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Re: [Freesurfer] Strange Segmentation
by Antonin Skoch 30 Jan '18

30 Jan '18

Dear Arkadiy, I see sometimes these kind of errors. I think they are caused by local mis-segmentation due to WM hypointensities (enlarged perivascular spaces or other lesions, usually benign) located just under GM. Sometimes it is hard to discern where it is a hypointensity and where it is just a sulcus. I recommend to assess them using all 3 slice orientations. I correct them by editing wm.mgz (filling in voxels by value 255). Regards, Antonin Skoch Dear Experts, This brain looks a little bit strange to us, and I was wondering if someone might be able to chime in about whether this is worth editing, based on the screenshots of different slices from the sagittal view.. Thank you for your expertise. -Arkadiy

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A question about FS6 hippocampal subfield segmentation output file
by Darko Komnenić 30 Jan '18

30 Jan '18

Dear FreeSurfer experts, in the txt files [lr]h.hippoSfVolumes-T1.v10.txt we can see the volumes of individual hippocampal subfields - I was wondering what are the units in which volume is given? Millimeters cubic, voxels, or something else? Thanks in advance! Best, Darko

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Re: [Freesurfer] To Yendiki, Anastasia on TRACULA (Yendiki, Anastasia)
by Renew Andrade 30 Jan '18

30 Jan '18

What is the configuration file or where can I find it?

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Programmer/Research Tech position available at Washington University in St. Louis
by Westerhaus, Elizabeth 30 Jan '18

30 Jan '18

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Calculating cortex scalp distance of a region of interest
by Lucia B 30 Jan '18

30 Jan '18

Dear Freesurfer experts, I would like to calculate the mean distance from cortex to the scalp in a region of interest (the area under the stimulator), to investigate the influence of this distance on tDCS effects. A similar question was asked in the archives, and the use of mris_distance_transform was suggested. I am new to freesurfer, and I wasn't able to figure out if this approach is suitable for me and, if yes, what files I need to load in. I checked mris_distance_transform -help, yet I am still missing some parts. Could you point me to the right direction? As <label>, can I load in the ROI of the area under the scalp electrode? I tried to run the function with lh.pial and the lh.BA45.label just to see how it works, and I also have questions concenring the output: mris_distance_transform surf/lh.pial label/lh.BA45_exvivo.label unsigned lh.dist writing surface values to surf/lh.dist.w. avg = 101.288, stdev = 50.852, min = 0.206, max = 207.610 distance transform took 0.1 minutes How can I view the output file lh.dist.w.? And what do the values mean (is it by any chance already the mean distance from the surface to the label I am looking for, and if yes, what is the dimension)? Any suggestions would be highly appreciated! Many thanks! Lucia

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Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx?
by Yendiki, Anastasia 29 Jan '18

29 Jan '18

As a sanity check, you can downsample one of the data sets that fail to 2mm iso, and see if it runs that way. This would tell you if it's a data size issue. ________________________________ From: Carissa Nicole Weis <cnweis(a)uwm.edu> Sent: Monday, January 29, 2018 5:53:59 PM To: Yendiki, Anastasia Subject: RE: [Freesurfer] TRACULA path segmentation fault error because of bedpostx? I went back and checked and it was just a mistake in our paperwork. All of the subjects’ data were acquired at 1x1x2 resolution, but for some reason some of the subjects would run through bedp on the first pass while others required several passes. I’ve requested additional memory on our cluster to run the subjects who stalled, but that didn’t make a difference. If you don’t see any potential issues from your end, then I’m beginning to think it could be a technical issue with our cluster perhaps it’s timing out or freezing after running for too long. I’ll look into this more to see if I can find any issues there. Do you have any other recommendations for troubleshooting at this point? Thanks, Carissa From: Yendiki, Anastasia [mailto:AYENDIKI@mgh.harvard.edu] Sent: Monday, January 29, 2018 1:54 PM To: Carissa Nicole Weis <cnweis(a)uwm.edu> Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx? The subjects that run through with no problems have 2mm isotropic resolution and the subjects that give you the segmentation fault have higher resolution? Then it sounds like a problem of insufficient memory. ________________________________ From: Carissa Nicole Weis <cnweis(a)uwm.edu<mailto:cnweis@uwm.edu>> Sent: Sunday, January 28, 2018 9:44:08 PM To: Yendiki, Anastasia Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx? My mistake. It was acquired that way. Also, after running my subjects through the -bedp step several times I’ve now only got one subject who is lingering there, but some subjects had to run 7+ times through bedp before finishing properly. I do have another dataset to analyze that was acquired with the same parameters so it’s quite possible this issue may arise again. Thanks again for your help, Carissa 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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Re: [Freesurfer] aparc-aseg vs aseg label maps
by elisabetta_delre＠hms.harvard.edu 29 Jan '18

