Freesurfer

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30099 discussions

Re: [Freesurfer] major lobes
by Juranek, Jenifer 25 Mar '14

25 Mar '14

Hi Doug, I recently saw your solution to a reported problem with grabbing StrictLobes WM & GM (posted on the Freesurfer forum 12/04/2013; thread title= major lobes). I have successfully grabbed the StrictLobes WM, but I am having trouble with the GM. According to the forum (posted 12/04/2013), the solution that worked was a link (you provided) to download a new binary for mri_annotation2label from the following location:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_… However, this link appears to be broken now that I am attempting to utilize your fix on my RHEL6 workstation. I checked the download site , but there is no new version of Freesurfer since May 2013. Any chance you could provide a link to the new binary for mri_annotation2label you had made available back in Dec 2013? Many Thanks, Jenifer Juranek

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Request for feedback on challenges/hurdles to using/learning Nipype
by Satrajit Ghosh 25 Mar '14

25 Mar '14

hi all, we are looking for feedback on learning/using/installing Nipype - any challenge or hurdle that may have derailed you, wasted your time, left you wanting a photon torpedo, etc.,. we are in the process of re-architecting components of Nipype and feedback would help a lot. please post/discuss at: http://neurostars.org/p/73/ cheers, satra

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Convert volume label to surface label
by Karen Marie Sandø Ambrosen 25 Mar '14

25 Mar '14

Hi Freesurfer experts, I have a volume label only which is only different from zero in the white matter-gray matter boundary. I am trying to convert this volume label to a surface label in order to visualize it in tksurfer. I am using mri_vol2surf: mri_vol2surf --mov volume_label.nii --out volume_label2surf.mgh --out_type mgh --hemi lh --regheader H01 --surf white --ref volume_label.nii However, when I load this surface as an overlay in tksurfer, to check the correctness, the original surface is not fully covered by the surface created by mri_vol2surf. Is there any way to make the surface fully cover the original surface so it doesn't look speckled? After creating the surface I want to convert the surface to labels by mri_cor2label and finally to an annotation file by mris_label2annot. Best, Karen

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R: Re: TRACULA statistics concern
by stdp82＠virgilio.it 24 Mar '14

24 Mar '14

Ciao Eugenio, thank you very much for your prompt and kind response.Yes, I'm looking average over the entire support of the path distribution and their differences among 2 pathological and 1 control groups.I haven't a strong hypothesis.When I performed MANOVA, Tukey or Bonferroni post hoc find differences but p for Wilk's lambda is not significant.If I understand your suggestion, I should performed a simple t-test for each tract.Bur, for Bonferroni's correction, I should consider: A. 0.05/18 tracts X 3 groups (I suspected that it should be too hard)orB. 0.05/18 tractsor more simplyC. 0.05/3 groups Thanks, Stefano ----Messaggio originale---- Da: iglesias(a)nmr.mgh.harvard.edu Data: 24-mar-2014 22.11 A: <stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] TRACULA statistics concern Ciao Stefano, can you be a bit more specific about what you're exactly trying to to? Am I correctly assuming that you are looking at differences between your groups? Are you looking at average FA/MD/RD/AD over whole tracts, or at values along them? Do you have any strong hypothesis on which tract will give you differences? In any case, people often look at the tracts of interest one by one (which a simple test, e.g., t-test) and then apply Bonferroni correction. Kind regards, /Eugenio On Mon, 2014-03-24 at 21:39 +0100, stdp82(a)virgilio.it wrote: > Hi list, > > > I'm performing TRACULA on three groups for all 18 tracts and for FA, > MD, RD, AD. > > > Which is the best way to perform statistic on TRACULA outcomes? I > think that MANCOVA is too hard and it delete interesting and > consolidate (in literature) results. > > > Thanks, > > > > > Stefano > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > 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 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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TRACULA statistics concern
by stdp82＠virgilio.it 24 Mar '14

24 Mar '14

Hi list, I'm performing TRACULA on three groups for all 18 tracts and for FA, MD, RD, AD. Which is the best way to perform statistic on TRACULA outcomes? I think that MANCOVA is too hard and it delete interesting and consolidate (in literature) results. Thanks, Stefano

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Re: [Freesurfer] Hemisphere stats question
by Douglas N Greve 24 Mar '14

