[Freesurfer] pathstats.byvoxel.txt
Hi Anastasia, I noticed that my pathstats.byvoxel.txt files are missing the last four values (AD_Avg RD_Avg MD_Avg FA_Avg) even though I'm certain I ran trac-all -path -c dmrircFile correctly. Do you have any idea why this might be? e.g. a configuration file change? Thank you! -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear* ___ 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] pathstats.byvoxel.txt
Hi Anastasia, I believe the issue I had with the pathstats.byvoxel.txt not displaying the last four values (AD_Avg RD_Avg MD_Avg FA_Avg ) is owing to the fact that trac-all was run with FREESURFER 5.1. I believe that FREESURFER 5.2 may be needed to generate path.pd.trk, and from that, the above values are derived. Is this correct? Thank you again, and have a good day! -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear* ___ 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] Editing the endpoint ROIs, and re-running trac-all -path
Hi Anastasia, For one of my subjects, I am noticing that the right uncinate fasciculus is very diffuse and more importantly, erroneously crosses from the frontal to the temporal lobe. I looked at the original endpoint ROI generated by trac-all -prior (rh.unc_AS_avg33_mni_bbr_end1.nii.gz) and the dilated endpoint ROI in the temporal lobe (rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz) and noticed that the endpoints appeared to cross over into the frontal lobe. Attached is a snapshot for your perusal. On the left side is a display of the subject/dmri/dtifit_FA.nii with the subject/dpath/rh.unc_AS_avg33_mni_bbr/path.pd.nii.gz tract superimposed over. As you can see, the right unc tract crosses from the frontal to the temporal lobe. On the right side is a display of the subject/dmri/brain_anat_mni.nii.gz with the endpoints subject/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2.nii.gz in green and subject/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1.nii.gz in blue (the red dots are control points). As you can see, the blue endpoints bleed over from the temporal to the frontal lobe. I tried to eliminate these blue points with fslview and then writing over rh.unc_AS_avg33_mni_bbr_end1.nii.gz. I performed a similar function manually editing rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz to better reflect the boundaries . I subsequently tried to re-run trac-all -path, and unfortunately, all my tracts looked much worse. Do you know if incorrectly placed endpoints impair the path reconstruction? Do you think you can help me? Any advice you can give would be much appreciated. -- Susie Kuo NIH Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear* attachment: incorrect_endpoint_roi.png___ 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] any way to parallelize Tracula?
Hi Anastasia, I apologize for jumping in here, but I have run bedpostx parallelized on a cluster. Are there files that we can modify to run the script in parallel? I noticed the '-prior' step is particularly long and cumbersome. Thank you! Susie Kuo NIH On Fri, May 17, 2013 at 12:47 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Matt - Have you ever ran any parallelized FSL program (like bedpostx) on your SGE cluster? Our scripts have built on the FSL scripts, adding support for our PBS cluster, but in theory the SGE functionality is still there, so it should be possible to make it work. Of course practice is often somewhat more complicated than theory... a.y On Thu, 16 May 2013, Hoptman, Matthew wrote: Hi all, I have access to a cluster computer. Is there any way to parallelize tracula using SGE without having to make a unique dmrirc for each subject? If I could pass subject numbers to the dmrirc that would be great, for example. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. __**__** __ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ___ 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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear* ___ 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] any way to parallelize Tracula?
Hi Anastasia, I am operating on 5.1... I'm glad to know that there is such a huge difference in versions; and that there's so much gain in upgrading. I will look at the fsl_sub_mgh script, and I'll post back what I figure out (if anything), if other people are interested. Otherwise, it's vox clamantis en deserto... Thank you! Susie Kuo NIH On Fri, May 17, 2013 at 1:02 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - The underlying script doing the job submission is called fsl_sub_mgh (a modification of fsl_sub). BTW, the -prior step should be about 70% less long and cumbersome in 5.2/5.3 than it was in 5.1. Which version are you running? a.y On Fri, 17 May 2013, Susan Kuo wrote: Hi Anastasia, I apologize for jumping in here, but I have run bedpostx parallelized on a cluster. Are there files that we can modify to run the script in parallel? I noticed the '-prior' step is particularly long and cumbersome. Thank you! Susie Kuo NIH On Fri, May 17, 2013 at 12:47 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Matt - Have you ever ran any parallelized FSL program (like bedpostx) on your SGE cluster? Our scripts have built on the FSL scripts, adding support for our PBS cluster, but in theory the SGE functionality is still there, so it should be possible to make it work. Of course practice is often somewhat more complicated than theory... a.y On Thu, 16 May 2013, Hoptman, Matthew wrote: Hi all, I have access to a cluster computer. Is there any way to parallelize tracula using SGE without having to make a unique dmrirc for each subject? If I could pass subject numbers to the dmrirc that would be great, for example. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. __**__** _ _ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. 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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https
[Freesurfer] Which space is TRACULA statistics in?
