Re: [Freesurfer] mris resample: Command not found. This error is permanent after new patch download
Stefano, step 4 should be: chmod +x $FREESURFER_HOME/bin/mris_resample When you do an ls -l in the $FREESURFER_HOME/bin directory, you need to see the to see the x's next to mris_resample just like you do with all the other files in that directory. -Zeke On 06/07/2013 11:49 AM, std...@virgilio.it wrote: Hi list, during trac-all -prep I have this error: MRISregister() return, current seed 0 writing registered surface to /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg... expanding nbhd size to 1 mris_resample: Command not found. Darwin iMac I have performed my analysis by the following steps (as recommended by Zeke and Lilla): 1. download unKnow file (7.6 MB) at ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample 2. put file in $FREESURFER/bin/ 4. chmod +x ~/mris_resample as recommended by Daniel (in the first test I did not use this command) 5. start trac-all -prep 6. ERROR (in inter-reg step) What's happen? Thank you very much, Stefano ___ 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] R: Re: mris resample: Command not found. This error is permanent after new patch download
Hi Zeke, thank you very much. I have download a file that named unknown. I should rename it as mris_resample? Stefano Messaggio originale Da: zkauf...@nmr.mgh.harvard.edu Data: 7-giu-2013 18.02 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] mris resample: Command not found. This error is permanent after new patch download Stefano, step 4 should be: chmod +x $FREESURFER_HOME/bin/mris_resample When you do an ls -l in the $FREESURFER_HOME/bin directory, you need to see the to see the x's next to mris_resample just like you do with all the other files in that directory. -Zeke On 06/07/2013 11:49 AM, std...@virgilio.it wrote: Hi list, during trac-all -prep I have this error: MRISregister() return, current seed 0 writing registered surface to /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg... expanding nbhd size to 1 mris_resample: Command not found. Darwin iMac I have performed my analysis by the following steps (as recommended by Zeke and Lilla): 1. download unKnow file (7.6 MB) at ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample 2. put file in $FREESURFER/bin/ 4. chmod +x ~/mris_resample as recommended by Daniel (in the first test I did not use this command) 5. start trac-all -prep 6. ERROR (in inter-reg step) What's happen? Thank you very much, Stefano ___ 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 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] Parameterization Optseq
Dear Doug, Thank you for your e-mail. Please find attached our command line. We felt that the first two lines of code should essentially yield the same timing of events. In the first we included the fixed duration of the fix (1.0) in our event duration (4.0) and meant to ask for extra null events of a minimum duration of 0.0 sec. In the second, we did not include the fixed duration of the fix in our event duration (4.0) and meant to ask for this by inserting null events of at least 1.0 sec. Since the second line of code yielded an error, we run the third line. Is this helpful? Best, Laura 2013/6/5 Douglas N Greve gr...@nmr.mgh.harvard.edu Hi Laura, what is your command line? doug On 06/04/2013 09:02 AM, Laura Dekkers wrote: Dear Dr Greve, Together with Dr Hilde Huizenga I am implementing an fMRI study in which we would like to optimize the design by using Optseq2. We have a few questions. Could you please help us out? Our task consists of 3 runs of 72 trails each, in which participants are presented with a fixation cross that remains on the screen for a fixed duration of 1 sec, followed by one out of nine different stimuli that remains on the screen for a fixed duration of 4 sec. This gives a scan duration of 360 sec. We would then like to add 25% jitter, which results in a scan duration of 450 sec, and as TR = 2.0, this results in 225 time points. However, Optseq yields an error if ntp is set to 225, ev duration set to 4.0, psdwin dPSD to 1.0 , tnullmin to 1.0 and tnullmax to 6.0 ERROR: could not enforce tNullMax=6 (ntries=10) You will need to reduce the number of time points or increase the number of presentations. However, reducing the number of time points makes Optseq to only insert null events of 1.0 or rarely 2.0 sec without much variation. Optimization with ntp set to 225, ev duration set to 5.0 (=fixed duration of fix + stimulus), psdwin dPSD to 1.0 , tnullmin to 0.0 (1.0 does not work) and tnullmax to 6.0 does work. However, this renders Optseq to insert null events of a fixed duration op 1.0 sec, which is not what we want. Could you please advise us in how to set these parameters? Thank you in advance. Best regards, Laura Dekkers -- Laura M.S. Dekkers, MSc Research assistant University of Amsterdam - Department of Developmental Psychology Weesperplein 4 1018 XA Amsterdam - The Netherlands E-mail: lmsdekk...