Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

mri_glmfit files
by Joshua deSouza 27 May '13

27 May '13

Hello all, I would just like to know what is the significance of the files that are produced after a glmfit is done. I was trying to find a write up online but I was not able to. They include : - cnr.mgh - F.mgh - gamma.mgh - gammavar.mgh - sig.mgh Thank you

2 1

Re: [Freesurfer] FMRI surface transformation for vertex-wise connectivity analysis
by Bruce Fischl 27 May '13

27 May '13

you would change fsaverage5 to fsaverage4 (fewer vertices) or fsaverage6 (more vertices) On Thu, 16 May 2013, Ludovico Minati wrote: > Hi Thomas > > many thanks. So, in the example you have sent me, how should I go > about if I wished to vary the granularity? Are there different meshes > to reshape or should I generate them somehow? > > Ludovico > > > On 16 May 2013 14:47, Thomas Yeo <ythomas(a)csail.mit.edu> wrote: >> Hi Ludovico, >> >> The mri_vol2surf example I sent you directly resample to fsaverage5, >> which is around 4mm spacing, resulting in 18715 vertices for both >> hemispheres combined after excluding the medial wall in the surfaces. >> >> I am also including the freesurfer mailing list in the email as >> suggested by Bruce. >> >> --Thomas >> >> On Thu, May 16, 2013 at 8:25 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >>> Hi Ludovico >>> >>> I wouldn't downsample before calling mri_surf2surf. We have tools for >>> uniformly parcellating the cortex (mris_make_face_parcellation) that can be >>> used for this purpose after sampling the timecourses to the cortex. >>> >>> >>> cheers >>> Bruce >>> On Thu, 16 May 2013, Ludovico Minati wrote: >>> >>>> Hi Bruce, >>>> >>>> many thanks. Yes sorry I shall use the list from now on. But let me >>>> just ask you a clarification as we are already on these questions >>>> >>>> For our connectivity analyses, at present we parcellated in 3D volume >>>> space the cortex into a pre-set number of roughly equal volume >>>> parcels, ranging in number between around 500 to 10,000. I would need >>>> to translate this approach to the surface space in Freesurfer, i.e. be >>>> able to smooth on the cortical surface and undersample it. What is the >>>> best approach that can be used? >>>> >>>> Along this like: you wrote around 150k vertices/hemisphere. For our >>>> purposes that's an enormous number, much larger than the number of EPI >>>> voxels. How can we mesh downsample before calling mri_vol2surf? >>>> >>>> Again thanks for your kind help and patience >>>> >>>> Ludovico >>>> >>>> >>>> On 16 May 2013 14:09, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >>>>> >>>>> Hi Ludovico >>>>> >>>>> can we move this discussion to the FreeSurfer list in the future so >>>>> others >>>>> can answer? >>>>> >>>>> 1. Hard to say as sometimes one works better than the other, you'll just >>>>> have to try. The transform should be rigid (6DOF) since the scalings are >>>>> read from the header, why would you want affine? I think Doug has worked >>>>> on >>>>> this and you can specify it in the bbregister command line, but I've >>>>> never >>>>> used it. >>>>> >>>>> 2. About 150K vertices/hemisphere. They are distributed initially at 1mm >>>>> spacing (the surface of the voxels), and cannot be tuned. There are some >>>>> tools around for mesh downsampling if you want, and this is even easier >>>>> if >>>>> you go to fsaverage space (with mri_surf2surf) where we have >>>>> representations >>>>> based on recursive icosahedral supersamplings. >>>>> >>>>> 3. This is due to a bug in the initial nifti format that didn't allow >>>>> any >>>>> one dimension greater than 64K. If you output in .mgz it should be >>>>> nvertices >>>>> x 1 x 1 x ntimepoints. >>>>> >>>>> 4. Search for "coordinate systems" on our wiki. This is documented >>>>> extensively. >>>>> >>>>> there are also matlab i/o functions for reading/writing all our formats >>>>> (e.g. MRIread.m) >>>>> >>>>> cheers >>>>> Bruce >>>>> >>>>> >>>>> On Thu, 16 May 2013, Ludovico Minati wrote: >>>>> >>>>>> Hi Thomas, >>>>>> >>>>>> thanks. A few quick questions, which hopefully will take little of >>>>>> your time but save me a lot of hassle: >>>>>> >>>>>> 1) bbregister. Do you advise using FLIRT or SPM for initialization? Is >>>>>> this a rigid-body transformation, or an affine one? Any way I can >>>>>> control the DOF? If I use SPM shall I feed the mean realigned volume >>>>>> here, as I expect? >>>>>> >>>>>> 2) recon-all. What is the typical number of vertices for the cortex? >>>>>> Any way I can control it, i.e. sample more or less finely? This would >>>>>> be particularly relevant for our task. >>>>>> >>>>>> 3) mri_vol2surf. Perhaps naively I was expecting an output file simply >>>>>> consisting of a list of values, i.e. one per vertex (assuming a single >>>>>> input