Hi FreeSurfing researchers, I am looking at the pathstats.overall.txt, and wanted to see if anybody knew which space these voxels are in - I assume MNI space (given that I used the MNI template) and not individual diffusion space, but would like to confirm. Does anybody know for certain what space this data is reported in? Thanks! -- Susie Kuo ___ 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] Which space is TRACULA statistics in?
Thank you, Anastasia! I will keep this in mind when I analyze the group statistics. On Wed, May 1, 2013 at 11:07 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susan - All outputs of tracula are in native diffusion space. Tractography is performed in the native space, without any transformationon the DWIs to another space. a.y On Wed, 1 May 2013, Susan Kuo wrote: Hi FreeSurfing researchers, I am looking at the pathstats.overall.txt, and wanted to see if anybody knew which space these voxels are in - I assume MNI space (given that I used the MNI template) and not individual diffusion space, but would like to confirm. Does anybody know for certain what space this data is reported in? Thanks! -- Susie Kuo The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. 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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear* ___ 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] Use our own training subjects?
Thank you, Anastasia. I think we can recruit some hard-working neuroanatomists here to help us with the labeling. I believe I will give this a shot for the IFO. Again, thanks for your support on this - I really appreciate it! Susie Kuo On Wed, May 1, 2013 at 11:04 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susan - Currently the only way to read in the manually labeled streamlines from the training subjects is in .trk format, which is what trackvis writes out. If you prefer to use another program for manual labeling, then its output would have to be converted to .trk format. This format is described in the online documentation for trackvis. The priors are generated by trac-all on the fly, given the .trk files and aparc+aseg for each of the training subjects. So once the manual labeling is done, it's just about transforming these files to the template space and passing the list to trac-all. I'm happy to document this part. The hard work is the manual labeling! Hope this helps, a.y On Wed, 1 May 2013, Susan Kuo wrote: Hi Anastasia, I would like to add several tracts of interest to our priors, e.g. the IFO and sections of the corpus callosum. Would it be possible for you to document how your group created your priors? Are we constrained to trackvis as a program? I know this is a lot of documentation, but I would be happy to help. I'm located on the NIH campus, and can travel up to help with the documentation if you'd like. It would be a good learning process for me. Thank you! Susan Kuo On Fri, Apr 26, 2013 at 1:42 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - If you can label the connection that you want in trackvis consistently in a set of subjects, then yes, it'd be possible to create your own mini atlas. You'd have to map the .trk files with the trackvis streamlines and the aparc+aseg's from all the training subjects to either the MNI or the CVS template. Then there's a trainfile variable that you can set in the configuration file that tells trac-all where to find the training data. If you decide to go through with this, I can try to document it in more detail on the wiki. a.y On Mon, 15 Apr 2013, Susan Kuo wrote: Hi Anastasia, We were viewing the arcuate fasiculus tract created by TRACULA, and noticed that the tract did not reach Broca's area. While there exists literature that now challenges this neuroanatomical convention, I would like to investigate the possibility of creating and inputting on our own training subjects as priors. Do you know if we can try this? Thank you! -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. 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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear* ___ 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] Use our own training subjects?