@gmail.com mailto:lmsdekk...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Laura M.S. Dekkers, MSc Research assistant University of Amsterdam - Department of Developmental Psychology Weesperplein 4 1018 XA Amsterdam - The Netherlands E-mail: lmsdekk...@gmail.com Test2 --ntp 255 --tr 2.0 --tprescan 4.0 --psdwin 0.0 16.0 1.0 --ev Gain2 5.0 8.0 --ev Gain4 5.0 8.0 --ev Gain6 5.0 8.0 --ev Gain8 5.0 8.0 --ev Loss2 5.0 8.0 --ev Loss4 5.0 8.0 --ev Loss6 5.0 8.0 --ev Loss8 5.0 8.0 --ev Catch 5.0 8.0 --tnullmin 0.0 --tnullmax 6.0 --tsearch .25 -focb 10 -ar1 .37 --evc 1 1 1 1 -1 -1 -1 -1 0 --evc -1.5 -.5 .5 1.5 -1.5 -.5 .5 1.5 0 --evc -1.5 -.5 .5 1.5 1.5 .5 -.5 -1.5 0 --cost eff --nkeep 3 --o output_test2 Test3 --ntp 255 --tr 2.0 --tprescan 4.0 --psdwin 0.0 16.0 1.0 --ev Gain2 4.0 8.0 --ev Gain4 4.0 8.0 --ev Gain6 4.0 8.0 --ev Gain8 4.0 8.0 --ev Loss2 4.0 8.0 --ev Loss4 4.0 8.0 --ev Loss6 4.0 8.0 --ev Loss8 4.0 8.0 --ev Catch 4.0 8.0 --tnullmin 1.0 --tnullmax 6.0 --tsearch .25 -focb 10 -ar1 .37 --evc 1 1 1 1 -1 -1 -1 -1 0 --evc -1.5 -.5 .5 1.5 -1.5 -.5 .5 1.5 0 --evc -1.5 -.5 .5 1.5 1.5 .5 -.5 -1.5 0 --cost eff --nkeep 3 --o output_test3 Test4 --ntp 180 --tr 2.0 --tprescan 4.0 --psdwin 0.0 16.0 1.0 --ev Gain2 4.0 8.0 --ev Gain4 4.0 8.0 --ev Gain6 4.0 8.0 --ev Gain8 4.0 8.0 --ev Loss2 4.0 8.0 --ev Loss4 4.0 8.0 --ev Loss6 4.0 8.0 --ev Loss8 4.0 8.0 --ev Catch 4.0 8.0 --tnullmin 1.0 --tnullmax 6.0
[Freesurfer] R: Re: R: Re: mris resample: Command not found. This error is permanent after new patch download
Ok, now I think that I have downloaded the correct file. I try to rerun trac-all -prep and at the end I'll send you a feedback. Thanks, Stefano Messaggio originale Da: zkauf...@nmr.mgh.harvard.edu Data: 7-giu-2013 18.18 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: mris resample: Command not found. This error is permanent after new patch download I dont know why your getting a file named unknown. If you click this link you should be able to download a file called mris_resample: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/ Download it and place it in $FREESURFER_HOME/bin (Usually Applications/freesurfer/bin on Macs). Then make it executable by typing chmod +x Applications/freesurfer/bin/mris_resample on the command line. -Zeke If you go this this link On 06/07/2013 12:09 PM, std...@virgilio.it wrote: Hi Zeke, thank you very much. I have download a file that named unknown. I should rename it as mris_resample? Stefano Messaggio originale Da: zkauf...@nmr.mgh.harvard.edu Data: 7-giu-2013 18.02 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] mris resample: Command not found. This error is permanent after new patch download Stefano, step 4 should be: chmod +x $FREESURFER_HOME/bin/mris_resample When you do an ls -l in the $FREESURFER_HOME/bin directory, you need to see the to see the x's next to mris_resample just like you do with all the other files in that directory. -Zeke On 06/07/2013 11:49 AM, std...@virgilio.it wrote: Hi list, during trac-all -prep I have this error: MRISregister() return, current seed 0 writing registered surface to /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg... expanding nbhd size to 1 mris_resample: Command not found. Darwin iMac I have performed my analysis by the following steps (as recommended by Zeke and Lilla): 1. download unKnow file (7.6 MB) at ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample 2. put file in $FREESURFER/bin/ 4. chmod +x ~/mris_resample as recommended by Daniel (in the first test I did not use this command) 5. start trac-all -prep 6. ERROR (in inter-reg step) What's happen? Thank you very much, Stefano ___ 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 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] AR2 Error
Hi Doug-- Running: recon-all -s freesurfer -autorecon2 -autorecon3 produced the same error. Could you send me the new version of the program? Thanks! Erin Browning On Thu, Jun 6, 2013 at 3:01 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: OK, this is a known problem when running recon-all with -autorecon1 -autorecon2 but not autorecon3. If you run it with -autorecon3, then it should run all the way through without a problem. Alternatively, I can give you a new version of the offending program (mri_segstats) that will allow you to use just ar1 and ar2. doug On 06/06/2013 03:46 PM, Erin Browning wrote: Here is the log file. http://gate.nmr.mgh.harvard.edu/filedrop2/?p=zrh2oi9 Thank you! On Thu, Jun 6, 2013 at 2:43 PM, Erin Browning brown...@uwm.edu mailto:brown...