Re: [Freesurfer] [FreeSurfer] : Convert asl data from fsaverage (surface) to MNI305 (volume)
Hello Douglas, I have download the new version of mri_surf2vol you supplied me, and have copied it in the FS5.3 /bin installation files. But when I tried to launch with my precedent command lines, the error message appeared : *gdiagno = -1Using identity matrix for registration--GNU libc version: 2.19ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://surfer.nmr.mgh.harvard.edu/registration.html http://surfer.nmr.mgh.harvard.edu/registration.html--gdiagno = -1Using merge volume as templateUsing identity matrix for registrationniiRead(): error opening file /home/fatmike/sebastien/FS5.1/207020_T0/asl/lh.MNI305.asl.nii.gzmri_surf2vol ERROR: reading /home/fatmike/sebastien/FS5.1/207020_T0/asl/lh.MNI305.asl.nii.gz headerMatrix from regfile: 0.998 -0.007 0.018 0.957;-0.013 -0.009 0.997 -17.816;-0.015 -1.001 0.002 -18.550; 0.000 0.000 0.000 1.000;movvol /home/global//fsl50/data/standard/MNI152_T1_2mm.nii.gztargvol /home/fatmike/sebastien/FS5.1/207020_T0/asl/MNI305.asl.nii.gzoutvol /home/fatmike/sebastien/FS5.1/207020_T0/asl/lh.MNI152.asl.nii.gzregfile /home/global//freesurfer5.3//average/mni152.register.datinvert 1tal 0talres 2regheader 0noresample 0interp nearest (0)precision float (3)Gdiag_no -1Synth 0SynthSeed 1427897150Invert!niiRead(): error opening file /home/fatmike/sebastien/FS5.1/207020_T0/asl/MNI305.asl.nii.gz* What shoul I do ? Best regards, Matthieu 2015-03-26 21:27 GMT+01:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: That version had a bug. Try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol On 03/26/2015 12:16 PM, Matthieu Vanhoutte wrote: Dear experts, I have some asl data on fsaverage surface and would like to compute them on MNI305 volume. So I executed the commands below, but when merging left and right hemispheres it seems that the /--fillribbon /option on /MNI305.asl.nii.gz/ output data didn't work for right hemisphere : /mri_surf2vol --surfval lh.fsaverage.asl --fillribbon --identity fsaverage --template fsaverage/mri/T1.mgz --hemi lh --o lh.MNI305.asl.nii.gz mri_surf2vol --surfval rh.fsaverage.asl --fillribbon --identity fsaverage --merge lh.MNI305.asl.nii.gz --hemi rh --o MNI305.asl.nii.gz/ What should I have to do ? Many thanks in advance for helping ! Best regards, Matthieu ___ 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_watershed Error: indices out of bounds
Hello Edgar, Could you upload the whole subject folder? I could try to run it through recon all here and see if I can reproduce the error. It would also allow me to look through your log files to see if I can spot anything that could be causing this issue. You can use FileDrop2.0 if the directory is under 2GB https://gate.nmr.mgh.harvard.edu/filedrop2/ Thank you, Ani Varjabedian On 03/25/2015 11:06 AM, Edgar Busovaca wrote: Hello Bruce, I took a look at the file with freeview and I can't identify anything peculiar about the data. The file is named Indices_oob.nii and has been uploaded to /transfer/incoming on the FTP file exchange server. Thank you for your swift reply and in advance for your time. Best regards, Edgar Busovaca On Tue, Mar 24, 2015 at 5:34 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: Hi Edgar the LINE SEARCH thing is not a real problem. I've never seen indices out of bounds before though. Is there anything strange about your dataset? Does freeview display it properly (that is, are what freeview thinks the RAS dirs the correct anatomical ones)? If you upload the dataset we'll see if we can replicate and fix the problem cheers Bruce On Tue, 24 Mar 2015, Edgar Busovaca wrote: Dear Freesurfer users, I have attempted to process a subject (.nii type input) through recon-all -all, but for some reason the processing gambit is terminated early ( during the skullstrip). During skullstripping the following warning appears twice: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO=3 POSSIBLE CAUSES FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof WuasiNewtonEMA: 007: -log(p) = 10341.8 tol 0.10 following the skullstrip step in ***WATERSHED the following appears: mri_watershed Error: indices out of bounds Oddly, this particular subject failed where the rest of the data set successfully completed recon-all -all. As a reference I am running freesurfer 5.1 Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 RedHat release: CentOS release 6.5 (Final) Kernel info: Linux 2.6.32-431.11.2.e16.x86_64 x86_64 Is there a flag to push this subject through recon-all? Thanks in advance for your time. Best, Edgar Busovaca ___ 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. ___ 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] [FreeSurfer] : Convert asl data from fsaverage (surface) to MNI305 (volume)