Hi Anastasia, We were viewing the arcuate fasiculus tract created by TRACULA, and noticed that the tract did not reach Broca's area. While there exists literature that now challenges this neuroanatomical convention, I would like to investigate the possibility of creating and inputting on our own training subjects as priors. Do you know if we can try this? Thank you! -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear* ___ 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] Incomplete and poorly formed tracts
Hi Anastasia, I'm attaching the graphic I arrived at with the command: freeview -tv subjectID/dlabel/diff/aparc+aseg.flt.nii.gz -v subjectID/dmri/dtifit_FA.nii.gz Here, I used the subject I send you (Sa69845.5) for the subjectID. I could not detect spill over in these images, mostly because the frontal lobe is a little cut off. Did you perhaps use a different viewer? I'm hoping to be able to detect these mis-registrations better for myself in the future. Thanks for all your help! Sincerely, Susie Kuo NIH On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - Everything under dlabel/diff is mapped to DWI space (either with flirt or with bbregister, whichever you use). The one in my screenshot was dlabel/diff/aparc+aseg.flt.**nii.gz. a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, I see what you mean. I had previously used the dtifit_FA.nii.gz image and overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using freeview. I didn't end up with the same images as you, however. Can you tell me which images you used to obtain this overlay? I am going to run bbregister tonight, and I'll let you know how it goes -- I'm hopeful! Thank you again! Susie Kuo NIH On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - I'm attaching a snapshot from your subject, showing the aparc+aseg overlaid on the FA map. The registration has failed. The frontal lobe has spilled out of the brain, the white matter has spilled into the ventricles. I strongly recommend using bbregister for the intra-subject registration, which is the default in the latest version of trac-all. Hope this helps, a.y On Tue, 26 Mar 2013, Susan Kuo wrote: Hi Anastasia, I did as you recommended and checked the diffusion-to-anatomical registration, and the overlay of aparc+aseg_mask on FA, and these views seem to be good. Upon closer inspection, what I find is that there are incipient 'bits' of all the tracts, but they seem to not have 'grown', though they are in the proper space (comparing them to good brains that yielded the full complement of tracts). Is there a configuration in your TRACULA that controls the growing of the tracts specifically? Perhaps I should look into that. Thank you, btw, for your very prompt reply yesterday- it was much appreciated! Sincerely, Susie Kuo NIH On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susan - Good to hear that you get good results for most of your subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical registration for the subjects that are failing? I'd check the aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if there are any holes or misregistration. a.y On Mon, 25 Mar 2013, Susan Kuo wrote: Hi FreeSurfers and Anastasia, TRACULA is working great for me, generating tracts for a sample of 20 subject brains I'm working with. However, for 3 of the brains, I'm receiving incomplete and poorly formed tracts. I've re-run trac-all at least 2x on each subject in case there was a mistake in my original configuration. However, I am reproducing the same results. Does anybody have an idea why I would see these spotty tracts? Thank you for all your help! -- Susie Kuo NIH The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. 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. -- Susie Kuo Mediocrity knows nothing higher than
Re: [Freesurfer] Incomplete and poorly formed tracts
Hi Anastasia, Thank you! I can see that the aparc+aseg spilled over badly. I am going to try bbregister, and then re-betting (Brain Extraction Tool-ing) the original image, since the dtifit_FA looks to include non-brain near the frontal lobe. I'll keep you and the FS community updated on the results, in case anybody is curious. Sincerely, Susie Kuo NIH On Wed, Mar 27, 2013 at 10:41 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - The -tv (tract volume) option of freeview is designed specifically to display the merged*.mgz output files of tracula. For a regular volume, use -v or no option at all. For best displaying the aparc+aseg, select it in freeview and choose Lookup Table from the Color map menu. Hope this helps, a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, I'm attaching the graphic I arrived at with the command: freeview -tv subjectID/dlabel/diff/aparc+**aseg.flt.nii.gz -v subjectID/dmri/dtifit_FA.