May 28, 2013 at 8:03 PM, Martijn Steenwijk martijnsteenw...@gmail.com mailto:martijnsteenw...@gmail.com wrote: Thanks Doug for your quick reply. But mri_segstats computes the average value inside the cortical region in the volume, right? That's not wat I want to have, I want to know the average value of the data in the volume on the wm/gm surface (i sampled with projfrac = 0). Any thoughts? On Tue, May 28, 2013 at 7:46 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I would use mri_segstats and specify the --annot option doug On 05/28/2013 01:28 PM, Martijn Steenwijk wrote: Dear all, I've created a custom '.mgh' file containing values on the cortical surface using mri_vol2surf. I would like to compute some statistics on this surface in the aparc-areas computed by freesurfer. Can I then just use mri_anatomical_stats with option -t specifying the custom mgh file as 'thickness' input? Or does mri_anatomical_stats something more complex than just averaging the values inside each region? Best, Martijn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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 mailto: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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_anatomical_stats segmentation fault
how did you create the label? If it has more vertices than the subject has then something is very wrong. You don't always get segfaults, you might just get garbage and never know it. doug On 05/28/2013 02:32 PM, Rob Tennyson wrote: Hi Doug, It appears that the subject I'm having the PHC issue with has fewer than 163798 vertices - it has 123249 vertices - however, it seems that all of our subjects have fewer vertices and I do not run into an error with any other subjects with this label. Also, I'm able to load the label onto my data in freeview without any issue. I'm having some problems opening my surfaces with tksurfer on my lab desktop, though. Should I upload the subjects in question so you can take a look? Thanks! Rob On Tue, May 28, 2013 at 10:06 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Nothing looks like it is wrong with that label. Can you verify that the white surface has not been changed since the label was created? Check how many vertices the white surface has with mris_info. The PHC label references a vertex index as high as 163798. If the white surface does not have that many veritices, then that could cause the problem. doug On 05/28/2013 10:33 AM, Rob Tennyson wrote: Hi Doug, Attached are the three labels I'm having an issue with (each with a different subject). These are built from areas that we found functional differences between a healthy control group and a MDD group. I was going to take a look at the anatomical stats to see if there are thickness or volume differences as well. I am also going to review the white surface soon as Bruce suggested. On Tue, May 28, 2013 at 9:26 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Rob, can you send me your label? doug On 05/27/2013 01:00 PM, Rob Tennyson wrote: Hi All, I'm running mris_anatomical_stats with a few manually defined labels. For a few of my subjects, I am getting the error: Segmentation fault on one of the labels. However, the other manually defined labels process without any errors on these same subjects. For example, I am running mri_anatomical_stats on subject 33_bay6 with a manually defined ERC label, a manually defined PHC label, and a manually defined medial frontal gyrus label. The only label that runs an error for this subject is the PHC label. This PHC label runs without any errors on the rest of my subjects. Here is what is displayed when running a label that fails: mris_anatomical_stats -f PHC.stats.04.txt -l lh.PHC_1.label -b 33_bay6 lh limiting computations to label lh.PHC_1.label. reading volume /Volumes/BigRaid/Rob/subjects/33_bay6/mri/wm.mgz... reading input surface /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... reading input pial surface /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.pial... reading input white surface /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... Segmentation fault Does anyone know what may be causing the Segmentation fault and what steps I should take to fix it? Thank you for your help! Rob ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Re: [Freesurfer] mri_anatomical_stats segmentation fault
The labels are built from areas that showed between-group functional differences. I am able to view the label on the subject in question in freeview. Maybe I'm looking at the wrong place in the output of mris_info? Or perhaps in the wrong file. I looked at nvertices in our lh.white file. On Tue, May 28, 2013 at 1:52 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: how did you create the label? If it has more vertices than the subject has then something is very wrong. You don't always get segfaults, you might just get garbage and never know it. doug On 05/28/2013 02:32 PM, Rob Tennyson wrote: Hi Doug, It appears that the subject I'm having the PHC issue with has fewer than 163798 vertices - it has 123249 vertices - however, it seems that all of our subjects have fewer vertices and I do not run into an error with any other subjects with this label. Also, I'm able to load the label onto my data in freeview without any issue. I'm having some problems opening my surfaces with tksurfer on my lab desktop, though. Should I upload the subjects in question so you can take a look? Thanks! Rob On Tue, May 28, 2013 at 10:06 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: Nothing looks like it is wrong with that label. Can you verify that the white surface has not been changed since