Freesurfer November 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
214 discussions

Pial medial line crossover at hemispheres
by Hampton, Jackie 15 Nov '16

15 Nov '16

In some of my subjects, the medial pial line crosses over the hemispheres. It mislabels in both brainmask and aseg. So the part that it crosses too far over in the left hemisphere is now mislabeled. I have seen this issue in the forums before, but it didn’t seem that there was a definitive fix to the issue. I am just hoping someone will be able to give me some direction. I have tried deleting voxels to no avail. Thank you! I have attached screenshots of the issue that I am having. Jackie Hampton Clinical Research Study Assistant Nico Dosenbach, MD, PhD & Deanna Greene, PhD Department of Neurology Washington University School of Medicine 660 S. Euclid Ave. | Campus Box 8111 St. Louis, MO 63110 Phone: 314-362-4154 jackiehampton(a)wustl.edu<mailto:jackiehampton@wustl.edu> [cid:5AAC79BE-115F-42BD-8A62-90FBF1552F21][cid:9C620881-C7CB-4917-AB7E-675324F74007] ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] Cluster Color
by Timothy Hendrickson 15 Nov '16

15 Nov '16

It seems that this message has been ignored. I really do need an answer on this. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay)

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Wm edits not used in -autorecon2-wm
by jari gool 15 Nov '16

15 Nov '16

Dear all, In three of my subjects one of the sides of the T1 scan is brighter than the other side (probably a coil problem). This resulted in the recon-all processing stream identifying not enough white and gray matter, even though the brainmask.mgz included the whole brain. Since I will use my T1 scans as registration for my DTI scans only the white matter is of importance and loss of gray matter is not really an issue. I manually edited the wm.mgz using the voxel edit function. I tried to rerun the pipeline in the same subject folder with this command: recon-all -autorecon2-wm -autorecon3 -s 0008_smri_t1 with the wm.mgz being replaced by my edited version (red overlay in attached screenshot). It finished without errors according to the log files (one is attached), but no changes were made to the output files (e.g. aparc+aseg and lh.white) as can been seen in the screenshots. Do you have any idea why the white matter that I added in wm.mgz has not been included in the new output files? Secondly, do you have any idea how I could fix this? I am still a bit new to Freesurfer, so help would be very welcome! Kind regards, Jari Gool Department of Neurology - Leiden University Medical Center - The Netherlands

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localGI command
by Lauren Gascoyne 15 Nov '16

15 Nov '16

Dear Freesurfer developers, I am attempting to run the localGI command to calculate the gyrification of a group of subjects. Freesurfer version 5.3.0 was used all the way through the process. The command I have been using is as follows: recon-all -s <subjid> -localGI However it crashes straight away with the following error: ERROR: cannot find /opt/magres/freesurfer-v5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs When I look for the file mentioned in the error, the following file is there instead: lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs Do you know why the folder contains a different file from the one the command is looking for? I cannot find this error reported elsewhere. Any ideas are much appreciated, thanks. Thanks very much Lauren This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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MP2RAGEs
by Torrisi, Sam (NIH/NIMH) [E] 15 Nov '16

15 Nov '16

hi there, will FS 6.0 have any special options for MP2RAGE sequences? specifically i'm trying to decide whether to collect MPRAGE or MP2RAGE T1s; either would be at 0.7mm iso (7T data). i've heard skull-stripping is the main issue with the MP2RAGE and so i'm curious if FS 6.0 will have any adaptations for that. improved subcortical gm/wm contrast is what's drawing me towards MP2RAGE. thanks! -Sam Section on Neurobiology of Fear and Anxiety National Institute of Mental Health

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Re: [Freesurfer] nuisance dichotomous variables
by Dominic Dwyer 14 Nov '16

14 Nov '16

Hi Prof. Greve, Thanks for the response and sorry for the confusion. I mean can we use dichotomous variables in the "Nuisance Factors" box of qdec? i.e., if we don't explicitly define them as categorical variables. I was thinking that if it's a GLM then it should be ok? We want to do this because we have more than one dichotomous variable that we want to control for. Many thanks, Dom -------------------------------------------------------------------- Dom Dwyer, PhD Psychiatry & Psychotherapy LMU Munich A: Nußbaumstr. 7, Munich, 80336 E: dominic.dwyer(a)med.uni-muenchen.de T: +49 (0)89 4400 55880 I'm not sure what you mean. Dichotomous variables can be used. Our tutorial has an example of using gender. On 11/9/16 5:05 AM, Dominic Dwyer wrote: Dear FS experts, Sorry for my confusion here, but I'm wondering why dichotomous nuisance variables (e.g., gender) can't be used in qdec? I was thinking that if it uses a generalized linear model then it should be ok? I read other posts and understand why discrete factors can't be used with more than 2 levels, but was thinking that dichotomous variables should be different. NB. we're trying to run a simple two group comparison, but we two dichotomous variables that we want to control for. Many thanks for your help, Dom -------------------------------------------------------------------- *Dom Dwyer, PhD* Psychiatry & Psychotherapy LMU Munich A: Nußbaumstr. 7, Munich, 80336 E: dominic.dw...(a)med.uni-muenchen.de <mailto:dominic.dw...@med.uni-muenchen.de> T: +49 (0)89 4400 55880