volume that is). But the documentation says: "The output will be >>>>>> a data set with Nv/R colums, 1 row, R slices, and Nf frames..." What >>>>>> is the reshaping factor R for? How do I deal with this, i.e. how do I >>>>>> simply get a value per vertex? Or am I missing something here? Is >>>>>> mri_vol2surf averaging over neighbouring vertices? >>>>>> >>>>>> 4) Where do I read the Euclinean co-ordinates of the vertices from? >>>>>> >>>>>> Cheers >>>>>> >>>>>> Ludovico >>>>>> >>>>>> On 16 May 2013 04:30, Thomas Yeo <ythomas(a)csail.mit.edu> wrote: >>>>>>> >>>>>>> >>>>>>> Hi Ludovico, >>>>>>> >>>>>>> Just remember that you need to run "recon-all" on your T1 anatomical >>>>>>> first. >>>>>>> >>>>>>> For bbregister, the command goes something like this: bbregister >>>>>>> --bold --s $anat_s --init-fsl --mov $input --reg $reg. I find the >>>>>>> bbregister cost function value a good indication of whether the >>>>>>> registration has good well. Below 0.5 is good. Below 0.6 is probably >>>>>>> acceptable. >>>>>>> >>>>>>> For mri_vol2surf, the command goes something like this: mri_vol2surf >>>>>>> --mov $f --reg $reg --hemi $hemi --projfrac 0.5 --trgsubject >>>>>>> fsaverage5 --o $output --reshape --interp trilinear >>>>>>> >>>>>>> Cheers, >>>>>>> Thomas >>>>>>> >>>>>>> On Wed, May 15, 2013 at 8:57 PM, Bruce Fischl >>>>>>> <fischl(a)nmr.mgh.harvard.edu> wrote: >>>>>>>> >>>>>>>> >>>>>>>> Hi Ludovico >>>>>>>> >>>>>>>> you can get vertex-level timecourse by using bbregister to register >>>>>>>> the >>>>>>>> EPI >>>>>>>> data to the surface, then mri_vol2surf to sample onto the surface. >>>>>>>> >>>>>>>> cheers >>>>>>>> Bruce >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Wed, 15 May 2013, Ludovico Minati wrote: >>>>>>>> >>>>>>>>> Hello Thomas, >>>>>>>>> >>>>>>>>> yes sure. Our area of interest is early dementia diagnosis, and we >>>>>>>>> are >>>>>>>>> exploring the predictive value of graph topological indices. As you >>>>>>>>> know >>>>>>>>> there are major volume changes in dementia, and from the literature I >>>>>>>>> have >>>>>>>>> convinced myself we may be better off resolving this confound through >>>>>>>>> working on the surface, rather than playing around with ad-hoc >>>>>>>>> atlases >>>>>>>>> for >>>>>>>>> volumetric normalization. >>>>>>>>> >>>>>>>>> I have got plenty of signal processing code to perform the analyses >>>>>>>>> from >>>>>>>>> BOLD timeseries; what I am looking for now is a way to apply >>>>>>>>> Freesurfer >>>>>>>>> normalization to obtain vertex-level time-courses. >>>>>>>>> >>>>>>>>> Hence, I am so far only interested in solving the following problem >>>>>>>>> with >>>>>>>>> Freesurfer: we have as input an individual T1 scan and a series of >>>>>>>>> EPI >>>>>>>>> volumes, we want to preprocess/coregister/normalize them with >>>>>>>>> Freesurfer and >>>>>>>>> extract the BOLD timecourses for each vertex. No fMRI analysis in >>>>>>>>> Freesurfer, no group analysis. >>>>>>>>> >>>>>>>>> Hopefully it is not too complex? I am dwarfed by the range of >>>>>>>>> commands >>>>>>>>> available! >>>>>>>>> >>>>>>>>> Thank you very much in advance >>>>>>>>> >>>>>>>>> Ludovico >>>>>>>>> >>>>>>>>> -----Original Message----- >>>>>>>>> From: Thomas Yeo <ythomas(a)csail.mit.edu> >>>>>>>>> Sender: yeoyeo02(a)gmail.com >>>>>>>>> Date: Wed, 15 May 2013 10:07:00 >>>>>>>>> To: Bruce Fischl<fischl(a)nmr.mgh.harvard.edu> >>>>>>>>> Cc: lminati(a)ieee.org<lminati(a)ieee.org>; Dennis >>>>>>>>> Chan<D.Chan(a)bsms.ac.uk> >>>>>>>>> Subject: Re: FMRI surface transformation for vertex-wise connectivity >>>>>>>>> analysis >>>>>>>>> >>>>>>>>> Hi Ludovico, >>>>>>>>> >>>>>>>>> Can you give me the context of what you need? >>>>>>>>> >>>>>>>>> Cheers, >>>>>>>>> Thomas >>>>>>>>> >>>>>>>>> On Wed, May 15, 2013 at 9:52 AM, Bruce Fischl >>>>>>>>> <fischl(a)nmr.mgh.harvard.edu> wrote: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Hi Ludovico >>>>>>>>>> Thomas Yeo (ccd) has a set of scripts for this purpose >>>>>>>>>> Cheers >>>>>>>>>> Bruce >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On May 14, 2013, at 8:50 PM, "Ludovico Minati" <lminati(a)ieee.org> >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> Ludovico >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> The information in this e-mail is intended only for the person to >>>>>>>>>> whom >>>>>>>>>> it >>>>>>>>>> is >>>>>>>>>> addressed. If you believe this e-mail was sent to you in error and >>>>>>>>>> the >>>>>>>>>> e-mail >>>>>>>>>> contains patient information, please contact the Partners Compliance >>>>>>>>>> HelpLine at >>>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>>>>>>> you >>>>>>>>>> in >>>>>>>>>> error >>>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>>> and >>>>>>>>>> properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>> >>>> >>>> >>> > > >