**nii.gz Here, I used the subject I send you (Sa69845.5) for the subjectID. I could not detect spill over in these images, mostly because the frontal lobe is a little cut off. Did you perhaps use a different viewer? I'm hoping to be able to detect these mis-registrations better for myself in the future. Thanks for all your help! Sincerely, Susie Kuo NIH On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - Everything under dlabel/diff is mapped to DWI space (either with flirt or with bbregister, whichever you use). The one in my screenshot was dlabel/diff/aparc+aseg.flt.**nii.gz. a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, I see what you mean. I had previously used the dtifit_FA.nii.gz image and overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using freeview. I didn't end up with the same images as you, however. Can you tell me which images you used to obtain this overlay? I am going to run bbregister tonight, and I'll let you know how it goes -- I'm hopeful! Thank you again! Susie Kuo NIH On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - I'm attaching a snapshot from your subject, showing the aparc+aseg overlaid on the FA map. The registration has failed. The frontal lobe has spilled out of the brain, the white matter has spilled into the ventricles. I strongly recommend using bbregister for the intra-subject registration, which is the default in the latest version of trac-all. Hope this helps, a.y On Tue, 26 Mar 2013, Susan Kuo wrote: Hi Anastasia, I did as you recommended and checked the diffusion-to-anatomical registration, and the overlay of aparc+aseg_mask on FA, and these views seem to be good. Upon closer inspection, what I find is that there are incipient 'bits' of all the tracts, but they seem to not have 'grown', though they are in the proper space (comparing them to good brains that yielded the full complement of tracts). Is there a configuration in your TRACULA that controls the growing of the tracts specifically? Perhaps I should look into that. Thank you, btw, for your very prompt reply yesterday- it was much appreciated! Sincerely, Susie Kuo NIH On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susan - Good to hear that you get good results for most of your subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical registration for the subjects that are failing? I'd check the aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if there are any holes or misregistration
Re: [Freesurfer] Incomplete and poorly formed tracts
Hi Anastasia, I saved out some of the completed trac-all.cmds following each TRACULA 'step', and I see where aparc+aseg is mapped to diffusion space. Thank you again for all your help - my project is starting to look a lot better! Sincerely, Susie Kuo NIH On Wed, Mar 27, 2013 at 12:02 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Actually the brain mask used on the diffusion data *is* the aparc+aseg mapped to diffusion space, so the reason you see that extra non-brain stuff in the FA map is because the aparc+aseg was not aligned well to it. So you just need to switch on bbregister and switch off flirt in your configuration file, and then rerun trac-all. If the DWI-to-T1 registration is good, then the masking issue will be solved too. Good luck! a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, Thank you! I can see that the aparc+aseg spilled over badly. I am going to try bbregister, and then re-betting (Brain Extraction Tool-ing) the original image, since the dtifit_FA looks to include non-brain near the frontal lobe. I'll keep you and the FS community updated on the results, in case anybody is curious. Sincerely, Susie Kuo NIH On Wed, Mar 27, 2013 at 10:41 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - The -tv (tract volume) option of freeview is designed specifically to display the merged*.mgz output files of tracula. For a regular volume, use -v or no option at all. For best displaying the aparc+aseg, select it in freeview and choose Lookup Table from the Color map menu. Hope this helps, a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, I'm attaching the graphic I arrived at with the command: freeview -tv subjectID/dlabel/diff/aparc+** aseg.flt.nii.gz -v subjectID/dmri/dtifit_FA.**nii.gz Here, I used the subject I send you (Sa69845.5) for the subjectID. I could not detect spill over in these images, mostly because the frontal lobe is a little cut off. Did you perhaps use a different viewer? I'm hoping to be able to detect these mis-registrations better for myself in the future. Thanks for all your help! Sincerely, Susie Kuo NIH On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - Everything under dlabel/diff is mapped to DWI space (either with flirt or with bbregister, whichever you use). The one in my screenshot was dlabel/diff/aparc+aseg.flt.**nii.gz. a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, I see what you mean. I had previously used the dtifit_FA.nii.gz image and overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using freeview. I didn't end up with the same images as you, however. Can you tell me which images you used to obtain this overlay? I am going to run bbregister tonight, and I'll let you know how it goes -- I'm hopeful! Thank you again! Susie Kuo NIH On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - I'm attaching a snapshot from your subject, showing the aparc+aseg overlaid on the FA map. The registration has failed. The frontal lobe has spilled out of the brain, the white matter has spilled into the ventricles. I strongly recommend using bbregister for the intra-subject registration, which is the default in the latest version of trac-all. Hope this helps, a.y On Tue, 26 Mar 2013, Susan Kuo wrote: Hi Anastasia, I did as you recommended and checked the diffusion-to-anatomical