the label was created? Check how many vertices the white surface has with mris_info. The PHC label references a vertex index as high as 163798. If the white surface does not have that many veritices, then that could cause the problem. doug On 05/28/2013 10:33 AM, Rob Tennyson wrote: Hi Doug, Attached are the three labels I'm having an issue with (each with a different subject). These are built from areas that we found functional differences between a healthy control group and a MDD group. I was going to take a look at the anatomical stats to see if there are thickness or volume differences as well. I am also going to review the white surface soon as Bruce suggested. On Tue, May 28, 2013 at 9:26 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: Rob, can you send me your label? doug On 05/27/2013 01:00 PM, Rob Tennyson wrote: Hi All, I'm running mris_anatomical_stats with a few manually defined labels. For a few of my subjects, I am getting the error: Segmentation fault on one of the labels. However, the other manually defined labels process without any errors on these same subjects. For example, I am running mri_anatomical_stats on subject 33_bay6 with a manually defined ERC label, a manually defined PHC label, and a manually defined medial frontal gyrus label. The only label that runs an error for this subject is the PHC label. This PHC label runs without any errors on the rest of my subjects. Here is what is displayed when running a label that fails: mris_anatomical_stats -f PHC.stats.04.txt -l lh.PHC_1.label -b 33_bay6 lh limiting computations to label lh.PHC_1.label. reading volume /Volumes/BigRaid/Rob/subjects/**33_bay6/mri/wm.mgz... reading input surface /Volumes/BigRaid/Rob/subjects/**33_bay6/surf/lh.white... reading input pial surface /Volumes/BigRaid/Rob/subjects/**33_bay6/surf/lh.pial... reading input white surface /Volumes/BigRaid/Rob/subjects/**33_bay6/surf/lh.white... Segmentation fault Does anyone know what may be causing the Segmentation fault and what steps I should take to fix it? Thank you for your help! Rob __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_anatomical_stats segmentation fault
The label that you sent applies to fsaverage. If you want to use it on a different subject, you should map it to that subject with mri_label2label doug On 05/28/2013 03:00 PM, Rob Tennyson wrote: The labels are built from areas that showed between-group functional differences. I am able to view the label on the subject in question in freeview. Maybe I'm looking at the wrong place in the output of mris_info? Or perhaps in the wrong file. I looked at nvertices in our lh.white file. On Tue, May 28, 2013 at 1:52 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: how did you create the label? If it has more vertices than the subject has then something is very wrong. You don't always get segfaults, you might just get garbage and never know it. doug On 05/28/2013 02:32 PM, Rob Tennyson wrote: Hi Doug, It appears that the subject I'm having the PHC issue with has fewer than 163798 vertices - it has 123249 vertices - however, it seems that all of our subjects have fewer vertices and I do not run into an error with any other subjects with this label. Also, I'm able to load the label onto my data in freeview without any issue. I'm having some problems opening my surfaces with tksurfer on my lab desktop, though. Should I upload the subjects in question so you can take a look? Thanks! Rob On Tue, May 28, 2013 at 10:06 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Nothing looks like it is wrong with that label. Can you verify that the white surface has not been changed since the label was created? Check how many vertices the white surface has with mris_info. The PHC label references a vertex index as high as 163798. If the white surface does not have that many veritices, then that could cause the problem. doug On 05/28/2013 10:33 AM, Rob Tennyson wrote: Hi Doug, Attached are the three labels I'm having an issue with (each with a different subject). These are built from areas that we found functional differences between a healthy control group and a MDD group. I was going to take a look at the anatomical stats to see if there are thickness or volume differences as well. I am also going to review the white surface soon as Bruce suggested. On Tue, May 28, 2013 at 9:26 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Rob, can you send me your label? doug On 05/27/2013 01:00 PM, Rob Tennyson wrote: Hi All, I'm running mris_anatomical_stats with a few manually defined labels. For a few of my subjects, I am getting the error: Segmentation fault on one of the labels. However, the other manually defined labels process without any errors on these same subjects. For example, I am running mri_anatomical_stats on subject 33_bay6 with a manually defined ERC label, a manually defined PHC label, and a manually defined medial frontal gyrus label. The only label that runs an error for this subject is the PHC label. This PHC label runs without any errors on the rest of my subjects. Here is what is displayed when running a label that fails: mris_anatomical_stats -f PHC.stats.04.txt -l lh.PHC_1.label -b 33_bay6 lh limiting computations to label lh.PHC_1.label. reading volume /Volumes/BigRaid/Rob/subjects/33_bay6/mri/wm.mgz... reading input surface
Re: [Freesurfer] mri_anatomical_stats segmentation fault
