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Re: [Freesurfer] question about qdec Stats Data Import for Longitudinal Workflow
by Martin Reuter 01 Jul '14

01 Jul '14

Hi I don't know what you mean. The word 'generate' does not appear on that web page. Best Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Salil Soman <salsoman(a)stanford.edu> Date:07/01/2014 9:50 PM (GMT+01:00) To: free surfer <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] question about qdec Stats Data Import for Longitudinal Workflow When following the longitudinal qdec tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel) does using the generate Stats Data Tables option extract data for the difference between time point1 and 2, or something else? Thank you. Salil Soman, MD, MS

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Re: [Freesurfer] longitudinal QDEC question
by Martin Reuter 01 Jul '14

01 Jul '14

Hi salil, the command for that are on the wiki. You'd do a one sample group mean (-osgm) . This asks if the variable of interest is significantly different from zero. Since you ran long mris slopes, that variable would be for example the rate of change or the percent change (one measure per subject). Best Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Salil Soman <salsoman(a)stanford.edu> Date:07/01/2014 9:40 PM (GMT+01:00) To: free surfer <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] longitudinal QDEC question Hi, I have been following the steps for longitudinal processing from here (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel) and was hoping for some advice on how to setup the GLM. I have a set of data where I have 2 time points for all subjects, have run recon-all, qcache, the base and cross steps of processing. I also ran the long mri_slopes step, created my long.qdec table, then created the simplified table for qdec. I would like to perform a whole brain analysis where I identify any brain regions that changed (volume or cortical thickness) from time point 1 and time point 2. I am a little unclear on what the explanatory variable should be performing this analysis. Any suggestions on how best to structure the analysis would be greatly appreciated. Best wishes, Salil Soman, MD, MS

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longitudinal QDEC question
by Salil Soman 01 Jul '14

01 Jul '14

Hi, I have been following the steps for longitudinal processing from here ( https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel) and was hoping for some advice on how to setup the GLM. I have a set of data where I have 2 time points for all subjects, have run recon-all, qcache, the base and cross steps of processing. I also ran the long mri_slopes step, created my long.qdec table, then created the simplified table for qdec. I would like to perform a whole brain analysis where I identify any brain regions that changed (volume or cortical thickness) from time point 1 and time point 2. I am a little unclear on what the explanatory variable should be performing this analysis. Any suggestions on how best to structure the analysis would be greatly appreciated. Best wishes, Salil Soman, MD, MS

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Re: [Freesurfer] Mean diffusivity (MD)
by Alshikho, Mohamad J. 01 Jul '14

01 Jul '14

Thanks Doug, Actually I want to calculate the MD just for the right and left hemispheric white matter. The output of dt_recon doesn't include anything about the mean diffusivity (i.e we have just the eignvals.nii ) so what is the best way to generate the MD as a nifty file? Is it by using fslsplit on eignvals.nii or as I did fslmaths command line to divide eignvals to L1, L2, L3 as I did in my first step or what do you think? Mohamad -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, July 01, 2014 10:54 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mean diffusuvuty MD I don't know about the first step but 2 and 3 look ok. But why are you using the aseg? It will just give you the lh and rh cerebral WM On 06/30/2014 03:11 PM, Alshikho, Mohamad J. wrote: > > Hi Fs Experts, > > In order to calculate the mean diffusivity MD in my DTI data I did the > following: > > 1.For the Eigvals.nii (the output of dt_recon) I used the following > command line: fslmaths eigvals -div 3 md.nii > > 2.mri_vol2vol -mov md.nii --reg register.dat --fstarg -- interp > nearest -- o md.anat.mgh > > 3.mri_segstats --seg $SUBJECTS_DIR/mri/aseg.mgz --ctab > $FREESURFER_HOME/FreeSurferColorLUT.txt --seg-erode 2 --i md.anat.mgh > --sum md.stats > > is this correct ? > > I highly appreciate any suggestions and advices > > Mohamad > > > > _______________________________________________ > 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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Skull-Stripping Atlas Usage
by Teo Gelles 01 Jul '14

