Freesurfer

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6 participants
30076 discussions

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

3 2

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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Re: [Freesurfer] Extracting structural measures from trend-level PET clusters
by Elijah Mak 14 Nov '16

14 Nov '16

Hi, A bit more info: the stack of thickness maps consists of lh.thickness.fwhm15.fsaverage.mghs that were created after -qcache. I used mri_concat --f --o to create the stack of mghs. I also noticed that the vertex values are in the range of 20-30, whereas those in the lh.thickness.fsvaerage mghs are in the expected range. Should I be using this for the calculation of the thickness in the clusters instead? Best Wishes, Elijah On Sat, Nov 12, 2016 at 12:15 AM, Elijah Mak <fkm24(a)medschl.cam.ac.uk> wrote: > Thanks, Doug. > > It works but I am not sure if the values I'm getting are correct. Is this > supposed to be reporting the mean cortical thickness of each cluster? I > have pasted the output below from the avgwf below. The names of the > clusters correspond to the regions from the "summary" text, am I right? > > > Group lh_fusiform lh_precentral lh_insular lh_precuneus lh_parsorbitalis > 1 24.29454 29.53935 14.24736 28.97924 31.54577 > 1 25.68872 28.26156 17.47828 28.20604 30.38902 > 2 25.46281 30.75879 19.34943 29.59019 32.0404 > 2 25.55514 27.23871 17.27937 29.14274 29.75657 > > Another related question: Is it possible to simply take the mean cortical > thickness across the voxels exceeding p<0.001 from the uncorrected sig.mgh? > > Thanks again! > > Best Wishes, > Elijah > > -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

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Invalid FreeSurfer license key problem
by Xiangzhen Kong 14 Nov '16

14 Nov '16

Hi, Anyone has solved a similar problem with 'Invalid FreeSurfer license key'? I have just got a license though email, and put the four-line code in a file named license.txt. Now the file is in the folder where I installed freesurfer. It should work well but it didn't. When I used tksurfer, something was printed out. "ERROR: Invalid FreeSurfer license key found in license file xxxxx/freesurfer/license.txt" Please help. Thanks, Xiangzhen -- ----------------------------------------------------------------------------------------- Kong Xiangzhen State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China, 100875.

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Voxel time series after nuisance regressors removal using fsfast
by Ladan Shahshahani 13 Nov '16

13 Nov '16

Dear fsfast users, I've just started to use fsfast for resting state fMRI data processing. I wonder if I could have a 4-D nifti file after nuisance regressors are removed. I do not want to perform any functional connectivity analysis. I just need each voxel time series after nuisance regressors are removed. Any ideas? Thanks in advance. Ladan

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dtrecon
by John Anderson 13 Nov '16

13 Nov '16

2 1

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