Freesurfer

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30083 discussions

Top Quartile of Active Voxels
by Dave Brohawn 16 Dec '08

16 Dec '08

Hello, I ran the following analysis to target task-specific voxels at a certain contrast and offset. func2roi-sess -roidef dACC10_lh -analysis EMerror -anatlabel dACC-lh -maskcontrast ASevfix -maskframe 5 -maskthresh 1 -masktail pos -maskmap sig -sf Subject_files/MTHFRn18-list -d $SUBJECTS_DIR We would like to create a functional constraint including only the 25% most active voxels (top quartile). Is there a command that can achieve this? Thanks, Dave Brohawn

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func2roi-sess command issue
by Dave Brohawn 15 Dec '08

15 Dec '08

Hello, In the stable 3 environment, I ran the func2roi-sess command. This is what was included: func2roi-sess -roidef dACC99_rh -analysis EMerror -anatlabel dACC-rh -maskcontrast ASevfix -maskframe 5 -maskthresh 0.0043648054 -masktail pos -maskmap sig -sf Subject_files/MTHFRn18-list -d $SUBJECTS_DIR I then ran this summary generating command: roisummary-sess -roidef dACC99_rh -analysis EMerror -sf Subject_files/MTHFRn18-list -d $SUBJECTS_DIR -sumfile $SUBJECTS_DIR/dACC999_rh.txt I've viewed the summary file, and found that there are negative values listed for some of the conditions time points (e.g conditon 1, 2 sec after stimulus onset). How can this be if I included the masktail pos flag? I thought that only captured positive activation. If there is a way to solve this issue and capture only positive activation, please post when you can. Thank you, Dave Brohawn

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mri_convert 3D set to a single 4D ?
by Siddharth Srivastava 15 Dec '08

15 Dec '08

hi everyone, is it possible to combine, using mri_convert, a set of 3D spm/analyze files into a 4D analyze file ? can anyone help me out with the syntax, if possible? thanks, sid.

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nature of bug in mris_wm_volume
by Michael Harms 15 Dec '08

15 Dec '08

Hello, The ReleaseNotes for v4.1.0 and v4.0.5 indicate refer to a bug in 'mris_wm_volume' related to the white matter parcellation. Was there actually a bug in mris_wm_volume itself? Or, is the issue that the aseg.mgz had some incorrect labeling of "non-white" structures relevant to the mris_wm_volume calculation? I guess I'm confused about what precisely is "incorrect" in aseg.stats? Is it just the lines for {Left,Right}-Cerebral-White-Matter? Or, the lines in the "intro" for "surface-based-volume mm3 {lh,rh}-cerebral- white-matter"? Or both? thanks for clarifying, -Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Water threshold for skull strip : 1% is still too high
by Julien Dubois 15 Dec '08

15 Dec '08

Hi all I can't get freesurfer to strip the skull properly, even with a water threshold of 1%. There is still so much skull (csf) remaining that a manual edit is not doable. Is there a way to preprocess the anatomical scan to correct this? ( I tried a water threshold of 0% although I'm not sure that it makes any sense - the result is attached, this time too much skull disappeared). - Julien

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make_average
by p.s.bjerkan＠studmed.uio.no 15 Dec '08

15 Dec '08

Hi, Trying to make an average of about 60 subjects. The problem is that the proper files are not produced. In average/mri/ I only have the mni305.cor.mgz and the folder "transforms". There should more. During processing I can see the following repeating at some point: "tail: cannot open `+3´ for reading: No such file or directory". Not sure what +3 means... Further, in the end of output (also in the make_average_volume.log, attached) we have the ERROR: failure writing /...../....../..../xxxx.mgh where xxxx is the first of the subjects in the "list". If I try to remove it and rerun, it only complain about the next in line... Don´t know what to do here...:) Petr

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.mat/.hdr and orientation
by Susie Heo 15 Dec '08