That explains a lot about my problem subjects. Just to confirm, I should use mri_label2label with fsaverage as the source subject and the subject in question as the target? Having this run for all of my subjects will then allow me to use mris_anatomical_stats for each subject. Thanks for the help! On Tue, May 28, 2013 at 2:06 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: The label that you sent applies to fsaverage. If you want to use it on a different subject, you should map it to that subject with mri_label2label doug On 05/28/2013 03:00 PM, Rob Tennyson wrote: The labels are built from areas that showed between-group functional differences. I am able to view the label on the subject in question in freeview. Maybe I'm looking at the wrong place in the output of mris_info? Or perhaps in the wrong file. I looked at nvertices in our lh.white file. On Tue, May 28, 2013 at 1:52 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: how did you create the label? If it has more vertices than the subject has then something is very wrong. You don't always get segfaults, you might just get garbage and never know it. doug On 05/28/2013 02:32 PM, Rob Tennyson wrote: Hi Doug, It appears that the subject I'm having the PHC issue with has fewer than 163798 vertices - it has 123249 vertices - however, it seems that all of our subjects have fewer vertices and I do not run into an error with any other subjects with this label. Also, I'm able to load the label onto my data in freeview without any issue. I'm having some problems opening my surfaces with tksurfer on my lab desktop, though. Should I upload the subjects in question so you can take a look? Thanks! Rob On Tue, May 28, 2013 at 10:06 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: Nothing looks like it is wrong with that label. Can you verify that the white surface has not been changed since the label was created? Check how many vertices the white surface has with mris_info. The PHC label references a vertex index as high as 163798. If the white surface does not have that many veritices, then that could cause the problem. doug On 05/28/2013 10:33 AM, Rob Tennyson wrote: Hi Doug, Attached are the three labels I'm having an issue with (each with a different subject). These are built from areas that we found functional differences between a healthy control group and a MDD group. I was going to take a look at the anatomical stats to see if there are thickness or volume differences as well. I am also going to review the white surface soon as Bruce suggested. On Tue, May 28, 2013 at 9:26 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: Rob, can you send me your label? doug On 05/27/2013 01:00 PM, Rob Tennyson wrote: Hi All, I'm running mris_anatomical_stats with a few manually defined labels. For a few of my subjects, I am getting the error: Segmentation fault on one of the labels. However, the other manually defined labels process without any errors on these same subjects. For example, I am running mri_anatomical_stats on subject 33_bay6 with a manually defined ERC label, a manually defined PHC label, and a manually defined medial frontal gyrus label. The only label that runs
Re: [Freesurfer] mri_anatomical_stats segmentation fault
yes On 05/28/2013 03:15 PM, Rob Tennyson wrote: That explains a lot about my problem subjects. Just to confirm, I should use mri_label2label with fsaverage as the source subject and the subject in question as the target? Having this run for all of my subjects will then allow me to use mris_anatomical_stats for each subject. Thanks for the help! On Tue, May 28, 2013 at 2:06 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: The label that you sent applies to fsaverage. If you want to use it on a different subject, you should map it to that subject with mri_label2label doug On 05/28/2013 03:00 PM, Rob Tennyson wrote: The labels are built from areas that showed between-group functional differences. I am able to view the label on the subject in question in freeview. Maybe I'm looking at the wrong place in the output of mris_info? Or perhaps in the wrong file. I looked at nvertices in our lh.white file. On Tue, May 28, 2013 at 1:52 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: how did you create the label? If it has more vertices than the subject has then something is very wrong. You don't always get segfaults, you might just get garbage and never know it. doug On 05/28/2013 02:32 PM, Rob Tennyson wrote: Hi Doug, It appears that the subject I'm having the PHC issue with has fewer than 163798 vertices - it has 123249 vertices - however, it seems that all of our subjects have fewer vertices and I do not run into an error with any other subjects with this label. Also, I'm able to load the label onto my data in freeview without any issue. I'm having some problems opening my surfaces with tksurfer on my lab desktop, though. Should I upload the subjects in question so you can take a look? Thanks! Rob On Tue, May 28, 2013 at 10:06 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Nothing looks like it is wrong with that label. Can you verify that the white surface has not been changed since the label was created? Check how many vertices the white surface has with mris_info. The PHC label references a vertex index as high as 163798. If the white surface does not have that many veritices, then that could cause the problem. doug On 05/28/2013 10:33 AM, Rob Tennyson wrote: Hi Doug, Attached are the three labels I'm having an issue with (each with a different subject). These are built from areas that we found functional differences between a healthy control group and a MDD group. I was going to take a look at the anatomical stats to see if there are thickness or volume differences as well. I am also going to review the white surface soon as Bruce suggested. On Tue, May 28, 2013 at 9:26 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Rob, can you send me your label?
