Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

Restart from somewhere in the middle of mri_ca_register
by Joshua Lee 16 Jul '12

16 Jul '12

Is it possible/pracitcal? This is a long step, and unfortunately my analysis computer was rebooted in the middle of this step, and I was hoping to present the volumes tomorrow.. ouch. - Josh

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ROI functional & anatomical cross
by Huiting Liu 16 Jul '12

16 Jul '12

Hello, I'm trying to do an ROI analysis that crosses the group-level functional activation with specific anatomical structures. Currently the clusters found for our group-level functional activation are too large and need to be separated into many structures. Is there a command I could use that would cross the group level map with each cortical structure generated by freesurfer's recon-all? Thanks.

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plotting cortical parcellation surfaces using 2009 atlas
by Maria Kharitonova 16 Jul '12

16 Jul '12

Hello, I apologize if my question is too basic, but I am trying to pull up cortical parcellation surfaces for my data, like shown here: http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation I tried typing in "tksurfer subjec_number lh inflated -aparc", but that produces the lateral surface using the 2005 atlas. Can you help me by suggesting which command can pull up parcellated surfaces using the 2009 atlas? Putting in "-aparc.a2009s" does not seem to work (no parcellation is shown). I would like to see both lateral and medial surfaces, if possible. Thank you in advance! Sincerely, Maria **************************************** Maria Kharitonova, Ph.D. Laboratory of Cognitive Neuroscience Children's Hospital Boston

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parcellations to fmri space
by Christopher Bell 16 Jul '12

16 Jul '12

Hello Freesurfers, I have developed a pipeline that uses mri_label2vol to take freesurfer parcellations to native fmri space, and uses dilation (within mri_label2vol) to make the ROIs larger since our resolution is only 3.5x3.5x4 we would end up with only a few voxels for some ROIs due to large voxel size and partial voluming wihout the dilation. However, since the lh and rh are done separately by mri_label2vol, I now have overlap on the midline and have to go through a bunch of masking steps to eliminate it. My question is; is there a tool that will take both lh/rh parcellations to a new coordinate system, do dilation, and most importantly control for lh/rh overlap? Or any other similar suggestions. Thanks! Basically I am looking to rework my pipeline, and it seems I should be able to find a more parsimonious solution, than my "Rube Goldberg" approach. Chris

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the make_average_subject without aparc.annot
by Leon 16 Jul '12

16 Jul '12

Hi, Doug I found from the archive that you made a version of make_average_surface without the need for aparc.annot. I tried to download it but the link is not valid anymore. Could you please send me a copy of the file? I need to generate an averaged surface for a group of non-human primates and I was asked to input these annotation files that do not exist for non-human primate data. Many thanks! Leon Re: [Freesurfer] how to generate aparc.annotion files? Douglas N Greve Mon, 08 Nov 2010 09:55:49 -0800 It is needed in make_average_surface. I've created a new version that does not use the aparc (thought I have not tested it). You can get it from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_… Make a backup of your current version of make_average_surface and then copy this one over it douig

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Clusterwise correction for multiple comparisons
by Ed Gronenschild 16 Jul '12

16 Jul '12

Hi, I'm performing a clusterwise correction for multiple comparisons with the command mri_glmfit-sim --glmdir my_glmdir --sim mc-z 5000 1.3 basename \ --sim-sign abs For version v4.5.0 this took about 40 hours to complete. However, for v5.1.0 it is now running for more than 6 days and from the csd file I can read that it still has more than 1000 steps to go. Is it possible that it takes that much time? Cheers, Ed

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annot 2 label file conversion
by Arnaud Messé 16 Jul '12

16 Jul '12

Hi there, I've some troubles with parcellisation schemes. I've used mri_annotation2label to extract labels within annot file. When I read the annot file within matlab (read_annotation.m), I found 869 entries, everything looks good so far. However, when I look at the output directory of labels, I only found 770 label file. For another parcellisation scheme, I found 325 entries in annot file and 496 label files... These findings are consistent across several subjects. So my question is how mri_annotation2label processes annot file? and how to find correspondence between annot and label files? Any advice would be greatly appreciate, -- Arnaud Messé, PhD Laboratoire d'imagerie fonctionnelle (LIF) UMRS 678 Inserm/UPMC CHU Pitié-Salpêtrière 91 boulevard de l'Hôpital F-75634 Paris Cedex 13 +33(0)1538284 03 (fax: 48) Arnaud.Messe(a)imed.jussieu.fr http://www.imed.jussieu.fr

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Repost: fsgd file
by Jacobs H (NP) 16 Jul '12

16 Jul '12

Dear FreeSurfers, I hope you can help me out with a problem in coding my fsgd file. I want to examine the spatial difference between two cognitive measures on cortical thickness in one group. Furthermore, I will correct for age (centered covariate). So, I have 4 variables: group (class), 2 cognitive scores (continuous) and age (continuous). How can I compare two continuous variables? I have tried to list them as two variables in the fsgd (so not class): e.g: Input101 group 2.3 1.9 -0.5 (number of subject / group / score 1/ score 2/ age) Then I ran the dods model with the contrast 0 -1 1 0, which ended up with a surface sig file. However, when I look at the scatterplot in tksurfer, I cannot see the two cognitive variables at the same time. Is there a better way to do this? Thanks a zillion times :) Best wishes Heidi ================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jacobs(a)maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================

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Coordinate Transformations
by jmd33 16 Jul '12

16 Jul '12

Hi, I'm working on a project project comparing the cortical thickness in epileptic patients to the corresponding brain area of a control subject. To do this, I have been trying to transform the patient RAS coordinates to talairach coordinates and then transforming the talairach coordinates into the RAS coordinates of the control. In doing this, I have two problems. First, when I use the transformation matrix provided in the free surfer subject folder (multiply RAS coordinate by transformation matrix in /mri/transforms/talairach.xfm) the coordinates seem to map to similar although not exactly the same area. Second, what is the best way to transform a set a talairach coordinates to RAS coordinates? Thank you for your help, Jared

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ROI from left to right hemi - cortical thickness
by Irene Altarelli 16 Jul '12

16 Jul '12

Dear all, I have a ROI on the left hemisphere and I'd like to extract cortical thickness values from the homologous region in the right hemisphere. For this I applied the interhemispheric registration process and got my ROI mapped into the right hemisphere in /subject/xhemi/label. However when I tried to run mris_anatomical_stats on /subject/xhemi it failed, as there is no wm.mgz file in /subject/xhemi/mri. Any suggestion would be greatly appreciated. Thank you, Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75230 Paris Cedex 05 tel. +33 (0)1 44 32 26 23

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