@uwm.edu wrote: Yes, it was. I tried copy and pasting it and just attaching the log file. Can I paste urls here? I'll just upload it to pastebin or something like that. On Thu, Jun 6, 2013 at 2:38 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: That's weird, people upload their recon-all.log files all the time. Was the email kicked back to you? On 06/06/2013 03:27 PM, Erin Browning wrote: The log file for recon-all is too large. How should I send it? On Thu, Jun 6, 2013 at 1:48 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Erin, thanks for reposting. Can you post the recon-all.log file? doug On 06/06/2013 02:37 PM, Erin Browning wrote: Hi everyone-- I emailed the other day about hyperintensity after running motioncor. We've skipped motioncor in our processing now, but we keep getting this error while running AR2. \n mri_ca_register -invert-and-save transforms/talairach.m3z \n mri passed volume size is different from the one used to create M3D data Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z gunzip -c transforms/talairach.m3z Inverting GCAM ERROR: mri_ca_register with non-zero status 0 Darwin cerebrum.uwm.edu http://cerebrum.uwm.edu http://cerebrum.uwm.edu http://cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 recon-all -s freesurfer exited with ERRORS at Wed Jun 5 19:32:56 CDT 2013 I tried rerunning recon-all -s freesurfer -talairach before running AR2, and that didn't fix the error. What's going wrong? Thanks, Erin Browning ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] AR2 Error
Could it be that since we skip motioncor, we skip the mri_add_xform_to_header program as well? Should I be running that separately? Thanks, Erin Browning On Fri, Jun 7, 2013 at 11:54 AM, Erin Browning brown...@uwm.edu wrote: Hi Doug-- Running: recon-all -s freesurfer -autorecon2 -autorecon3 produced the same error. Could you send me the new version of the program? Thanks! Erin Browning On Thu, Jun 6, 2013 at 3:01 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: OK, this is a known problem when running recon-all with -autorecon1 -autorecon2 but not autorecon3. If you run it with -autorecon3, then it should run all the way through without a problem. Alternatively, I can give you a new version of the offending program (mri_segstats) that will allow you to use just ar1 and ar2. doug On 06/06/2013 03:46 PM, Erin Browning wrote: Here is the log file. http://gate.nmr.mgh.harvard.edu/filedrop2/?p=zrh2oi9 Thank you! On Thu, Jun 6, 2013 at 2:43 PM, Erin Browning brown...@uwm.edu mailto:brown...@uwm.edu wrote: Yes, it was. I tried copy and pasting it and just attaching the log file. Can I paste urls here? I'll just upload it to pastebin or something like that. On Thu, Jun 6, 2013 at 2:38 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: That's weird, people upload their recon-all.log files all the time. Was the email kicked back to you? On 06/06/2013 03:27 PM, Erin Browning wrote: The log file for recon-all is too large. How should I send it? On Thu, Jun 6, 2013 at 1:48 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Erin, thanks for reposting. Can you post the recon-all.log file? doug On 06/06/2013 02:37 PM, Erin Browning wrote: Hi everyone-- I emailed the other day about hyperintensity after running motioncor. We've skipped motioncor in our processing now, but we keep getting this error while running AR2. \n mri_ca_register -invert-and-save transforms/talairach.m3z \n mri passed volume size is different from the one used to create M3D data Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z gunzip -c transforms/talairach.m3z Inverting GCAM ERROR: mri_ca_register with non-zero status 0 Darwin cerebrum.uwm.edu http://cerebrum.uwm.edu http://cerebrum.uwm.edu http://cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 recon-all -s freesurfer exited with ERRORS at Wed Jun 5 19:32:56 CDT 2013 I tried rerunning recon-all -s freesurfer -talairach before running AR2, and that didn't fix the error. What's going wrong? Thanks, Erin Browning ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] Xhemi question
Hi Daria, the only way is to map the individual curvature to the group space (fsaverage_sym) and see if the curvatures seem to align. doug ps. Please post questions to the FreeSurfer list. Thanks! On 06/07/2013 11:13 AM, Daria Boratyn wrote: Hi Doug, We are experimenting with adding xhemi to our processing stream. Is there is a way to QC the results at an individual subject level? Best, Daria Daria A. Boratyn, Clinical Research Coordinator MS Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FS-FAST - ERROR: mapping surfaces