Re: [Freesurfer] Incomplete and poorly formed tracts
Hi Anastasia, I did as you recommended and checked the diffusion-to-anatomical registration, and the overlay of aparc+aseg_mask on FA, and these views seem to be good. Upon closer inspection, what I find is that there are incipient 'bits' of all the tracts, but they seem to not have 'grown', though they are in the proper space (comparing them to good brains that yielded the full complement of tracts). Is there a configuration in your TRACULA that controls the growing of the tracts specifically? Perhaps I should look into that. Thank you, btw, for your very prompt reply yesterday- it was much appreciated! Sincerely, Susie Kuo NIH On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susan - Good to hear that you get good results for most of your subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical registration for the subjects that are failing? I'd check the aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if there are any holes or misregistration. a.y On Mon, 25 Mar 2013, Susan Kuo wrote: Hi FreeSurfers and Anastasia, TRACULA is working great for me, generating tracts for a sample of 20 subject brains I'm working with. However, for 3 of the brains, I'm receiving incomplete and poorly formed tracts. I've re-run trac-all at least 2x on each subject in case there was a mistake in my original configuration. However, I am reproducing the same results. Does anybody have an idea why I would see these spotty tracts? Thank you for all your help! -- Susie Kuo NIH The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. 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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear* ___ 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] Incomplete and poorly formed tracts
Hi Anastasia, I see what you mean. I had previously used the dtifit_FA.nii.gz image and overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using freeview. I didn't end up with the same images as you, however. Can you tell me which images you used to obtain this overlay? I am going to run bbregister tonight, and I'll let you know how it goes -- I'm hopeful! Thank you again! Susie Kuo NIH On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - I'm attaching a snapshot from your subject, showing the aparc+aseg overlaid on the FA map. The registration has failed. The frontal lobe has spilled out of the brain, the white matter has spilled into the ventricles. I strongly recommend using bbregister for the intra-subject registration, which is the default in the latest version of trac-all. Hope this helps, a.y On Tue, 26 Mar 2013, Susan Kuo wrote: Hi Anastasia, I did as you recommended and checked the diffusion-to-anatomical registration, and the overlay of aparc+aseg_mask on FA, and these views seem to be good. Upon closer inspection, what I find is that there are incipient 'bits' of all the tracts, but they seem to not have 'grown', though they are in the proper space (comparing them to good brains that yielded the full complement of tracts). Is there a configuration in your TRACULA that controls the growing of the tracts specifically? Perhaps I should look into that. Thank you, btw, for your very prompt reply yesterday- it was much appreciated! Sincerely, Susie Kuo NIH On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susan - Good to hear that you get good results for most of your subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical registration for the subjects that are failing? I'd check the aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if there are any holes or misregistration. a.y On Mon, 25 Mar 2013, Susan Kuo wrote: Hi FreeSurfers and Anastasia, TRACULA is working great for me, generating tracts for a sample of 20 subject brains I'm working with. However, for 3 of the brains, I'm receiving incomplete and poorly formed tracts. I've re-run trac-all at least 2x on each subject in case there was a mistake in my original configuration. However, I am reproducing the same results. Does anybody have an idea why I would see these spotty tracts? Thank you for all your help! -- Susie Kuo NIH The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. 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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear* ___ 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] TRACULA trac-all -path giving 'Segmentation error (core dumped) error'