4 3

contrast selection and group analyses
by Damien MARIE 27 May '13

27 May '13

Dear FreeSurfer experts, I was using VBM for group analysis but I am now working with FreeSurfer 5.3 which is pretty new for me. I have to compare two groups but I'm confused about the results and I have a coupe of questions about that. How can we select contrasts? I mean Qdec propose this with Cortical Thickness for example: " Does the average thickness differ between group 1 and group 2 ? ". Thus I was thinking that when I choose this question, the result will correspond to the contrast " group 1 - group 2 " but I'm not sure since the results presented then looks like corresponding to the inverse, the contrast " group 2 - group 1 ". Anyway I have to check both contrasts. 1) How identify the contrast presented? 2) How select the contrast? Best regards, Damien Marie - Doctorant / PhD student E-mail: damien.marie(a)u-bordeaux2.fr Phone: +33 (0)5 57 82 09 39 Homepage: www.gin.cnrs.fr/spip.php?article23&lang=en Researchgate: www.researchgate.net/profile/Damien_Marie/ _______________________________________________ GIN (Groupe d'Imagerie Neurofonctionnelle) UMR 5296 - Université Bordeaux II Ségalen - CNRS - CEA 146, rue Léo Saignat - Case 71 33076 Bordeaux cedex _______________________________________________

2 1

nuintensitycor and skullstrip problems
by LAOUCHEDI MAKHLOUF 27 May '13

27 May '13

hi all i run recon_all on some subjects having 512x512x154 , i noticed (using tkmedit) that there are no problems with orig.mgz, and rawavg.mgz but most of them were cropped (more than half of the brain disappeared) after the "-nuintensity" step (nu.mgz); for one of these patients, the nu.mgz is ok but the T1.mgz produced after skullstrip is bad : the skull was largely still there on the right hemisphere. i read in the "recon-all.local-copy" file (in the SUBJECTS_DIR/subj/scripts folder) that we must include the "-cw256" flag if the "FOV" is beyond 256x256x256 (just to be sure, is it the FOV -in mm- or the just the GRID). but when reading in the recon-all.log file, this step seems to be a default one when running "recon_all -all" command. in the recon-all.log file it is written : Original Data has (0.4883, 0.4883, 1.2) mm size and (512, 494, 154) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation thank you for your help

2 1

very slow analysis with recon-all
by stdp82＠virgilio.it 26 May '13

26 May '13

Hi list, I'm running recon-all on two T1 but the command is for two days on CORRECTING DEFECT 11 (vertices=55538, convex hull=7811). Is it ok? What's happen? Thanks, Stefano