Re: [Freesurfer] LME toolbox - univariate
Hi Yolanda, since you have the intercept you don't need both group1 and group2 (as one is 1 - the other), so drop beta 5 and 6 terms. If you want to test if the slope is different between the groups differ just look at beta4 which is checking if slope1-slope2 different from zero. If it is negative slope2 is larger, if positive slope1 is larger. Note that if your slopes are negative, e.g. atrophy, then larger means closer to zero = less atrophy. Best, Martin On 05/28/2013 11:57 AM, Yolanda Vives wrote: Dear FreeSurfer experts, I am trying to use the LME toolbox to analyse the hippocampal change over time in a group and also among 2 groups (2 scans per subject). When I estimate the parameters with lme_fit_FS I become a warning saying that the matrix is singular and my results are NaN. I guess that my design matrix X is not correct, can you please help me? I have followed the example from the wiki. My model for the two groups study is the following: Y_ij = ß_1 + ß_2 *t_ij +ß_3 *Group1 + ß_4 *Group1 *t_ij + ß_5 *Group2 + ß_6 *Group2 *t_ij + ß_7 *Gender_i + ß_8 *Age_i + ß_9 *ICV_i + b_1i + b_2i *t_ij + e_ij 1) intercept (all ones) 2) time (t_ij ) . Here I have 0s for the first scan of each subject and a number in years for the second scans. Is it correct? 3) one for Group1 and zero otherwise 4) colum 3) .* time 5) one for Group2 and zero otherwise 6) colum 5) .* time 7) Gender 8) Age of the subject at each scan moment. 9) ICV (converted to liters). Thank you in advance, Yolanda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] recon-all error: v5.0.0 - dataset 1
BEST FITNESS (M) is 984.24263 mri =0.000 curv = 4.318 unmri = -1001.515 ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) 63 patches have been generated - 38 self-intersected max face = 36973(40653) - loop = 46 (73) - ntries = [27,14799] ERROR: _FindFacePath: could not find path! Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s xtyzW exited with ERRORS at Tue May 21 05:48:38 EDT 2013 ___ 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] recon-all error: v5.0.0 - dataset 3
CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces vertex 88778 has 0 face No such file or directory Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s ghjG exited with ERRORS at Thu May 16 05:11:49 EDT 2013 ___ 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] recon-all error: v5.0.0 - dataset 2
=== *WATERSHED** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all. Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s cbvfB exited with ERRORS at Fri May 17 17:45:23 EDT 2013 == ___ 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] recon-all errors: v5.0.0; dataset 4
CORRECTING DEFECT 1 (vertices=33, convex hull=57) After retessellation of defect 1, euler #=-41 (88676,260208,171491) : difference with theory (-61) = -20 CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces vertex 88778 has 0 face No such file or directory Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s IN387G exited with ERRORS at Thu May 16 05:11:49 EDT 2013 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all error: v5.0.0 - dataset 1
the new topo fixer will correct this problem Bruce On Tue, 28 May 2013, Sudhin A. Shah wrote: BEST FITNESS (M) is 984.24263 mri =0.000 curv = 4.318 unmri = -1001.515 ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) 63 patches have been generated - 38 self-intersected max face = 36973(40653) - loop = 46 (73) - ntries = [27,14799] ERROR: _FindFacePath: could not find path! Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s xtyzW exited with ERRORS at Tue May 21 05:48:38 EDT 2013 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all error: v5.0.0 - dataset 2
Hi Sudhin you need to track down why this happened. First thing to look at is the tal xform Bruce On Tue, 28 May 2013, Sudhin A. Shah wrote: === *WATERSHED** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all. Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s cbvfB exited with ERRORS at Fri May 17 17:45:23 EDT 2013 == ___ 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] hipposubfields and data