Hi FreeSurfer Community, I am trying to run TRACULA's last step, 'trac-all -path -c path-to-dmrirc-config-script', and am receiving the error: Segmentation fault(core dumped) Moreover, when I look to standard output (terminal), I noticed that the initial 'dmri_paths' command is incomplete. The terminal shows that the command includes the '--init' switch and several arguments (e.g. 'subject ID/dlabel/diff/rh.atr_PP_avg33_mni_flt_cpts_5.txt'), the last of which is terminated mid-pathname. Can anyone suggest a reason why this would be the case? Thank you, Susie Kuo ___ 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] Parallelizing on a different kind of cluster
Hi TRACULA Experts, Is there a way of parallelizing BEDPOSTX on a cluster, not using the bedpostx_seychelles option since I'm on a non-MGH cluster? Thanks! Susie Kuo ___ 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] Parallelizing on a different kind of cluster
I see. So I will discriminate between what bedpostx requires from the more inclusive bedpostx_seychelles script. Thank you for your help. I sincerely appreciate it. Best, Susie Kuo On Tue, Feb 12, 2013 at 1:56 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Everything that's in bedpostx is also in bedpostx_seychelles. I've just added to it. But if you want to run bedpostx directly on the command line instead of going through trac-all -bedp, you can do that, too. On Tue, 12 Feb 2013, Susie Kuo wrote: Thank you very much for your response. Is there a way to use bedpostx instead of bedpostx_seychelles? If not, no worries. I will look at your script and compose one of our own. Best, Susie Kuo On Feb 12, 2013, at 11:56 AM, Anastasia Yendiki wrote: Hi Susie - FSL's bedpostx script works for parallelization on the type of cluster they have at Oxford, and bedpostx_seychelles is a modified version of it that also works on our cluster. Other than that, support for all possible cluster setups at other centers is beyond the scope of our research, but perhaps the existing script is useful as a starting point for making it work on your cluster. Hope this helps, a.y On Tue, 12 Feb 2013, Susan Kuo wrote: Hi TRACULA Experts, Is there a way of parallelizing BEDPOSTX on a cluster, not using the bedpostx_seychelles option since I'm on a non-MGH cluster? Thanks! Susie Kuo The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Trying to email out on the FreeSurfer mailing list
Hi, I've been trying to email out for help to the FreeSurfer community, using the below addresses. However, I am not receiving my own email back, though I am a member of the mailing list via this email address. Can you tell me what I'm doing wrong? Thank you! Susan Kuo -- Forwarded message -- From: Susan Kuo susan.kuo@gmail.com Date: Wed, Feb 6, 2013 at 4:57 PM Subject: Troubleshooting the preproc To: ayend...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Hi FreeSurfer community, I am currently trying to troubleshoot my preprocessing part of TRACULA with the tutorial dataset (for *Diff001* as the subject, specifically), running *trac-all -corr -c config dmrirc*. I am running the commands in * subjectID/scripts/trac-all.cmd* one by one because I've had problems with some of the steps. Specifically, *flip4fsl* didn't work. I instead used *fslswapdim -x -y z* (*flip4fsl* uses *fslswapdim x -y z*, which doesn't generate the correct orientation for FSL in fact), followed by *fslorient -forceradiological*. I successfully ran *eddy_current *thereafter. Now I am stuck again, at FreeSurfer's *xfmrot, *which should look like: * * *xfmrot transform file input vector file [output vector file]* I specifically typed in: *xfmrot /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi.ecclog /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/bvecs.norot /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/bvecs* and received the following iterative errors: * avscale: Command not found. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. * Can any of you help me? Thank you, Susie K ___ 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] BEDPOSTX - seychelles option
Hi FreeSurfer community, I would like to run '-bedp' with TRACULA, to run the bedpostx option. I see from the *./subjID/scripts/trac-all.cmd* file that the actual command issued was *bedpostx_seychelles*, which allows for the PBS queueing system running on seychelles and is used by the Martinos Center folks to parallelize computation. I have 2 questions regarding this modification: 1 - Can I switch to strictly *bedpostx*? Is there a text file I can alter to reflect changes to the commands issued? I believe *trac-all.cmd* is actually created at runtime, not prior. 2 - I work at NIH and have the Biowulf cluster to work with. Can I parallelize bedpostx on Biowulf (which uses a Altair's PBS Pro batching system) with TRACULA's *trac-all -bedp* command, or any of *trac-all*? Thank you for your attention! Susie Kuo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Problem with flip4fsl
