Freesurfer

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30090 discussions

problem in installation practices
by Yagmur Ozdemir 19 07 Jul '17

07 Jul '17

Hello, I am testing my FreeSurfer installation by doing the practices shown on the page. Regardless of command-although I managed to convert the sample to nifti format- this error on line 2 shows up. Can anyone explain what that could be caused by and point me in the right direction to fix it? I do not have a good coding background. lab@lab-ThinkStation-E31:/mnt/sbd/freesurfer/freesurfer$ recon-all -i sample-001.nii.gz -s bert -all bash: /mnt/sbd/freesurfer/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory lab@lab-ThinkStation-E31:/mnt/sbd/freesurfer/freesurfer/subjects$ recon-all -s bert -all bash: /mnt/sbd/freesurfer/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory lab@lab-ThinkStation-E31:/mnt/sbd/freesurfer/freesurfer/subjects$ freeview -v bash: /mnt/sbd/freesurfer/freesurfer/bin/freeview: /bin/tcsh: bad interpreter: No such file or directory Thank you! an undergraduate student

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MNI Coordinates
by AKUDJEDU, THEOPHILUS 07 Jul '17

07 Jul '17

Hi All, I am trying to visualise nodes of a brain network reconstructed using FreeSurfer Desikan-Killiany Atlas parcellation scheme (aparc+aseg.mgz) on Brain Net Viewer and Network Based Statistics software. In order to do so, I need to upload a .txt file listing Freesurfer labels coordinates in MNI space. Is there any way I can get a list of MNI coordinates for my set of labels? Many thanks, Theo

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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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Re: [Freesurfer] PVC on DTI
by Victor Montal Blancafort 07 Jul '17

07 Jul '17

Dear Doug, We are trying to compute partial volume correction in DWI images, using your PEtsurf approach, to correct CSF contamination. Afterwards, we will compute whatever DTI metric from the corrected data and project it to surface. As you suggested in your previous post (https://www.mail-archive.com/ freesurfer(a)nmr.mgh.harvard.edu/msg52436.html) we used the psf=0, so the algorithm will just perform TFE. However, we have some concerns. When we perform this correction in symptomatic subjects (e.g AD patients), we have seen that in certain regions (mainly non atrophied areas), the PVC effect is overestimated. If I am not wrong, the WM coefficient obtained from the SGTM takes into account ALL the superficial WM, and thus, will take intro account both atrophied and non atrophied regions. This is important because, unlike PET, the superficial WM diffusion, resembles the GM diffusion and it would be interesting to treat them as one compartment. Therefore, my question is if there is any option in mri_gtmpvc to use a 3-compartiment model (WM+GM, CSF, SKULL) instead of the default 4-compartment. Once we have the PVC volume, we project our DTI metric to surface using mri_vol2surf with proj-fract 0.5. However, since we used a GM thr of 30% (as in your NI paper), there are several regions with no signal (i.e 0 in the native surface). How do you solve this issue? Smooth of the data? Exclude those vertices from further analysis? Thank you in advance for your help!! Regards, Victor M

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ROI analyses using SPM AAL ROIs
by M Janani 07 Jul '17

07 Jul '17

Hi Team, Currently I'm working on ROI analyses. I saw one article related to VolumeROICorticalThickness in Free surfer wiki. Could anyone please tell me what is the anatomical file(TT_avg152T1.nii) they are referring to? I took AAL ROIs from SPM. In that case, which anatomical file should I use for my analyses? Any help would be really grateful. Thanks in advance. Regards, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ----------------------------------------------------------------------------------------------------------------------------------------------------

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GLM question
by Yann Ying Chye 07 Jul '17

07 Jul '17

Dear FreeSurfer mailing list, I've got two questions regarding the freesurfer GLM analysis. 1. I am trying to run mri_glmfit on the cortical thickness of a dataset that has a few interacting factors of unequal levels. For example, my dataset may have groups A, B, C, and D. Within the groups, subjects are further divided by gender - male and female. However, group A only has males, such that the classes in my FSGD file = A-male, B-male, B-female, C-male, C-female, D-male, and D-female. Will this design be a problem? Will it be statistically sound? Additionally if I was looking for an effect of gender, how would I weigh my contrast? I was thinking 0.25 0.25 -0.33 0.25 -0.33 0.25 -0.33. Would that be valid? 2. Does mri_glmfit have a limit to the number of subjects it can run with? If I have say upwards of a few thousand subjects, will this be possible to run/how long would that take? Thanks for your help! Regards Yann

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ERROR: dimension mismatch between input volume and seg - VolumeROICorticalThickness
by M Janani 07 Jul '17

07 Jul '17

Hi Team, I'm attempting to extract cortical thickness values for a region-of-interest (ROI) defined in volume spacesubject for PiB MRI. I got the below mentioned error while computing the stats value cwd cmdline mri_segstats --seg freesurfer/subjects/fsaverage/surf/lh.fsaverage.CBLROI.mgh --in lh.thickness.fsaverage.mgh --sum segstats-CBLROI.txt sysname Linux hostname teslak80 machine x86_64 user lakshman UseRobust 0 Loading /freesurfer/subjects/fsaverage/surf/lh.fsaverage.CBLROI.mgh Loading lh.thickness.fsaverage.mgh ERROR: dimension mismatch between input volume and seg input 27307 1 6 seg 23406 1 7 I tried with the solution provided in the below mail, but it didn't work for me https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-January/027405.…<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-January/027405.h…> Any help would be really helpful. Regards, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ----------------------------------------------------------------------------------------------------------------------------------------------------

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remove skull from gtmseg.mgz
by miracle ozzoude 07 Jul '17

07 Jul '17

Hello Freesurfer, After running the first step of PETsurfer ( https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer) I viewed the image it created using freeview. When I change, the color map to Lookup Table, the image also included the skull. How can I remove the skull from gtmseg.mgz/prevent it from showing? Any help will be appreciated. Thanks. Please, see attached image Best, Paul

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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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