Re: [Freesurfer] beta
Hi Bruce- The teams at UCSF and the SFVAMC would be more than willing to provide letters of support. Regards, Wil ─── William Irwin | Imaging Core Supervisor University of California | Mission Bay Sandler Neurosciences Building Memory and Aging Center | MC: 1207 675 Nelson Rising Lane | Suite 190 San Francisco | CA | 94158 wirwin |at| memory.ucsf.edu p: 415-502-7146 | f: 415-476-1816 -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Wednesday, January 30, 2013 9:43 AM To: Joshua Lee Cc: freesurfer@nmr.mgh.harvard.edu; Ed Gronenschild Subject: Re: [Freesurfer] beta thanks Joshua I wish study sections agreed with you. We will probably put in another support grant in the next year when I work up the energy to write one (they are quite dull). I'll probably request support letters at that time. cheers Bruce On Wed, 30 Jan 2013, Joshua Lee wrote: This news is most unfortunate. We all appreciate the Freesurfer team's work. Freesurfer, and project's like these, provide a substantial multiplier effect to the productivity of the neuroscience community. There should be more funding for these types of neuroscience research infrastructure. - Joshua On Wed, Jan 30, 2013 at 7:50 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Ed I mean that the grant funding FreeSurfer maintainance didn't get renewed. We certainly will continue support and development, but it does have a substantial negative impact on the engineering we can do, such as getting rid of the 1mm restrictions. cheers Bruce On Wed, 30 Jan 2013, Ed Gronenschild wrote: Hi Bruce, What do you mean: no support anymore or no new development? Cheers, Ed On 30 Jan 2013, at 13:41, Jacobs H (NP) wrote: Message: 7 Date: Mon, 21 Jan 2013 19:19:25 -0500 (EST) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] beta To: Colin Reveley reve...@gmail.com Cc: Joshua Lee jki...@ucdavis.edu, freesurfer@nmr.mgh.harvard.edu, Nick Schmansky ni...@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.00.1301211918340.29...@entry.nmr.mgh.harvard.edu Content-Type: text/plain; charset=iso-8859-1 Hi Colin yes, but we simply don't have the person power to do it at the moment. Our FS support grant ends in a month and is not going to get renewed, so it's going to be hard to do anytime soon. sorry Bruce ___ 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] QA Tools Snaps Scrambled - Follow up
Hi Louis- I dug a little deeper and examined the rgb files before conversion. The problem is not with the IM conversion, it is with the capture. For example, 'subject_curv_lh_lat.rgb' is just fine, but from the same subject 'snapshot-talairach-H-128.rgb' is garbage. Any ideas on this? Thanks, Wil -Original Message- From: Irwin, William Sent: Wednesday, January 09, 2013 6:22 AM To: Louis Nicholas Vinke Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William Subject: RE: [Freesurfer] QA Tools Snaps Scrambled - Clairification Hi Louis- I was speaking cryptically and/or imprecisely. Of course there are dependencies for IM-- in fact about 8 libraries which are uniquely required by IM. I was thinking about a higher (or lower) level of dependency. This would suggest a more system-level problem, but I'm not having problems with any of the other apps running on my system. Obviously I'm not asking you to help diagnose the health of my system, but though you might have some thoughts/suggestions. Regards, Wil -Original Message- From: Irwin, William Sent: Wednesday, January 09, 2013 5:37 AM To: Louis Nicholas Vinke Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William Subject: RE: [Freesurfer] QA Tools Snaps Scrambled Hi Louis- No problem doing command line conversion of an rgb to either jpg or gif in terms of error messages. However, the converted files are scrambled. Might there be a dependency on which ImageMagick relies which still in place, but corrupted? I was under the impression ImageMagick was self-contained. This is a real mystery -Wil -Original Message- From: Louis Nicholas Vinke [mailto:vi...@nmr.mgh.harvard.edu] Sent: Tuesday, January 08, 2013 6:29 PM To: Irwin, William Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QA Tools Snaps Scrambled Hi Irwin, It sounds like the snapshots from tksurfer are fine, but the ones from tkmedit are not being generated properly. It may be this peculiar bug where ImageMagick has trouble reading rgb files. Try converting an rgb file to a jpg 'convert file.rgb file.jpg'. You may get the error 'Improper image header'. The tksurfer tcl script saves tiff files, the tkmedit tcl script saves rgbs, which may explain why some images are fine. -Louis On Tue, 8 Jan 2013, Irwin, William wrote: Hi- I’ve come across a peculiar behavior with recon_checker, and am hoping someone can shed some light on this. I have used it 100’s of times in the past, but not for about 2 months. I recently processed a large set of cases I wanted to QC. When I ran it, some, but not all, of the snaps were corrupted. Specifically the talairach, aseg, surfs, and all the ‘detailed snaps’, which are basically additional instances of the aforementioned types. The inflated, curv, and parc are all just fine. As the process runs, all images are being displayed in the pop-up windows, and the html page is created. While there have been no system changes which should affect this, I upgraded from ImageMagick 6.5.4 to 6.8.1 to see if this would fix the problem. The problem remains. And the problem remains w/ or w/o the flag for detailed snaps. If all of the images were corrupted, I would have certainly concluded something has gone awry with my system. The fact that only some of the images are corrupted makes me scratch my head. Thoughts? Suggestions? Thanks, Wil 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] QA Tools Snaps Scrambled