3 2

Re: [Freesurfer] Freesurfer Digest, Vol 111, Issue 37
by Yongxia Zhou 26 May '13

26 May '13

Dear Dr. Greve, Thank you very much for your information. I double checked the data, and realizes that the anatomical volume linked to fsaverage subject, which should be induvidual subject. Sorry that I missed your reply yesterday. I will try to run everything again to make sure data format and processing are all done correct. Thanks very much again. Best regards Yongxia On Sunday, May 26, 2013, wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Freesurfer Digest, Vol 111, Issue 34 (Yongxia Zhou) > 2. Re: Freesurfer Digest, Vol 111, Issue 34 (Douglas Greve) > 3. Re: possible to use freesurfer segmentations to get mean > values for anatomic structures from other sequences (Douglas Greve) > 4. Re: possible to use freesurfer segmentations to get mean > values for anatomic structures from other sequences (Salil Soman) > 5. Re: possible to use freesurfer segmentations to get mean > values for anatomic structures from other sequences (Douglas Greve) > 6. Correction for multiple comparisons error (Fotiadis, Panagiotis) > 7. minor bug report (Joseph Dien) > 8. Fwd: BBR Register failing (Salil Soman) > 9. Re: BBR Register failing (Salil Soman) > 10. Re: BBR Register failing (Salil Soman) > 11. very slow analysis with recon-all (stdp82(a)virgilio.it) > 12. contrast selection and group analyses (Damien MARIE) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 25 May 2013 12:05:10 -0400 > From: Yongxia Zhou <yongxiazhou(a)gmail.com> > Subject: Re: [Freesurfer] Freesurfer Digest, Vol 111, Issue 34 > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CAMYv_=v0mvsPYnyS-TTXNhxYfPj9nyPyz3sjhiT1AE7Ra2m= > rA(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Freesurfer experts, > > thank you very much for your suggestion. This is the error message > > when I specify the -analysis folder. It seems coming from the > > preprocessing registration step. > > Any of your advice will be greatly appreciated. > > > > best regards > > yongxia > > > > fslregister --s andrew_fsaverage --mov > > bold/tmp.bbregister.65172/template.nii --reg > > bold/tmp.bbregister.65172/reg.init.dat --niters 1 --maxangle 90 > > --nobetmov --tmp bold/tmp.bbregister.65172/fslregister --dof 6 > > > > Log file is bold/tmp.bbregister.65172/reg.init.dat.fslregister.log > > > > Fri May 24 08:40:39 EDT 2013 > > --s andrew_fsaverage --mov bold/tmp.bbregister.65172/template.nii > > --reg bold/tmp.bbregister.65172/reg.init.dat --niters 1 --maxangle 90 > > --nobetmov --tmp bold/tmp.bbregister.65172/fslregister --dof 6 > > $Id: fslregister,v 1.34.2.1 2011/03/28 20:35:36 greve Exp $ > > YongxiaZhous-MacBook.local > > Darwin YongxiaZhous-MacBook.local 9.6.1 Darwin Kernel Version 9.6.1: > > Sun Dec 21 19:45:33 PST 2008; root:xnu-1228.9.75~4/RELEASE_I386 i386 > > nIters 1 > > -------------------------------------- > > /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/sess02 > > mri_convert > > > /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/andrew_fsaverage/mri/brainmask.mgz > > bold/tmp.bbregister.65172/fslregister/refvol.fslregister.nii > > mri_convert > > > /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/andrew_fsaverage/mri/brainmask.mgz > > bold/tmp.bbregister.65172/fslregister/refvol.fslregister.nii > > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > > reading from > > > /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/andrew_fsaverage/mri/brainmask.mgz... > > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (-1, 0, 0) > > j_ras = (0, 0, -1) > > k_ras = (0, 1, 0) > > writing to > bold/tmp.bbregister.65172/fslregister/refvol.fslregister.nii... > > -------------------------------------- > > /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/sess02 > > mri_convert bold/tmp.bbregister.65172/template.nii > > bold/tmp.bbregister.65172/fslregister/movvol.fslregister.nii --frame 0 > > mri_convert bold/tmp.bbregister.65172/template.nii > > bold/tmp.bbregister.65172/fslregister/movvol.fslregister.nii --frame 0 > > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > > reading from bold/tmp.bbregister.65172/template.nii... > > TR=7.00, TE=0.00, TI=0.00, flip angle=0.00 > > warning: input volume axes are not orthogonal:i_dot_j = 0.000000, > > i_dot_k = 1.000000, j_dot_k = 0.000000 > > i_ras = (-1, -0, 0) > > j_ras = (-0, -0, -1) > > k_ras = (-1, -0, 0) > > warning: output volume axes are not orthogonal:i_dot_j = 0.000000, > > i_dot_k = 1.000000, j_dot_k = 0.000000 > > i_ras = (-1, -0, 0) > > j_ras = (-0, -0, -1) > > k_ras = (-1, -0, 0) > > keeping frame 0 > > writing to > bold/tmp.bbregister.65172/fslregister/movvol.fslregister.nii... > > WARNING: bad orientation matrix (determinant = 0) in nifti1 file ... > > ... continuing. > > Mov determinant is 0 > > /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/sess02 > > tkregister2_cmdl --mov > > bold/tmp.bbregister.65172/fslregister/movvol.fslregister.nii --reg > > bold/tmp.bbregister.65172/fslregister/reg0.65212.dat --regheader > > --fslregout bold/tmp.bbregister.65172/reg.init.dat.fsl.mat0 --s > > andrew_fsaverage --noedit > > tkregister_tcl /Applications/freesurfer/tktools/tkregister2.tcl > > INFO: no target volume specified, assuming FreeSurfer orig volume. > > target volume orig > > movable volume > bold/tmp.bbregister.65172/fslregister/movvol.fslregister.nii > > reg file bold/tmp.bbregister.65172/fslregister/reg0.65212.dat > > LoadVol 0 > > ZeroCRAS 0 > > $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ > > Diagnostic Level -1 > > INFO: loading target > > > > > /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/andrew_fsaverage/mri/orig.mgz > > Ttarg: -------------------- > > -1.000 0.000 0.000 128.000; > > 0.000 0.000 1.000 -128.000; > > 0.000 -1.000 0.000 128.000; > > 0.000 0.000 0.000 1.000; > > INFO: loading movable > > bold/tmp.bbregister.65172/fslregister/movvol.fslregister.nii > > Tmov: -------------------- > > -0.508 0.000 0.000 130.000; > > 0.000 0.000 9.600 -14.400; > > 0.000 -0.508 0.000 130.000; > > 0.000 0.000 0.000 1.000; > > MatrixMultiply: m2 is null! > > > > mkheaderreg = 1, float2int = 0 > > Computing reg from header (and possibly input matrix) > > ERROR: tkregister2_cmdl > > if ( $status ) exit 1 ; > > if ( 1 ) exit 1 > > exit 1 > > > > > > On 5/24/13, freesurfer-request(a)nmr.mgh.harvard.edu <javascript:;> > > <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > > > Send Freesurfer mailing list submissions to > > > freesurfer(a)nmr.mgh.harvard.edu > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > or, via email, send a message with subject or body 'help' to > > > freesurfer-request(a)nmr.mgh.harvard.edu > > > > > > You can reach the person managing the list at > > > freesurfer-owner(a)nmr.mgh.harvard.edu > > > > > > When replying, please edit your Subject line so it is more specific > > > than "Re: Contents of Freesurfer digest..." > > > > > > > > > Today's Topics: > > > > > > 1. Re: command not found (Louis Nicholas Vinke) > > > 2. Re: A question of running fsfast in mac (Douglas N Greve) > > > 3. Re: p-value visualization (Douglas N Greve) > > > 4. Re: command not found (clelia pellicano) > > > 5. Re: problem with alignment of labeling files generated from > > > the rh.area file (Douglas N Greve) > > > 6. Re: FreeSurfer v 5.3.0 compatibility with Mac OS X 10.4.11 > (Z > > K) > > > 7. Re: mri_concat --conjunct (Caspar M. Schwiedrzik) > > > 8. Re: p-value visualization (MCLAREN, Donald) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Fri, 24 May 2013 12:09:59 -0400 (EDT) > > > From: Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> > > > Subject: Re: [Freesurfer] command not found > > > To: clelia pellicano <pellicanoc(a)gmail.com> > > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > > Message-ID: <alpine.LRH.2.03.1305241206080.43202(a)nmr.mgh.harvard.edu> > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Hi Clelia, > > > That mv command is failing presumably because SetUpFreeSurfer.txt does > > not > > > exist in that directory. What are you trying to do with the mv > command? > > > > > > It does look like freesurfer was sourced successfully. Are the > > FreeSurfer > > > related commands still not found? > > > > > > Don't forget to cc the freesurfer mailing list. > > > -Louis > > > > > > On Fri, 24 May 2013, clelia pellicano wrote: > > > > > >> Hi Louise, > > >> I'm now using tcsh. Here what I did > > >> > > >> [dyn1097-8:~] cpellica% setenv FREESURFER_HOME > > >> /Applications/freesurfer > > >> [dyn1097-8:~] cpellica% source > > >> /Applications/freesurfer/SetUpFreesurfer.csh > > >> -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- > > >> Setting up environment for FreeSurfer/FS-FAST (and FSL) > > >> FREESURFER_HOME ? /Applications/freesurfer > > >> FSFAST_HOME ? ? ? /Applications/freesurfer/fsfast > > >> FSF_OUTPUT_FORMAT nii.gz > > >> SUBJECTS_DIR ? ? ?/Applications/freesurfer/subjects > > >> MNI_DIR ? ? ? ? ? /Applications/freesurfer/mni > > >> FSL_DIR ? ? ? ? ? /usr/local/fsl > > >> [dyn1097-8:~] cpellica% mv ?SetUpFreeSurfer.txt SetUpFreeSurfer.csh? > > >> mv: rename SetUpFreeSurfer.txt to SetUpFreeSurfer.csh: No such file or > > >> directory > > >> > > >> Do you have any advice? > > >> > > >> Thanks > > >> > > >> Clelia > > >> > > >> > > >> > > >> > > >> > > >> On Fri, May 24, 2013 at 3:04 PM, Louis Nicholas Vinke > > >> <vinke(a)nmr.mgh.harvard.edu> wrote: > > >> Hi Clelia, > > >> What do you run to source FS and do you get any output in your > > >> ter >

