Re: [Freesurfer] Script to get recon processing time
no, but if you add the flag -time to recon-all, you will get lines like this in the recon-all.log: time:: 0:11.49 cmd:: mris_anatomical_stats where you can grep on 'time::' to get command run times, although you'd have to add together some commands to get times for a stage. note: runtimes can vary quite a bit, some subjects take a lot longer to correct than others, and the newer intel nehalem architecture runs in less than half the time as the older amd opteron and p4s. n On Wed, 2010-07-28 at 17:19 -0400, Chris Watson wrote: Hello, Do you guys have a script that parses recon-all.log and spits out the processing time for each step? Something that would be similar to this in recon-all --help: -nomotioncor 5 min -nonuintensitycor 3 min -notalairach 4 min -nonormalization 3 min -noskullstrip 1 min -nogcareg 8 min -nocanorm 1 min -nocareg 10 hours and so on. Thanks, Chris ___ 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] recon-all error
you will need to get a fixed version of mri_ca_label from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc n. On Wed, 2010-07-28 at 22:40 -0400, Watson, Christopher wrote: I was running a subject, and got this error: recon-all exited with ERRORS at Wed Jul 28 21:50:47 EDT 2010 make: *** [/usr/local/freesurfer/freesurfer-4.5.0/subjects/zhang_r/mri/aseg.mgz] Error 1 The disk is not full, and permissions are in order. I've run several other subjects with no problems. Initially my command line was recon-all -autorecon2 -s zhang_r; then I tried again except with -make autorecon2, and saw the same error. It exits at SubCort Seg (mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/freesurfer/current/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz) The last several lines of output are: mri_ca_label GCA sequential renormalization: label 28 not consistently computed. not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.01 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux cwatson.homeunix.net 2.6.18-194.3.1.el5.centos.plus #1 SMP Wed May 19 09:14:46 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux Any ideas? Chris ___ 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] Script to get recon processing time
fyi, attached is the grep time:: output from a recent run (which took 27.5 hours). this should at least spare you from having to run recon-all -time yourself. it was run on a 2GHz amd opteron. n. On Thu, 2010-07-29 at 11:38 -0400, Nick Schmansky wrote: no, but if you add the flag -time to recon-all, you will get lines like this in the recon-all.log: time:: 0:11.49 cmd:: mris_anatomical_stats where you can grep on 'time::' to get command run times, although you'd have to add together some commands to get times for a stage. note: runtimes can vary quite a bit, some subjects take a lot longer to correct than others, and the newer intel nehalem architecture runs in less than half the time as the older amd opteron and p4s. n On Wed, 2010-07-28 at 17:19 -0400, Chris Watson wrote: Hello, Do you guys have a script that parses recon-all.log and spits out the processing time for each step? Something that would be similar to this in recon-all --help: -nomotioncor 5 min -nonuintensitycor 3 min -notalairach 4 min -nonormalization 3 min -noskullstrip 1 min -nogcareg 8 min -nocanorm 1 min -nocareg 10 hours and so on. Thanks, Chris ___ 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 time:: 0:05.93 cmd:: mri_convert time:: 0:05.93 cmd:: mri_convert time:: 0:10.52 cmd:: mri_convert time:: 0:03.88 cmd:: mri_add_xform_to_header time:: 2:41.60 cmd:: mri_nu_correct.mni time:: 1:26.74 cmd:: talairach_avi time:: 0:00.28 cmd:: talairach_afd time:: 5:26.60 cmd:: mri_normalize time:: 1:02:34 cmd:: mri_em_register time:: 2:10.99 cmd:: mri_watershed time:: 1:11.88 cmd:: mri_gcut time:: 53:11.75 cmd:: mri_em_register time:: 4:00.77 cmd:: mri_ca_normalize time:: 9:15:42 cmd:: mri_ca_register time:: 2:26.80 cmd:: mri_ca_register time:: 2:41.19 cmd:: mri_remove_neck time:: 49:59.14 cmd:: mri_em_register time:: 42:13.88 cmd:: mri_ca_label time:: 1:29.74 cmd:: mri_cc time:: 8:22.76 cmd:: mri_normalize time:: 0:06.26 cmd:: mri_mask time:: 2:15.52 cmd:: mri_segment time:: 1:08.39 cmd:: mri_edit_wm_with_aseg time:: 0:14.25 cmd:: mri_pretess time:: 1:47.44 cmd:: mri_fill time:: 0:07.82 cmd:: mri_pretess time:: 0:06.26 cmd:: mri_tessellate time:: 0:05.53 cmd:: mris_extract_main_component time:: 0:08.82 cmd:: mris_smooth time:: 1:32.37 cmd:: mris_inflate time:: 11:54.58 cmd:: mris_sphere time:: 32:29.24 cmd:: mris_fix_topology time:: 0:06.86 cmd:: mris_remove_intersection time:: 27:53.18 cmd:: mris_make_surfaces time:: 0:00.17 cmd:: mris_calc time:: 0:00.07 cmd:: mris_calc time:: 0:00.10 cmd:: mris_calc time:: 0:08.37 cmd:: mris_smooth time:: 1:44.29 cmd:: mris_inflate time:: 2:53.10 cmd:: mris_curvature time:: 0:12.38 cmd:: mris_curvature_stats time:: 2:59:01 cmd:: mris_sphere time:: 1:42:58 cmd:: mris_register time:: 0:04.70 cmd:: mris_jacobian time:: 0:03.92 cmd:: mrisp_paint time:: 2:34.75 cmd:: mris_ca_label time:: 1:33.53 cmd:: mris_anatomical_stats time:: 2:49.94 cmd:: mris_ca_label time:: 1:54.05 cmd:: mris_anatomical_stats