Freesurfer June 2017

freesurfer@nmr.mgh.harvard.edu

116 participants
186 discussions

Regarding_ Midbrain_misalignment
by Dr Sampada Sinha 07 Jul '17

07 Jul '17

Dear freesurfer experts, I am trying to over brainstem mask of my patients' group on mmi_colin_t1hires atlas. I had no problems in overlaying thalamus or amygdala mask, but somehow the midbrain mask is shifted from the actual place (please see attachment). Can you please let me know how do I correct this error? Thanks for all your help. Kind regards, Sam -- Dr Sampada Sinha Research medical scientist (B) Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 , Uttar Pradesh India

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cluster analysis in longitudinal analysis
by Livia Liu 07 Jul '17

07 Jul '17

Dear FS experts, I are analysing longitudinal data - the difference of the cortical thickness, surface area and volume between 2 groups (1 and 0) with 2 time points for each group (0, 1 --all the same time interval: a month). I followed the page http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels in wiki. According to experts' advice in the mail-list, I used voxel-wise mixed model “lhstats = lme_mass_fit_vw(X,[1],Y,ni,lhcortex)” to do analysis. And I got the result “sig.mgh” (Freesurfer significance map -log10(p-value)). 1. I loaded the “sig.mgh” to do the FDR correction in the qdec tool. When I press the button of ‘set using FDR ’, the threshold value changes. But the minimum value in the color bar is a little bit small than the value in the table. I used the value in the color bar to get the correction result. Q: Can I do FDR correction like this? And could you give me some more advices about the correction? And how to do other multiple comparison correction like Monte Carlo simulation in longitudinal analysis? 2.To get more infotmation about the cluster, I used the cmd “mri_surfcluster --in sig.mgh --subject fsaverage --surf inflated --hemi lh –thmin *( minimum value in above FDR correction) --sign abs –annot aparc –-sum lh.t.cluster.summary” to generate the set of detected clusters and their anatomical coordinates. Q: I want to know if I use the correct command? 3.I saved clusters’ label file manually in qdec tool. Then I use the cmd "mri_label2label" and "mris_anatomical_stats" to get the value of thickness. Just like the page: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI For area and volume, can I get in the same way? For example, in the stats:# ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd lh.1.label 25 19 51 3.044 0.237 0.105 0.068 0 0 I think that the “SurfArea” is the value of area, “GrayVol” is the value of volume. I wonder that it may be wrong way. In my other GLM analysis, I found that cortical surface area or volume is not an integer in the file “…y.ocn.dat”. Q:Is it right way to get the cluster value? What methods do you recommend to extract the cluster’s mask and the value within the cluster? Thank you very much, and looking forward to reply. Kind regards, Livia

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glm results : opposite direction between whole-brain analysis and feature extraction in the significant clusters
by Damien MARIE 07 Jul '17

07 Jul '17

Hi, I am working on R1 maps. I ran a very simple glm on smoothed R1 maps, FWHM = 8 mm, population 1, population 2 , and age as nuisance factor. After POS MC simulation CW correction, I had two significant clusters resulting from this in the planum temporale and Heschl’s sulcus. The contrast being population 1 - population 2, my interpretation was higher R1 values in these two clusters in Pop 1 as compared to Pop 2. After that I wanted to run some post-hoc tests let say, in a statistical software similar to SPSS, JMP, on the mean R1 values from each of these clusters. The strategy I picked was to stay in the common space, fsaverage, and apply mri_segstats: #Extract mean R1 in montecarlo's significantcluster for i in `cat subjects` do mri_segstats --mul 1000 --annot fsaverage lh PT_mc-z.pos.sig.ocn --i $SUBJECTS_DIR/${i}/surf/lh.R1.fsaverage.fwhm8.mgh --sum lh.PT.R1.${i}.stats done for i in `cat subjects` do mri_segstats --mul 1000 --annot fsaverage lh HS_mc-z.pos.sig.ocn --i $SUBJECTS_DIR/${i}/surf/lh.R1.fsaverage.fwhm8.mgh --sum lh.HS.R1.${i}.stats done Everything when fine but as compared to my glm analysis when looking at mean group differences in my stat software I have the opposite : larger R1 values in Pop 2 as compared to Pop 1 (after removing the effect of age or not, and removing one outlier or not). I went back to my glm and checked everything, fsgd file, matrix and so on, everything seems ok I am not mistaken on the direction of my glm contrast (pop 1 - pop 2) so I do not get it at all. Any advices? For now I am thinking about going back in the individual space, registering my clusters in the individual surfaces (label2surf something like that) and then extract my mean R1 values, or extract values in non-smoothed maps, but I do not think it will change anything. Damien

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Re: [Freesurfer] Brainmask Shifted
by KALEY E ELLIS 07 Jul '17