1 0

Fwd: BBR Register failing
by Salil Soman 25 May '13

25 May '13

---------- Forwarded message ---------- From: Salil Soman <salsoman(a)stanford.edu> Date: Sat, May 25, 2013 at 8:00 PM Subject: BBR Register failing To: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Dear Doug, I attempted to run the process we discussed earlier today for registering a different tissue contrast to the T1 after freesurfer 5.3 was run. I had run an FSSPGR for my subject using the following command: recon-all -i SPGR/*.gz -s WMR3T_0015z_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all It finished without any problems. Then I tried running the bbrregister command: bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold (this version was with bold contrast, but I get the same error if I try t1 or t2). The process fails and I get the following error log (below). Any suggestions on what I am doing wrong? Thanks, Sal ---------- Forwarded message ---------- From: Salil Soman <salsoman(a)stanford.edu> Date: Sat, May 25, 2013 at 7:54 PM Subject: bbregister fail log To: salsoman(a)stanford.edu Logfile for bbregister Sat May 25 19:51:15 PDT 2013 setenv SUBJECTS_DIR /mnt/glusterfs/salsoman/output/FS cd /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS /mnt/glusterfs/salsoman/freesurfer/bin/bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux corn18.stanford.edu 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /mnt/glusterfs/salsoman/freesurfer mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from QSM_906.nii.gz... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) writing to ./tmp.bbregister.26724/template.nii... fslregister --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask Log file is ./tmp.bbregister.26724/reg.init.dat.fslregister.log Sat May 25 19:51:17 PDT 2013 --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ corn18.stanford.edu Linux corn18.stanford.edu 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii mri_convert: extra arguments ("not" and following) type mri_convert -u for usage -------------------------------------- /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ./tmp.bbregister.26724/template.nii ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 mri_convert ./tmp.bbregister.26724/template.nii ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.bbregister.26724/template.nii... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) keeping frame 0 writing to ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii... Mov determinant is -0.984886 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS tkregister2_cmdl --mov ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --reg ./tmp.bbregister.26724/fslregister/reg0.26760.dat --regheader --fslregout ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 --s WMR3T_0015z_FS --noedit tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii reg file ./tmp.bbregister.26724/fslregister/reg0.26760.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.000 0.000 0.000 112.000; 0.000 0.000 0.985 -83.715; 0.000 -1.000 0.000 112.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; Determinant 1 subject = WMR3T_0015z_FS RegMat --------------------------- 1.000 -0.000 -0.000 1.591; -0.000 -0.950 0.313 0.719; 0.000 -0.313 -0.950 -5.896; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.984886, ref det = -1 Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/fsl/etc/flirtsch/xyztrans.sch -init ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort Sat May 25 19:51:22 PDT 2013 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.26724/reg.init.dat.fsl.mat -init ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule /mnt/glusterfs/salsoman/freesurfer/bin/flirt.newdefault.20080811.sch ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.26724/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.26724/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.26724/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort tkregister2_cmdl --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --fslreg ./tmp.bbregister.26724/reg.init.dat.fsl.mat --noedit tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl ERROR: cannot open ./tmp.bbregister.26724/reg.init.dat.fsl.mat cat: ./tmp.bbregister.26724/reg.init.dat: No such file or directory tmp: Subscript out of range. Started at Sat May 25 19:51:17 PDT 2013 Ended at Sat May 25 19:51:23 PDT 2013 fslregister Done To check results, run: tkregister2 --mov ./tmp.bbregister.26724/template.nii --reg ./tmp.bbregister.26724/reg.init.dat --surf orig mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg ./tmp.bbregister.26724/reg.init.dat --out-reg ./tmp.bbregister.26724/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/reg.init.dat mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg ./tmp.bbregister.26724/bbr.pass1.dat --out-reg register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param --surf white --cur-reg ./tmp.bbregister.26724/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.26724/bbr.pass1.dat Cleaning up Started at Sat May 25 19:51:15 PDT 2013 Ended at Sat May 25 19:51:24 PDT 2013 BBR-Run-Time-Sec 9 bbregister Done To check results, run: tkregister2 --mov QSM_906.nii.gz --reg register.dat --surf

