Freesurfer March 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
153 discussions

thickness of frontal lobe
by Liukarl 02 Mar '10

02 Mar '10

Hello, I looked at the results from stage 3 and found out it has 1100 regions (we might not use qdec since we have many other variables to control). But it is beyond manageable levels. What we want might two things: The first one might be a general measure of thickness (or volume) of each lobe (frontal, parietal,…) or which one from these 1100 regions? And we are particularly interested in the prefrontal lobe and behavior. Is there any finer measure of frontal lobe (thickness/volume, dorsal frontal/ventral frontal)? Thanks a lot Karl _________________________________________________________________ 约会说不清地方？来试试微软地图最新msn互动功能！ http://ditu.live.com/?form=TL&swm=1

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Standard Desikan map and/or qdec blurb?
by Dankner, Nathan (NIH/NIMH) [F] 02 Mar '10

02 Mar '10

Hi all, I'm about to start writing up a paper, and was curious as to whether there is a standard figure displaying the Desikan parcellations that is floating around out there, and also whether or not there is a standard blurb describing QDEC's GLM analyses. Thanks! Nathan

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cortex bad segmentation...
by Gonzalo Rojas Costa 02 Mar '10

02 Mar '10

Hi: In a patient, I got a bad cortex segmentation... I try to adjust the skull stripping, but I couldn't got a better stripping... How can I correct that segmentation ?... Sincerely, Gonzalo Rojas Costa

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Loading new data into Freesurfer
by Janani Dhinakaran 02 Mar '10

02 Mar '10

Hello to everyone! Hope the new month is bringing better weather to all of you. I am trying to load new data. I cd-d to the location of the files (.hdr and .img). Now I am trying to convert the data. It doesn't recognise the information. I've manually created the files JS, MRI, and Orig within to allocate an appropriate path for it. Here is a copy of what I did. Please let me knwo what I need to do. Thank you! s0964091@CRIC-0012:~/Desktop/Newdata/RAW_DATA$ cd 1_1 s0964091@CRIC-0012:~/Desktop/Newdata/RAW_DATA/1_1$ mri_convert /Desktop/Newdata/RAW_DATA/1_1 /Desktop/Newdata/JS mri_convert /Desktop/Newdata/RAW_DATA/1_1 /Desktop/Newdata/JS mri_convert: can't determine type of output volume s0964091@CRIC-0012:~/Desktop/Newdata/RAW_DATA/1_1$ mri_convert /Desktop/Newdata/RAW_DATA/1_1 /Desktop/Newdata/JS/001.mgz mri_convert /Desktop/Newdata/RAW_DATA/1_1 /Desktop/Newdata/JS/001.mgz file not found or unknown file type for file /Desktop/Newdata/RAW_DATA/1_1 s0964091@CRIC-0012:~/Desktop/Newdata/RAW_DATA/1_1$ mri_convert /Desktop/Newdata/RAW_DATA/1_1 /Desktop/Newdata/JS/mri/orig/001.mgz mri_convert /Desktop/Newdata/RAW_DATA/1_1 /Desktop/Newdata/JS/mri/orig/001.mgz file not found or unknown file type for file /Desktop/Newdata/RAW_DATA/1_1 -- I am the Sun, I know no darkness.

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signal loss in the orbitofrontal cortex
by Cindy Eckart 02 Mar '10

02 Mar '10

Dear FreeSurfers, in the FreeSurfer cortical parcellation procedure, a volume measure is calculated for the lateral orbitofrontal cortex and in my study population I indeed do find a significant group difference in the volumes of this region. However, there certainly is signal loss of the MR signal in the orbitofrontal region... However, I am not quite sure how much of the lateral orbitofrontal cortex is concerned by this phanomenon. Thus, my question: Is there any data how reliable the volume measurement of the FreeSurfer cortical parcellation might be in the lateral orbitofrontal cortex? Is there a way to check how much of this parcel is concered from signal loss in my own data? And do you have any experience how reasonable it may be to interpret a group difference in this region? Thank you very much in advance! Cindy ___________________________________________________________ GRATIS für alle WEB.DE-Nutzer: Die maxdome Movie-FLAT! Jetzt freischalten unter http://movieflat.web.de

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software versions
by Roser Sala 02 Mar '10

02 Mar '10

Hello freesurfers, we have several data processed (with recon-all) using FreeSurfer v.4.3.1, but we are thinking in moving to v.4.5. Do we have to re-run recon-all again for all the subjects, or can we just run the new features implemented in the new version (If so, is there any 'easy way' to do it?) Thanks in advance, - Roser -

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continue longitudinal processing...
by Gonzalo Rojas Costa 02 Mar '10

02 Mar '10

Hi: I was processing a longitudinal processing using a command line like: recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all but it couldn't finished because the power cut produced by a 8.8 magnitude earthquake here in Chile... How can I continue the processing without starting again from the beginning ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Santiago Chile

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Covariates in qdec
by Dankner, Nathan (NIH/NIMH) [F] 01 Mar '10

01 Mar '10

Hi all, I've covaried age in a group difference analyses on cortical thickness data both in qdec for vertex-based and in spss for the gyral-based data. For the vertex-based data, covarying age has almost no effect, and if anything intensifies the group differences. However, when run in qdec, covarying age in this dataset wipes out almost any group differences. Is covarying in qdec to be trusted? It seems strange to me that these two methods would result in such extreme differences in results. Thanks, Nathan

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mri_convert dicom conversion
by Satrajit Ghosh 01 Mar '10

01 Mar '10

hi, mri_convert TrioTim/123456-10-1.dcm test.nii.gz will scan all files in the dicom directory to get at series 10. in the above scenario, i know that the files corresponding to the run are 123456-10-*.dcm. is there a way to leverage this information, so that it does not scan the entire directory? cheers, satra

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ICV Error fs 4.3.1
by Jeff Sadino 01 Mar '10

01 Mar '10

Hello, I reconed 149 subjects using freesurfer 4.3.1 automatically using our cluster. When I did asegstats2table, all 149 subjects had the exact same icv: # Measure IntraCranialVol, ICV, Intracranial Volume, 1948106.000000, mm^3 Running mri_segstats manually, here is the beginning of the output: mri_segstats --seg mri/aseg.mgz --sum stats/aseg2.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --ctab $FREESURFER_HOME/ASegStatsLUT.txt --subject 040002_S04 atlas_icv (eTIV) = 1948106 mm^3 (det: 1.000000 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 246101 rh white matter volume 251160 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1766623 # brainmaskvolume 1766623.0 # nbrainsegvoxels 1310448 # brainsegvolume 1310448.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation 1 2 Left-Cerebral-White-Matter 247216 247216 Looking at the log files for several other subjects, they all have a determinant of 1. However, all of the other numbers - brainmask, brain seg volume, individual regions - are all unique and correct. It is just the icv. Can anyone point me in the right direction of how to investigate the determinant value? Here is the mri_segstats version: # cvs_version $Id: mri_segstats.c,v 1.33.2.5 2009/02/11 22:38:51 nicks Exp $ Thanks! Jeff Sadino

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Freesurfer March 2010