24 Mar '14

Is this the difference you mean? [t:D:mri-> grep Cortex ~/tmp/lh.total.stats # Measure Cortex, NumVert, Number of Vertices, 118847, unitless # Measure Cortex, SurfArea, Surface Area, 78090, mm^2 [t:D:mri-> grep Cortex ~/tmp/lh.aparc.stats # Measure Cortex, NumVert, Number of Vertices, 111237, unitless # Measure Cortex, SurfArea, Surface Area, 72998.7, mm^2 If so this is just the difference in the vertices coverted by cortex.label vs aparc On 03/24/2014 12:49 PM, _andreia_(a)sapo.pt wrote: > Hi Doug, > > I've attached the files. To contextualize a little bit, I'm using > Brodmann Areas measures (CT, surface area and volume, thresholded to > the correct probability) and I'll be extracting the surface area using > pial and white surface. However, I'll be also analyzing whole brain > using the aparc stats (again, CT, surface area and volume) - should I > use the file that is in agreement with aparc? > > I don't understand why total.stats gives different values from > cortex.stats since I've created the total.stats file using the command: > > mris_anatomical_stats -l ../label/lh.cortex.label -f lh.total.stats -b > SUBJ lh white > > > > One more question: is the ?hCortexvol value from aseg that I should > use to get the total volume of each hemisphere? > > Sorry for so many questions... > > Thank you! > > Andreia > > > Quoting Douglas Greve <greve(a)nmr.mgh.harvard.edu>: > >> How much of a difference is there? There should not be much, but there >> will be some because the aparc does not cover the exact same vertices as >> cortex.label >> doug >> >> >> >> On 3/24/14 8:04 AM, _andreia_(a)sapo.pt wrote: >>> Hello list, >>> >>> I have a question regarding what stats are more correct to use to get >>> whole hemisphere surface area and mean thickness. >>> >>> The cortex.label values extracted using the two bottom command lines >>> don't match aparc stats, however they match in the number of vertices >>> between them, and using pial or white surface also results in values >>> that make sense comparing each one (higher surface area using pial, >>> same thickness, same volumes). >>> >>> In the past I've been using the two first command lines (in which >>> values agree in the same way as cortex.label between them but are also >>> in agreement with aparc.stats), however now I'm having this question: >>> which one is the correct one to use? >>> >>> And why does this difference exists? >>> >>> >>> mris_anatomical_stats -l ../label/lh.cortex.label -f lh.total.stats -b >>> SUBJ lh white (matches aparcstats) >>> >>> mris_anatomical_stats -l ../label/lh.cortex.label -f >>> lh.total_pial.stats -b SUBJ lh pial (matches aparcstats) >>> >>> >>> mris_anatomical_stats -mgz -f ../stats/lh.cortex_pial.stats SUBJ lh >>> pial (does not match aparcstats) >>> >>> mris_anatomical_stats -mgz -f ../stats/lh.cortex_white.stats SUBJ lh >>> white (does not match aparcstats) >>> >>> >>> Thank you in advance, >>> Andreia >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> 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 >> >> >> 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. > > -- 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/

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Re: [Freesurfer] Difference in volumes btw 5.1 and 5,3
by Ed Gronenschild 24 Mar '14