I have read that the hippo-subfield algorithm uses the aseg for initialization, and then uses the original MRI data. By original, does that mean it up-samples the conformed 1mm data to .5mm, or does that mean it takes the original original input (i.e. my 0.7 mm isotropic MPRAGE) and upsamples it to .5mm? 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] hipposubfields and data
Hi Josh, as of now, it uses nu.mgz, which is conformed and bias field corrected with N3. Koen, do you think we should add a flag to change this? The algorithm is pretty resolution-independent, and could certainly benefit from higher-res data. Cheers, /Eugenio On Tue, 2013-05-28 at 13:34 -0700, Joshua Lee wrote: I have read that the hippo-subfield algorithm uses the aseg for initialization, and then uses the original MRI data. By original, does that mean it up-samples the conformed 1mm data to .5mm, or does that mean it takes the original original input (i.e. my 0.7 mm isotropic MPRAGE) and upsamples it to .5mm? Josh ___ 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 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 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] hipposubfields and data
I think the resolution is important. The CA1 subfield is only about 2-2.5 mm thick after all. If this is a feature request thread now, let me add that it would be nice if the actual training algorithm was integrated into Freesurfer. There is a lot of disagreement about the most appropriate subfield boundaries, and the ability to make custom training sets would be helpful. Right now there is little guidance on what kind of data-sets are appropriate to use with this algorithm. I am concerned that users are trying to segment subfields with older data-sets that probably aren't appropriate (e.g. 1.5 Tesla or 1.5 mm isotropic data). Josh On Tue, May 28, 2013 at 1:44 PM, Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu wrote: Hi Josh, as of now, it uses nu.mgz, which is conformed and bias field corrected with N3. Koen, do you think we should add a flag to change this? The algorithm is pretty resolution-independent, and could certainly benefit from higher-res data. Cheers, /Eugenio On Tue, 2013-05-28 at 13:34 -0700, Joshua Lee wrote: I have read that the hippo-subfield algorithm uses the aseg for initialization, and then uses the original MRI data. By original, does that mean it up-samples the conformed 1mm data to .5mm, or does that mean it takes the original original input (i.e. my 0.7 mm isotropic MPRAGE) and upsamples it to .5mm? Josh ___ 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 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. 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] recon-all error: v5.0.0 - dataset 1
Hi! Can you please send this to me? On May 28, 2013, at 4:24 PM, Bruce Fischl wrote: the new topo fixer will correct this problem Bruce On Tue, 28 May 2013, Sudhin A. Shah wrote: BEST FITNESS (M) is 984.24263 mri =0.000 curv = 4.318 unmri = -1001.515 ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) 63 patches have been generated - 38 self-intersected max face = 36973(40653) - loop = 46 (73) - ntries = [27,14799] ERROR: _FindFacePath: could not find path! Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s xtyzW exited with ERRORS at Tue May 21 05:48:38 EDT 2013 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] SUMA and FSFAST
I was wondering if someone could give me a summary as to how SUMA and FSFAST differ? In other words, user interface aside, what would be reasons to use one or the other? Joe Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Subcortical Structures not included in GM surfaces
It doesn't need fixing. Those regions aren't part of cortex and the surfaces are arbitrary there (but excluded from thickness calculations) On May 28, 2013, at 7:39 PM, Jonathan Holt whats...@umich.edu wrote: Is this normal, attached slide shows a rather common occurrence for me. Half of the amygdala (blue) is included in pial surface, while the other is not. How should I go about fixing, the local WM is perfectly fine so I'm not sure where to start. Screen Shot 2013-05-28 at 7.37.17 PM.png ___ 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] Fwd: Re: mris_resample: Command not found.