15 Dec '08

Hello, I am hoping that someone can help me to solve my orientation/angle acquisition problem: 1) I have an EPI oblique slice in Analyze format with incorrect orientation/angle acquisition information in the .hdr file (no .mat file) 2) I have a distorted image of the same slice in Analyze format with the correct orientation/angle information in the .hdr/.mat files 3) I would like to change the .hdr/(.mat?) file of 1) to conform to the orientation/angle specs of 2). I have tried: 1) Replacing 1).hdr w/ 2).hdr--incorrect orientation; image off center; same as if kept 1).hdr 2) Replacing 1).hdr w/ 2).hdr and 2).mat--correct slice angle, image flipped -y and possibly -x? 3) mri_convert <input> <output> --iid -1 0 0 -ijd 0 1 0 -ikd 0 0 1 where <input> = 1).img, 2).hdr, 2).mat --lost slice angle, correct orientation Any tips? What exactly do the .hdr and .mat files contain? Susie

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Re: [Freesurfer] Aparc and aseg description table
by Maartje Katzenbauer 15 Dec '08

15 Dec '08

Hello Julia, Besides the definitions above the tables, there are some articles mentioned on the wiki site- main page, scroll down- giving information about the definitions of the areas. F.e. Desikan, 2006, about cortical parcellation. Kind regards, Maartje Katzenbauer ----- Original Message ----- From: Julia Altenburg <juliaaltenburg(a)yahoo.de> Date: Monday, December 15, 2008 1:24 pm Subject: [Freesurfer] Aparc and aseg description table Hi all, It would be *really* great if there was a page somewhere (or just a file) giving some info on the various measures that are captured in the aseg and aparc files. For each measure (in the table or the "comments" above the table): -- Description of what it includes -- some are obvious from the name, others not. -- Whether it's deprecated. Is there anything like that? Thanks a lotJulia _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Aparc and aseg description table
by Julia Altenburg 15 Dec '08

15 Dec '08

Hi all, It would be *really* great if there was a page somewhere (or just a file) giving some info on the various measures that are captured in the aseg and aparc files. For each measure (in the table or the "comments" above the table): -- Description of what it includes -- some are obvious from the name, others not. -- Whether it's deprecated. Is there anything like that? Thanks a lotJulia

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Some questions about my analysis
by Christian Scheel 15 Dec '08

15 Dec '08

Dear all, I have got several questions about the analysis of my data. Maybe you can help me out: 1) Regarding the different levels of smoothing (FWHM) in Qdec are there already some 'standards' that one should usually stick to? My results look better when I set the smoothing level to 15 or even 20, but is it really appropriate to use such high levels of smoothing? 2) In Qdec is there a possibilty to set something like an 'Extent threshold' in order to display only clusters of a certain size and hide all clusters that are smaller? 3) Am I correct that the best way to get the total gray and white matter volume is a) for the gray matter volume: mris_volume ?h.pial minus mris_volume ?h.white b) for the white matter volume: mris_wm_volume subject ?h I read that the values for white and gray matter in the aseg.stats are not that accurate, but what about the GrayVol value in the ?h.aparc.stats files? I was a bit surprised that the sum of these GrayVol values is not the same as the total gray matter volume calculated with mris_volume (although it comes quite close) 4) All of recon-all has been run with Freesurfer 4.02 for all subjects - is it OK to use Freesurfer 4.05 or 4.10 for the analysis? 5) I have tried loading my data into the qdec version shipped with Freesurfer 4.05 and noticed that now there is an option to chose between DODS and DOSS. In my study I wish to compare the thickness of a group of patients and a group of controls accounting for gender and age. Did I understand Dougs freshly updated wiki page correctly and can I use DOSS in case I assume that age has the same effect on patients and controls (so same slope) and they are only starting at different thickness levels? And when chosing DOSS is age really still in the calculation as a covariate? I was surprised to see that I can only chose the question 'Does the average thickness, accounting for gender, differ between patient and control' but not 'accounting for gender and age'. 6) I would like to have a look at the local gyrification index aswell but still need to buy Matlab for it. Do I also need some extra toolboxes to run the lgi calculation - or do I just need the core programm? Any help is greatly appreciated. Best wishes, Christian Scheel --- University of Cologne Department of Psychiatry

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