24 Mar '14

Dear Kim, This may be of interest to you: http://dx.plos.org/10.1371/journal.pone.0038234 Cheers, Ed On 24 Mar, 2014, at 17:00, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 3 > Date: Mon, 24 Mar 2014 12:28:29 +0900 > From: jh kim <jhkim.merrf(a)gmail.com> > Subject: Re: [Freesurfer] Difference in volumes btw 5.1 and 5,3 > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CADiwdtbtNUbiXaaQgoR9bwLBrEwFDfu4 > +Zv5VhViDhz3nfQOCg(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Prof. Fischl > > Thanks for the valuable comments. > > Kim > > > 2014-03-23 3:26 GMT+09:00 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > >> Hi Kim >> >> we of course always strive to make things more accurate, but in >> the end >> it will depend on the details of your acquisition and such. I >> don't think >> I have a better answer than that, other than to say look at the >> segmentations and see if you think they are more accurate in one case >> than the other. >> >> sorry >> Bruce >> On Sun, 23 Mar 2014, jh kim wrote: >> >>> Dear Prof. Fischl >>> Thanks for the prompt response. >>> >>> The more specific reason of my query is that there was a >>> difference in >>> statistical significance between two FS versions. >>> For example, the result of group comparison of left thalamic volumes >> (ANCOVA >>> controlling for age and eICV) is statistically significant (p = >>> 0.04) >> when >>> using FS 5.1, whereas the result is no longer significant at all >>> (p = >> 0.28) >>> in case of FS 5.3. >>> I'm a little confused about this discrepancy. >>> Which result should I trust? >>> >>> Thank you in advance for your comments. >>> >>> Kim >>> >>> >>> 2014-03-23 2:59 GMT+09:00 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >>> Hi Kim >>> >>> there are probably lots of little reasons for the differences. >>> This is >>> always true for different versions, and the reason we never >>> mix >>> versions >>> >>> cheers >>> Bruce >>> On >>> Sun, 23 Mar 2014, jh kim wrote: >>> >>>> Dear FS lists >>>> When I measured subcortical GM volumes in the same subjects by >>> using both >>>> version 5.1 and 5.3, I have observed a considerable difference >>> in volumes >>>> between the two versions. >>>> For instance, please see the left thalamic volumes below. >>>> I cannot figure out why there is much difference between the >>> versions. >>>> Which result is more reliable? >>>> >>>> Left-Thalamus-Proper_5.3 >>>> Left-Thalamus-Proper_5.1 >>>> 10313 >>>> 9757 >>>> 8924.8 >>>> 7746 >>>> 9834.8 >>>> 8287 >>>> 7935.2 >>>> 7034 >>>> 8764.1 >>>> 7747 >>>> 9411.8 >>>> 8037 >>>> 7636.7 >>>> 8051 >>>> 9334.7 >>>> 8255 >>>> 10024.3 >>>> 8171 >>>> 8757.7 >>>> 6900 >>>> 9540.9 >>>> 8316 >>>> 9294.4 >>>> 8369 >>>> 8091 >>>> 7366 >>>> 9103.7 >>>> 7818 >>>> 9310.2 >>>> 7974 >>>> 7583 >>>> 6872 >>>> 9838.9 >>>> 8911 >>>> 8829.6 >>>> 8004 >>>> 9094.8 >>>> 6973 >>>> 9492.3 >>>> 8922 >>>> 8821.6 >>>> 7691 >>>> 7971.6 >>>> 7376 >>>> 9901.2 >>>> 8936 >>>> 9773.9 >>>> 8855 >>>> 9283.7 >>>> 7615 >>>> 8801.6 >>>> 7690 >>>> 8505.1 >>>> 7325 >>>> 8981 >>>> 7258 >>>> 9644.7 >>>> 8860 >>>> 9104.2 >>>> 8298 >>>> 8494.8 >>>> 7402 >>>> 9024.9 >>>> 7721 >>>> 8117.8 >>>> 7226 >>>> 8001.8 >>>> 7548 >>>> 8392.3 >>>> 7668 >>>> 8606.6 >>>> 8173 >>>> 9126.7 >>>> 7595 >>>> 8093 >>>> 7885 >>>> 8317.7 >>>> 7157 >>>> 10556 >>>> 9307 >>>> 8669.6 >>>> 8374 >>>> 8034.7 >>>> 7338 >>>> 8148.5 >>>> 7276 >>>> 9048.1 >>>> 8064 >>>> 8160.1 >>>> 7014 >>>> 8747.9 >>>> 7894 >>>> 8329.9 >>>> 6866 >>>> 8415.8 >>>> 8189 >>>> 9246.9 >>>> 8256 >>>> 8194.1 >>>> 7183 >>>> 9629.2 >>>> 9579 >>>> 7688.2 >>>> 6398 >>>> 8349.2 >>>> 8238 >>>> 8366.2 >>>> 7348 >>>> 8436.5 >>>> 7616 >>>> 8372.3 >>>> 6977 >>>> 9396.4 >>>> 7589 >>>> 9327.5 >>>> 7684 >>>> 10001.8 >>>> 8627 >>>> 9762.4 >>>> 9228 >>>> 8841 >>>> 8532 >>>> 8342.4 >>>> 8024 >>>> 8645.7 >>>> 7725 >>>> >>>> Any comment would be appreciated. >>>> Thank you. >>>> >>>> Kim >>>> >>>> >>> _______________________________________________ >>> 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. >>> >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>

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Flipping left-right hemispheres
by Peggy Skelly 24 Mar '14

24 Mar '14

Hi All, Although the question of flipping hemispheres has come up before, I still struggling with it. I'm working on a longitudinal study with stroke subjects (half with lh lesions, half with rh lesions). We want to compare only the non-lesioned, healthy, hemispheres at 2 timepoints (pre- and post-therapy). Using the tutorial (http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial_freeview) as a guide, I've completed the longitudinal analysis (cross-base-long steps) for both lh- and rh-lesioned subjects. I've done the thickness data qcache for the right/healthy hemi for the lh-lesioned group: long_mris_slopes --qdec long_qdec_lh_lesion_subjects_table.dat --meas thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time my_time_var --qcache fsaverage_sym --sd $SUBJECTS_DIR Convert the long_qdec_lh_lesion_subjects_table.dat into a cross.qdec.table.dat to use in qdec. This works well---I can look for clusters where athe average thickness-rate is different from 0. How can I combine the rh-lesioned group with the first group? I thought I could flip hemispheres of the results at each subject's longitudinal output timepoint with: surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi but this terminated with an error: > recon-all -sb s1311_15T_post.long.s1311_15T_base/xhemi -talairach > > ERROR: Are you trying to run or re-run a longitudinal time point? > If so, please specify the following parameters: > > \' -long <tpNid> <templateid> \' > > where <tpNid> is the time point id (SAME as cross sectional > ID) and <templateid> is the ID created in the -base run. > The directory <tpNid>.long.<templateid> will be created > automatically or used for output, if it already exists. I know it's recommended to flip hemispheres after processing (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg34040.html) When (and how) is it best done? Thanks, Peggy

