[Freesurfer] Qdec - generate stats data table
Hello, I was running the tutorial on Qdec, when I went to generate stats data, it started running fine, and then I got the following error message: aparcstats2table --hemi rh --parc aparc.a2005s --meas area --tablefile /mnt/hgfs/VBM/freesurfer_EONCS/EONCS/buckner_data/tutorial_subjs/qdec/stats_tables//rh.aparc.a2005s.area.stats.dat --subjects 140 049 141 084 021 093 080 091 040 017 138 106 108 092 124 129 103 130 039 123 095 067 004 133 097 073 149 045 136 144 032 131 145 111 102 074 114 008 128 099 Number of subjects : 40 Building the table.. ERROR: cannot find /mnt/hgfs/VBM/freesurfer_EONCS/EONCS/buckner_data/tutorial_subjs/140/stats/rh.aparc.a2005s.stats Use --skip flag if you want to continue in such cases -- aparcstats2table --hemi rh --parc aparc.a2005s --meas volume --tablefile /mnt/hgfs/VBM/freesurfer_EONCS/EONCS/buckner_data/tutorial_subjs/qdec/stats_tables//rh.aparc.a2005s.volume.stats.dat --subjects 140 049 141 084 021 093 080 091 040 017 138 106 108 092 124 129 103 130 039 123 095 067 004 133 097 073 149 045 136 144 032 131 145 111 102 074 114 008 128 099 Number of subjects : 40 Building the table.. ERROR: cannot find /mnt/hgfs/VBM/freesurfer_EONCS/EONCS/buckner_data/tutorial_subjs/140/stats/rh.aparc.a2005s.stats Use --skip flag if you want to continue in such cases -- aparcstats2table --hemi rh --parc aparc.a2005s --meas thickness --tablefile /mnt/hgfs/VBM/freesurfer_EONCS/EONCS/buckner_data/tutorial_subjs/qdec/stats_tables//rh.aparc.a2005s.thickness.stats.dat --subjects 140 049 141 084 021 093 080 091 040 017 138 106 108 092 124 129 103 130 039 123 095 067 004 133 097 073 149 045 136 144 032 131 145 111 102 074 114 008 128 099 Number of subjects : 40 Building the table.. ERROR: cannot find /mnt/hgfs/VBM/freesurfer_EONCS/EONCS/buckner_data/tutorial_subjs/140/stats/rh.aparc.a2005s.stats Use --skip flag if you want to continue in such cases -- aparcstats2table --hemi rh --parc aparc.a2005s --meas meancurv --tablefile /mnt/hgfs/VBM/freesurfer_EONCS/EONCS/buckner_data/tutorial_subjs/qdec/stats_tables//rh.aparc.a2005s.meancurv.stats.dat --subjects 140 049 141 084 021 093 080 091 040 017 138 106 108 092 124 129 103 130 039 123 095 067 004 133 097 073 149 045 136 144 032 131 145 111 102 074 114 008 128 099 Number of subjects : 40 Building the table.. ERROR: cannot find /mnt/hgfs/VBM/freesurfer_EONCS/EONCS/buckner_data/tutorial_subjs/140/stats/rh.aparc.a2005s.stats Use --skip flag if you want to continue in such cases Completed creation of aseg and aparc stats data tables. Is this the same problem as before, where I might have an older bundle of data that doesn't contain these certain files? Is there a way I can recreate them and continue running the tutorial? Thanks, Fatima E-pos vrywaringsklousule Hierdie e-pos mag vertroulike inligting bevat en mag regtens geprivilegeerd wees en is slegs bedoel vir die persoon aan wie dit geadresseer is. Indien u nie die bedoelde ontvanger is nie, word u hiermee in kennis gestel dat u hierdie dokument geensins mag gebruik, versprei of kopieer nie. Stel ook asseblief die sender onmiddellik per telefoon in kennis en vee die e-pos uit. Die Universiteit aanvaar nie aanspreeklikheid vir enige skade, verlies of uitgawe wat voortspruit uit hierdie e-pos en/of die oopmaak van enige l?ers aangeheg by hierdie e-pos nie. E-mail disclaimer This e-mail may contain confidential information and may be legally privileged and is intended only for the person to whom it is addressed. If you are not the intended recipient, you are notified that you may not use, distribute or copy this document in any manner whatsoever. Kindly also notify the sender immediately by telephone, and delete the e-mail. The University does not accept liability for any damage, loss or expense arising from this e-mail and/or accessing any files attached to this 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] editing pial surface
Hi freesurfer experts, I am trying to correct the pial surfaces of my data. I was able to remove voxels with the right button of my mouse, but unfortunately, it didn't work out to add voxels. Can somebody please help me with that? Do I need a middle button on the mouse for it? Attached you may find a slice of the brain data. The red line (indicating the pial surface) and green line (indicating the grey matter/white matter boundary) cross, which should not happen in my opinion. Is there any possibility to change the lines so that they don't cross anymore? Cheers, Julia ___ 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] Robust register