Hi Ronny, there is a dimension mismatch which usually means that the surfaces for that subject are out of synch, ie, it has not been run through to the end. This often happens when a subject is run all the way through, then edited and re-run but the re-run only runs autorecon1 and autorecon2 but not autorecon3. Try running recon-all -make all -s subj007. You can also just check if the subject is out of synch with vno_match_check subj007 doug On 06/07/2013 11:03 AM, preci...@nmr.mgh.harvard.edu wrote: I am having an issue when running the preprocess script in fs-fast. It failed once and I tried something and ran the script again and it failed the same way. The command I ran is: preproc-sess -s subj007 -fsd bold -stc siemens -surface fsaverage lhrh -mni305 -fwhm 5 -per-run Below is the part where the error appears to occur, but the full log is attached. Any help would be appreciated. -Ronny 1/1 subj007 1/1 subj007 008 lh - Fri Jun 7 10:50:50 EDT 2013 mri_vol2surf --mov /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/masks/brain.nii.gz --reg /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/register.dof6.dat --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/masks/brain.fsaverage.lh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/masks/brain.nii.gz srcreg = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.cortex.label Reading surface /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.white Done reading source surface Reading thickness /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 19272 Reading source surface registration /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.sphere.reg Done loading source registration surface surf2surf_nnfr(): Vals and Reg dimension mismatch nVals = 157755, nReg 157894 Reading target registration /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (subj007 - fsaverage) ERROR: mapping surfaces ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FS-FAST - ERROR: mapping surfaces
Thanks Doug, I did make some manual edits to wm.mgz and brainmask.mgz then reran the subject a couple times using: recon-all -autorecon2-wm -subjid subj007 Shouldn't -autorecon2-wm run through -autorecon2 and -autorecon3? Will running 'recon-all -make all -s subj007' do away with my manual edits? -Ronny Hi Ronny, there is a dimension mismatch which usually means that the surfaces for that subject are out of synch, ie, it has not been run through to the end. This often happens when a subject is run all the way through, then edited and re-run but the re-run only runs autorecon1 and autorecon2 but not autorecon3. Try running recon-all -make all -s subj007. You can also just check if the subject is out of synch with vno_match_check subj007 doug On 06/07/2013 11:03 AM, preci...@nmr.mgh.harvard.edu wrote: I am having an issue when running the preprocess script in fs-fast. It failed once and I tried something and ran the script again and it failed the same way. The command I ran is: preproc-sess -s subj007 -fsd bold -stc siemens -surface fsaverage lhrh -mni305 -fwhm 5 -per-run Below is the part where the error appears to occur, but the full log is attached. Any help would be appreciated. -Ronny 1/1 subj007 1/1 subj007 008 lh - Fri Jun 7 10:50:50 EDT 2013 mri_vol2surf --mov /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/masks/brain.nii.gz --reg /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/register.dof6.dat --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/masks/brain.fsaverage.lh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/masks/brain.nii.gz srcreg = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.cortex.label Reading surface /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.white Done reading source surface Reading thickness /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 19272 Reading source surface registration /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.sphere.reg Done loading source registration surface surf2surf_nnfr(): Vals and Reg dimension mismatch nVals = 157755, nReg 157894 Reading target registration /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (subj007 - fsaverage) ERROR: mapping surfaces ___ 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 ___ 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] FS-FAST - ERROR: mapping surfaces
