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30099 discussions

Tracula trac-all -stat flag -stat unrecognized
by Cat Chong 18 Jul '14

18 Jul '14

Hello Anastasia, I have just converted pathstas.overall.txt files to a table for group analyses. Now, I am trying to convert pathstats.byvoxel.txt files to a table for group analyses using the command: trac-all -stat -c I am receiving the error message: ERROR: flag -stat unrecognized I am working on a mac using bash script using Freesurfer version 5.3 Do you have any ideas? Cheers, Cat

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transforming Base surfaces to Cross space
by prasser 18 Jul '14

18 Jul '14

Dear All, For longitudinal data sets, is there a way that the lh.pial surface from the Base can be transformed into the brainmask.mgz space of a Cross so that it can be viewed with tkmedit on the Cross brainmask.mgz? Thanks, Paul

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Group differences in pc1 (longitudinal stage2)
by Tudor Popescu 18 Jul '14

18 Jul '14

Dear FS list, (dear Martin!) I have a longitudinal design, 3 groups, 2 timepoints, and I created three different QDEC tables (two groups at a time) in order to be able to compare each pair of groups in terms of percentage change from pre to post (what's referred to as "pc1" in the first stage of the two-stage-model). I look at thickness, area and lGI as dependent variables. Group is a categorical factor of interest, gender as the other categorical factor (not interested in its effect), and age as (continuous) nuisance. I'm interested in the contrast "Does the average ..., accounting for gender, differ between G1 and G2?" Say that, for some analysis (e.g. group 1 vs group 2, thickness, LH) I get a certain cluster that survives the MonteCarlo Null-Z correction. If the cluster is redish, I take it to mean that group 1 has a higher signed value of pc1 than group 2, and vice-versa if the cluster is blueish. However, because pc1 is (I think) a signed statistic, i.e. is negative for thickness decrease and positive for thickness increase, this makes me unsure how to interpret the stage2 (cross-sectional) result. As I understand it, having a significant red cluster in the group comparison can mean either of these 3 scenarios: 1. Both groups have pc1>0 2. G1 has pc1>0 and G2 has pc1<0 3. Both groups have pc1<0 ..but that the pc1 of G1 is always greater, as a signed number, than that of G2, since that is what defines the cluster. The problem is that, when I run the same analysis but keeping only subjects of one group in at one time, i.e. for each group separately and looking at the contrast "Does the average ... differ from zero?", in most cases I don't get the same cluster that appeared in the group comparison. My question is therefore: can a cluster appearing in the between-groups analysis be trusted if the same (or similar) cluster does *not *appear in each of the two within-groups (one-sample test) analyses? And if the latter analysis produces null results but the former does have sig clusters, does it still make sense to look at the sign of each group's mean pc1 in order to find the effect of the longitudinal treatment (atrophy or increase), even if that group in fact did not have a pc1 that was significantly different from zero? Many thanks for your help! Tudor

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Spatial smoothing in Matlab
by Reza Rajimehr 18 Jul '14

18 Jul '14

Hi, For a simulation purpose, I want to load a surface into Matlab, assign a random value (taken from a normal distribution) to each vertex, do spatial smoothing on the surface with a given FWHM (e.g. 5mm), then do some computations with the smoothed values. I am wondering if there is a Matlab code that I can use for surface smoothing, similar to what FS-FAST preprocessing does in Freesurfer version 5 and above. Thanks, Reza ***************** Reza Rajimehr, MD Postdoctoral Research Fellow McGovern Institute for Brain Research Massachusetts Institute of Technology (MIT) NMR Martinos Center Massachusetts General Hospital (MGH) Harvard University *****************

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retinotopic mapping using selxavg3-sess
by Alan Lee 18 Jul '14

18 Jul '14

Hello freesurferers, I ran this command (33333 is my subject name): selxavg3-sess -a Retinotopy.33333.lh -s 33333 and got this error message: # ---------- Using FSL's BET to Extract Brain------------------ # /usr/local/freesurfer/subjects/Retinotopy/33333/Retinotopy bet.fsl /tmp/mkbrainmask_14781/in.nii /tmp/mkbrainmask_14781/brain -m -f 0.1 /usr/lib/fsl/5.0/bin/bet2: error while loading shared libraries: libfslvtkio.so: cannot open shared object file: No such file or directory It seems that something is wrong with the file libfslvtkio.so, or perhaps some path problem (I've manually set $FSLDIR to /usr/lib/fsl/5.0/). Any feedback would be greatly appreciated. Below are the versions of software I'm using: Linux debian 3.2.0-4-486 #1 Debian 3.2.57-3+deb7u1 i686 GNU/Linux (run in virtualbox with a Windows 8 Host) FSL 5.0.6 freesurfer-Linux-centos4-stable-pub-v5.3.0 Many thanks, Alan -- Alan Lee sites.google.com/site/alanlflee/

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Re: [Freesurfer] Spatial smoothing in Matlab
by Reza Rajimehr 18 Jul '14

18 Jul '14

Thanks Doug! I need to do this procedure 100 times, so I have to automate it. Do you have an example C-shell script for this? Or is there a way to call mri_surf2surf inside a "for loop" of Matlab? Thanks, Reza not that I know of. When I have to do this, I save the data to a file, then call mri_surf2surf with a system call, then load the result back into matlab.