01 Jul '14

Hi Everyone, I am trying to skullstrip an mri image without using an atlas. Does the following command use an atlas at any point? If so, is there a way to run the skullstripping algorithm without using information from an atlas? recon-all -s bert/ -clean-bm -skullstrip Thanks. Teo Gelles

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Edits, where art thou?
by Max Svensson 01 Jul '14

01 Jul '14

Hi! When I edit my data, for instance wm editing, I do not see the changes applied to the original image. To make you understand what I do: Open up freeview, load the image, Wm and brainmask, with wm at the top. Then I go into voxel edit, press recon edit, and start filling in topographical defects and do some wm editing. HOWEVER, after I run recon all (recon-all -autorecon2 -autorecon3 -subjid anon)and it's finished without problems, I do not see the edits done on my image. Sure, I see the yellow colour which I filled some spots with, but I was thinking that I would see an edited image, that is with pia (topographical defects) and wm surface going out to the areas I edited. Not only yellow filling which was there before since I edited. Am I doing something wrong? Is the reconprocessed images hidden out there somewhere? Freesurfer team, please help! Best, MAX

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Re: [Freesurfer] Longitudinal preprocessing troubleshooting
by Martin Reuter 01 Jul '14

01 Jul '14

Hi Bryan, I can answer the longitudinal question (2), the rest is about cross sectional editing and can probably better be answered by someone else. So yes, I would run the base and check brainmask and surfaces there before going too deep into editing the cross. Best Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: "Chiu, Bryan (PHTH)" <bryan.chiu(a)ubc.ca> Date:06/26/2014 8:06 PM (GMT+01:00) To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal preprocessing troubleshooting Hi all, I have a set of data with ~75 subjects with up to 4 timepoints of scans. The structure of the data indicates that it would be best processed using a longitudinal design. I have recon-all most of the scans. There are a few scans that I am worried about and wondering how to treat each case. I do one sanity check with freeview using a modified version of bert's command: "freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red" 1a) Skull strip or underanalysis errors: I have attached one screenshot of a very severe case of an underanalysis. How should I treat this case? I have recently read about Editing a Recon in Freeview, but I'm not sure how to proceed with this. b) Skull strip errors -- Some scans have a very small amount of cerebral cortex labelling into the dura mater/ skull. Does this warrant the manual removal via freeview of the skull? 2) Since I am running this through the longitudinal processing, could I be able to skip #1 hoping that the averaging of the timepoints into a 'base' will remove these issues? 3) I have 2 brains that are completely whited out in Freeview (see attached). However the analysis went through and it looks good to me. Opening the raw Nifti file in mricroGL does not show this at all. What is going on and should I be concerned? 4) I have 2 other brains that failed the recon-all. One of them is a Talairach fail and the other one failed mri_watershed. Looking at these brains in mricroGL shows a dark shadow being cast over the brain running diagonally from the front of the head to the back. I think this is the root of the problem. Is there a way to fix this or should I consider these scans problematic and exclude them? Regards, - Bryan

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Flip ROI left-right qdec
by Raphael F.C. 01 Jul '14

01 Jul '14

Dear experts, I am new to freesurfer, and please forgive me if this is not the right way to present my issue. I drew a ROI in QDEC, in the left hemisphere of a template and saved it as a Label file (a .txt file) I would like to flip this ROI to the right hemisphere. Does anybody know an easy way of doing it? I tried manipulating the .txt file, but I could not do it. Thanks in advance, Raphael

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problem with qdec stats tables
by Kristina Kuhlmann 01 Jul '14

01 Jul '14

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tkmedit coronal view - y coordinate issue
by DeCross, Stephanie N. 01 Jul '14

01 Jul '14

Hi, In FreeSurfer 5.3, when I click around in a coronal view slice, the Talairach y coordinate changes (in both the cursor column and the mouse column). This doesn’t make sense - it’s the same coronal slice, so shouldn’t anywhere on that same plane still have the same y coordinate? When I take a screenshot of the brain map and report the y coordinate, is there a standardized procedure for where in the slice I should click to take that coordinate to report? Thanks, Stephanie Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 Phone: 617-724-3283 Fax: 617-726-4078

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