Hi Louis- No problem doing command line conversion of an rgb to either jpg or gif in terms of error messages. However, the converted files are scrambled. Might there be a dependency on which ImageMagick relies which still in place, but corrupted? I was under the impression ImageMagick was self-contained. This is a real mystery -Wil -Original Message- From: Louis Nicholas Vinke [mailto:vi...@nmr.mgh.harvard.edu] Sent: Tuesday, January 08, 2013 6:29 PM To: Irwin, William Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QA Tools Snaps Scrambled Hi Irwin, It sounds like the snapshots from tksurfer are fine, but the ones from tkmedit are not being generated properly. It may be this peculiar bug where ImageMagick has trouble reading rgb files. Try converting an rgb file to a jpg 'convert file.rgb file.jpg'. You may get the error 'Improper image header'. The tksurfer tcl script saves tiff files, the tkmedit tcl script saves rgbs, which may explain why some images are fine. -Louis On Tue, 8 Jan 2013, Irwin, William wrote: Hi- I’ve come across a peculiar behavior with recon_checker, and am hoping someone can shed some light on this. I have used it 100’s of times in the past, but not for about 2 months. I recently processed a large set of cases I wanted to QC. When I ran it, some, but not all, of the snaps were corrupted. Specifically the talairach, aseg, surfs, and all the ‘detailed snaps’, which are basically additional instances of the aforementioned types. The inflated, curv, and parc are all just fine. As the process runs, all images are being displayed in the pop-up windows, and the html page is created. While there have been no system changes which should affect this, I upgraded from ImageMagick 6.5.4 to 6.8.1 to see if this would fix the problem. The problem remains. And the problem remains w/ or w/o the flag for detailed snaps. If all of the images were corrupted, I would have certainly concluded something has gone awry with my system. The fact that only some of the images are corrupted makes me scratch my head. Thoughts? Suggestions? Thanks, Wil 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] QA Tools Snaps Scrambled - Clairification
Hi Louis- I was speaking cryptically and/or imprecisely. Of course there are dependencies for IM-- in fact about 8 libraries which are uniquely required by IM. I was thinking about a higher (or lower) level of dependency. This would suggest a more system-level problem, but I'm not having problems with any of the other apps running on my system. Obviously I'm not asking you to help diagnose the health of my system, but though you might have some thoughts/suggestions. Regards, Wil -Original Message- From: Irwin, William Sent: Wednesday, January 09, 2013 5:37 AM To: Louis Nicholas Vinke Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William Subject: RE: [Freesurfer] QA Tools Snaps Scrambled Hi Louis- No problem doing command line conversion of an rgb to either jpg or gif in terms of error messages. However, the converted files are scrambled. Might there be a dependency on which ImageMagick relies which still in place, but corrupted? I was under the impression ImageMagick was self-contained. This is a real mystery -Wil -Original Message- From: Louis Nicholas Vinke [mailto:vi...@nmr.mgh.harvard.edu] Sent: Tuesday, January 08, 2013 6:29 PM To: Irwin, William Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QA Tools Snaps Scrambled Hi Irwin, It sounds like the snapshots from tksurfer are fine, but the ones from tkmedit are not being generated properly. It may be this peculiar bug where ImageMagick has trouble reading rgb files. Try converting an rgb file to a jpg 'convert file.rgb file.jpg'. You may get the error 'Improper image header'. The tksurfer tcl script saves tiff files, the tkmedit tcl script saves rgbs, which may explain why some images are fine. -Louis On Tue, 8 Jan 2013, Irwin, William wrote: Hi- I’ve come across a peculiar behavior with recon_checker, and am hoping someone can shed some light on this. I have used it 100’s of times in the past, but not for about 2 months. I recently processed a large set of cases I wanted to QC. When I ran it, some, but not all, of the snaps were corrupted. Specifically the talairach, aseg, surfs, and all the ‘detailed snaps’, which are basically additional instances of the aforementioned types. The inflated, curv, and parc are all just fine. As the process runs, all images are being displayed in the pop-up windows, and the html page is created. While there have been no system changes which should affect this, I upgraded from ImageMagick 6.5.4 to 6.8.1 to see if this would fix the problem. The problem remains. And the problem remains w/ or w/o the flag for detailed snaps. If all of the images were corrupted, I would have certainly concluded something has gone awry with my system. The fact that only some of the images are corrupted makes me scratch my head. Thoughts? Suggestions? Thanks, Wil 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] QA Tools Snaps Scrambled
Hi- I've come across a peculiar behavior with recon_checker, and am hoping someone can shed some light on this. I have used it 100's of times in the past, but not for about 2 months. I recently processed a large set of cases I wanted to QC. When I ran it, some, but not all, of the snaps were corrupted. Specifically the talairach, aseg, surfs, and all the 'detailed snaps', which are basically additional instances of the aforementioned types. The inflated, curv, and parc are all just fine. As the process runs, all images are being displayed in the pop-up windows, and the html page is created. While there have been no system changes which should affect this, I upgraded from ImageMagick 6.5.4 to 6.8.1 to see if this would fix the problem. The problem remains. And the problem remains w/ or w/o the flag for detailed snaps. If all of the images were corrupted, I would have certainly concluded something has gone awry with my system. The fact that only some of the images are corrupted makes me scratch my head. Thoughts? Suggestions? Thanks, Wil ___ 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] Error with updated freeview.bin