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mri_convert issue
by DaWoon Heo 14 Nov '16

14 Nov '16

Dear Freesurfer experts, I would like to use the ‘mir_convert --out_orientation LAS’ to change the orientation of my data (i.e. fMRI T1 data). >From several materials, I could find it is not a good idea to change the orientation. However, to improve the efficacy of ‘bet’, it seems converting the orientation is necessary. The problem is, when I use ‘mir_convert --out_orientation LAS’, I could find some top of the skull and brain areas were severed. Thus, may I ask you for an advice to solve this problem? Many thanks in advance. Best regards, DaWoon

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Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label
by Matthieu Vanhoutte 14 Nov '16

14 Nov '16

Thank you Douglas for giving me a way to compute area from segmented surface data. Are vertices equally spaced along cortex or do triangles all have same area ? Best, Matthieu Le 11 nov. 2016 10:55 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> a écrit : If you want to do it on fsaverage, then mris_segstats --i $SUBJECTS/fsaverage/surf/lh.white.avg.area.mgh --seg lh.sign_clust.bin.mgh --excludeid 0 --sum lh.bin.area.sum --accumulate On 11/11/2016 04:48 PM, Matthieu Vanhoutte wrote: > > Dear Douglas, > > Yes I would like to in order to compute mean of some means. Maybe not > if it is equivalent to number of vertices (are vertices distributed > equaly distant on the cortical surface ?) > > In case I need surface area, do I have to convert overlay to > annotation file to be used with mri_segstats ? > > Best regards, > Matthieu > > > Le 11 nov. 2016 9:21 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> a écrit : > > NVox is the number of vertices. The Volume_mm3 is not meaningful. > Do you > want area? > > > On 11/11/2016 04:53 AM, Matthieu Vanhoutte wrote: > > Dear Douglas, > > > > I come back to you concerning stats made from binary .mgh > surface data > > file: > > > > mri_segstats --i lh.fsaverage.sm10.mgh --seg lh.sign_clust.bin.mgh > > --excludeid 0 --sum lh.bin.sum --avgwf lh.wav.bin.txt > > > > In the output file « lh.bin.sum » all is considered as volume > > input/output as you could see below: > > > > /# InVolFileTimeStamp 2016/04/28 09:46:19 / > > /# InVolFrame 0 / > > /# ExcludeSegId 0 / > > /# Only reporting non-empty segmentations/ > > /# VoxelVolume_mm3 1 / > > /# TableCol 1 ColHeader Index / > > /# TableCol 1 FieldName Index / > > /# TableCol 1 Units NA / > > /# TableCol 2 ColHeader SegId / > > /# TableCol 2 FieldName Segmentation Id/ > > /# TableCol 2 Units NA/ > > /# TableCol 3 ColHeader NVoxels / > > /# TableCol 3 FieldName Number of Voxels/ > > /# TableCol 3 Units unitless/ > > /# TableCol 4 ColHeader Volume_mm3/ > > /# TableCol 4 FieldName Volume/ > > /# TableCol 4 Units mm^3/ > > /# TableCol 5 ColHeader Mean / > > /# TableCol 5 FieldName Intensity Mean/ > > /# TableCol 5 Units unknown/ > > /# TableCol 6 ColHeader StdDev/ > > /# TableCol 6 FieldName Itensity StdDev/ > > /# TableCol 6 Units unknown/ > > /# TableCol 7 ColHeader Min/ > > /# TableCol 7 FieldName Intensity Min/ > > /# TableCol 7 Units unknown/ > > /# TableCol 8 ColHeader Max/ > > /# TableCol 8 FieldName Intensity Max/ > > /# TableCol 8 Units unknown/ > > /# TableCol 9 ColHeader Range/ > > /# TableCol 9 FieldName Intensity Range/ > > /# TableCol 9 Units unknown/ > > /# NRows 1 / > > /# NTableCols 9 / > > /# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev > > Min Max Range / > > / 1 1 11510 11510.0 Seg0001 7.6819 1.4396 > > 4.4862 10.9042 6.4180 / > > > > As my inputs are all surface data could I consider that NVoxels is > > equal to NVertices and Volume_mm3 is equal to SurfaceArea_mm2 ? > > > > Best regards, > > Matthieu > > > >> Le 10 nov. 2016 à 23:18, Matthieu Vanhoutte > >> <matthieuvanhoutte(a)gmail.com > <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com > <mailto:matthieuvanhoutte@gmail.com>>> a > >> écrit : > >> > >> Thank you Douglas ! > >> > >> > >> Le 10 nov. 2016 7:21 PM, "Douglas N Greve" > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > >> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> a écrit : > >> > >> You need to weight by the number of vertices > >> > >> n = [27805 2321 552]; > >> m = [8.8194 10.3661 10.3365]; > >> sum(n.