On 06/07/2013 02:24 PM, preci...@nmr.mgh.harvard.edu wrote: Thanks Doug, I did make some manual edits to wm.mgz and brainmask.mgz then reran the subject a couple times using: recon-all -autorecon2-wm -subjid subj007 Shouldn't -autorecon2-wm run through -autorecon2 and -autorecon3? No, you have to add -autorecon3 to run autorecon3 Will running 'recon-all -make all -s subj007' do away with my manual edits? No, FS never deletes manual edits unless you explicitly tell it to. Running -make all tells it to update things that need to be based on modification dates on the file. doug -Ronny Hi Ronny, there is a dimension mismatch which usually means that the surfaces for that subject are out of synch, ie, it has not been run through to the end. This often happens when a subject is run all the way through, then edited and re-run but the re-run only runs autorecon1 and autorecon2 but not autorecon3. Try running recon-all -make all -s subj007. You can also just check if the subject is out of synch with vno_match_check subj007 doug On 06/07/2013 11:03 AM, preci...@nmr.mgh.harvard.edu wrote: I am having an issue when running the preprocess script in fs-fast. It failed once and I tried something and ran the script again and it failed the same way. The command I ran is: preproc-sess -s subj007 -fsd bold -stc siemens -surface fsaverage lhrh -mni305 -fwhm 5 -per-run Below is the part where the error appears to occur, but the full log is attached. Any help would be appreciated. -Ronny 1/1 subj007 1/1 subj007 008 lh - Fri Jun 7 10:50:50 EDT 2013 mri_vol2surf --mov /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/masks/brain.nii.gz --reg /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/register.dof6.dat --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/masks/brain.fsaverage.lh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/masks/brain.nii.gz srcreg = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.cortex.label Reading surface /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.white Done reading source surface Reading thickness /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 19272 Reading source surface registration /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.sphere.reg Done loading source registration surface surf2surf_nnfr(): Vals and Reg dimension mismatch nVals = 157755, nReg 157894 Reading target registration /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (subj007 - fsaverage) ERROR: mapping surfaces ___ 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 ___ 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
Re: [Freesurfer] FS-FAST - ERROR: mapping surfaces
Hi Ronny you should have run recon-all -autorecon2-wm -subjid subj007 -autorecon3 at this point you should be fine running -make all. It should retain all your manual edits cheers Bruce On Fri, 7 Jun 2013, preci...@nmr.mgh.harvard.edu wrote: Thanks Doug, I did make some manual edits to wm.mgz and brainmask.mgz then reran the subject a couple times using: recon-all -autorecon2-wm -subjid subj007 Shouldn't -autorecon2-wm run through -autorecon2 and -autorecon3? Will running 'recon-all -make all -s subj007' do away with my manual edits? -Ronny Hi Ronny, there is a dimension mismatch which usually means that the surfaces for that subject are out of synch, ie, it has not been run through to the end. This often happens when a subject is run all the way through, then edited and re-run but the re-run only runs autorecon1 and autorecon2 but not autorecon3. Try running recon-all -make all -s subj007. You can also just check if the subject is out of synch with vno_match_check subj007 doug On 06/07/2013 11:03 AM, preci...@nmr.mgh.harvard.edu wrote: I am having an issue when running the preprocess script in fs-fast. It failed once and I tried something and ran the script again and it failed the same way. The command I ran is: preproc-sess -s subj007 -fsd bold -stc siemens -surface fsaverage lhrh -mni305 -fwhm 5 -per-run Below is the part where the error appears to occur, but the full log is attached. Any help would be appreciated. -Ronny 1/1 subj007 1/1 subj007 008 lh - Fri Jun 7 10:50:50 EDT 2013 mri_vol2surf --mov /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/masks/brain.nii.gz --reg /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/register.dof6.dat --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/masks/brain.fsaverage.lh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/masks/brain.nii.gz srcreg = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.cortex.label Reading surface /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.white Done reading source surface Reading thickness /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 19272 Reading source surface registration /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.sphere.reg Done loading source registration surface surf2surf_nnfr(): Vals and Reg dimension mismatch nVals = 157755, nReg 157894 Reading target registration /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (subj007 - fsaverage) ERROR: mapping surfaces ___ 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 ___ 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] subfield algorithm and subject intensity differences