Daniel, Stefano, Others, A patch is now available for the mris_resample : Command not found error you encountered. Simply download the file from the following link and place it in your $FREESURFER_HOME/bin directory: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample Feel free to contact me if you have any additional questions/issues. -Zeke Original Message Subject: Re: [Freesurfer] mris_resample: Command not found. Date: Tue, 28 May 2013 11:41:21 -0400 From: Z K zkauf...@nmr.mgh.harvard.edu To: Barron, Daniel S barr...@livemail.uthscsa.edu CC: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu, Lilla Zollei lzol...@nmr.mgh.harvard.edu Hello Daniel, This is a confirmed issue with the 64bit Mac build. A patch to fix the issue will be available shortly (~hours). I will email the list and you personally once it is available. Sorry for the inconvenience. -Zeke On 05/28/2013 11:36 AM, Barron, Daniel S wrote: Hi Lilla, I'm using OSX 10.8.3 Thanks, Daniel From: Lilla Zollei [lzol...@nmr.mgh.harvard.edu] Sent: Tuesday, May 28, 2013 10:04 AM To: Barron, Daniel S Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: mris_resample: Command not found. Hi Daniel, What operating system are you using? Lilla On Tue, 28 May 2013, Barron, Daniel S wrote: Hello, I am trying to perform an inter-subject registration using mri_cvs_register on version 5.3. When I ran mri_cvs_check, my feedback was I needed to find mri_cvs_register.settings.txt but I didn't worry about this per Lilla's post: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.html mri_cvs_register kicks off well, but eventually it ends with: mris_resample: Command not found. I go into my $FREESURFER_HOME/bin directory and note that mris_resample is truly not there. Did I not install 5.3 properly? I have attached a log file in case this helps. Cheers, Daniel The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_resample: Command not found.
Thanks for the path, Zeke. Because it didn't download as an executable file to my computer, I used chmod +x ~/mris_resample (FYI for others?) It looks to be running normally. Will report back when finished! Thanks again, Daniel On May 28, 2013, at 11:25 PM, zkauf...@nmr.mgh.harvard.edu wrote: Daniel, Stefano, Others, A patch is now available for the mris_resample : Command not found error you encountered. Simply download the file from the following link and place it in your $FREESURFER_HOME/bin directory: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample Feel free to contact me if you have any additional questions/issues. -Zeke Original Message Subject: Re: [Freesurfer] mris_resample: Command not found. Date: Tue, 28 May 2013 11:41:21 -0400 From: Z K zkauf...@nmr.mgh.harvard.edu To: Barron, Daniel S barr...@livemail.uthscsa.edu CC: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu, Lilla Zollei lzol...@nmr.mgh.harvard.edu Hello Daniel, This is a confirmed issue with the 64bit Mac build. A patch to fix the issue will be available shortly (~hours). I will email the list and you personally once it is available. Sorry for the inconvenience. -Zeke On 05/28/2013 11:36 AM, Barron, Daniel S wrote: Hi Lilla, I'm using OSX 10.8.3 Thanks, Daniel From: Lilla Zollei [lzol...@nmr.mgh.harvard.edu] Sent: Tuesday, May 28, 2013 10:04 AM To: Barron, Daniel S Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: mris_resample: Command not found. Hi Daniel, What operating system are you using? Lilla On Tue, 28 May 2013, Barron, Daniel S wrote: Hello, I am trying to perform an inter-subject registration using mri_cvs_register on version 5.3. When I ran mri_cvs_check, my feedback was I needed to find mri_cvs_register.settings.txt but I didn't worry about this per Lilla's post: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.html mri_cvs_register kicks off well, but eventually it ends with: mris_resample: Command not found. I go into my $FREESURFER_HOME/bin directory and note that mris_resample is truly not there. Did I not install 5.3 properly? I have attached a log file in case this helps. Cheers, Daniel The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] beta weights from FS-Fast analysis
I need to extract the beta weights from a cluster identified with FS-Fast in order to compute percentage signal change. 1) I see a file called beta.nii.gz that appears to have the beta weight information. It has a four dimensional structure and the fourth dimension appears to be the beta weights. Is there an index somewhere as to which beta weight is which? Or if not, how are they organized? 2) In order to extract the cluster, it looks like I would use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a volume where the voxels are tagged with the number of the corresponding cluster. I could then use that to generate masks to extract the information I need for each cluster from beta.nii.gz. Is that correct? 3) The final information that I would need is the canonical hrf shape generated by FSFAST for a single event. I guess I could generate that by setting up a dummy analysis run with a single event of the desired duration and then look in the X variable in the resulting X.mat file? Sorry for all the questions! Joe Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