Hi, I would like to use mri_robust_register to co-register b-volumes to the reference b0-volume in a DTI dataset. The documentation informs that it is not quite suitable in case of large intensity differences which apply to my case. How to proceed? Is a dev version available for this purpose? Cheers, Ed ___ 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] mkheadsurf and smseghead
Hi Will Doug is out of email contact until next week, and I suspect he's the best one to help you. If you haven't heard by mid week can you repost? cheers Bruce On Thu, 22 Mar 2012, Will Woods wrote: Hi, In my previous lab, which I no longer have access to, we ran mkheadsurf as part of postprocessing, and it generated smseghead files. The latest version of Freesurfer which I recently downloaded (with mkheadsurf version v 1.8 2011/03/02 20:16:39 nicks Exp) does not generate these files - and moreover the smheadsurf environment variable (which defaults to 'smseghead') in the mkheadsurf script does not appear to be used for anything in that script. Have I forgotten to do something in the earlier processing stages, or have things changed? Will ___ 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] editing pial surface
Hi Julia it's really hard to tell from just this image. If the problem is the skull strip removing voxels you can use the clone tool to paint them back in from another volume like the T1.mgz. Are you sure it's not dura or pial vessels? Where in the brain do you mean? cheers Bruce On Thu, 22 Mar 2012, Richter, Julia wrote: Sorry, this time with attachment :). Hi freesurfer experts, I am trying to correct the pial surfaces of my data. I was able to remove voxels with the right button of my mouse, but unfortunately, it didn't work out to add voxels. Can somebody please help me with that? Do I need a middle button on the mouse for it? Attached you may find a slice of the brain data. The red line (indicating the pial surface) and green line (indicating the grey matter/white matter boundary) cross, which should not happen in my opinion. Is there any possibility to change the lines so that they don't cross anymore? Cheers, Julia ___ 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] mkheadsurf and smseghead
Hi Will, I noticed this as well. I don't know Doug's thinking, but I suspect it was just to avoid generating lots of files. The new script overwrites the lh.seghead, when smoothing. I would just update your script to use lh.seghead instead of lh.smseghead. HTH D Will Woods wrote: Hi, In my previous lab, which I no longer have access to, we ran mkheadsurf as part of postprocessing, and it generated smseghead files. The latest version of Freesurfer which I recently downloaded (with mkheadsurf version v 1.8 2011/03/02 20:16:39 nicks Exp) does not generate these files - and moreover the smheadsurf environment variable (which defaults to 'smseghead') in the mkheadsurf script does not appear to be used for anything in that script. Have I forgotten to do something in the earlier processing stages, or have things changed? Will ___ 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] editing pial surface
Hi Julia, Are you editing on a Mac? -Louis On Thu, 22 Mar 2012, Richter, Julia wrote: Hi freesurfer experts, I am trying to correct the pial surfaces of my data. I was able to remove voxels with the right button of my mouse, but unfortunately, it didn't work out to add voxels. Can somebody please help me with that? Do I need a middle button on the mouse for it? Attached you may find a slice of the brain data. The red line (indicating the pial surface) and green line (indicating the grey matter/white matter boundary) cross, which should not happen in my opinion. Is there any possibility to change the lines so that they don't cross anymore? Cheers, Julia ___ 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] Displaying results from qdec on a single subject
Hi All, Is it possible to resample a .sig file from a group thickness analysis in qdec so that the results could be displayed on a single subject's anatomy rather than the fsaverage anatomy in tksurfer? Thanks, Emily -- Emily J Rogalski, PhD Assistant Research Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogal...@gmail.com ___ 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] Displaying results from qdec on a single subject
Hi Emily yes, mri_surf2surf should do this for you. cheers Bruce On Thu, 22 Mar 2012, Emily Rogalski wrote: Hi All, Is it possible to resample a .sig file from a group thickness analysis in qdec so that the results could be displayed on a single subject's anatomy rather than the fsaverage anatomy in tksurfer? Thanks, Emily -- Emily J Rogalski, PhD Assistant Research Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogal...@gmail.com ___ 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] Future of freesurfer
