Freesurfer March 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

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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fsaverage documentation
by Emily Rogalski 21 Mar '12

21 Mar '12

Hi All, I was looking for documentation on the fsaverage brain but I do not have permission to access the *Buckner40<http://surfer.nmr.mgh.harvard.edu/fswiki/Buckner40>page for notes on building fsaverage*. http://surfer.nmr.mgh.harvard.edu/fswiki/Buckner40 Has the information on this page been relocated? If so, can you point me to the new location? 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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Skull strip and white matter
by Vincent 21 Mar '12

21 Mar '12

Hi, I am having an issue where some dura remains behind after the skull strip and is being mistakenly classified as white matter. Since it is just dura, and not skull, would it be better to edit the white matter volume or should I start by adjusting the skull strip since occurs earlier in the recon-all processing stream? --Vincent

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interpreting cluster results
by Govindarajan, Koushik Athreya 21 Mar '12

21 Mar '12

Dear FS group, This may be a trivial question. Could not find answer in the archives. When Freesurfer outputs cluster summary files, it displays number of vertices (NVtxs). What is the size of each of these vertices. In other words, is there a standard correspondence between number of vertices and area of the cluster. Thanks Koushik

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Tkmedit question
by Antonella Kis 21 Mar '12

21 Mar '12

Dear All, I am trying to understand what should be my -fthresh and -fmax or -fmin and -fmax values while visualizing in tkmedit the significant map of uncorrected results so I can see all the clusters in this map. Further,I want to see what clusters from this map did not survived after corrections by multiple comparison for cluster voxel-wise equal 3. Thank you. Antonella

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Structural images quality
by Cícero Nardini Querido 21 Mar '12

21 Mar '12

Hi everyone, I am going to use FreeSurfer to analyze cortical thickness in some structural images. In order to generate the individual output, Freesurfer asks for 2 different input images. If I have two acquisitions from the same subject, but they present different degrees of quality (such as movement index), would it be better to use just one of them? Is there any problem in doing that? Also, is there a reliable index to assess the images level of movement before I use them on FreeSurfer? Thanks for that!

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Freesurfer March 2012