1 0

Re: [Freesurfer] Freesurfer Digest, Vol 111, Issue 34
by Yongxia Zhou 25 May '13

25 May '13

Dear Dr. Greve, thank you very much for your suggestion. This is the error message when I specify the -analysis folder. It seems coming from the preprocessing registration step. best regards yongxia fslregister --s andrew_fsaverage --mov bold/tmp.bbregister.65172/template.nii --reg bold/tmp.bbregister.65172/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/tmp.bbregister.65172/fslregister --dof 6 Log file is bold/tmp.bbregister.65172/reg.init.dat.fslregister.log Fri May 24 08:40:39 EDT 2013 --s andrew_fsaverage --mov bold/tmp.bbregister.65172/template.nii --reg bold/tmp.bbregister.65172/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/tmp.bbregister.65172/fslregister --dof 6 $Id: fslregister,v 1.34.2.1 2011/03/28 20:35:36 greve Exp $ YongxiaZhous-MacBook.local Darwin YongxiaZhous-MacBook.local 9.6.1 Darwin Kernel Version 9.6.1: Sun Dec 21 19:45:33 PST 2008; root:xnu-1228.9.75~4/RELEASE_I386 i386 nIters 1 -------------------------------------- /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/sess02 mri_convert /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/andrew_fsaverage/mri/brainmask.mgz bold/tmp.bbregister.65172/fslregister/refvol.fslregister.nii mri_convert /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/andrew_fsaverage/mri/brainmask.mgz bold/tmp.bbregister.65172/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/andrew_fsaverage/mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to bold/tmp.bbregister.65172/fslregister/refvol.fslregister.nii... -------------------------------------- /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/sess02 mri_convert bold/tmp.bbregister.65172/template.nii bold/tmp.bbregister.65172/fslregister/movvol.fslregister.nii --frame 0 mri_convert bold/tmp.bbregister.65172/template.nii bold/tmp.bbregister.65172/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from bold/tmp.bbregister.65172/template.nii... TR=7.00, TE=0.00, TI=0.00, flip angle=0.00 warning: input volume axes are not orthogonal:i_dot_j = 0.000000, i_dot_k = 1.000000, j_dot_k = 0.000000 i_ras = (-1, -0, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) warning: output volume axes are not orthogonal:i_dot_j = 0.000000, i_dot_k = 1.000000, j_dot_k = 0.000000 i_ras = (-1, -0, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) keeping frame 0 writing to bold/tmp.bbregister.65172/fslregister/movvol.fslregister.nii... WARNING: bad orientation matrix (determinant = 0) in nifti1 file ... ... continuing. Mov determinant is 0 /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/sess02 tkregister2_cmdl --mov bold/tmp.bbregister.65172/fslregister/movvol.fslregister.nii --reg bold/tmp.bbregister.65172/fslregister/reg0.65212.dat --regheader --fslregout bold/tmp.bbregister.65172/reg.init.dat.fsl.mat0 --s andrew_fsaverage --noedit tkregister_tcl /Applications/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/tmp.bbregister.65172/fslregister/movvol.fslregister.nii reg file bold/tmp.bbregister.65172/fslregister/reg0.65212.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/andrew_fsaverage/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable bold/tmp.bbregister.65172/fslregister/movvol.fslregister.nii Tmov: -------------------- -0.508 0.000 0.000 130.000; 0.000 0.000 9.600 -14.400; 0.000 -0.508 0.000 130.000; 0.000 0.000 0.000 1.000; MatrixMultiply: m2 is null! mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ERROR: tkregister2_cmdl if ( $status ) exit 1 ; if ( 1 ) exit 1 exit 1 On 5/24/13, freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: command not found (Louis Nicholas Vinke) > 2. Re: A question of running fsfast in mac (Douglas N Greve) > 3. Re: p-value visualization (Douglas N Greve) > 4. Re: command not found (clelia pellicano) > 5. Re: problem with alignment of labeling files generated from > the rh.area file (Douglas N Greve) > 6. Re: FreeSurfer v 5.3.0 compatibility with Mac OS X 10.4.11 (Z K) > 7. Re: mri_concat --conjunct (Caspar M. Schwiedrzik) > 8. Re: p-value visualization (MCLAREN, Donald) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 24 May 2013 12:09:59 -0400 (EDT) > From: Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] command not found > To: clelia pellicano <pellicanoc(a)gmail.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <alpine.LRH.2.03.1305241206080.43202(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Clelia, > That mv command is failing presumably because SetUpFreeSurfer.txt does not > exist in that directory. What are you trying to do with the mv command? > > It does look like freesurfer was sourced successfully. Are the FreeSurfer > related commands still not found? > > Don't forget to cc the freesurfer mailing list. > -Louis > > On Fri, 24 May 2013, clelia pellicano wrote: > >> Hi Louise, >> I'm now using tcsh. Here what I did >> >> [dyn1097-8:~] cpellica% setenv FREESURFER_HOME >> /Applications/freesurfer >> [dyn1097-8:~] cpellica% source >> /Applications/freesurfer/SetUpFreesurfer.csh >> -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- >> Setting up environment for FreeSurfer/FS-FAST (and FSL) >> FREESURFER_HOME ? /Applications/freesurfer >> FSFAST_HOME ? ? ? /Applications/freesurfer/fsfast >> FSF_OUTPUT_FORMAT nii.gz >> SUBJECTS_DIR ? ? ?