Hi all, I'm currently compiling/installing freesurfer on mac osx lion, ubuntu 12.04 (will be relased soon) and lots of packages which are required by freesurfer appear to be outdated. Is there any step-by-step installation/compilation tutorial somewhere in the web? Therefore I have a couple of questions: Do you plan to update the default libraries to newer versions sometimes soon? (I'm not sure for how long building against old packages will build viable?) Shouldn't freesurfer links against the current release of each library? Regarding the build system, do you consider switching to cmake? It would make easier to maintain, keep up to date and deploy freesurfer over mac and linux? Best, Nicolas ___ 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] calculating DLPFC or frontal lobe grey and white matter volumes
Dear All We want to find frontal lobe grey and white matter volumes in a patient group to compare it with control group. In particular, we want to see the grey and white matter volumes in the dorsolateral prefrontal cortex (DLPFC). However we seem to be having problems finding this region on the processed data for white matter volume (after recon-all command). It was previously suggested in this mailing list that we can get grey matter volume for the DLPFC by combining the following volumes: $hemi.G_frontal_middle.label $hemi.S_frontal_inferior.label $hemi.S_frontal_middle.label We are wondering how to get white matter volumes in the same region... If getting the DLPFC volume is difficult then can we just use the frontal grey and white matter volumes to make between group comparisons. From aseg and aparc files in the stats folder, adding all the following values below would give us frontal white and grey matter volumes. Or is there a simpler and less time consuming way to calculate grey and white matter volume in the frontal lobe? Frontal lobes - White Matter volume caudalmiddlefrontal lateralorbitofrontal medialorbitofrontal paracentral parsopercularis parsorbitalis parstriangularis precentral rostralmiddlefrontal superiorfrontal frontalpole Frontal lobes - Grey Matter volumes G_and_S_frontomargin G_and_S_paracentral G_and_S_subcentral QQQ??? G_and_S_transv_frontopol G_front_inf-Opercular G_front_inf-Orbital G_front_inf-Triangul G_front_middle G_front_sup G_precentral S_front_inf S_front_middle S_front_sup Thanks in advance Sam ___ 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] Spot Opened in Boston FreeSurfer course
Hi everyone, We had a last minute drop-out from our Boston FreeSurfer course which takes place April 2nd through the 4th. If anyone is interested in taking this spot, please let me know. Details about the course content, the registration fee, and other logistics can be found here: http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription Allison ___ 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] Checkout release and stable branch
Hi all,
I followed the instructions on the wiki but it seems impossible to checkout
the stable and release branches?
[toor@linux:x86_64-Linux]...or/cvsroot/test$cvs -d
:pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P -r
stable5 stable
cvs server: cannot find module `stable' - ignored
cvs [checkout aborted]: cannot expand modules
Did their name changed?
Is there a good way with cvs to list the available branches?
('cvs ls' not woking)
Thanks,
Nicolas
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Re: [Freesurfer] Checkout release and stable branch
the last arg should be 'dev', not 'stable'.
Hi all,
I followed the instructions on the wiki but it seems impossible to
checkout
the stable and release branches?
[toor@linux:x86_64-Linux]...or/cvsroot/test$cvs -d
:pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P -r
stable5 stable
cvs server: cannot find module `stable' - ignored
cvs [checkout aborted]: cannot expand modules
Did their name changed?
Is there a good way with cvs to list the available branches?
('cvs ls' not woking)
Thanks,
Nicolas
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
Re: [Freesurfer] Checkout release and stable branch
Thanks for the quick answer :)
I'm not very familiar with cvs and was assuming 'stable' was only the name
of the directory in which the code would be checked out!
Thanks!
Nicolas
On Thu, Mar 22, 2012 at 3:09 PM, Nick Schmansky
ni...@nmr.mgh.harvard.eduwrote:
the last arg should be 'dev', not 'stable'.
Hi all,
I followed the instructions on the wiki but it seems impossible to
checkout
the stable and release branches?
[toor@linux:x86_64-Linux]...or/cvsroot/test$cvs -d
:pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P
-r
stable5 stable
cvs server: cannot find module `stable' - ignored
cvs [checkout aborted]: cannot expand modules
Did their name changed?
Is there a good way with cvs to list the available branches?