time:: 0:09.09 cmd:: mri_pretess time:: 0:06.06 cmd:: mri_tessellate time:: 0:05.07 cmd:: mris_extract_main_component time:: 0:08.84 cmd:: mris_smooth time:: 1:41.04 cmd:: mris_inflate time:: 11:16.03 cmd:: mris_sphere time:: 43:49.82 cmd:: mris_fix_topology time:: 0:08.65 cmd:: mris_remove_intersection time:: 27:23.40 cmd:: mris_make_surfaces time:: 0:00.43 cmd:: mris_calc time:: 0:00.07 cmd:: mris_calc time:: 0:00.10 cmd:: mris_calc time:: 0:08.76 cmd:: mris_smooth time:: 1:21.45 cmd:: mris_inflate time:: 2:51.19 cmd:: mris_curvature time:: 0:12.80 cmd:: mris_curvature_stats time:: 2:10:09 cmd:: mris_sphere time:: 1:48:06 cmd:: mris_register time:: 0:04.58 cmd:: mris_jacobian time:: 0:04.08 cmd:: mrisp_paint time:: 2:34.42 cmd:: mris_ca_label time:: 1:54.71 cmd:: mris_anatomical_stats time:: 2:50.40 cmd:: mris_ca_label time:: 2:04.81 cmd:: mris_anatomical_stats time:: 34:49.65 cmd:: mris_volmask time:: 18:39.54 cmd:: mri_segstats time:: 7:07.57 cmd:: mri_aparc2aseg time:: 7:02.38 cmd:: mri_aparc2aseg time:: 16:53.63 cmd:: mri_aparc2aseg time:: 28:07.75 cmd:: mri_segstats time:: 0:00.02 cmd:: ln time:: 0:18.98 cmd:: mri_label2label time:: 0:22.28 cmd:: mri_label2label time:: 0:18.37 cmd:: mri_label2label time:: 0:20.10 cmd:: mri_label2label time:: 0:19.96 cmd:: mri_label2label time:: 0:18.64 cmd:: mri_label2label time:: 0:29.49 cmd:: mri_label2label time:: 0:18.81 cmd:: mri_label2label time:: 0:17.79 cmd:: mri_label2label time:: 0:19.80 cmd:: mri_label2label time:: 0:23.95 cmd:: mri_label2label time:: 0:16.81 cmd:: mri_label2label time:: 0:03.92 cmd:: mris_label2annot
[Freesurfer] Overlay Thickness Files in tkmedit
Hi, is there a way to visualize the lh.thickness or rh.thickness files as an overlay in tkmedit. Thanks, Michael ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all error
Thanks, that did the trick. Chris Nick Schmansky wrote: you will need to get a fixed version of mri_ca_label from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc n. On Wed, 2010-07-28 at 22:40 -0400, Watson, Christopher wrote: I was running a subject, and got this error: recon-all exited with ERRORS at Wed Jul 28 21:50:47 EDT 2010 make: *** [/usr/local/freesurfer/freesurfer-4.5.0/subjects/zhang_r/mri/aseg.mgz] Error 1 The disk is not full, and permissions are in order. I've run several other subjects with no problems. Initially my command line was recon-all -autorecon2 -s zhang_r; then I tried again except with -make autorecon2, and saw the same error. It exits at SubCort Seg (mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/freesurfer/current/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz) The last several lines of output are: mri_ca_label GCA sequential renormalization: label 28 not consistently computed. not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.01 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux cwatson.homeunix.net 2.6.18-194.3.1.el5.centos.plus #1 SMP Wed May 19 09:14:46 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux Any ideas? Chris ___ 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] skull strip
I have a question regarding the skull stripping process. I ran my data through recon-all but still had much skull intact. I then followed the recommended process per the freesurfer wiki to change the watershed threshold levels on the recon process. I did so at the 20, 15, 10, 5, and 0 threshold with little improvement to the amount of skull removed. I know a similar question has been asked but in that scenario freesurfer was not including the skull as part of the cortical matter while in my scenario it is. Do you have any further suggestions as to how to remove the skull from my images? Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Overlay Thickness Files in tkmedit
you could sample it into the volume then visualize that I guess. On Thu, 29 Jul 2010, Michael Scheel wrote: Hi, is there a way to visualize the lh.thickness or rh.thickness files as an overlay in tkmedit. Thanks, Michael ___ 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] monkey brain recon outputs
Hi Ali, On Jul 27, 2010, at 12:00 PM, Arslan, Ali wrote: Hi, I finished reconstructing a monkey's surface following the scripts on the wiki. The output surfaces seems to be a bit distorted and rough around the edges. This reconstruction is done with a volume normalized by using ~400 white matter control points. The resolution of the scan is 1x1x1 mm. Here are some pictures to look at: http://www.flickr.com/photos/52445...