Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30135 discussions

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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annotation files for cortical labels?
by pavitrak＠nmr.mgh.harvard.edu 01 Jul '14

01 Jul '14

Hi Freesurfer Team, I'd like to view a multicolored quilt of individual cortical icosahedron subdivisions. I have labels for these subdivisions stored in the SUBJECT/label folder I can also batch load all these labels and view them in Freeview but am not sure how to randomize their colors for a multicolored appearance. I looked up how to use annotation files and tried to amalgate all left cortical labels in the SUBJECT/label/ folder as below: - cd $SUBJECTS_DIR/$SUBJECT/label - mris_label2annot --s $SUBJECT --h lh --a leftall.annot But it asks for a color table file - it seems like editing the Freesurfer color table file will be quite involved. I have all the labels data and vertices in a w-file - can I use it to somehow create the colortable that I need, or the annotation file itself? Is this the correct way for my goal? Thank you. Best Regards Pavitra

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Optseq2 Help!!
by Elise Cardinale 01 Jul '14

01 Jul '14

Hello! I am trying to use optseq to optimize my study design and cannot get it to accept the parameters I need for my task and I have officially stumped those helping me at my institution so I need your help! I am trying to run a very simple design where my stimuli are presented for 3.5 seconds and I have 60 stimuli: 10 Montreal Pain 10 Montreal Neutral 10 Ekman Neutral 10 Ekman Fear 10 Ekman Anger 5 Montreal Anger 5 Montreal Fear I calculated that at 3.5 seconds each that equals a total of 210 seconds of task and I added 40 seconds of null (~20% of task). Totaling to 250 seconds. My TR is 2.5 seconds giving me 100 time points. I tried to run the following Optseq command: optseq2 --ntp 100 --tr 2.5 --tprescan 0 --psdwin 0 16 .5 --ev angerE 3.5 10 --ev fearE 3.5 10 --ev angerM 3.5 5 --ev fearM 3.5 5 --ev neutralE 3.5 10 --ev neutralM 3.5 10 --ev pain 3.5 10 --nsearch 10000 --nkeep 6 --o EmotionalFaces_Donor_FINAL2 When I do I get the following: INFO: Setting srand48() seed to 374226 optseq2 $Id: optseq2.c,v 2.15 2009/05/26 18:13:45 greve Exp $ NoSearch = 0 nSearch = 10000 nKeep = 6 PctUpdate = 10.000000 nCB1Opt = 0 seed = 374226 Ntp = 100 TR = 2.5 TPreScan = 0 PSD Window = 0 16 0.5 nEvTypes = 7 EvNo Label Duration nRepsNom 1 angerE 3.500 10 2 fearE 3.500 10 3 angerE 3.500 5 4 fearE 3.500 5 5 neutralE 3.500 10 6 neutralM 3.500 10 7 pain 3.500 10 PctVarEvReps = 0 VarEvRepsPerCond = 0 PolyOrder = -1 tNullMax = -1 tNullMin = 0 outstem = EmotionalFaces_Donor_FINAL2 AR1 = 0 No refractory penalty Cost = eff OutStem = EmotionalFaces_Donor_FINAL2 Summary File = EmotionalFaces_Donor_FINAL2.sum nTaskAvgs = 224 ERROR: DOF Constraint Violation: number of estimates (224) is greater than or equal to the number of time points (100). To fix: (1) increase the number of time points to 225, or (2) decrease the number of event types, or, (3) reduce the size of the PSD window, or (4) increase the dPSD. If I decrease the PDS window it comes back with 10000/10000 being unusable. I can't change my dPSD interval as my TR is 2.5 and my event is 3.5 and even if I increase my time points (which is not an option- I cannot double the length of my task) it still comes back as 10000/10000 being unusable. Any advice on how to fix this? Thank you so much! -Elise Cardinale --- Laboratory on Social and Affective Neuroscience Georgetown University White Gravenor Hall 302 email: emc62(a)georgetown.edu phone: 202-687-6853

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Mean diffusuvuty MD
by Alshikho, Mohamad J. 01 Jul '14

01 Jul '14

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

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Pons and midbrain segmentation....
by Gonzalo Rojas Costa 01 Jul '14

01 Jul '14

Hi: How can I segment the pons and midbrain using freesurfer ?... or any other segmentation software that do such task ?... Sincerely, Gonzalo Rojas Costa -------------------------------- Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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