Hi FreeSurfer community, I am trying to run 'trac-all -corr -c config file' on the tutorial data, specifically for the single subject: Diff001. To start from 'scratch', I've deleted all but the './scripts' and the './orig' directories in the Diff001 parent folder. When I run the following command: trac-all -corr -c config file I receive the following error: ERROR BEGINS flip4fsl /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig.nii.gz /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8 fslswapdim /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig.nii.gz x -y z /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig_flip.nii.gz Cannot open volume /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig_flip for reading! ERROR ENDS Looking in my 'Diff001/dmri' directory, I cannot locate a 'dwi_orig_flip.nii.gz' file. I assume this is where the script breaks. I tried to run the 'flip4fsl' command singly, but received the same error. I'm working on a: 3.2.0-35-generic #55-Ubuntu SMP Wed Dec 5 17:42:16 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux I've unsuccessfully searched through the mailing list archive to find if others had encountered the same issue previously. Does anybody have any suggestions? Thanks! Susie ___ 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] Troubleshooting the preproc
Hi FreeSurfer community, I am currently trying to troubleshoot my preprocessing part of TRACULA with the tutorial dataset (for *Diff001* as the subject, specifically), running *trac-all -corr -c config dmrirc*. I am running the commands in * subjectID/scripts/trac-all.cmd* one by one because I've had problems with some of the steps. Specifically, *flip4fsl* didn't work. I instead used *fslswapdim -x -y z* (*flip4fsl* uses *fslswapdim x -y z*, which doesn't generate the correct orientation for FSL in fact), followed by *fslorient -forceradiological*. I successfully ran *eddy_current *thereafter. Now I am stuck again, at FreeSurfer's *xfmrot, *which should look like: * * *xfmrot transform file input vector file [output vector file]* I specifically typed in: *xfmrot /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi.ecclog /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/bvecs.norot /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/bvecs* and received the following iterative errors: * avscale: Command not found. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. * Can any of you help me? Thank you, Susie K ___ 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: Problems in testing out newly installed Freesurfer with autorecon-1 option
Thank you, Nick. I tried using fixup_mni_paths, but received a poor result. I copied the stdout below: *** yocto/j/dti7/Susie/freesurfer/subjects su Password: root@yocto:/j/dti7/Susie/freesurfer/subjects# fixup_mni_paths fixup_mni_paths: command not found root@yocto:/j/dti7/Susie/freesurfer/subjects# cd $FREESURFER_HOME/bin root@yocto:/usr/local/freesurfer/bin# fixup_mni_paths fixup_mni_paths: command not found root@yocto:/usr/local/freesurfer/bin# ./fixup_mni_paths Using perl '/usr/bin/perl' Patching autocrop...(original file saved to autocrop.old) Patching field2imp...(original file saved to field2imp.old) Patching imp2field...(original file saved to imp2field.old) Patching make_template...(original file saved to make_template.old) Patching mritoself...(original file saved to mritoself.old) Patching mritotal...(original file saved to mritotal.old) Patching nu_correct...(original file saved to nu_correct.old) Patching nu_estimate...(original file saved to nu_estimate.old) Patching nu_estimate_np_and_em...(original file saved to nu_estimate_np_and_em.old) Patching nu_evaluate...(original file saved to nu_evaluate.old) Patching resample_labels...(original file saved to resample_labels.old) Patching sharpen_volume...(original file saved to sharpen_volume.old) Patching xfmtool...(original file saved to xfmtool.old) done. Here are the changes: diff autocrop autocrop.old diff field2imp field2imp.old diff imp2field imp2field.old diff make_template make_template.old diff mritoself mritoself.old diff mritotal mritotal.old diff nu_correct nu_correct.old diff nu_estimate nu_estimate.old diff nu_estimate_np_and_em nu_estimate_np_and_em.old diff nu_evaluate nu_evaluate.old diff resample_labels resample_labels.old diff sharpen_volume sharpen_volume.old diff xfmtool xfmtool.old done. Note: not all systems will require a patch, and may not show any differences. Now a test of the MNI tool 'nu_correct'... nu_correct: Command not found. A version number and usage message should have been displayed. *** I double-checked that /usr/bin/perl exists, so that's ok. I've been crawling the forums, but I can't find a good answer for what appears to be a simple problem. Can I fix this manually? Thanks! Susie On Wed, Jan 9, 2013 at 4:29 PM, Nick Schmansky ni...