07 Jul '17

Hi Doug, Our freeview command is: freeview -v ${fs_id}/mri/T1.mgz ${fs_id}/mri/brainmask.mgz:colormap=heat:opacity=0.4 Thank you, Kaley Message: 7 Date: Wed, 14 Jun 2017 16:32:38 +0200 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Brainmask Shifted To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <02f67013-f90c-699f-0307-9f1bf9b131be(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" what is your freeview command? On 6/14/17 3:51 PM, KALEY E ELLIS wrote: > > Dear FreeSurfer Developers, > > > We are using FreeSurfer v6.0 and our operating system is OS X El > Capitan version 10.11.6. > > > We are going through the manual editing process and are checking the > brainmask by following these instructions: > > http://freesurfer.net/fswiki/FsTutorial/SkullStripFixV6.0 > > We have two subjects who appear to have brainmasks that are shifted up > considerably (see attached image). The recon-all.log file indicates > that it finished without errors: > > > reading volume > /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/mri/wm.mgz... > reading input surface > /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.white... > reading input pial surface > /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.pial... > reading input white surface > /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.white... > INFO: assuming MGZ format for volumes. > > table columns are: > number of vertices > total surface area (mm^2) > total gray matter volume (mm^3) > average cortical thickness +- standard deviation (mm) > integrated rectified mean curvature > integrated rectified Gaussian curvature > folding index > intrinsic curvature index > structure name > > 277 173 970 3.493 0.659 0.107 0.039 3 0.4 > ./rh.entorhinal_exvivo.label > > #------------------------------------------ > > Started at Thu Jun 8 10:50:24 CDT 2017 > Ended at Fri Jun 9 00:06:58 CDT 2017 > #@#%# recon-all-run-time-hours 13.276 > recon-all -s 2083_base finished without error at Fri Jun 9 00:06:58 > CDT 2017 > > Could you please advise me on how to correct this issue? We have run > all of these subjects the same way, but only two have had this problem. > > > Thank you! > > Kaley > > > Associate Research Specialist > Center for Healthy Minds > Waisman Center for Brain Imaging and Behavior > University of Wisconsin-Madison > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Freesurfer Info Page - Harvard University<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...

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glmfit_sim for CVS mapped data
by Magnús Ingvi 07 Jul '17

07 Jul '17

Hi, I've been trying to run glmfit_sim on a glm analysis with data in the AVG_35_CVS space but it doesn't seem to finish (tried almost two weeks). Does anyone have an idea what might be going on here? I used mc_full for 1000 iterations for my simlation.

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bbregister vs spmregister vs mri_coreg
by John Anderson 06 Jul '17

06 Jul '17

Dear Freesurfer experts, I see that the tool "mri_coreg" has been implemented recently in Free Surfer 6 and I really wanted to know what are the differences between the registration tools "bbregister", " spmregister" and "mri_coreg"! Kindly: 1. Are these tools similar? if not what are the differences ? 2. Is there any preference of using a tool over the others for specific type of data. For example: A. If I want to register FA map to T1 image which tool is more robust? B. if I want to register FA map to MNI space which tool is more robust? I highly appreciate your input on this! John

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Raw Cortical thickness values
by Muhammad Naveed Iqbal Qureshi 06 Jul '17

06 Jul '17

Dear Community, I need to know how can I read the numeric cortical thickness values from freesurfer processed files. (as there are too many in the surf folder) Thank you. Best Regards Naveed

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Average myelination within ROI
by SHAHIN NASR 06 Jul '17

06 Jul '17

Hi Surfers, I want to measure the average amount of myelinations within my ROI(s), I have already generated my myelination maps on surfaces (e.g. lh.myelin_ProjFrac0p5.nii ). Then I used mri_segstats as below: mri_segstats --i lh.myelin_ProjFrac0p5.nii --slabel SBJ_001 lh lh.V1 --sum V1_Stats.txt --accumulate but the numbers don't make any sense. For instance: # ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 125261 82573.4 Seg0000 110280.4453 0.2922 -5.5000 51.0000 56.5000 2 1 1138 764.8 Seg0001 941.0988 0.1572 0.2675 1.4203 1.1527 How can mean=941.0988 when the max=1.4203 ??? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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content of "subjects_dir"
by Schumman Resonance 05 Jul '17

05 Jul '17

Dear free surfer community, Silly question here. I note the default "subjects_dir" in freesurfer contains a bunch of directories and files. If I set the environment so that my "subjects_dir" is not the default location, do I need to move any of the files in the original location to the new one? I hope this makes sense. Thanks, Kev

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Question mri_glmfit fwhm smoothing
by Van Der Deijl, Rosanne 05 Jul '17

05 Jul '17

Hi, I have a question about mri_glmfit. As an input, you give e.g. the stacked thickness data from all subjects, smoothed with a certain fwhm. But then as an output file, it gives an fwhm.dat file, which, at least in my case, contains another smoothing level. I noticed this because I ran mri_glmfit-sim forclusterwise multiple comparison correction, which gives me the error: ERROR: cannot find /usr/local/freesurfer/stable6/average/mult-comp-cor/fsaverage/rh/cortex/fwhm33/abs/th13/mc-z.csd As input I gave data smoothed to 25fwhm, and not fwhm33, as it seems to think. But indeed, in the fwhm.dat file it gives fwhm = 32.940499. I read in the tutorial that the fwhm.dat file contains the average FWHM of the residual. But still my questions are: - what this means - why mri_glmfit-sim would need this number, and whether/how I can run the mult. comparison correction on the 25fwhm-smoothed data. Thank you in advance! - Rose Commands: mri_glmfit: mri_glmfit --fsgd $CALMGREY/CALM_FSGD.txt dods --C CALMlong_contrast1.mat --C CALMlong_contrast2.mat --C CALMlong_contrast3.mat --C CALMlong_contrast4.mat --glmdir rh.CALMlong.thickness-spc.fwhm25 --y rh.CALMlong.thickness-spc.stack.fwhm25.mgh --cortex --surf fsaverage rh mri_glmfit-sim: mri_glmfit-sim --glmdir rh.CALMlong.thickness-spc.fwhm0 --cache 1.3 neg --cwp --2spaces

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Freesurfer June 2017