@n05/sets/72157624471174691/ Are those real 1.0 mm isotropic volumes or 0.5 mm isotropic volumes faked to appear 1.0 mm isotropic? Interestingly, white matter and gray matter boundaries seem to be intermingled for some reason. I was hoping control points would take care of that problem but they didn't. This can be observed by the 2 vol_surf images in the set. Can you post screen shots of the brain.final.mgz and brain.mgz? The most obvious defects can be seen on the white matter. There are small protrusions over the gyri, and the surfaces are generally very rough, unlike a successful human reconstruction. It pretty much looks like the segmentation in white and gray matter failed badly for the final surface. Also notice how the initial segmentation (wm.mgz) that produces the green line actually traces somewhere in between the white and gray matter boundary? It pretty much looks like the normalization of your images is not helpful for freesurfer. Alas, I have no real help to offer right now (I am struggling with similar issues tight now). In case I find a work around I might post a fresh set of processing scripts... I was wondering if you have any ideas as to the source of the problem. Skull stripping was done with FSL's bet, and it looks successful. Can it be a problem with intensity normalization? I agree, the normalization does not really work out. I have no solution to offer right now. Well, except to have visually inspect the rawavg.mgz see whether you think there is enough dynamic contrast inthere that you could trace the white/gray matter boundary by hand. If yes, it should be possibly to convince freesurfer to do it for you. If not then you will need new scans. Best Sebastian Regards, Ali Arslan ___ 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. -- Sebastian Moeller telephone: 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 moel...@caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkmedit scripting question
Hi Sebastian I was able to manipulate the dialogue like this %set gEditBrush(1,cloneSource) 1 %set gEditBrush(1,mode) 1 Try a combination of 0 or 1 for the last argument. And spaces ( or lack of them ) are absolutely important. Don't leave any space in gEditBrush(1,mode) The first argument of gEditBrush denotes the brush. 0 means Brush 2 and 1 means Brush 3. Let us know if it works -Krish On Jul 28, 2010, at 3:22 PM, Sebastian Moeller wrote: Aloha fellow surfers, I am trying to script a few steps of my freesurfer pipeline. At the moment I am facing the problem that all my brainmasks need some manual intervention. Following advice from the wiki I try to set up tkmedit to clone from the aux to the main volume on the pressing button 3. Now my question how do I configure Button 3 from a tcl script so that my users do not have to do this manually every time? I would expect something like SetBrushInfo that takes more arguments than just brush, low, high, new, but my tcl-foo is very weak. If someone has a pointer how to set Button 3 to clone from aux vol I would be happy to hear it. Thanks in advance. Best Sebastian -- Sebastian Moeller telephone: 626-395-6713 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 moel...@caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA ___ 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] [fsfast]: temporal overlap of stimuli and concurrent presentation
Dear fellow Surfers, is it possible to model several independent event streams for fs-fast? That is, using the 5 column paradigm file, is it okay to have different condition ID codes that have identical stimulus onset time (well only some of the time)? Or would I have to model that by specifying a TER and have both staggered around the real onset time? I would be happy to receive any pointer. Thanks in advance best regards Sebastian -- Sebastian Moeller telephone: 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 moel...@caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA ___ 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] tkmedit scripting question
Hi Krish, thanks a lot. Unfortunately that only sets the values for the dialog but does not actually activate them. I will try my luck, now that you showed me how to set more involved tcl structures :). I will report back (once our computer system works again). Best Sebastian On Jul 29, 2010, at 2:21 PM, Krish Subramaniam wrote: Hi Sebastian I was able to manipulate the dialogue like this %set gEditBrush(1,cloneSource) 1 %set gEditBrush(1,mode) 1 Try a combination of 0 or 1 for the last argument. And spaces ( or lack of them ) are absolutely important. Don't leave any space in gEditBrush(1,mode) The first argument of gEditBrush denotes the brush. 0 means Brush 2 and 1 means Brush 3. Let us know if it works -Krish On Jul 28, 2010, at 3:22 PM, Sebastian Moeller wrote: Aloha fellow surfers, I am trying to script a few steps of my freesurfer pipeline. At the moment I am facing the problem that all my brainmasks need some manual intervention. Following advice from the wiki I try to set up tkmedit to clone from the aux to the main volume on the pressing button 3. Now my question how do I configure Button 3 from a tcl script so that my users do not have to do this manually every time? I would expect something like SetBrushInfo that takes more arguments than just brush, low, high, new, but my tcl-foo is very weak. If someone has a pointer how to set Button 3 to clone from aux vol I would be happy to hear it. Thanks in advance. Best Sebastian -- Sebastian Moeller telephone: 626-395-6713 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 moel...@caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA ___ 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. -- Sebastian Moeller telephone: 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 moel...@caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