Hello- I just downloaded the updated freeview.bin (8/23/2012) file (from: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/). I am running Linux 64-bit (2.6.32-279.5.1.el6.x86_64 #1 SMP Tue Aug 14 16:11:42 CDT 2012 x86_64 x86_64 x86_64 GNU/Linux). When I tried to execute freeview, I got the following error: freeview.bin: symbol lookup error: freeview.bin: undefined symbol: _ZN9QListData11detach_growEPii I'm assuming there are updates, improvements to the newer version, which I what motivated me to update. Please advise. Thanks, Wil ___ 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] Error with updated freeview.bin
Hi Nick- Yes, library dependency issues which don't appear to easily be solved. Presumably they would be easier to solve if I moved to the centos6 version of 5.1, but the centos4 version is working just fine. Thanks for your help. -Wil |-Original Message- |From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] |Sent: Tuesday, October 09, 2012 1:52 PM |To: Irwin, William |Cc: freesurfer@nmr.mgh.harvard.edu |Subject: Re: [Freesurfer] Error with updated freeview.bin | |Wil, | |I've just uploaded the latest-greatest dev build of freeview.bin for |centos6 here: | |ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux- |centos6_x86_64/ | |hopefully that will work. there could be library dependency issues though. | |Nick | |On Tue, 2012-10-09 at 18:32 +, Irwin, William wrote: | Hello- | | | I just downloaded the updated freeview.bin (8/23/2012) file (from: | ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux- |centos4_x86_64/). | I am running Linux 64-bit (2.6.32-279.5.1.el6.x86_64 #1 SMP Tue Aug 14 | 16:11:42 CDT 2012 x86_64 x86_64 x86_64 GNU/Linux). | When I tried to execute freeview, I got the following error: | freeview.bin: symbol lookup error: freeview.bin: undefined symbol: | _ZN9QListData11detach_growEPii | I’m assuming there are updates, improvements to the newer version, | which I what motivated me to update. | Please advise. | Thanks, | Wil | | | | ___ | 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] Questions on QA Tools
Hi- This is an useful addition. I have a couple of questions about the outputs: 1. subject has 36 outliers: I assume this refers to the volumetrics as compared to FS Average, where an outlier is a volume +/- 2 SDs? 2. 7927 vertices did not have an annotation!: I understand what this means, but what are the QA implications? Thanks, Wil ___ 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] RB*2008-03-26.gca vs. RB*2011-10-25.gca files
Hello-
The 'RB_all_2008-03-26.gca' and 'RB_all_withskull_2008-03-26.gca' files are
packaged with the 5.1 release.
Is there any reason the 2011 versions ('RB_all_2011-10-25.gca'
'RB_all_withskull_2011-10-25.gca ')are not included in the 5.1 release or users
should not update to these newer versions?
Thanks,
Wil
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Re: [Freesurfer] Reading/loading posterior_* files from hippocampal subfield segmentation
Hi Koen,
Yes, Thanks. A stupid syntax/typo on my part.
-Wil
|-Original Message-
|From: Koen Van Leemput [mailto:k...@nmr.mgh.harvard.edu]
|Sent: Monday, April 09, 2012 12:35 AM
|To: Irwin, William
|Cc: freesurfer@nmr.mgh.harvard.edu
|Subject: Re: [Freesurfer] Reading/loading posterior_* files from hippocampal
|subfield segmentation
|
|Hi Irwin,
|
|The command should do exactly as you describe, but it seems to work when I
|try it.
|
|I did notice that the filename you specified
|(hippoposterior_right_CA4-DG.mgz.gz) has an extra hippo in front - could
|you please double-check?
|
|Thanks,
|
|Koen
|
|
|On Sat, Apr 7, 2012 at 10:07 PM, Irwin, William wir...@memory.ucsf.edu
|wrote:
| Hi-
|
|
|
| This is probably a question for Koen, but perhaps others could help me out.
|
|
|
| I want to read into Matlab the 'posterior_*.mgz' files generated by
| the subfield segmentation. I'm not exactly sure the format/content of
| these files, but in addition to any information (e.g., some coordinate
| reference), I'm assuming it contains the posterior probability (0 -
| 255, scaled) for each (sub) voxel for each of the regions/fields.
|
|
|
| I tried the obvious Matlab file (i.e., load_mgh.m), but that results
| in an error (the current Matlab directory contains the files and if I
| include the full path the same error obtains):
|
|
|
| [vol M] = load_mgh('hippoposterior_right_CA4-DG.mgz');
|
| gzip: hippoposterior_right_CA4-DG.mgz.gz: No such file or directory
|
| ERROR: problem reading fname
|
| SWITCH expression must be a scalar or string constant.
|
|
|
| Error in load_mgh (line 156)
|
| switch type
|
|
|
| Given what I know (or think I know) about the procedure by which the
| subfields are labeled, it likely isn't surprising the genearl Matlab
| scripts don't properly deal with the posterior subfield files.
|
|
|
| My objective is to be able to evaluate the distribution of voxels
| values (posterior probabilities) which exist for each of the
subfields/regions.
|
|
|
| Thanks,
|
| Wil
|
|
| ___
| 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.
|
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[Freesurfer] Clarification on centos version/updates/patches
Hi- It would appear the stable release for centos6 is ready for primetime 'stable5.1-bin.tgz'; Is this correct? There is an updated version of 'mri_info' based on file size (ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/). mri_info in 'stable5.1-bin.tgz': 9787048 04-Oct-2011 13:45 mri_info outside of 'stable5.1-bin.tgz': 9866032 04-Oct-2011 11:32 Which version is the most current? Can the contents of 'stable5.1-bin.tgz' be extracted into /freesurfer/bin to overwrite the extant files? Additionally, there is a versioning discrepancy between 'trac-all' located in (http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/) '$Id: trac-all,v 1.35 2011/09/02 19:19:22 ayendiki Exp $'a and the version packaged with the cenos6_x86_65 'stable5.1-bin.tgz' '$Id: trac-all,v 1.22.2.9 2011/09/02 19:21:03 ayendiki Exp $' I did not comprehensively look for any other discrepancies-these just happened to stand out based on the work I was doing today. Thanks much, Wil ___ 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] Reading/loading posterior_* files from hippocampal subfield segmentation
Hi-
This is probably a question for Koen, but perhaps others could help me out.
