Freesurfer August 2014

freesurfer@nmr.mgh.harvard.edu

146 participants
208 discussions

bblabel
by Agoston Mihalik 07 Aug '14

07 Aug '14

Dear All I have problems using bblabel and would like to ask for expertise. At first, I tried to make a coronal cut in the following way: 'bblabel --l lh.DLPFCsd.label --o lh.out.label --ymin 26' I got a runtime error with: 'echo: No match' Then I used the example in bblabel help: 'bblabel --l lh.G_cuneus.label --o lh.out.label --xmin 0 --ymax -90 --zmin 10 --zmax 20' During running it seemed to be fine: 'bblabel done' However, inspecting the output label in freeview I got the following error: 'no data in label file' Any help would be appreciated. Thanks and regards Agoston

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Scatter plot after mri_glmfit
by Righart, Ruthger 07 Aug '14

07 Aug '14

Hi All, In Tksurfer it is possible to view a scatter plot of a relationship analyzed by mri_glmfit, by File -> Load Group Descriptor File (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) Is this also possible in Freeview? I tried Tools -> Plot FSGD Data, but that does not work. Best, Ruthger Righart

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label to surf (.mgh file)
by Sarah Whittle 07 Aug '14

07 Aug '14

Hi, I would like to create an overlay from a number of labels from the standard 2005 aparc in order to perform an fdr correction of a significance map using a mask to restrict the search space. I would like to do this with fsaverage. As far as I can tell, there is no label or annotation to surf function?? What I have done so far is group my labels into one larger label using mri_mergelabels. Then I have converted this label to a nifti volume using mri_label2vol (I tried using this command to create an mgh file, and it did, but I was not able to subsequently open this as an overlay in tksurfer). What I then wanted to do was convert the volume to a surface using mri_vol2surf, BUT I don't have a registration file, as this has all been done with fsaverage. I feel like there should be a simpler way to do this though! Any advice appreciated. Thanks, Sarah

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distances on individual and mni brain
by pfannmoelj＠uni-greifswald.de 07 Aug '14

07 Aug '14

Dear Experts, I have calculated distances with mris_pmake on the individual brain of a subject. I would like to compute the distance between the corresponding points on the mni brain (fsaverage). Is there a simple way to transform the distances? Best pfannmoe

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random effects of individuals
by Ralf Veit 07 Aug '14

07 Aug '14

Dear list-members, I submitted a paper regarding cortical thickness in relation to body fat distribution. The analysis was based on the mri_glmfit procedure implemented in freesurfer 5.1. Version. Gender was defined as a categorical or group factor and age, Body Mass Index, total surface are, body fat distribution and education as continuous factors. In a first step, we tested whether the slope of males and females were different regarding the continuous covariates. We found no significant gender specific slopes and used therefore the simpler model with one regressor for each covariate. Now I received the comments of the reviewers. One reviewer asked: "How are results affected if mixed effects modelling is used to control for the random effects of individuals?" Does it mean I need a subject specific error term in my GLM? Is there an option in freesurfer to perform such an analysis? Best Ralf Ralf Veit PhD Institute of Medical Psychology and Behavioral Neurobiology Otfried-Müller str. 47 72076 Tübingen phone: +49-7071-2987703 fax: +49-7071-295706

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FW: YANQ follow-up
by Krieger, Donald N. 06 Aug '14