/Applications/freesurfer/subjects >> MNI_DIR ? ? ? ? ? /Applications/freesurfer/mni >> FSL_DIR ? ? ? ? ? /usr/local/fsl >> [dyn1097-8:~] cpellica% mv ?SetUpFreeSurfer.txt SetUpFreeSurfer.csh? >> mv: rename SetUpFreeSurfer.txt to SetUpFreeSurfer.csh: No such file or >> directory >> >> Do you have any advice? >> >> Thanks >> >> Clelia >> >> >> >> >> >> On Fri, May 24, 2013 at 3:04 PM, Louis Nicholas Vinke >> <vinke(a)nmr.mgh.harvard.edu> wrote: >> Hi Clelia, >> What do you run to source FS and do you get any output in your >> terminal after doing so? ?What operating system are >> you running? ?You might try using c-shell instead of bash. >> -Louis >> >> On Fri, 24 May 2013, clelia pellicano wrote: >> >> Hi Louis, >> thank you for your answer.? >> I sourced freesurfer again, but I still ?get 'command not >> found'. >> What can I try? >> Thank you, >> >> Clelia >> >> >> On Thu, May 23, 2013 at 7:15 PM, Louis Nicholas Vinke >> <vinke(a)nmr.mgh.harvard.edu> wrote: >> ? ? ? Hi Clelia, >> ? ? ? If this is in a new terminal then you'll have to source >> freesurfer again. See here for details: >> ? ? ? >> https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration >> ? ? ? -Louis >> >> ? ? ? On Wed, 22 May 2013, clelia pellicano wrote: >> >> ? ? ? ? ? ? Hi, >> ? ? ? ? ? ? I have run recon-all -s bert -all to try my >> installation and it worked. >> ? ? ? ? ? ? Now, when I try to use other command (and also >> again?recon-all -s bert -all) I always get >> this: >> >> ? ? ? ? ? ? dyn1097-8:subjects cpellica$ tkmedit bert >> orig.mgz >> ? ? ? ? ? ? -bash: tkmedit: command not found >> ? ? ? ? ? ? dyn1097-8:subjects cpellica$ tkmedit -s bert >> orig.mgz >> ? ? ? ? ? ? -bash: tkmedit: command not found >> ? ? ? ? ? ? dyn1097-8:subjects cpellica$ tksurfer -s bert rh >> pial >> ? ? ? ? ? ? -bash: tksurfer: command not found >> ? ? ? ? ? ? dyn1097-8:subjects cpellica$ qdec >> ? ? ? ? ? ? -bash: qdec: command not found >> ? ? ? ? ? ? dyn1097-8:subjects cpellica$ recon-all help >> ? ? ? ? ? ? -bash: recon-all: command not found >> ? ? ? ? ? ? dyn1097-8:subjects cpellica$ recon-all -s bert >> -all >> ? ? ? ? ? ? -bash: recon-all: command not found >> >> >> ? ? ? ? ? ? I don't know how to do. Please, could you help >> me? >> >> ? ? ? ? ? ? Thanks >> >> ? ? ? ? ? ? Clelia >> >> >> >> >> The information in this e-mail is intended only for the person >> to whom it is >> addressed. If you believe this e-mail was sent to you in error >> and the e-mail >> contains patient information, please contact the Partners >> Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was >> sent to you in error >> but does not contain patient information, please contact the >> sender and properly >> dispose of the e-mail. >> >> >> >> >> >> > > ------------------------------ > > Message: 2 > Date: Fri, 24 May 2013 12:14:51 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] A question of running fsfast in mac > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <519F91FB.8070709(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Sharon, you have to specify an analysis (as created by > mkanalysis-sess) as the argument to -analysis > doug > > > > > > > On 05/24/2013 10:35 AM, Yongxia Zhou wrote: >> Dear Freesurfer experts: >> hi, I'm one of the attendees of the multi-modality training program. I >> had tried running fsfast in the mac and got an error message. Below is >> the detail information. Any of your suggestions is highly appreciated >> and thank you very much. >> -Sharon >> >> OS: Mac OS X 10.5.6 >> >> [YongxiaZhous-MacBook:~/Desktop/DICOM/13051914] Young% pwd >> /Users/Young/Desktop/DICOM/13051914 >> [YongxiaZhous-MacBook:~/Desktop/DICOM/13051914] Young% selxavg3-sess >> -s sess01 -analysis >> /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/001/test01.sm05.lh >> -no-preproc -c music_silence.mat >> -------------------------------------------------------------- >> selxavg3-sess logfile is >> /Users/Young/Desktop/DICOM/13051914/log/selxavg3-sess-bold-test01.sm05.lh-130524090501.log >> -------------------------------------------------------------- >> ------------------------------------------- >> /Users/Young/Desktop/DICOM/13051914/sess01 >> Fri May 24 09:05:02 EDT 2013 >> anadir = /Users/Young/Desktop/DICOM/13051914/sess01/bold/test01.sm05.lh >> DoGLMFit = 1 >> DoContrasts = 1 >> UpdateNeeded = 1 >> ------------------------------------------ >> ------- matlab output -------------------- >> Warning: Unable to open display iconic, MATLAB is starting without a >> display. >> You will not be able to display graphics on the screen. >> >> < M A T L A B > >> Copyright 1984-2007 The MathWorks, Inc. >> Version 7.4.0.287 (R2007a) >> January 29, 2007 >> >> Warning: Duplicate directory name: /Users/Young/matlab. >> Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has >> the same name as a MATLAB builtin. We suggest you rename the function >> to avoid a potential name conflict. >> To get started, type one of these: helpwin, helpdesk, or demo. >> For product information, visit www.mathworks.com >> <http://www.mathworks.com/>. >> Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has >> the same name as a MATLAB builtin. We suggest you rename the function >> to avoid a potential name conflict. >> > In hgrc at 132 >> In matlabrc at 105 >> Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has >> the same name as a MATLAB builtin. We suggest you rename the function >> to avoid a potential name conflict. >> > In path at 110 >> In startup at 5 >> In