I want to read into Matlab the 'posterior_*.mgz' files generated by the
subfield segmentation. I'm not exactly sure the format/content of these files,
but in addition to any information (e.g., some coordinate reference), I'm
assuming it contains the posterior probability (0 - 255, scaled) for each (sub)
voxel for each of the regions/fields.
I tried the obvious Matlab file (i.e., load_mgh.m), but that results in an
error (the current Matlab directory contains the files and if I include the
full path the same error obtains):
[vol M] = load_mgh('hippoposterior_right_CA4-DG.mgz');
gzip: hippoposterior_right_CA4-DG.mgz.gz: No such file or directory
ERROR: problem reading fname
SWITCH expression must be a scalar or string constant.
Error in load_mgh (line 156)
switch type
Given what I know (or think I know) about the procedure by which the subfields
are labeled, it likely isn't surprising the genearl Matlab scripts don't
properly deal with the posterior subfield files.
My objective is to be able to evaluate the distribution of voxels values
(posterior probabilities) which exist for each of the subfields/regions.
Thanks,
Wil
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dispose of the e-mail.
Re: [Freesurfer] lobar WM volumes
Thanks, Doug. I actually want lobar both GM and WM. So would this be the correct syntax to generate lobar GM and WM labels? mri_aparc2aseg --ssubject --labelwm --rip-unknown --ctxseg aparc+aseg.mgz --annot lobe Yes, I started to do as you suggest with tkmedit using FreeView, but I thought there might be a less manual way of doing this. Thanks, Wil |-Original Message- |From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] |Sent: Thursday, April 05, 2012 8:30 AM |To: Irwin, William |Cc: freesurfer@nmr.mgh.harvard.edu |Subject: Re: [Freesurfer] lobar WM volumes | |You don't need to do 2b if all you want are the lobar wm segmentations. |2b should just copy the cortical labels into the new seg. | |mri_segstats --seg mri/newseg.mgz --sum stats/newseg.stats --pv |mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent -- |subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units |MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab newcolortable -- |subjectsubject | | |You can load the newseg.mgz into tkmedit as both a segmentation (-seg) and |as the aux volume. When you click on a point, you can see the seg value |associated with the given label. | |doug | | | |On 04/04/2012 11:15 PM, Irwin, William wrote: | Hi Doug- | | I wanted to follow up on this procedure and ask for a bit of clarification. As |an extension from Ines' efforts, I believe one can produce a ' lobe+aseg.mgz' |lobar volume with both WM and GM for both RH and LH. | | 1: | mri_annotation2label --ssubject --hemi rh --lobesStrict lobe | mri_annotation2label --ssubject --hemi lh --lobesStrict lobe | | 2(a): | mri_aparc2aseg --ssubject --labelwm --annot lobe | | 2(b) | mri_aparc2aseg --ssubject --rip-unknown --ctxseg aparc+aseg.mgz -- |annot lobe | I'm not sure if this the correct syntax to be analogous to that for WM in 2(a). | | What would be the correct syntax to combine 2(a) and 2(b) into one |command? | | 3: | Per your suggestion for syntax, this can be found in recon-all.log following |that for wmparc (and I have identified that). There is similar syntax for |GM/ctx. I'm not sure if the following would need to be slightly modified for |my objective: | | mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv | mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent | --subcortgray --in mri/norm.mgz --in-intensity-name norm | --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol | --totalgray --ctab /usr/local/freesurfer/ASegStatsLUT.txt | --subjectsubject | | But, before proceeding with the step 3, how can one determine the lobar |label numbers assigned such that a custom LUT can be created. The output of |the 2(b) (if the syntax is correct) indicates that 8 entries are read (Frontal, |Temporal, Parietal, Occipital for LH and RH?). | | Thanks for your help. | | -Wil | | |-Original Message- | |From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] | |Sent: Monday, April 02, 2012 10:39 AM | |To: freesurfer@nmr.mgh.harvard.edu | |Subject: Re: [Freesurfer] lobar WM volumes | | | |use mri_segstats. You can look in subjid/scripts/recon-all.log for | |example command lines (look for the one with wmparc). The command | |will require a color table. The ones in the log file will use the | |default table, but this will not have the numbers/names of your | |lobar regions, so you'll need to create a new color table (or add to the one |that is there). | |doug | | | |On 04/02/2012 12:58 PM, Inês Violante wrote: | | Dear all, | | | | I need to obtain the white matter volume per lobe for a given | | numer of | |subjects. | | I started by using the following: | | | | mri_annotation2label --subjectsubjid --hemi rh --lobesStrict lobe | | | | mri_aparc2aseg --ssubjid --labelwm --annot lobe | | | | and now I have a lobe+aseg.mgz file. How can I create a stats | | file containing the wm volume for each lobe? | | | | Thank you, | | | | ines | | | | ___ | | 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html | | | | | | | |-- |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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html | | | |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
Re: [Freesurfer] lobar WM volumes