I'm trying to understand Leemput's subfield algorithm better as implemented in Freesurfer. Does the algorithm make use of intensity differences in the internal hippocampal lamina from the subject's T1 image to warp meshes and assign subfield probabilities? Or does it depend only on outward boundaries of the hippocampus and probability priors to determine the inner boundaries between CAs and dentate gyrus? - Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] subfield algorithm and subject intensity differences
Hi Josh it depends on intensity differences if it can find them as well as boundary/geometry. cheers Bruce On Fri, 7 Jun 2013, Joshua Lee wrote: I'm trying to understand Leemput's subfield algorithm better as implemented in Freesurfer. Does the algorithm make use of intensity differences in the internal hippocampal lamina from the subject's T1 image to warp meshes and assign subfield probabilities? Or does it depend only on outward boundaries of the hippocampus and probability priors to determine the inner boundaries between CAs and dentate gyrus? - Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] subfield algorithm and subject intensity differences
Dear Josh, at this point, and given that the boundaries between these subfields cannot really be seen in 1mm T1 scans, the algorithm assumes that all the subfields other than fimbria and fissure share the same image intensity properties. Therefore, using your own words: depend only on outward boundaries of the hippocampus and probability priors to determine the inner boundaries between CAs and dentate gyrus Cheers, /Eugenio - Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] subfield algorithm and subject intensity differences
Thanks Bruce and Eugenio, Suppose I had two identical images of a subject, but in one image I reduced the contrast of internal lamina while leaving the rest of the image intact...just removing internal intensity differences, but leaving the outer boundary contrast intact. Would the images result in very different subfield segmentations? Josh - Joshua Lee Graduate Student Center for Mind and Brain Department of Psychology University of California, Davis 530.747.3805 On Fri, Jun 7, 2013 at 12:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Josh it depends on intensity differences if it can find them as well as boundary/geometry. cheers Bruce On Fri, 7 Jun 2013, Joshua Lee wrote: I'm trying to understand Leemput's subfield algorithm better as implemented in Freesurfer. Does the algorithm make use of intensity differences in the internal hippocampal lamina from the subject's T1 image to warp meshes and assign subfield probabilities? Or does it depend only on outward boundaries of the hippocampus and probability priors to determine the inner boundaries between CAs and dentate gyrus? - Josh 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] Hypointense lesions
Hi FreeSurfer Community, I was wondering whether there is an automatic tool that outlines the hypointense lesions in a SWI scan. Thank you, Panos ___ 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] AR2 Error
you need to include the -autorecon3 flag simultaneously with the -autorecon1 and -autorecon2 flags. On 06/07/2013 05:45 PM, Erin Browning wrote: It fails before ar3 runs. On Jun 7, 2013 2:54 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: There is no indication in this log file that you ran autorecon3 doug On 06/07/2013 02:51 PM, Erin Browning wrote: Here's the log. I ran mri_add_xform_to_header after it failed again last time and am currently rerunning AR2+3 on it, so you can probably ignore the latest modifications to it. http://gate.nmr.mgh.harvard.edu/filedrop2/?p=iowkgmv We're running Mac OSX 10.6.8. Thanks, Erin On Fri, Jun 7, 2013 at 12:22 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hmmm, I don't know. I think that something strange is happening. Can you send me the new recon-all.log file? Also, tell me what platform you are using and I'll send you a new version of mri_segstats doug On 06/07/2013 01:14 PM, Erin Browning wrote: Could it be that since we skip motioncor, we skip the mri_add_xform_to_header program as well? Should I be running that separately? Thanks, Erin Browning On Fri, Jun 7, 2013 at 11:54 AM, Erin Browning brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu wrote: Hi Doug-- Running: recon-all -s freesurfer -autorecon2 -autorecon3 produced the same error. Could you send me the new version of the program? Thanks! Erin Browning On Thu, Jun 6, 2013 at 3:01 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: OK, this is a known problem when running recon-all with -autorecon1 -autorecon2 but not autorecon3. If you run it with -autorecon3, then it should run all the way through without a problem. Alternatively, I can give you a new version of the offending program (mri_segstats) that will allow you to use just ar1 and ar2. doug On 06/06/2013 03:46 PM, Erin Browning wrote: Here is the log file. http://gate.nmr.mgh.harvard.edu/filedrop2/?p=zrh2oi9 Thank you! On Thu, Jun 6, 2013 at 2:43 PM, Erin Browning brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu wrote: Yes, it was. I tried copy and pasting it and just attaching the log file. Can I paste urls here? I'll just upload it to pastebin or something like that. On Thu, Jun 6, 2013 at 2:38 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