06 Aug '14

Thanks for posting back so quickly, Bruce, and for the direction. Just to clarify, here is the command which I am using so you can see the types of files on which I am operating. The working directory is ${FREESURFER_HOME}/subjects/bert . I'm putting each switch on a separate line: mri_label2label --s Sub125 --srclabel label/rh.cortex.label --trglabel testLabels/rh.cortext.label --xfm mri/transforms/talairach.xfm --xfm-invert --regmethod volume I plotted the output vectors for a single 1 mm slice using my tools. This is shown in the left panel of the attached jpg. The right panel shows the same vectors translated by hand to "fit." The size and shape are close so this appears to be in the right direction. I would like to find the freesurfer coords --> MRI coords transform and try it in place of talairach.xfm . I assume that the inverse of talairach.xfm is not the correct transform to get from freesurfer --> MRI coordinates. Is there a way to extract the correct transform? It must have existed early in the "recon-all" run and must also be accessible to mri_convert -rl ... I tried --nt as you suggested but my version of mri_label2label (stable5) does not recognize it. I tried --regmethod surface --hemi rh and found that it gives identical results whether using --xfm-invert or not ! Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [mailto:freesurfer- > bounces(a)nmr.mgh.harvard.edu<mailto:bounces@nmr.mgh.harvard.edu>] On Behalf Of Bruce Fischl > Sent: Friday, August 01, 2014 9:29 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] FW: YANQ follow-up > > Hi Don > > try mri_label2label. Also, the if you are transforming label volumes > you need to use nearest neighbor interpolation, so include the -rt nearest switch. > > cheers > Bruce > On Fri, 1 Aug 2014, Krieger, Donald N. wrote: > > > > > Hi All, > > > > > > > > I am still in need of finding the tool sequence to generate an ASCII > > file containing (1) voxel RAS coordinates (2) for a specific label > > (3) using the original MRI coordinates rather than freesurfer coordinates. > > > > > > > > mri_convert -rl rawavg.mgz <input vol> <output vol> > > > > does generate a new output volume containing the "labelled" voxels > > contained in <input vol> . I can tell because this volume shows up > > more or less correctly in freeview although the color mapping > > appears to have changed or perhaps freeview is doing some kind of "fill" > > operation differently depending on the loaded volume. I assume > > these are in the coordinates for rawavg.mgz but cannot tell for sure. > > > > > > > > I need to generate a list of these voxel coordinates from <output > > vol> to check and for my work. > > > > (1) Do I need to generate a new annotation file from <output vol> > > and then use mri_annotation2label to get there? I have not been > > able to find the tool sequence which generates the .annot files. > > > > (2) An alternative appears to be mri_label2label with -xfm > > xfmfile and possibly including --xfm-invert . I did get this > > command to complete successfully using mri/transforms/talaraich.xfm > > but I presume this is not the correct transform. > > > > > > > > Thanks and best regards, > > > > > > > > Don > > > > > > > > Don Krieger, Ph.D. > > > > Department of Neurological Surgery > > > > University of Pittsburgh > > > > (412)648-9654 Office > > > > (412)521-4431 Cell/Text > > > > > > > > From: Krieger, Donald N. > > Sent: Thursday, July 31, 2014 9:36 AM > > To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> > > Subject: YANQ follow-up > > > > > > > > Thanks again for the pointer, Bruce. > > > > > > > > You wrote: > > > > ... mri_convert -rl rawavg.mgz <input vol> <output vol> > > > > which does produce an output volume from which I now need to extract > > RAS voxel coordinates. > > > > A pointer to a keyboard command would be most welcome. > > > > > > > > Of interest is the difference between the color mappings for the > > input and output volumes in freeview. > > > > When using the lookup table in freeview they are quite different > > whereas in grayscale they are almost identical. > > > > I wonder if this is contributing to my difficulty in finding a tool > > to extract the voxel coordinates. > > > > > > > > Thanks again. > > > > > > > > Regards, > > > > > > > > Don > > > > > > > > Don Krieger, Ph.D. > > > > Department of Neurological Surgery > > > > University of Pittsburgh > > > > (412)648-9654 Office > > > > (412)521-4431 Cell/Text > > > > > > > > > >

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license file not working
by Saemann Philipp 06 Aug '14

06 Aug '14

Hello users or support team, after using FS successfully for some time, now, after a trivial command such as mri_convert -it analyze T1.img -ot mgz 001.mgz an error appears as follows: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from T1.img... -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /net/PE1/raid1/enigma-mdd/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- I re-applied for a license file which was the EXACT one I already had at the specified location, and it still does produce the error message. What makes this licence "invalid" here? Is there some problem with C-compiler versions? (though I would not this should appear right now) Thanks for any ideas, Philipp Saemann Facharzt für Nervenheilkunde Arbeitsgruppe Neuroimaging Max-Planck-Institut für Psychiatrie Kraepelinstr. 2-10 80804 Munich Mail: saemann(a)mpipsykl.mpg.de Phone: 0049-89-30622-413