Hi Doug- I wanted to follow up on this procedure and ask for a bit of clarification. As an extension from Ines' efforts, I believe one can produce a ' lobe+aseg.mgz' lobar volume with both WM and GM for both RH and LH. 1: mri_annotation2label --s subject --hemi rh --lobesStrict lobe mri_annotation2label --s subject --hemi lh --lobesStrict lobe 2(a): mri_aparc2aseg --s subject --labelwm --annot lobe 2(b) mri_aparc2aseg --s subject --rip-unknown --ctxseg aparc+aseg.mgz --annot lobe I'm not sure if this the correct syntax to be analogous to that for WM in 2(a). What would be the correct syntax to combine 2(a) and 2(b) into one command? 3: Per your suggestion for syntax, this can be found in recon-all.log following that for wmparc (and I have identified that). There is similar syntax for GM/ctx. I'm not sure if the following would need to be slightly modified for my objective: mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject subject But, before proceeding with the step 3, how can one determine the lobar label numbers assigned such that a custom LUT can be created. The output of the 2(b) (if the syntax is correct) indicates that 8 entries are read (Frontal, Temporal, Parietal, Occipital for LH and RH?). Thanks for your help. -Wil |-Original Message- |From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] |Sent: Monday, April 02, 2012 10:39 AM |To: freesurfer@nmr.mgh.harvard.edu |Subject: Re: [Freesurfer] lobar WM volumes | |use mri_segstats. You can look in subjid/scripts/recon-all.log for example |command lines (look for the one with wmparc). The command will require a |color table. The ones in the log file will use the default table, but this will not |have the numbers/names of your lobar regions, so you'll need to create a |new color table (or add to the one that is there). |doug | |On 04/02/2012 12:58 PM, Inês Violante wrote: | Dear all, | | I need to obtain the white matter volume per lobe for a given numer of |subjects. | I started by using the following: | | mri_annotation2label --subjectsubjid --hemi rh --lobesStrict lobe | | mri_aparc2aseg --ssubjid --labelwm --annot lobe | | and now I have a lobe+aseg.mgz file. How can I create a stats file | containing the wm volume for each lobe? | | Thank you, | | ines | | ___ | 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html | ___ 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] QATools
Hi - The link to download the QATools script (http://surfer.nmr.mgh.harvard.edu/fswiki/QATools) for non-MGH users is broken, and I couldn't find it by looking through the ftp download directories. Regards, Wil ___ 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] Performance questions
Hi Nick- I was explicitly told by you there was not stable centos5 release of 5.1. And unless it is located elsewhere, it is not located in: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/ Can you please clarify this? Thanks, Wil |-Original Message- |From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] |Sent: Wednesday, January 18, 2012 10:10 AM |To: Bruce Fischl |Cc: freesurfer@nmr.mgh.harvard.edu; Malcolm Tobias |Subject: Re: [Freesurfer] Performance questions | |Malcolm, | |actually, they (IBM) are looking at openmp (to allow multiple threads to |process for-loops) and SSE3 instructions (better vectorization). | |recon-all --help contains some timings for an AMD processor. centos4 vs. |centos5 itself should not account for any speed differences, but it is true that |our centos5 build was built with gcc 4.1 while our centos4 build uses gcc 3.4.7, |so those compiler difference likely account for speed differences. | |another major factor that affects runtime is whether the Intel Nahalem |architecture exists on your system. this memory controller is much better at |handling the wide memory layout of freesurfer structures (minimizing cache- |line hits). | |Nick | | |On Fri, 2012-01-13 at 09:13 -0500, Bruce Fischl wrote: | Hi Malcolm | | in collaboration with IBM we are also looking at MPI and pthreads. | | cheers | Bruce | | On Fri, | 13 Jan 2012, Malcolm Tobias wrote: | | | Is there a standard benchmark for FreeSurfer? | I've been using the data under subjects (Bert?/Ernie?) and running a | recon- | all: | | recon-all -s ernie -i ./sample-001.mgz -i ./sample-002.mgz -all | | On our hardware using the 5.1 distributed binary (freesurfer-Linux- | centos4_x86_64-stable-pub-v5.1.0.tar.gz) it takes about 12 hours. | | I was surprised that 5.1 was running so much faster than 5.0. With | 5.0 | (freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0.tar.gz) it was | taking about | 18 hours. Did anyone else notice a big speed-up from 5.0 to 5.1? | Maybe it's a difference between centos5 vs. centos4? If so, | wouldn't you expect the former to be faster? | | If I back-port the changes Nick made to configure.in for the dev | branch to the stable release of 5.1 and build from source on our | systems, I'm able to run in | ~10 hours. I'm guessing this is mostly due to the difference in the | versions of gcc used on our system (4.1.2) vs. those used for the | centos4 distributed binary? | | For the dev release, it's taking about ~11 hours. I'm guessing the | dev branch is mostly focused on features/bug-fixes and performance | is only looked at before a release? | | Besides GPUs, what else are people doing to increase performance? | | Cheers, | Malcolm | | | ___ | 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] Hanging or running at 'SubCort Seg'?
