Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30066 discussions

Fwd: surface inaccuracies around the optic chiasm
by Gabor Perlaki 10 Jul '17

10 Jul '17

Somehow, my last email didn't appear on the Freesurfer forum. I'm resending it without the attachments. Dear Bruce, I'm not interested in the chiasm, but the medialorbitofrontal cortex would be interesting. In most of the subjects pial and white surfaces intrude into the area around the optic chiasm, which is clearly not a cortical region. However, I think that until this region is segmented as a subcortical label (i.e. opic chiasm) or nothing in the aparc.DKTatlas+aseg.mgz file my cortical measures won't be affected, but if it's labeled as medialorbitofrontal cortex or wm then I should correct it. 1. Could you please confirm that these surface inacuracies don't matter as long as the area is not segmented as a cortical region (i.e. medialorbitofrontal) or white matter in the aparc.DKTatlas+aseg.mgz file? 2. I think I should correct the wm.mgz, but I'm not sure about how to correct it without loosing my earlier corrections. I'm ready with all of the other corrections inclding wm, brainmask and aseg corrections as well? I'm trying to resend some images showing the missegmented area. Best Regards, Gabor

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Re: [Freesurfer] help with code interpretation
by Leanne Hunt 10 Jul '17

10 Jul '17

Hi, I am currently using free surfer to analyse my brain imaging and i was wondering if you could tell me what G_S stands for in the rh.aparc.a2009s.stats and lh.aparc.a2009s.stats folders? for example: G_and_S_frontomargin Many thanks Leanne

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surface inaccuracies around the optic chiasm
by Gabor Perlaki 09 Jul '17

09 Jul '17

Dear all, I use Freesurfer 6. In some of my subjects the surfaces (both pial and white) intruding into the optic chiasm. However, when I check the aparc.DKTatlas+aseg.mgz it seems that although the surfaces are wrong, the region is segmented as optic chiasm. Can I ignore this type of surface inaccuracies similarly to surface inacurracies around the amygdala and hippocampus? Best Regards, Gabor

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recon-all on newborn
by Das S. 08 Jul '17

08 Jul '17

Dear Freesurfer expert, I want to perform recon-all pipeline on neonates data.Can I do so? I was going through some mail archives and there it is said that on T1 image of neonates data we can't perform recon-all. But again there is another paper where it says Freesurfer can perform segmentation of neonates image. Any input will be appreciated. Thanks S Das

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convert .mgz to .nii format
by Almarshad F. 08 Jul '17

08 Jul '17

Hi everyone; is it possible to convert T1.mgz back to T1.nii.gz I'm using the examples in the tutorial data which does not have the original T1.nii i tried to use the command mri_convert but i don't think the file it created is correct ! any advice regards to this issue will be very helpful .. kindest regards, Fatima

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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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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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