Freesurfer September 2011

freesurfer@nmr.mgh.harvard.edu

119 participants
181 discussions

questions about mapping volume data to brain surface and extracting cortical thickness
by ZhiLiangLong 06 Sep '11

06 Sep '11

Hi FS experts: I have two questions about FS. (1) Is there a way that can map volume data(.hdr and .img file) to brain surface in FS? (2) I find a way that can extract cortical thickness automatically,first,the statistical significant areas derived from group analysis on qdec are converted to annotation file using mri_surfcluster,then i use mri_annotation2label to convert the annotation file to label file,finally, mri_label2label and mri_anatomical_stats are used to map the label file to each subject and obtain cortical thickness. I want to know if the process is correct. any help appreciated

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Re: [Freesurfer] FS-FAST modeling question
by Benjamin Matthew Deen 06 Sep '11

06 Sep '11

Hi, I have an update to this query. I tried using mkanalysis-sess instead of the ".new" version, and now I do seem to be able to get rid of intensity normalization and prewhitening (or at least, adding these flags now has an effect on betas/t-stats, and in the expected directions). The code I'm using is mkanalysis-sess -analysis ToMLoc-1 -TR 2 -p para.para -dt blocked -fsd bold -funcstem f -runlistfile runlist1 -polyfit 0 -nc 2 -spmhrf 0 -tw 40 -no-inorm -nowhiten -noautostimdur # mkcontrast stuff here... selxavg3-sess -sf sessid -df sessdir -analysis ToMLoc-1 However, I have a few remaining questions about the results. 1) When I look at the regressors used in the analysis, they have a surprisingly large magnitude -- the HRF peaks at a value of ~20. Is there any way to alter the analysis such that these peaks are comparable to the values used in FSL/SPM, which is around .8, so that beta values will be directly comparable across analyses? If not, I can just scale the betas by the relevant factor, but it would be nice if this were possible. 2) When I compare the results of this analysis to results obtained with FSL or SPM, I find that the spatial pattern of beta/t-stats is very similar, but the t-stats have a noticeably reduced magnitude across the brain. Is there anything that may differ about FS-FAST's implementation of the GLM, such that t-stats would differ? 3) I saw in a ppt presentation on FS-FAST that the option -hpf can be used to add a highpass temporal filter to the model. However, when I use this option with mkanalysis-new, the script says that the flag isn't recognized. Is there another way to add such a filter? Thanks in advance for any help. Cheers, Ben ________________________________________ Date: Sun, 4 Sep 2011 13:15:51 -0400 From: Benjamin Matthew Deen <bdeen(a)mit.edu> Subject: [Freesurfer] FS-FAST modeling question To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <D0755B22EA5ED64C941ED568237AEC8D1764DCC5E3(a)EXPO11.exchange.mit.edu> Content-Type: text/plain; charset="us-ascii" Hi, I'm trying to run a model in fs-fast using no intensity normalization and no autocorrelation correction, for the purpose of comparing results with other software packages, and comparing results with/without autocorrelation correction. However, I haven't been able to get this to work so far. I've tried using the -noinorm and -nowhiten flags for mkanalysis-sess.new, but these don't seem to have any effect on the results: noinorm doesn't change the beta values, and nowhiten doesn't change either betas or t-stats, at all. The commands I'm using are: mkanalysis-sess.new -analysis ToMLoc-1 -TR 2 -p para.para -dt blocked -fsd bold -funcstem f -runlistfile runlist1 -polyfit 0 -nc 2 -spmhrf 0 -tw 40 -noinorm -nowhiten mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope1 -a 1 -c 2 mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope2 -a 2 -c 1 mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope3 -a 1 -a 2 -c 0 mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope4 -a 0 -c 1 -c 2 selxavg3-sess -sf sessid -df sessdir -analysis ToMLoc-1 Any idea what might be going wrong, or how I can get this to work? Thanks, Ben ------------------------------

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Regarding Segmentation of Hippocampal Subfield
by mohan boddu 06 Sep '11

06 Sep '11

Hello, When I segmented the Hippocampal Subfields (using the process stated in http://www.freesurfer.net/fswiki/HippocampalSubfieldSegmentation ) it generated two files by name *"posterior_Left-Hippocampus.mgz"* and * "posterior_Right-Hippocampus.mgz*". I would like to know what actually are those since they are not actual Hippocampus. When I am generating the crisp images do I need to use those files also, if so what are the labels of those regions. Also, what about the *right_alveus, right_fornix, left_alveus, left_fornix*regions. They haven't generated in the segmentation. Is there a way to generate those regions also. Any help regarding would be appreciated. Thank you. -- With Thanks & Regards, Mohan Boddu

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two questions: asymmetry and controlling for global thickness abnormality
by Tetiana Dadakova 05 Sep '11

05 Sep '11

Dear list, I have two question: 1. Is it possible to do the asymmetry analysis in FS, I mean to compare left and right hemispheres within one group? 2. Is it necessary to somehow control for global abnormality of thickness while looking at regional abnormality, e.g. if one group has thinner brain overall, but also thinner brain in some regions? (Similar to dividing by total brain volume in volumetric analysis) Thank you and best wishes, Tanja.