Hi Bruce- We'll this was insightful: The norm.mgz file was empty and when I looked at the original input after (after MRI convert) the sagittal view was rotate by 90 degrees. I'm not sure what caused this, as the input is correctly oriented. The discrepancy between input and conversion to .mgz seem likely to explain why the Talairach transform failed. Suggested on what would cause this glitch? Thanks, Wil |-Original Message- |From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] |Sent: Monday, October 17, 2011 6:27 AM |To: Irwin, William |Cc: freesurfer@nmr.mgh.harvard.edu |Subject: RE: [Freesurfer] Hanging or running at 'SubCort Seg'? | |hmmm, looks like it is almost finished with mri_cc but doesn't complete. |It usually only takes like 2 minutes for this process, so something must be |wrong. Can you send me aseg.auto_noCCseg.mgz and norm.mgz for this |subject? You can probably just email them. | |cheers |Bruce | | |On Mon, 17 Oct 2011, Irwin, |William wrote: | | | Hi Bruce- | | | | It is still running, but the recon-all.log as it stands is attached. | | | | Thanks for your help. | | | | Regards, | | Wil | | | | From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] | Sent: Sunday, October 16, 2011 6:27 PM | To: Irwin, William | Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William | Subject: Re: [Freesurfer] Hanging or running at 'SubCort Seg'? | | | | Hi Wil | | Can you send us the full recon-all.log? | | Cheers | | Bruce | | | On Oct 16, 2011, at 3:53 PM, Irwin, William wir...@memory.ucsf.edu |wrote: | | Hi- | | | | I?m a bit stumped by a cased. The input volume looks very good. The first |error was the Talairach transform would not complete, so I used the | ?-notal-check? flag. As I have been focused on other things, I just let the |job run, but after 2 weeks, it is stuck (I assume) as indicated. It | is running on a fast processor with plenty of memory, so system | constraints are not the issue | | | | #@# SubCort Seg Sun Oct 9 16:41:44 PDT 2011 | | | | mri_ca_label -align -nobigventricles norm.mgz | transforms/talairach.m3z | /usr/local/freesurfer/average/RB_all_2008-03-26.gca as | | eg.auto_noCCseg.mgz | | | | mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz ?lta | /media/ClusterData2/data/localdata2/FreeSurfer/wirwin/wirwin_subject | | s/FT047-5/mri/transforms/cc_up.lta FT047-5 | | | | Any suggestions as to what might be the problem? | | | | Thanks much, | | Wil | | ___ | 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] Hanging or running at 'SubCort Seg'?
Hi- I'm a bit stumped by a cased. The input volume looks very good. The first error was the Talairach transform would not complete, so I used the '-notal-check' flag. As I have been focused on other things, I just let the job run, but after 2 weeks, it is stuck (I assume) as indicated. It is running on a fast processor with plenty of memory, so system constraints are not the issue #@# SubCort Seg Sun Oct 9 16:41:44 PDT 2011 mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca as eg.auto_noCCseg.mgz mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /media/ClusterData2/data/localdata2/FreeSurfer/wirwin/wirwin_subject s/FT047-5/mri/transforms/cc_up.lta FT047-5 Any suggestions as to what might be the problem? Thanks much, Wil ___ 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] Renaming a processed subject
That is not going to change the information in associated files, for example stats files. -Wil From: Pedro Paulo de Magalhães Oliveira Junior [mailto:p...@netfilter.com.br] Sent: Thursday, September 01, 2011 8:09 AM To: Irwin, William Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Renaming a processed subject You can just rename the directory ABC1234 to Case1 mv ABC1234 Case1 On Thu, Sep 1, 2011 at 12:01, Irwin, William wir...@memory.ucsf.edumailto:wir...@memory.ucsf.edu wrote: Hi For purposes of de-identification, is there an easy way to rename all the contents of data for a processed subject? For example, If I want to do share data or do reliability training on an existing subject (e.g., ABC1234), I want to rename everything associated with this case to Case1. Thanks Wil William Irwin | Imaging Core Supervisor UCSF | Memory and Aging Center 350 Parnassus Avenue, Suite 905 San Francisco CA 94143-1207 wir...@memory.ucsf.edumailto:wir...@memory.ucsf.edu | memory.ucsf.eduhttp://memory.ucsf.edu p: 415.476.1680tel:415.476.1680 | f: 415.476.1816tel:415.476.1816 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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] Renaming a processed subject
Hi Bruce- Not trivial to be sure! I was hoping there was an undocumented feature/command. Of course, everyone and their neighbor could suggest a useful feature to be added, but this one seems particularly useful. Thanks, Wil |-Original Message- |From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] |Sent: Thursday, September 01, 2011 8:58 AM |To: Irwin, William |Cc: freesurfer@nmr.mgh.harvard.edu |Subject: Re: [Freesurfer] Renaming a processed subject | |I think the .mgh/.mgz files and surfaces contain some cmdline info in them, so |it may not be so trivial. Reading and writing them in matlab will probably |remove all that stuff. | |cheers |Bruce | | |On Thu, 1 Sep 2011, Irwin, William wrote: | | | Hi | | | | For purposes of de-identification, is there an easy way to ?rename? | all the contents of data for a processed subject? | | | | For example, If I want to do share data or do reliability training on | an existing subject (e.g., ?ABC1234?), I want to rename everything | associated with this case to ?Case1?. | | | | Thanks | | Wil | | | | | William Irwin | Imaging Core Supervisor UCSF | Memory and Aging Center | 350 Parnassus Avenue, Suite 905 | San Francisco CA 94143-1207 | wir...@memory.ucsf.edu | memory.ucsf.edu | p: 415.476.1680 | f: 415.476.1816 | | | | | | | | | |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] Procedure to get amygdalar sub-regions and brainstem Brainstem consituents volumes
Thanks, Bruce. That was my assumption, but I thought it was worthwhile asking. Related, for the hippocampal subfield segmentation, I understand the voxel values are the probabilities of belonging to a given subfield. Is there way to extract a list of voxels with their values for each region? I realize this would generate a very long stream of data. But then one could post-hoc adjust the number of voxels per region by setting some criteria (e.g., the probability of belonging to the fornix has to be 95%). Thanks, Wil |-Original Message- |From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] |Sent: Wednesday, August 24, 2011 12:28 PM |To: Irwin, William |Cc: freesurfer@nmr.mgh.harvard.edu |Subject: Re: [Freesurfer] Procedure to get amygdalar sub-regions and |brainstem Brainstem consituents volumes | |Hi Wil | |sorry, we don't have anything for that yet, although we are actively working |on it. | |cheers |Bruce |On Wed, 24 Aug 2011, Irwin, William wrote: | | | Hello- | | | | In the FreeSurferColorLUT.txt,v 1.70.2.1 2011/05/02 file, there are labels for |sub-regions of interest. For example amygdala and brainstem. | | | | How does one go about extracting the volumes for these regions? | | | | Thank you in advance, | | Wil | | | | | | #No. Label Name: R G B A | | 7001 Lateral-nucleus 72 132 181 0 | | 7002 Basolateral-nucleus 243 243 243 0 | | 7003 Basal-nucleus 207 63 79 0 | | 7004 Centromedial-nucleus 121 20 135 0 | | 7005 Central-nucleus 197 60 248 0 | | 7006 Medial-nucleus 2 149 2 0 | | 7007 Cortical-nucleus 221 249 166 0 | | 7008 Accessory-Basal-nucleus 232 146 35 0 | | 7009 Corticoamygdaloid-transitio 20 60 120 0 | | 7010 Anterior-amygdaloid-area-AAA 250 250 0 0 | | 7011 Fusion-amygdala-HP-FAH 122 187 222 0 | | 7012 Hippocampal-amygdala-transition-HATA 237 12 177 0 | | 7013 Endopiriform-nucleus 10 49 255 0 | | 7014 Lateral-nucleus-olfactory-tract 205 184 144 0 | | 7015 Paralaminar-nucleus 45 205 165 0 | | 7016 Intercalated-nucleus 117 160 175 0 | | 7017 Prepiriform-cortex 221 217 21 0 | | 7018 Periamygdaloid-cortex 20 60 120 0 | | 7019 Envelope-Amygdala 141 21 100 0 | | 7020 Extranuclear-Amydala 225 140 141 0 | | | | | | # Label names and colors for Brainstem consituents | | # No. Label Name: R G B A | | 170 brainstem 119 159 176 0 | | 171 DCG 119 0 176 0 | | 172 Vermis 119 100 176 0 | | 173 Midbrain 119 200 176 0 | | 174 Pons 119 159 100 0 | | 175 Medulla 119 159 200 0 | | | | | |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] Longitudinal Subject/Base name errors
Hi-
Note, this bug still exists in 5.1. Below is my exchange with Martin and Nick a
several months ago.
-Wil
---
|-Original Message-
|From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
|Sent: Wednesday, May 25, 2011 3:52 PM
|To: Irwin, William; Martin Reuter
|Subject: RE: 5.1.0 Longitudial syntax question
|
|Martin,
|
|attached is his log. it seems like it will fail if the basename
|partially matches a timepoint name.
|
|
|
|Wil, there are two possible workarounds:
|
|1) edit line 5421 of recon-all to change:
|if ( ! $status) then
|
|to
|
|if ( 0 ) then
|
|
|so that this block is never run
|
|or
|
|2) change the name of the basename so that its not a sub-match, for
|instance change to xxx_base
|
|
|we'll have to figure out how this happened.
|
|n.
---
|-Original Message-
|From: Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu]
|Sent: Wednesday, August 10, 2011 10:10 AM
|To: Jeff Sadino
|Cc: freesurfer@nmr.mgh.harvard.edu
|Subject: Re: [Freesurfer] Longitudinal Subject/Base name errors
|
|Hi Jeff,
|
|this was a known bug in 5.0 and there are fixes on the web (release notes),
|just download the recon all from there (and did you grab the robust template
|binary)?.
|
|http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
|
|Best, Martin
|
|On Mon, 2011-08-08 at 17:43 -1000, Jeff Sadino wrote:
| Hello Experts,
|
|
| I am using fs 5.0.0. My naming convention is similar to 11_S01
| and 11_S02 for subject, and then 11 for the base. Now when I
| process the runs longitudinally, I get: ERROR: longitudinal base ID
| cannot be the same as a timepoint. I believe this is because of line
| 4845 in recon-all: grep $longbaseid
| ${longbasedir}/${BaseSubjsListFname} /dev/null. I can just as
| easily cut out this part of the code, or I could manipulate the
| base-tps file, or rename the base folder. But I do not know if there
| are other spots in the code that rely on the original naming
| conventions. Can anyone recommend one approach over the other?