Hello Douglas, I have downloaded a new license and it successfully runs ! Best regards, Matthieu 2015-03-31 12:39 GMT+02:00 Matthieu Vanhoutte matthieuvanhou...@gmail.com: Hello Douglas, I have download the new version of mri_surf2vol you supplied me, and have copied it in the FS5.3 /bin installation files. But when I tried to launch with my precedent command lines, the error message appeared : *gdiagno = -1Using identity matrix for registration--GNU libc version: 2.19ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://surfer.nmr.mgh.harvard.edu/registration.html http://surfer.nmr.mgh.harvard.edu/registration.html--gdiagno = -1Using merge volume as templateUsing identity matrix for registrationniiRead(): error opening file /home/fatmike/sebastien/FS5.1/207020_T0/asl/lh.MNI305.asl.nii.gzmri_surf2vol ERROR: reading /home/fatmike/sebastien/FS5.1/207020_T0/asl/lh.MNI305.asl.nii.gz headerMatrix from regfile: 0.998 -0.007 0.018 0.957;-0.013 -0.009 0.997 -17.816;-0.015 -1.001 0.002 -18.550; 0.000 0.000 0.000 1.000;movvol /home/global//fsl50/data/standard/MNI152_T1_2mm.nii.gztargvol /home/fatmike/sebastien/FS5.1/207020_T0/asl/MNI305.asl.nii.gzoutvol /home/fatmike/sebastien/FS5.1/207020_T0/asl/lh.MNI152.asl.nii.gzregfile /home/global//freesurfer5.3//average/mni152.register.datinvert 1tal 0talres 2regheader 0noresample 0interp nearest (0)precision float (3)Gdiag_no -1Synth 0SynthSeed 1427897150Invert!niiRead(): error opening file /home/fatmike/sebastien/FS5.1/207020_T0/asl/MNI305.asl.nii.gz* What shoul I do ? Best regards, Matthieu 2015-03-26 21:27 GMT+01:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: That version had a bug. Try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol On 03/26/2015 12:16 PM, Matthieu Vanhoutte wrote: Dear experts, I have some asl data on fsaverage surface and would like to compute them on MNI305 volume. So I executed the commands below, but when merging left and right hemispheres it seems that the /--fillribbon /option on /MNI305.asl.nii.gz/ output data didn't work for right hemisphere : /mri_surf2vol --surfval lh.fsaverage.asl --fillribbon --identity fsaverage --template fsaverage/mri/T1.mgz --hemi lh --o lh.MNI305.asl.nii.gz mri_surf2vol --surfval rh.fsaverage.asl --fillribbon --identity fsaverage --merge lh.MNI305.asl.nii.gz --hemi rh --o MNI305.asl.nii.gz/ What should I have to do ? Many thanks in advance for helping ! Best regards, Matthieu ___ 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] White matter and pial surfaces not tracking sulcus
Hi all, Sorry for the repost, was just wondering whether someone might have some input regarding this issue. Thanks! Niels On Thu, Mar 26, 2015 at 12:10 PM, Niels Bergsland theni...@gmail.com wrote: Hi all, I have run into an issue that I am having trouble correcting. http://imgur.com/a/4KqpJ I have checked the aseg to see if it was labeled as ventricle. This does not seem to be the cause. Any other suggestions? I am happy to upload the case if that is necessary. Best regards, Niels ___ 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] isxconcat-sess problem
Hi list, I'm performing the FS-FAST analysis. Some months ago, I have already preformed this analysis on some subjects without problem. Now, I have added some subjects. When I rerun the analysis i have these error: for isxconcat-sess -sf sessidlist —analysis fc.lthalseed.surf.lh -contrast L_Thalamus -o my-group_thal_LHERROR: finding sessionsSess47 /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess15 /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess48 /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess49 /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess50[iMac-di-Stefano:freesurfer/subjects/FUNCTIONAL_DATA] Stefano% and for isxconcat-sess -s Sess01 -s Sess02 -s Sess03 -s Sess04 -s Sess05 -s Sess06 -s Sess07 -s Sess08 -s Sess09 -s Sess10 -s Sess11 -s Sess12 -s Sess13 —s Sess14 -s Sess15 -s Sess16 -s Sess30 -s Sess31 -s Sess32 -s Sess33 -s Sess34 -s Sess35 -s Sess36 -s Sess37 -s Sess39 -s Sess40 -s Sess41 -s Sess42 -s Sess43 -s Sess44 -s Sess45 -s Sess46 -s Sess47 -s Sess48 —s Sess49 -s Sess50 —analysis fc.lthalseed.surf.lh -contrast L_Thalamus -o my-group_THAL_LEFTERROR: Flag —s unrecognized. FUNCTIONAL_DATA directory contains: file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.lamgseed.surf.lh/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.lthalseed.surf.lh/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.ramgseed.surf.rh/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.rthalseed.surf.rh/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/file.fsgdfile:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/g1g2.intercept.mtxfile:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group.diff.mtxfile:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group1.mtxfile:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group2.mtxfile:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/GroupDescriptorFile%201file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/log/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.L_Amygdala.configfile:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.L_Thalamus.configfile:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.R_Amygdala.configfile:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.R_Thalamus.configfile:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess02/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess03/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess04/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess05/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess06/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess07/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess08/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess09/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess10/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess11/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess12/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess13/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess14/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess15/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess16/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess30/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess31/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess32/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess33/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess34/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess35/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess36/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess37/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess39/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess40/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess41/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess42/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess43/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess44/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess45/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess46/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess47/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess48/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess49/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess50/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/sessidlist for each subject, i.e. within
Re: [Freesurfer] longitudinal
Martin, Thanks for the advice. I'll have a think about which approach to take. Regards, Kate On Wed, Apr 1, 2015 at 2:24 AM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Kate, first you can check (and fix) the surface in the base. They are mapped from there to the time points, so improving the base will have an effect on both time points. checking surface placement can only be done by opening the images and surfaces manually. If you want to avoid that, you can run an ROI analysis on cortical regions and look for outliers but you'll miss cases that way. Best, Martin On 03/31/2015 12:55 AM, Kate Riggall wrote: Hello all, I am running a 2 time point longitudinal analysis of some structural brain images. I have noticed that there is some issues with the cortical surface reconstruction, i.e. some grey matter not recognised etc. As this is a short project, I do not have time to fix each image manually, but what I would like to be able to do is check whether there is at least a good match between time points within each subject. Is there an automated way to do this that would be more efficient than checking each subject manually? Thanks in advance, Kate Riggall ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology 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 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: drmirc parameteres with already processed and registered data
Hello, I am interested in using TRACULA for my data, but I have a few questions about modifying the dmrirc configuration file. I have already conducted eddycorrect, bet, and dtifit in FSL, registration of T1 and dti using ANTs, and I have also registered individual subject data to a template created in our lab (rather than MNI_T1_1mm_brain.nii.gz). We tried FSL flirt alignment initially, and it did not work well for our data, thus we used a different program that yielded better alignment for our data, and I'd like to be able to input the data files I have already registered (rather than re-registering them through fsl flirt). Additionally, as I already have the dtifit output, as well as the registration steps complete, I want to ensure that I am specifying the correct parameters in the dmrirc configuration file before running TRACULA on the data. I have set the dtroot, subjlist, dcmroot, dcmlist, bvecfile, and bvalfile to the appropriate locations for our data. I have set doeddy = 0, and was wondering what further specifications I need to provide in the dmrirc configuration file to use my already processed (dtifit) and registered data in the TRACULA steps. I greatly appreciate any assistance with the dmrirc setup. Thank you, Michelle ___ 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] longitudinal
Hi Kate, first you can check (and fix) the surface in the base. They are mapped from there to the time points, so improving the base will have an effect on both time points. checking surface placement can only be done by opening the images and surfaces manually. If you want to avoid that, you can run an ROI analysis on cortical regions and look for outliers but you'll miss cases that way. Best, Martin On 03/31/2015 12:55 AM, Kate Riggall wrote: Hello all, I am running a 2 time point longitudinal analysis of some structural brain images. I have noticed that there is some issues with the cortical surface reconstruction, i.e. some grey matter not recognised etc. As this is a short project, I do not have time to fix each image manually, but what I would like to be able to do is check whether there is at least a good match between time points within each subject. Is there an automated way to do this that would be more efficient than checking each subject manually? Thanks in advance, Kate Riggall ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology 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.