@nmr.mgh.harvard.eduwrote: Susan, there appear to be two problems here. the first and main problem is the one: nu_correct: Command not found. nu_correct is a script which has as its first line: #!/usr/bin/perl -w so can you check that you have perl installed at /usr/bin/perl? better yet, run this script: fixup_mni_paths which does the checking for you and attempts to fix the scripts. the other problem appears to be the fact that mri_nu_correct.mni doesnt exit upon finding the error that the files are missing. this is bad, although in looking at the script, it ought to. the next release will contain a double check. from the looks of your script, it appears that you are running recon-all with a subject that had its data already processed, so nu.mgz existed already, so it just used that and continued on. so the results are correct (assuming nu.mgz was decent to begin with), but resolving the nu_correct issue is the important thing to do. Nick On Wed, 2013-01-09 at 11:00 -0500, Susan Kuo wrote: Hi, I'm currently in the process of verifying that my install of Freesurfer works. I have an Ubuntu 12.04.1 LTS box. I encountered what appeared to be 4 errors after running recon-all -s bert -autorecon1. The last line I included here states that the command completed without error, so I'm not sure if I should be concerned thatnu_correct wasn't found, or that there were loading errors, and a mincREAD() error. Could you help me identify what I need to do to correct these issues? I've included the standard output for this command as a text file here. There appear to be 4 issues: ***ISSUE 1: cannot find nu_correct * nu_correct: Command not found. INFO: current FREESURFER_HOME does not match that of previous processing. ***ISSUE 2: No such file or directory error cp: cannot stat `./tmp.mri_nu_correct.mni.25253/nu2.mnc': No such file or directory mri_binarize --i ./tmp.mri_nu_correct.mni.25253/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.25253/ones.mgz mincRead(): can't find file ./tmp.mri_nu_correct.mni.25253/nu2.mnc ***ISSUE 3: Loading error** Loading ./tmp.mri_nu_correct.mni.25253/ones.mgz ERROR: loading ./tmp.mri_nu_correct.mni.25253/ones.mgz mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.25253/ones.mgz --i ./tmp.mri_nu_correct.mni.25253/nu2.mnc --sum ./tmp.mri_nu_correct.mni.25253/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25253/output.mean.dat mghRead(./tmp.mri_nu_correct.mni.25253/ones.mgz, -1): could not open file ***ISSUE 4: Loading error** Loading
[Freesurfer] Problems in testing out newly installed Freesurfer with autorecon-1 option
Hi, I'm currently in the process of verifying that my install of Freesurfer works. I have an Ubuntu 12.04.1 LTS box. I encountered what appeared to be 4 errors after running *recon-all -s bert -autorecon1.* The last line I included here states that the command completed without error, so I'm not sure if I should be concerned that*nu_correct* wasn't found, or that there were loading errors, and a *mincREAD()* error. Could you help me identify what I need to do to correct these issues? I've included the standard output for this command as a text file here. There appear to be 4 issues: ***ISSUE 1: cannot find *nu_correct* * nu_correct: Command not found. INFO: current FREESURFER_HOME does not match that of previous processing. ***ISSUE 2: No such file or directory error cp: cannot stat `./tmp.mri_nu_correct.mni.25253/nu2.mnc': No such file or directory mri_binarize --i ./tmp.mri_nu_correct.mni.25253/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.25253/ones.mgz mincRead(): can't find file ./tmp.mri_nu_correct.mni.25253/nu2.mnc ***ISSUE 3: Loading error** Loading ./tmp.mri_nu_correct.mni.25253/ones.mgz ERROR: loading ./tmp.mri_nu_correct.mni.25253/ones.mgz mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.25253/ones.mgz --i ./tmp.mri_nu_correct.mni.25253/nu2.mnc --sum ./tmp.mri_nu_correct.mni.25253/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25253/output.mean.dat mghRead(./tmp.mri_nu_correct.mni.25253/ones.mgz, -1): could not open file ***ISSUE 4: Loading error** Loading ./tmp.mri_nu_correct.mni.25253/ones.mgz ERROR: loading ./tmp.mri_nu_correct.mni.25253/ones.mgz (standard_in) 1: syntax error mris_calc -o ./tmp.mri_nu_correct.mni.25253/nu2.mnc ./tmp.mri_nu_correct.mni.25253/nu2.mnc mul mincRead(): can't find file ./tmp.mri_nu_correct.mni.25253/nu2.mnc This is the last line to standard output, and it seems reassuring** recon-all -s bert finished without error at Tue Jan 8 17:49:19 EST 2013 I appreciate whatever help you can give me, and thank you very much for your time! The attached is a text file. Best, S Kuo freesurfer Description: Binary data ___ 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.