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Hemisphere stats question
by _andreia_＠sapo.pt 24 Mar '14

24 Mar '14

Hello list, I have a question regarding what stats are more correct to use to get whole hemisphere surface area and mean thickness. The cortex.label values extracted using the two bottom command lines don't match aparc stats, however they match in the number of vertices between them, and using pial or white surface also results in values that make sense comparing each one (higher surface area using pial, same thickness, same volumes). In the past I've been using the two first command lines (in which values agree in the same way as cortex.label between them but are also in agreement with aparc.stats), however now I'm having this question: which one is the correct one to use? And why does this difference exists? mris_anatomical_stats -l ../label/lh.cortex.label -f lh.total.stats -b SUBJ lh white (matches aparcstats) mris_anatomical_stats -l ../label/lh.cortex.label -f lh.total_pial.stats -b SUBJ lh pial (matches aparcstats) mris_anatomical_stats -mgz -f ../stats/lh.cortex_pial.stats SUBJ lh pial (does not match aparcstats) mris_anatomical_stats -mgz -f ../stats/lh.cortex_white.stats SUBJ lh white (does not match aparcstats) Thank you in advance, Andreia

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Re: [Freesurfer] Group comparisons
by Tudor Popescu 24 Mar '14

24 Mar '14

Sorry, couple more questions: 1) I know that QDEC's/mri_glmfit's equivalent in FSL ("randomise") applies the GLM by doing permutations, and so already corrects for multiple comparisons in the process. How similar is this to what Monte-Carlo does (i.e. controlling FWE via repeated simulations) upon the initially uncorrected QDEC results? 2) In FSL, a comparison between groups A and B is tested by defining both a "A>B" as well as a "B>A" contrast - the reason being (as far as I understand) that taking the logical complement of "A>B", i.e. inverting the t-values in the statistical map, is *not* equal to the map produced by the cotnrast "B>A". How come, then, that QDEC phrases the group contrast in a "two-tailed" way (i.e. "do groups A and B differ")? Is the dichotomy not necessary in QDEC, or is it simply done behind the scenes? 3) I've read papers where the thickness from *native*-space was used in the analyses, even though initially T1-weighted images were initially aligned to the ICBM 152 template. Why isn't thickness from this *standard*-space used, as happens in FSLVBM with grey matter density? Why even register to the template in the first place if you're then going to go back and use native-space values? Thanks! On 6 March 2014 10:20, Tudor Popescu <tudor3(a)gmail.com> wrote: > Thank you very much Doug. > Tudor > > > On 6 March 2014 03:53, Douglas Greve <greve(a)nmr.mgh.harvard.edu> wrote: > >> >> On 3/5/14 5:25 PM, Tudor Popescu wrote: >> >> Hello, I have some questions on doing group comparisons with thickness, >> area and volume. Many thanks in advance for any help! >> >> 1) For a DOSS design with group and gender as categorical factors, I see >> that an interaction contrast ("Is there a group-gender interaction in the >> mean thickness?") still exists - but what does this contrast mean, given >> that DOSS by definition doesn't allow for interactions? >> >> Are you using QDEC? If so, don't use the DOSS as the contrasts are >> incorrect. It is possible to have an interaction among the categorical >> factors with a DOSS. >> >> >> 2) it makes sense that measures such as thickness are analysed >> vertex-wise in QDEC, however what does it mean when the dependent variable >> is area or volume - measures that do not make physical sense for a single >> vertex but only at the level of a region consisting of *several* vertices? >> >> The interpretation is a little more difficult. Each vertex is assigned an >> area equal to the average of the triangles adjacent to it. This is just a >> value that can be mapped to a common space like any other value (eg, >> thickness) (but there is a special jacobain correction to account for >> stretching or compression). Smoothing reduces the effect of having >> different sized triangles. One can think of it like this: in the common >> space (fsaverage) image having a patch of a certain size. When you mapped >> that patch back to each individual, how big would that patch be? You could >> then do group statistics on that number. In this way you could analyze the >> entire hemisphere. Now imagine doing this but making the patch smaller and >> smaller. >> >> >> 3) For values extracted from atlas regions with aparcstats2table, it >> seems that the product of the extracted CT and area is in the same order of >> magnitude as the extracted volume, but never really the same or even close >> - why, when the volume of a region should theoretically be the product of >> its surface area by its thickness? >> >> It is an issue of how it is computed. Sum(CT*Area) != Sum(CT)*Sum(Area). >> When computing volume, CT*Area is computed for each vertex then summed >> across vertices. >> doug >> >> >> Tudor >> >> >> _______________________________________________ >> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 >> >> >> 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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