[Freesurfer] environment variable FREESURFER_HOME
Can anyone advice me on how to set the environment variable FREESURFER_HOME for installing it in OS X 10.6.8 (with XQuartz installed)? My directory for Freesurfer: /Applications/freesurfer I know I also have to add: setenv FREESURFER_HOME /Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.cshBut I am not sure where exactly I should add these lines. Do I need to edit the .csh file in Freesurfer. How should I do this? using Text Edit from apple would work?Thanks,Pablo ___ 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] AR2 Error
The recon-all.log fail indicates that you did not use the -autorecon3 flag. In any event, I'm trying to get you a new version of mri_segstats, but it looks like our snowleopard build has not gone through since I made the change. I'll try again over the weekend or on Monday. doug On 06/07/2013 06:01 PM, Erin Browning wrote: The last thing I ran was recon-all -s freesurfer -autorecon2 -autorecon3 Which still failed. We quality check after ar1, so we need to run ar1 separately from ar2 and 3. On Jun 7, 2013 4:53 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: you need to include the -autorecon3 flag simultaneously with the -autorecon1 and -autorecon2 flags. On 06/07/2013 05:45 PM, Erin Browning wrote: It fails before ar3 runs. On Jun 7, 2013 2:54 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: There is no indication in this log file that you ran autorecon3 doug On 06/07/2013 02:51 PM, Erin Browning wrote: Here's the log. I ran mri_add_xform_to_header after it failed again last time and am currently rerunning AR2+3 on it, so you can probably ignore the latest modifications to it. http://gate.nmr.mgh.harvard.edu/filedrop2/?p=iowkgmv We're running Mac OSX 10.6.8. Thanks, Erin On Fri, Jun 7, 2013 at 12:22 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hmmm, I don't know. I think that something strange is happening. Can you send me the new recon-all.log file? Also, tell me what platform you are using and I'll send you a new version of mri_segstats doug On 06/07/2013 01:14 PM, Erin Browning wrote: Could it be that since we skip motioncor, we skip the mri_add_xform_to_header program as well? Should I be running that separately? Thanks, Erin Browning On Fri, Jun 7, 2013 at 11:54 AM, Erin Browning brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu wrote: Hi Doug-- Running: recon-all -s freesurfer -autorecon2 -autorecon3 produced the same error. Could you send me the new version of the program? Thanks! Erin Browning On Thu, Jun 6, 2013 at 3:01 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: OK, this is a known problem when running recon-all with -autorecon1
Re: [Freesurfer] environment variable FREESURFER_HOME
There should be a file called .cshrc in your home directory. Add the two lines to that file. -Zeke On 06/07/2013 05:53 PM, pablo najt wrote: Can anyone advice me on how to set the environment variable FREESURFER_HOME for installing it in OS X 10.6.8 (with XQuartz installed)? My directory for Freesurfer:*/Applications/freesurfer* * * I know I also have to add: setenv FREESURFER_HOME /Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh But I am not sure where exactly I should add these lines. Do I need to edit the .csh file in Freesurfer. How should I do this? using Text Edit from apple would work? Thanks, Pablo ___ 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] Installation trouble on Macbook Air (no such file or directory)
I am new to Unix and FreeSurfer, and I am having some trouble installing FreeSurfer on my Macbook Air (10.8). I've downloaded the .dmg file just fine, and when I start the installation steps, I'm instructed to add some lines to my .cshrc or .tcshrc files in my home directory. Can anyone point me to this file? Also, just below on the installation dialog, it says for sh or bash users: export FREESURFER_HOME=freesurfer_installation_directory/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh Can I use these instead of the first two lines of code? I tried to enter these bash lines one at a time into my terminal window. The first one (export) did not give me any errors but for the source one, I received the message: bash: /freesurfer/SetUpFreeSurfer.sh: No such file or directory. Any idea as to why I am getting this error? My apologies in advance for my lack of experience. Many thanks, Nate ___ 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.