|
|
| Thank you very much,
| Jeff Sadino
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[Freesurfer] MCSRCH ERROR
Hi- I'm at a bit of a loss as to how to address and/or fix these errors. The native input images are very good quality; the conversion to T1.mgz is fine; the brainmask.mgz is good, a bit of dura remained at the parietal/occipital region (very common); otherwise, the skull stripping is very clean. The recon-all finished but with errors as expected. Processing continued to the end, but there is no output except in /mri and /touch. Doing: #@# Skull Stripping First under Computing MAP estimate using 3481 samples... 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 QuasiNewtonEMA: 005: -log(p) = 10327.2 tol 0.10 Then several of the same under EM alignment process ... 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 TOLERANCESpass 2 through quasi-newton minimization... 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 TOLERANCESpass 3 through quasi-newton minimization... 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 TOLERANCESpass 4 through quasi-newton minimization... 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 TOLERANCESpass 5 through quasi-newton minimization... 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 QuasiNewtonEMA: 017: -log(p) = 1145822.4 tol 0.00 Then again at Computing MAP estimate using 2772 samples... 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 QuasiNewtonEMA: 009: -log(p) = 7006.0 tol 0.10 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 TOLERANCESpass 2 through quasi-newton minimization... 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 QuasiNewtonEMA: 013: -log(p) = 838978.4 tol 0.00 Thanks, Wil William Irwin | Brain Imaging Coordinator UCSF | Memory and Aging Center 350 Parnassus Avenue, Suite 905 San Francisco CA 94143-1207 wir...@memory.ucsf.edu | memory.ucsf.edu p: 415.476.1680 | f: 415.476.1816 ___ 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_segment optional flags problem
Hi Bruce- Is this fix going to be put on the site as a patch/fix download (e.g., ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/) or distributed on a per-user need? Thanks, Wil William Irwin | Brain Imaging Coordinator UCSF | Memory and Aging Center 350 Parnassus Avenue, Suite 905 San Francisco CA 94143-1207 wir...@memory.ucsf.edu | memory.ucsf.edu p: 415.476.1680 | f: 415.476.1816 |-Original Message- |From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] |Sent: Thursday, August 04, 2011 12:39 PM |To: Christopher Luna |Cc: freesurfer@nmr.mgh.harvard.edu |Subject: Re: [Freesurfer] mri_segment optional flags problem | |oops, I just fixed that. If you let us know what software/hardware env you are |using we'll give you an updated binary. | |Bruce | | |On Thu, 4 Aug 2011, Christopher Luna |wrote: | | Hello, | I'm trying to run mri_segment with some custom values in the optional | flags, such as -p for setting the percentage threshold with a float value. | | When I run the command though, | mri_segment -p 0.6 brain.mgz wm.seg.mgz | | The command properly sets the threshold to 60%, but also takes the 0.6 to |be in the input file name instead of brain.mgz. | | Is there another option I'm missing? Or have I unfortunately stumbled upon |a small bug? | | Thanks, | Christopher Luna | MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern | Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony | at MIT | | | ___ 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_segment optional flags problem
Bruce, Until it is determined if there is enough interest, how do I obtain it for centos4_x86_64? Thanks much, Wil |-Original Message- |From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] |Sent: Friday, August 05, 2011 12:10 PM |To: Irwin, William |Cc: Christopher Luna; freesurfer@nmr.mgh.harvard.edu |Subject: RE: [Freesurfer] mri_segment optional flags problem | |Hi Wil | |we can certainly post it if there is enough interest. | |cheers |Bruce |On Fri, 5 Aug 2011, |Irwin, William wrote: | | Hi Bruce- | | Is this fix going to be put on the site as a patch/fix download (e.g., |ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux- |centos4_x86_64/) or distributed on a per-user need? | | Thanks, | Wil | | William Irwin | Brain Imaging Coordinator UCSF | Memory and Aging | Center | 350 Parnassus Avenue, Suite 905 | San Francisco CA 94143-1207 | wir...@memory.ucsf.edu | memory.ucsf.edu | p: 415.476.1680 | f: 415.476.1816 | | | | |-Original Message- | |From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] | |Sent: Thursday, August 04, 2011 12:39 PM | |To: Christopher Luna | |Cc: freesurfer@nmr.mgh.harvard.edu | |Subject: Re: [Freesurfer] mri_segment optional flags problem | | | |oops, I just fixed that. If you let us know what software/hardware | |env you are using we'll give you an updated binary. | | | |Bruce | | | | | |On Thu, 4 Aug 2011, Christopher Luna | |wrote: | | | | Hello, | | I'm trying to run mri_segment with some custom values in the | | optional flags, such as -p for setting the percentage threshold with a float |value. | | | | When I run the command though, | | mri_segment -p 0.6 brain.mgz wm.seg.mgz | | | | The command properly sets the threshold to 60%, but also takes the | | 0.6 to | |be in the input file name instead of brain.mgz. | | | | Is there another option I'm missing? Or have I unfortunately | | stumbled upon | |a small bug? | | | | Thanks, | | Christopher Luna | | MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, | | McGovern Institute for Brain Research MIT Archery Club Alpha Kappa | | Psi Colony at MIT | | | | | | | | | | | | |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] Combining 'accelerated' vs 'non-accelerated' data in ongitudinal analyses
Hello- Our group occasionally encounters patients with various syndromes such that 'excessive' head movement is an issue. One solution on which we rely is acquiring an accelerated MPRAGE sequences (Siemens GRAPPA) which takes about ½ the time. For those not familiar with this method, the resulting image is noisier and the contrast-to-noise is reduced. Quantitatively, because of the increased noise in the accelerated acquisition, comparisons of the correlation between regional cortical thickness reveals that the covariance is different between data acquired with the accelerated vs. non-accelerated sequences. If the longitudinal processing stream is used, is the issue of differing covariance between the 2 acquisitions method an issue? If so, does anyone have a suggestion about to deal with this issue? I should add, there is no systematic issue such as one patient group always requires using the accelerated sequence. Regards, Wil ___ 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.