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Post-hoc test failure by ROI extraction after successful group analysis with FreeSurfer
by Yunxin Wang 06 Aug '14

06 Aug '14

Hi folks, I tried to extract the thickness/volume value of the ROI labels transferred from the annot files that're generated automatically by FreeSurfer after a succesful group analysis with corrected significant results. However, the thickness/volume values are no longer correlated with the independent variable that I used in the group analysis model earlier and even the direction of group difference seems to be inconsistent with the group analysis results as well. I have no idea how it went wrong and wondered maybe there's something wrong with my scripts. Have any of you run into such kind of problem? My script for ROI value extraction goes like this: #annot2label: mri_annotation2label --subject fsaverage --annotation onsetage_thickness --hemi rh --labelbase /expdata/wangyunxin/reconall_lj/fsaverage/labels/onsetage_thickness for i in sub* do #label2label: mri_label2label --srclabel fsaverage/labels/onsetage_thickness-001.label --srcsubject fsaverage --trglabel ./$i/labels/onsetage_thickness-001.label --trgsubject $i --regmethod surface --hemi rh #label2stats: mris_anatomical_stats -l $i/labels/onsetage_thickness-001.label -t $i/surf/rh.thickness -f $i/stats/rh.onsetage_thickness-001.stats -nsmooth 10 $i rh done #stats2table aparcstats2table --subjectsfile /expdata/wangyunxin/reconall_lj/music/sublist48 --hemi rh --meas thickness --parc onsetage_thickness-001 --tablefile music/onsetage_thickness-001_rh.txt Any suggestion would be great! Thanks! Best, Yunxin ------ Yunxin Wang Visiting PhD Student Gabrieli Lab McGovern Institute for Brain Research at MIT Office: 46-5107 Tel: 617-955-2809 http://gablab.mit.edu/index.php/gablab/people/14-sample-data-articles/220

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mri_cor2label: volume --> .label vectors
by Krieger, Donald N. 06 Aug '14

06 Aug '14

mri_cor2label does work for extracting vectors with FreesurferColorLUT.txt label numbers from .mgz volumes. The documentation at http://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2label states: --id labelid 0-255 value in COR volume The attached pdf shows the number of vectors which were extracted from each of 5 volumes for labels 1-255. You can see that volumes aseg, aparc+aseg, and wmparc yield nearly identical results. I ran several file pairs through spot checks and the vectors were identical in the ones I checked. Volume filled.mgz contains vectors for only 3 labels while volume T1.mgz contained vectors for all of them and in most cases, the numbers were higher. Questions: 1. Can mri_cor2label handle labelIDs > 255? 2. Is there a tool determining which labelIDs are represented in a .mgz volume? 3. Are there other volumes which I should be using for vector extraction for these labels. 4. Is there a way to extract labels with ids > 255? I assume that mri_cor2label is an older tool and the new approach is generate .annot files and then use mri_annotation2label. 5. How are .annot files created? I have been unable to find this even though it must be staring me in the face. Thanks, Don

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Crossing Segments
by Isaiah C. Smith 06 Aug '14

06 Aug '14

Hello All, Thank you for the help. I looked at my surface images in free view and they are crossing. The crossing seems to be taking place between the the brain and inner skull crossing over outer skull and outer skin. I believe that this is because the data that we have only goes down so far in the original mr images (Below). And when the individual surfaces are created they cross towards the posterior part of the head (Next Image). I attached the surfaces just in case to allow you to see. Would it be possible to extend outer skull and skin when using freesurfer, or get around this some other way. And lastly we are getting a very bumpy skin (Last Photo). Will this be a problem when creating the head model, finding the lead field matrix, etc. with MNE because the crossing sections prevent me from proceeding? Isaiah [cid:27A0E365-2791-4E78-879D-1A3490B5A655@host.ucla.edu][cid:42061E47-0F8E-43CF-B35C-AD40D52C02E9@host.ucla.edu][cid:10EB4B44-6FF2-4C08-9D07-7291D89BA9A2@host.ucla.edu]_______________________________________________

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Freesurfer August 2014