('cvs ls' not woking)
Thanks,
Nicolas
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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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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] make_average_subject failure
Dear Freesurfers, Command line: make_average_subject --out average --subjects ... (n=60) . . . . . Applying LTAtransformInterp (resample_type 1) writing to /Volumes/Macintosh/freesurfer/Kontrollen//average/tmp/make_average_vol-tmp-15056/orig-A2/WE.mgh... ERROR: failure writing /Volumes/Macintosh/freesurfer/Kontrollen//average/tmp/make_average_vol-tmp-15056/orig-A2/WE.mgh /Volumes/Macintosh/freesurfer/Kontrollen ERROR: mri_convert failed. ERROR: make_average_volume Surface averaging was done without any problem, but the volume averaging Any clue what's wrong? Thanks in advance Holger ___ 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: comparison in expression (FS with SGE)
I'm dredging this 2 year old post up for the benefit of Google and anyone else who wonders about the cause of this. It is a non-fatal error (for FreeSurfer, but perhaps not other things) that is caused by having set the variable: POSIXLY_CORRECT=1 It causes bc (on Debian/Ubuntu) systems to fail when making comparisons like: echo '3.5 2.5' | bc -l I am guessing (because this is what I was doing) that the poster was using fsl_sub to launch FreeSurfer jobs in SGE. fsl_sub sets this flag for some reason, but commenting it out seems not to cause any problems. Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Xue, Feng Sent: Sunday, March 14, 2010 1:37 PM To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ERROR: comparison in expression (FS with SGE) Thanks! I would check them later. On Mon, Mar 15, 2010 at 1:24 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: if it was a syntax error then recon-all wouldn't have finished, so I'm not sure what's going on. You should visually inspect the surfaces and segmentations to make sure they are all ok. cheers, Bruce On Mon, 15 Mar 2010, Xue, Feng wrote: Sorry, I didn't notice that the reply address was not the list, I've done re-post it. Is there any method to check whether it is ok? For SGE, it might only write errors to dot e files instead of warnings. It seemed like a shell syntax error, however, I don't have that experience to check the recon-all script. On Sun, Mar 14, 2010 at 11:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: can you post this to the list? There are others better qualified to say what's going on. But if everything finished ok is there really a problem? Maybe this is just a warning? On Sun, 14 Mar 2010, Xue, Feng wrote: Hi Bruce, Thanks for your reply. The recon-all.log said it finished without error. please find the whole scripts root in the attachment. I'm also running a raw testing with one subject and without SGEMaybe I can report the result the day after tomorrow. BTW, I found in my 64bit Debian nodes, I repeated got the error as below (standard_in) 2: Error: comparison in expression but in 32bit, I met both. for the GMail security restriction, I changed recon-all.cmd in the attachment to recon-all.cmds. On Sat, Mar 13, 2010 at 11:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: what does the recon-all.log say? Did the recon finish correctly? Does this happen if you just run it on the command line? Bruce On Sat, 13 Mar 2010, Xue, Feng wrote: Dear Bruce FS experts, Please forgive my re-post, for I havn't got any response from last post. I do appreciate if anyone could give me a hint or suggestion. ++ We are running freesurfer with Sun GridEngine. Currently, we repeatedly got this error in SGE's job error log file on some data when doing recon_all: $ cat recon_xf.e437 (standard_in) 2: Error: comparison in expression $ cat recon_xf.e431 (standard_in) 2: comparison in expression I also checked the recon-all-status.log file, but not error was found. Has anyone met this problem? Is it critical? Thanks in advance. -- Best Regards Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn == Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org ___ 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. -- Best Regards Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn == Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list
Re: [Freesurfer] make_average_subject failure
did you run out of disk space? Does that path exist? On Thu, 22 Mar 2012, Klein, Holger wrote: Dear Freesurfers, Command line: make_average_subject --out average --subjects ... (n=60) . . . . . Applying LTAtransformInterp (resample_type 1) writing to/Volumes/Macintosh/freesurfer/Kontrollen//average/tmp/make_average_vol-tmp-15056/o rig-A2/WE.mgh... ERROR: failure writing/Volumes/Macintosh/freesurfer/Kontrollen//average/tmp/make_average_vol-tmp-15056/o rig-A2/WE.mgh /Volumes/Macintosh/freesurfer/Kontrollen ERROR: mri_convert failed. ERROR: make_average_volume Surface averaging was done without any problem, but the volume averaging Any clue what's wrong? Thanks in advance Holger ___ 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] QDEC with cluster-wise p=.1
Hello FreeSurfers, I want to do several cluster-wise corrections at a p value of .1, preferably in QDEC. To create the new template cluster, I am using this command: mri_mcsim --o test --base mc-z --surf fsaverage lh --nreps 1 --fwhm 10 Is there a way that I can tell mri_mcsim to do a threshold of 1.00 (p=.1) and only the abs sign? Thank you, Jeff Sadino ___ 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] Jacobian Questions