Re: [Freesurfer] GLM_Fit Question
Thanks so much! That did the trick. Taylor Elrod ___ 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] 'current' FSL
It may help to provide a bit more context e.g. the email/instructions you where you found the reference to 'current' fsl version? HTH, D On Tue, Mar 31, 2015 at 3:31 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Other than someone's recollection, there is probably no verifiable means for determining this information. Sending an inquiry to Martinos Center Help Desk is your best bet. -Zeke On 03/31/2015 03:24 PM, Marco Loggia, PhD wrote: Hi all, If I wanted to find out what was the 'current' FSL version at the Martinos Center on May 1, 2012, how would i do it? Thanks! Marco __ Marco L. Loggia, PhD Assistant Professor of Radiology Harvard Medical School Massachusetts General Hospital 149 Thirteenth Street, Room 2301 Charlestown, MA 02129 Phone: (617) 643-7267 Fax: (617) 726-7422 Email: ma...@nmr.mgh.harvard.edu mailto:ma...@nmr.mgh.harvard.edu Web: scholar.harvard.edu/loggia http://scholar.harvard.edu/loggia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] 'current' FSL
I think he's referring to the convention used in the various /usr/pubsw/packages libraries where current points to a version number. For example as of right now: /usr/pubsw/packages/fsl/current - 5.0.7 But there is no real way of knowing the destination of that symlink at May 1 2012. At least not that I'm aware of. -Zeke On 03/31/2015 03:34 PM, dgw wrote: It may help to provide a bit more context e.g. the email/instructions you where you found the reference to 'current' fsl version? HTH, D On Tue, Mar 31, 2015 at 3:31 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Other than someone's recollection, there is probably no verifiable means for determining this information. Sending an inquiry to Martinos Center Help Desk is your best bet. -Zeke On 03/31/2015 03:24 PM, Marco Loggia, PhD wrote: Hi all, If I wanted to find out what was the 'current' FSL version at the Martinos Center on May 1, 2012, how would i do it? Thanks! Marco __ Marco L. Loggia, PhD Assistant Professor of Radiology Harvard Medical School Massachusetts General Hospital 149 Thirteenth Street, Room 2301 Charlestown, MA 02129 Phone: (617) 643-7267 Fax: (617) 726-7422 Email: ma...@nmr.mgh.harvard.edu mailto:ma...@nmr.mgh.harvard.edu Web: scholar.harvard.edu/loggia http://scholar.harvard.edu/loggia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] 'current' FSL
Other than someone's recollection, there is probably no verifiable means for determining this information. Sending an inquiry to Martinos Center Help Desk is your best bet. -Zeke On 03/31/2015 03:24 PM, Marco Loggia, PhD wrote: Hi all, If I wanted to find out what was the 'current' FSL version at the Martinos Center on May 1, 2012, how would i do it? Thanks! Marco __ Marco L. Loggia, PhD Assistant Professor of Radiology Harvard Medical School Massachusetts General Hospital 149 Thirteenth Street, Room 2301 Charlestown, MA 02129 Phone: (617) 643-7267 Fax: (617) 726-7422 Email: ma...@nmr.mgh.harvard.edu mailto:ma...@nmr.mgh.harvard.edu Web: scholar.harvard.edu/loggia http://scholar.harvard.edu/loggia ___ 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] 'current' FSL
Hi all, If I wanted to find out what was the 'current' FSL version at the Martinos Center on May 1, 2012, how would i do it? Thanks! Marco __ Marco L. Loggia, PhD Assistant Professor of Radiology Harvard Medical School Massachusetts General Hospital 149 Thirteenth Street, Room 2301 Charlestown, MA 02129 Phone: (617) 643-7267 Fax: (617) 726-7422 Email: ma...@nmr.mgh.harvard.edu Web: scholar.harvard.edu/loggia ___ 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] Accounting for lesions misclassified as non-brain matter
From: jennifer.fer...@alumni.ubc.ca Sent: Tuesday, March 31, 2015 11:04 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Accounting for lesions misclassified as non-brain matter Hi there, I am having an issue with stroke lesions that border onto the cortex being misclassfied by freesurfer. Often with lesions in this region the pial boudary gets dragged to surround the lesion, missing actual grey matter and inaccurately classifying the tissue. The trouble is that every fix I can think of does nothing to impact this misclassification. I have tried: filling in the lesion on wm.mgz (pictured here) filling it in with voxels set to 110 on brainmask.mgz and filling it in with voxels set to 77 (wm hypointensities) on apar.mgz yet still this problem persists. Are there any other fixes I can use to correct this issue? Alternately if this issue can't be corrected should I expect it to impact my data much? These lesions typically occur in the insula, but I am only interested in quantifying primary motor and sensory areas, so will the estimation of volumes in these areas still be accurate? Thanks for any insight anyone can provide! - Jenn ___ 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 NIFTI Images
Dear Colleagues, I'm having problem to process TRACULA. I already processed the T1 imagens (recon-all) but I can't go further with the DWI imagens. I think that the problem is my image type. I have 33 files (1 b0 and 32 different directions) and in the configuration file I pointed to the first image (b0). Tracula starts the first step (-prep) but hangs after 1h. Do you think I need to convert the images or do I need to use a 4D NIFTI file? Last but not least, I have to say that I don't have the DICOM files, just PAR/REC. Thank you. Lucas Lessa. ___ 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.
