Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Spot Opened in Boston FreeSurfer course
by Allison Stevens Player 22 Mar '12

22 Mar '12

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

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Future of freesurfer
by Nicolas Rannou 22 Mar '12

22 Mar '12

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on mac osx lion, ubuntu 12.04 (will be relased soon) and lots of packages which are required by freesurfer appear to be outdated.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

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Displaying results from qdec on a single subject
by Emily Rogalski 22 Mar '12

22 Mar '12

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 erogalski(a)gmail.com

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editing pial surface
by Richter, Julia 22 Mar '12

22 Mar '12

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

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mkheadsurf and smseghead
by Will Woods 22 Mar '12

22 Mar '12

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

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Robust register
by Ed Gronenschild 22 Mar '12

22 Mar '12

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

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(no subject)
by Richter, Julia 22 Mar '12

22 Mar '12

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

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Qdec - generate stats data table
by Ahmed, F, Me <fahmed＠sun.ac.za> 22 Mar '12

22 Mar '12

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.

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Skull strip failure
by Vincent 21 Mar '12

21 Mar '12

Hi, I have an image that is completing the skull strip with a lot of skull remaining and it is have a large effect on the surfaces. I've tried lowering the watershed threshold as low as 5 and I've tried adding the -gcut option, but the low threshold by itself does not eliminate the skull and gcut not only fails to remove the skull but it removes cerebellum as well. There is so much skull left that I am hesitant to try manual edits, but I don't know any other options. Are there any? By the way, this brain is from an older individual with pretty substantial atrophy. --Vincent

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custom making an overlay
by Linda Douw 21 Mar '12

21 Mar '12

Hi freesurfers, Is it possible to make an overlay to load into tksurfer containing any type of data (for instance, centrality measures computed with graph theory) for a particular annotation? In the mailing archive, I've found tips about creating a custom LUT table and making it a segmentation, but you need the coordinates of the labels for that. In my case, I've made my own parcellation by using mris_divide_parcellation, so then I would have to know where to find the coordinates (I don't). And do you think this is the most efficient method? Thanks! -- Linda Douw, Ph.D.

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