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FS-FAST modeling question
by Benjamin Matthew Deen 04 Sep '11

04 Sep '11

Hi, I'm trying to run a model in fs-fast using no intensity normalization and no autocorrelation correction, for the purpose of comparing results with other software packages, and comparing results with/without autocorrelation correction. However, I haven't been able to get this to work so far. I've tried using the -noinorm and -nowhiten flags for mkanalysis-sess.new, but these don't seem to have any effect on the results: noinorm doesn't change the beta values, and nowhiten doesn't change either betas or t-stats, at all. The commands I'm using are: mkanalysis-sess.new -analysis ToMLoc-1 -TR 2 -p para.para -dt blocked -fsd bold -funcstem f -runlistfile runlist1 -polyfit 0 -nc 2 -spmhrf 0 -tw 40 -noinorm -nowhiten mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope1 -a 1 -c 2 mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope2 -a 2 -c 1 mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope3 -a 1 -a 2 -c 0 mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope4 -a 0 -c 1 -c 2 selxavg3-sess -sf sessid -df sessdir -analysis ToMLoc-1 Any idea what might be going wrong, or how I can get this to work? Thanks, Ben

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what is thalamus-proper and clusters-table related question
by Tetiana Dadakova 04 Sep '11

04 Sep '11

Dear FS list, 1. What does a label Thalamus Proper include? Is it the same as thalamus? 2. After correcting for multiple comparisons, I get a table of clusters. I have several questions regarding this table: What do the columns Max, CWPLow, and CWPHigh represent? Regarding the NVtxs column: is it the number of vertexes in cluster? What kind of information can I get from this value? If two clusters have different areas but the same number of vertexes, does it mean something? Thank you very much for your help and for your time, Tanja.

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dcm2nii and recon all
by Carolina Valencia 02 Sep '11

02 Sep '11

Dear FS' users, I have a 3D T1 from a GE scanner which I convert with dcm2nii to use it with recon-all, but I got 3 images: o -- original oo -- orthogonal co -- cropped image Which I should use to run the command recon-all? thanks! Carolina

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Surface analysis FSL GFEAT results for multiple subjects with 4 runs each
by Michelle Umali 02 Sep '11

02 Sep '11

Hi Freesurfers, I've been looking at the wiki for information on doing an surface analysis using GFEAT results for within subject, across multiple runs. On the wiki, a fixed effects analysis was used because there were only two runs. I have four runs and FSL uses FLAME 1 and FLAME 1+2. 1. Should/how do I do I random effects for 4 runsb? 2. How does one do a group surface analysis this for multiple subjects who each have 4 runs? Thanks. Michelle

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Grad_Unwarp question
by Mohana Ramaratnam 02 Sep '11

02 Sep '11

Hello, We used to run: grad_unwarp with matlab invoked with -nodisplay option. The version information on this file is: version: Version for distribution, 1.0, author: SC----------- id: id9/01 13:34:11 I see that Freesurfer 5.1 has a grad_unwarp script, which I can modify to invoke matlab with -nodisplay, however, I dont see any sub-folder grad_unwarp_tables in FREESURFER_HOME. Where do I get these tables from? Am I missing some installation option? Regards Mohana

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Longitudinal aseg errors
by Jeff Sadino 02 Sep '11

02 Sep '11

Hello, I finished processing my first longitudinal subjects, but I have some errors. The TP3.long aseg.mgz file is poorly segmented (corpus callosum, see attachment). I am wondering where I should make edits to correct this. The surfaces of all 3 longitudinal timepoints look fine, so according to the wiki, I should only have to edit the TP3.long. Is that true? If not, then I will have to edit TP3.cross. Originally, the watershed for TP3.cross was bad. I edited this and re-ran autorecon2 and autorecon3, and exited with no errors. However, the cross aseg.mgz is still bad. I thought maybe the talairach.m3z file was bad, but the nu_noneck image was transformed fine. I see that the log file says during the mri_ca_label step that the CSF peak is too bright - rejecting (see attachment). After comparing the csf areas of the TP3.cross norm image with the csf areas of the TP1.cross norm image, they have values of 30 compared to values of 10. Previous posts have suggested to copy the orig.mgz image to the nu.mgz image for a similar problem. Can someone please advise me on where it would be best to make the edits so that my longitudinal reconstructions are accurate? Thank you! Jeff Sadino

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Freesurfer September 2011