Hello, Since the jacobian files contain only positive numbers, is there any way to make a distinction between a brain area that needs to be stretched bigger to fit the template versus a brain area that needs to be squished smaller? fsaverage is comprised of 40 subjects, but I wonder if the jacobian is most accurate only for my subjects that have the same age as the fsaverage mean? If so, then the younger subjects would need to be squished and the older subjects would need to be stretched. But since the jacobian is always positive, then on a scatterplot of jacobian versus age, this would look like a hump centered on the fsaverage mean age. Am I on the right track with this? Thank you, Jeff ___ 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] Cortical Normalization Questions
Hello, For cortical thickness normalizations, Bruce said not to normalize based on a HBM abstract ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html). Is this still the consensus? For cortical volume, it is pretty standard to normalize to eTIV. For cortical surface area (jacobian), I couldn't find any information on the wiki. Does anyone have any recommendations? Thank you, Jeff ___ 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] Jacobian Questions
Hi Jeff 1 means compressed and 1 means expanded. You can take the log if you want to turn it into the real line. I'm not sure age matters that much for the white matter surface, although it would for the pial one cheers Bruce On Thu, 22 Mar 2012, Jeff Sadino wrote: Hello, Since the jacobian files contain only positive numbers, is there any way to make a distinction between a brain area that needs to be stretched bigger to fit the template versus a brain area that needs to be squished smaller? fsaverage is comprised of 40 subjects, but I wonder if the jacobian is most accurate only for my subjects that have the same age as the fsaverage mean? If so, then the younger subjects would need to be squished and the older subjects would need to be stretched. But since the jacobian is always positive, then on a scatterplot of jacobian versus age, this would look like a hump centered on the fsaverage mean age. Am I on the right track with this? Thank you, Jeff ___ 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] Cortical Normalization Questions
Hi Jeff yes, I think this is still our recommendation for thickness, although perhaps David Salat can verify. As far as surface area, you might get Anderson Winkler to send you a preprint of his newly accepted paper on surface area comparisons and how to do them properly. I would have said normalize by the 2/3 root of ICV (maybe David can comment on this as well) cheers Bruce On Thu, 22 Mar 2012, Jeff Sadino wrote: Hello, For cortical thickness normalizations, Bruce said not to normalize based on a HBM abstract (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html). Is this still the consensus? For cortical volume, it is pretty standard to normalize to eTIV. For cortical surface area (jacobian), I couldn't find any information on the wiki. Does anyone have any recommendations? Thank you, Jeff ___ 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] Cortical Normalization Questions
Hi Jeff, I personally like the idea of using average thickness as a covariate to control for a reduction in whole brain thickness, and have used that approach in a paper. If the Abstract that you mentioned indicated that this is flawed, I'd be curious to know what the reason was... cheers, -MH On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote: Hi Jeff yes, I think this is still our recommendation for thickness, although perhaps David Salat can verify. As far as surface area, you might get Anderson Winkler to send you a preprint of his newly accepted paper on surface area comparisons and how to do them properly. I would have said normalize by the 2/3 root of ICV (maybe David can comment on this as well) cheers Bruce On Thu, 22 Mar 2012, Jeff Sadino wrote: Hello, For cortical thickness normalizations, Bruce said not to normalize based on a HBM abstract (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html). Is this still the consensus? For cortical volume, it is pretty standard to normalize to eTIV. For cortical surface area (jacobian), I couldn't find any information on the wiki. Does anyone have any recommendations? Thank you, Jeff ___ 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] Cortical Normalization Questions
Yes, I think Mike's approach is a good one also, although you have to be clear about the somewhat different hypothesis you are testing On Mar 22, 2012, at 9:15 PM, Michael Harms mha...@conte.wustl.edu wrote: Hi Jeff, I personally like the idea of using average thickness as a covariate to control for a reduction in whole brain thickness, and have used that approach in a paper. If the Abstract that you mentioned indicated that this is flawed, I'd be curious to know what the reason was... cheers, -MH On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote: Hi Jeff yes, I think this is still our recommendation for thickness, although perhaps David Salat can verify. As far as surface area, you might get Anderson Winkler to send you a preprint of his newly accepted paper on surface area comparisons and how to do them properly. I would have said normalize by the 2/3 root of ICV (maybe David can comment on this as well) cheers Bruce On Thu, 22 Mar 2012, Jeff Sadino wrote: Hello, For cortical thickness normalizations, Bruce said not to normalize based on a HBM abstract (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html). Is this still the consensus? For cortical volume, it is pretty standard to normalize to eTIV. For cortical surface area (jacobian), I couldn't find any information on the wiki. Does anyone have any recommendations? Thank you, Jeff ___ 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