*m)/sum(n) > >> > >> ans = > >> > >> 8.9637 > >> > >> > >> On 11/10/2016 06:44 AM, Matthieu Vanhoutte wrote: > >> > Dear Freesurfer's experts, > >> > > >> > Could anyone please explain me the difference I got with > >> command line > >> > in below mail ? > >> > > >> > Best regards, > >> > Matthieu > >> > > >> > 2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte > >> > <matthieuvanhoutte(a)gmail.com > <mailto:matthieuvanhoutte@gmail.com> > >> <mailto:matthieuvanhoutte@gmail.com > <mailto:matthieuvanhoutte@gmail.com>> > >> <mailto:matthieuvanhoutte@gmail.com > <mailto:matthieuvanhoutte@gmail.com> > >> <mailto:matthieuvanhoutte@gmail.com > <mailto:matthieuvanhoutte@gmail.com>>>>: > >> > > >> > Dear experts, > >> > > >> > I am in trouble with two ways of computing mean > intensity with > >> > mri_segstats. > >> > > >> > First I have used on .annot files with three > different labels > >> > inside (SegId 1 to 3) : > >> > > >> > /mri_segstats --annot fsaverage lh > cache.th23.pos.sig.ocn.annot > >> > --i lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum/ > >> > / > >> > / > >> > which give me those results: > >> > # ColHeaders Index SegId NVertices Area_mm2 > StructName Mean > >> > StdDev Min Max Range > >> > 1 1 27805 14182.6 cluster-001 8.8194 1.4351 > >> > 6.2105 14.2947 8.0842 > >> > 2 2 2321 1047.3 cluster-002 10.3661 > 1.0848 > >> > 8.8375 12.9317 4.0942 > >> > 3 3 552 313.1 cluster3 10.3365 0.4711 > >> > 9.3719 11.8694 2.4975 > >> > > >> > Second I have created on .label files containing the > three > >> > segmented labels (SegId 1 to 3) and used this label with > >> mri_segstats: > >> > > >> > /mri_segstats --slabel fsaverage lh > >> > lh.th23.cluster.thresh1.3.label --i > lh.PET.fsaverage.sm10.mgh > >> > --excludeid 0 --sum lh.pet.label.sum / > >> > / > >> > / > >> > which give me those results:/ > >> > / > >> > /# ColHeaders Index SegId NVertices Area_mm2 > StructName Mean > >> > StdDev Min Max Range / > >> > / 1 1 30678 15542.9 Seg0001 8.9637 1.4701 > 6.2105 > >> > 14.2947 8.0842 / > >> > / > >> > / > >> > I verified if I obtained the same results with the > two ways > >> > (.annot or .label) and everything is fine comparing > NVertices, > >> > Area_mm2 but Mean in first way gives me > >> (8.8194+10.3661+10.3365)/3 > >> > = 9.84066 and with .label file Mean = 8.9637. > >> > > >> > Did I have miss anything and how is computed mean > intensity ? > >> > > >> > Many thanks in advance. > >> > > >> > Best regards, > >> > Matthieu > >> > > >> > > >> > > >> > > >> > _______________________________________________ > >> > Freesurfer mailing list > >> > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > >> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > >> > >> -- > >> Douglas N. Greve, Ph.D. > >> MGH-NMR Center > >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > >> Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > >> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > >> > >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > >> <https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2>> > >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > >> Outgoing: > >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > >> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > >> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <http://www.partners.org/complianceline> > >> <http://www.partners.org/complianceline > <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(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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complement of a label
by Eryilmaz, H. Hamdi 14 Nov '16

14 Nov '16

Dear FreeSurfers, I was wondering if there is a standardized way to construct a label that is the complement of a regional label on freesurfer. For example, I have a customized DLPFC label and would like to create another label that encompasses the entire cortex except that DLPFC region. Thanks for your help. Best, Hamdi

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Surface-Edges
by Foteini Protopapa 14 Nov '16

14 Nov '16

Dear FS experts, I have a volume with specific clusters and I project it to a surface using mri_vol2surf. How can I determine the edges of my clusters now? Thanks in advance, Foteini.

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Freesurfer November 2016