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Re: [Freesurfer] mri_convert
by Douglas Greve 18 Jul '14

18 Jul '14

You can use mri_convert to change the orientation in the header. If you run mri_convert without options it will give you lots of documentation doug On 7/18/14 9:17 AM, Fan, Qiuyun wrote: > Hi Doug, > > I think I figured it out. It's the angulation of the image plane. ImageOreintation (should have been axial slices) reads "0.99995101907245\0.00923454555106\-0.0035612672513\-0.0089978930043\0.69829945291611\-0.7157491962821", and was thus identified as coronal. So, nothing went wrong with mri_convert. > > As a follow up question, although technically, there's nothing wrong with it, it does look confusing intuitively. I'm wondering if there's a way to fool the nifti to label it as LPS at all? > > Thanks a lot! > > Best, > > Qiuyun > ________________________________________ > From: Fan, Qiuyun > Sent: Thursday, July 03, 2014 4:19 PM > To: Douglas N Greve > Subject: mri_convert > > Hi, Doug, > > I found an error when using mri_convert to convert image from dicom to nifti. I have one odd subject, whose orientation labels were wrong. The dicom-info-dump looks the same as the other subjects, and the images look fine too. > > If you have a chance to take a look at the images, here's the path to the "odd" subject:/autofs/cluster/hcps/data_preproc/HCPS_017/dcm/diff_1k/ > > An example of a "good" subject can be found here: /autofs/cluster/hcps/data_preproc/HCPS_015/dcm/diff_1k/ > > BTW, I'm using /usr/local/freesurfer/stable5_3_0. > > Please let me know if you need more information from me. > > Thanks a lot! > > Best, > > Qiuyun > >

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Errors in Mapping of Brodmann Areas
by pfannmoelj＠uni-greifswald.de 18 Jul '14

18 Jul '14

Dear Experts, I am working with freesurfer 5.3 on Mac OSX. I applied recon-all to a data set. This has been done with the same data on a Linux system with Freesurfer 5.3 without any problems. Everything works fine on the Mac except of the labelling of Brodmann Areas. On the Mac the regions are not created as a single areal with a border at the outline. Instead they consist of an outside border and several small regions inside the label. I already tried to create the Brodmann Areas by myself using the command: mri_label2label --srclabel /.../subjects/fsaverage/label/lh.BA3b.label --srcsubject fsaverage --trglabel lh.BA3b.test.label --trgsubject subjid --regmethod surface --hemi lh This does not change the result. I attached a screen shot of the label in fsaverage and one of my subjects. Any help is highly appreciated. Regards pfannmoe

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mni152reg error
by JacobML＠nmr.mgh.harvard.edu 18 Jul '14

18 Jul '14

Hello Freesurfer Experts, I am trying to view stats generated with FsFast in fslview/MNIspace, and in doing so I have run mni152reg to generate the registration matrix. That said, mni152reg did not complete correctly and below I have pasted the terminal output: Thu Jul 17 09:58:10 EDT 2014 setenv SUBJECTS_DIR /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons cd /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons /usr/local/freesurfer/stable5_3_0/bin/mni152reg --s CD_cerv_pat4_sess1_recon Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux fslregister --mov /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz --s CD_cerv_pat4_sess1_recon --reg /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat --dof 12 mkdir: cannot create directory `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833': Permission denied Log file is /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat.fslregister.log Thu Jul 17 09:58:11 EDT 2014 --mov /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz --s CD_cerv_pat4_sess1_recon --reg /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat --dof 12 $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ purkinje Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons mri_convert /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii mri_convert /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii niiWrite(): error opening file /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz... TR=2530.00, TE=3.25, TI=1100.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (-0, -0, -1) k_ras = (0, 1, 0) writing to /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii... ERROR: failure writing /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii I tried to run the fslregister command from within the subject's directory (in hopes to possible correct what may be a permissions issue), but this produces the same final error, "ERROR: failure writing /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.24919/refvol.fslregister.nii." Lastly, probably to no surprise, the /.../mri/transforms/reg.mni152.2mm.dat file was never generated. Any ideas how I may be able to correct these errors? Thank you for the help! Jacob

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selxavg3-sess error in ==> fast_selxavg3 at 434
by pfannmoelj＠uni-greifswald.de 18 Jul '14

18 Jul '14

Dear Experts, during an fsfast analysis an error occured after selxavg3-sess was executed. The corresponding commands were: mkanalysis-sess -fsd bold -surface self lh -fwhm 0 -event-related -paradigm sensory.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 8 -polyfit 2 -analysis analysis.lh -delay 0 -per-run -force -mcextreg mkcontrast-sess -analysis analysis.lh -contrast stim-v-base -a 1 selxavg3-sess -s ./sessdir -analysis analysis.lh -no-preproc -force The output of selxavg3-sess was: >> >> >> >> >> >> >> sxa3pwd = /.../evaluation >> sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./sessdir -analysis analysis.lh -no-preproc -force >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# sessdir ############################### /.../evaluation/sessdir ------------------------- $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m ------------------------- outtop = /.../evaluation Extension format = nii.gz 1 stim-v-base.mat Excluding 8 points nruns = 1 autostimdur = outanadir = /.../evaluation/sessdir/bold/analysis.lh Excluding 8 points Found 145573/155188 (93.8) voxels in mask Creating Design Matrix ... creation time = 0.008 sec DoMCFit = 1 ntptot = 108, nX = 15, DOF = 93 Saving X matrix to /.../evaluation/sessdir/bold/analysis.lh/Xtmp.mat XCond = 64.7067 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.468819 (t=0.005249) 2 -0.25 -0.252194 (t=0.007053) 3 0 -0.0449419 (t=0.008126) 4 0.25 0.149516 (t=0.00935) 5 0.5 0.319324 (t=0.010795) AR1 Correction M: 0.0749452 1.26122 Computing contrast matrices OLS Beta Pass run 1 t= 0.0 Global Mean Global In-Mask Mean = (0.664951) ??? Error using ==> mrdivide Matrix dimensions must agree. Error in ==> fast_selxavg3 at 434 RescaleFactor = flac0.inorm/gmean; >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Do you have an idea what went wrong? Sincerely yours pfannmoe

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