29 Jan '18

Hi FS team, running FS 5.3 and checking the labelmaps, there are some differences between the aseg and the aparc-aseg maps. The aparc-aseg are more inclusive. My understanding is that volumes for global measures are calculated from aseg. Could that cause problems in accuracy? Thank you so much, best, Elisabetta > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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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Strange Segmentation
by Maksimovskiy, Arkadiy 29 Jan '18

29 Jan '18

Dear Experts, This brain looks a little bit strange to us, and I was wondering if someone might be able to chime in about whether this is worth editing, based on the screenshots of different slices from the sagittal view.. Thank you for your expertise. -Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School [cid:image001.png@01D39915.A264E300][cid:image002.png@01D39915.A264E300][cid:image003.png@01D39915.A264E300][cid:image004.png@01D39915.A264E300][cid:image005.png@01D39915.A264E300]

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To Yendiki, Anastasia on TRACULA
by Renew Andrade 29 Jan '18

29 Jan '18

Dear Anastasia: All the output I get is the if Expression Syntax.

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strange output from lme analysis - Max r value=inf
by Valsasina Paola 29 Jan '18

29 Jan '18

Dear all I am using the lme toolbox to perform a longitudinal comparison of cortical thickness among 4 patient groups. Following the lme tutorial, I concatenated all files and I built a design matrix with following columns: -one column for intercept (all ones) -one column for time -four columns for each group (1 for subjects belonging to the group, zero otherwise) -four columns for group by time interaction I then built appropriate contrasts to test the effects of time, group and time x group effect; e.g., to test time x group interaction between group 1 and group 2, I built the following contrast: CM.C=[0 0 0 0 0 0 1 -1 0 0] However, I obtain quite strange results, because I get a lot of very small, very significant clusters of difference (having max t value = inf or -inf). Do you have any idea of the reason why I am getting this strange output? In your opinion, is there anything wrong in my design matrix or in the way I defined the contrasts? This is the first time I am trying to compare four groups in the same LME models, I previously ran LME statistics including just one or two groups, and everything ran smoothly. Please see a snapshot of my output statistic below: # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs Annot 1 -inf 112586 0.96 -19.0 -95.2 8.3 1 lateraloccipital 2 -inf 93693 0.89 -22.0 54.4 16.4 1 rostralmiddlefrontal 3 inf 29207 0.86 -35.9 46.6 -9.9 1 parsorbitalis 4 inf 158564 0.78 -13.7 -98.8 2.3 1 lateraloccipital 5 -inf 67614 0.69 -8.3 35.1 25.4 1 superiorfrontal 6 -inf 123144 0.69 -40.3 19.5 29.8 1 caudalmiddlefrontal 7 -inf 2273 0.68 -55.6 -30.9 24.2 1 supramarginal 8 -inf 140663 0.67 -6.2 39.1 -4.4 1 rostralanteriorcingulate 9 -inf 5857 0.64 -35.5 8.6 50.8 1 caudalmiddlefrontal 10 inf 87756 0.61 -14.1 -98.2 1.7 1 lateraloccipital 11 inf 95576 0.56 -43.9 24.5 27.5 1 rostralmiddlefrontal 12 -inf 112122 0.56 -29.0 -62.8 35.9 1 inferiorparietal 13 inf 54800 0.54 -18.7 -59.3 2.6 1 lingual 14 -inf 140378 0.53 -19.0 -42.5 62.6 1 superiorparietal 15 inf 99044 0.49 -43.7 -20.0 52.6 1 postcentral 16 inf 119372 0.47 -52.1 -2.5 25.5 1 precentral 17 -inf 125951 0.47 -44.3 -55.1 12.7 1 inferiorparietal 18 inf 8776 0.46 -57.0 -2.0 11.7 1 precentral 19 inf 10137 0.44 -27.8 -49.8 -1.9 1 lingual 20 inf 20153 0.42 -6.6 13.8 29.5 1 caudalanteriorcingulate 21 -inf 19380 0.40 -61.6 -8.6 13.7 1 postcentral 22 -inf 38802 0.39 -23.9 -56.1 49.0 1 superiorparietal 23 inf 53936 0.38 -45.3 -25.9 46.7 1 postcentral 24 inf 45406 0.35 -38.8 -36.8 36.7 1 supramarginal 25 -inf 46213 0.32 -6.4 -47.6 15.7 1 isthmuscingulate 26 inf 41829 0.26 -61.1 -8.7 10.5 1 postcentral 27 -13.032 76609 0.40 -14.4 -15.8 64.7 1 precentral 28 12.272 78924 0.27 -6.0 -6.5 30.3 1 posteriorcingulate 29 -10.960 822 0.63 -51.8 -30.1 -17.2 1 inferiortemporal 30 10.326 96572 0.48 -31.7 11.6 0.5 1 insula 31 -8.509 43473 0.54 -62.2 -26.3 6.7 1 superiortemporal .. continued with a lot of significant clusters, all 1 vertex in size .. Thank you for any suggestion Best regards Paola Rispetta l'ambiente: non stampare questa mail se non ? necessario. Respect the environment: if it's not necessary, don't print this mail.

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