matlabrc at 255 >> Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has >> the same name as a MATLAB builtin. We suggest you rename the function >> to avoid a potential name conflict. >> > In path at 110 >> In startup at 14 >> In matlabrc at 255 >> >> >> >> >> >> >> >> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# sess01 ############################### >> /Users/Young/Desktop/DICOM/13051914/sess01 >> ------------------------- >> $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ >> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m >> /Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m >> /Applications/freesurfer/matlab/MRIread.m >> ------------------------- >> outtop = /Users/Young/Desktop/DICOM/13051914 >> Extension format = nii.gz >> 1 music_silence.mat >> ??? Error using ==> MRIread at 76 >> ERROR: cannot determine format of >> /Users/Young/Desktop/DICOM/13051914/sess01/bold/001/fmc.siemens.sm5 >> (MRIread) >> >> >> Error in ==> flac_customize at 87 >> mri = MRIread(fstem,1); >> >> Error in ==> fast_selxavg3 at 65 >> flac0 = flac_customize(flac0); >> >> >> 2013-05-24 09:05:32.710 MATLAB[65661:60b] Process manager already >> initialized -- can't fully enable headless mode. >> ------------------------------------------ >> ERROR: fast_selxavg3() failed\n >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 3 > Date: Fri, 24 May 2013 12:15:55 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] p-value visualization > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <519F923B.20300(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > We don't have a binary that does it. You can do it in matlab, but it > will take a bit of programming. > doug > > > On 05/24/2013 10:54 AM, Ludovici, Katharine (NIH/NIMH) [F] wrote: >> Hello, >> >> We are attempting to compare surface area for 46 regions of interest in >> subjects versus controls. We've created a list of p-values for each ROI >> using R Studio to compare the two groups. Is there any way to visualize >> these p-values mapped on to the ROI's? >> >> Thanks very much, >> >> Katie Ludovici >> Postbaccalaureate IRTA >> National Institute of Mental Health >> Child Psychiatry Branch >> 301-435-5557 >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 4 > Date: Fri, 24 May 2013 17:15:57 +0100 > From: clelia pellicano <pellicanoc(a)gmail.com> > Subject: Re: [Freesurfer] command not found > To: Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CAENN+0=nzuJnq+eSEVuYagRX+mPVd8D2DR=XkSFSEz4XDWVaYg(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Louise, > > yes, teh FreeSurfer related commands are still not found. The other thing > is that I had problem with license file. I have created a file in > Applications/Freesurfer named .license and tried to copy inside le license > key but I'm not sure that it worked beacuse if I write cd .license I get > 'it is not a file not a directory'. > Thanks > > Clelia > > On Fri, May 24, 2013 at 5:09 PM, Louis Nicholas Vinke < > vinke(a)nmr.mgh.harvard.edu> wrote: > >> Hi Clelia, >> That mv command is failing presumably because SetUpFreeSurfer.txt does >> not >> exist in that directory. What are you trying to do with the mv command? >> >> It does look like freesurfer was sourced successfully. Are the >> FreeSurfer >> related commands still not found? >> >> Don't forget to cc the freesurfer mailing list. >> >> -Louis >> >> On Fri, 24 May 2013, clelia pellicano wrote: >> >> Hi Louise, >>> I'm now using tcsh. Here what I did >>> >>> [dyn1097-8:~] cpellica% setenv FREESURFER_HOME >>> /Applications/freesurfer >>> [dyn1097-8:~] cpellica% source /Applications/freesurfer/** >>> SetUpFreesurfer.csh >>> -------- freesurfer-Darwin-lion-stable-**pub-v5.3.0 -------- >>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >>> FREESURFER_HOME /Applications/freesurfer >>> FSFAST_HOME /Applications/freesurfer/**fsfast >>> FSF_OUTPUT_FORMAT nii.gz >>> SUBJECTS_DIR /Applications/freesurfer/**subjects >>> MNI_DIR /Applications/freesurfer/mni >>> FSL_DIR /usr/local/fsl >>> [dyn1097-8:~] cpellica% mv SetUpFreeSurfer.txt SetUpFreeSurfer.csh >>> mv: rename SetUpFreeSurfer.txt to SetUpFreeSurfer.csh: No such file or >>> directory >>> >>> Do you have any advice? >>> >>> Thanks >>> >>> Clelia >>> >>> >>> >>> >>> >>> On Fri, May 24, 2013 at 3:04 PM, Louis Nicholas Vinke < >>> vinke(a)nmr.mgh.harvard.edu> wrote: >>> Hi Clelia, >>> What do you run to source FS and do you get any output in your >>> terminal after doing so? What operating system are >>> you running? You might try using c-shell instead of bash. >>> -Louis >>> >>> On Fri, 24 May 2013, clelia pellicano wrote: >>> >>> Hi Louis, >>> thank you for your answer. >>> I sourced freesurfer again, but I still get 'command not >>> found'. >>> What can I try? >>> Thank you, >>> >>> Clelia >>> >>> >>> On Thu, May 23, 2013 at 7:15 PM, Louis Nicholas Vinke < >>> vinke(a)nmr.mgh.harvard.edu> wrote: >>> Hi Clelia, >>> If this is in a new terminal then you'll have to >>> source >>> freesurfer again. See here for details: >>> https://surfer.nmr.mgh.**harvard.edu/fswiki/** >>> SetupConfiguration<https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration> >>> -Louis >>> >>> On Wed, 22 May 2013, clelia pellicano wrote: >>> >>> Hi, >>> I have run recon-all -s bert -all to try my >>> installation and it worked. >>> Now, when I try to use other command (and also >>> again recon-all -s bert -all) I always get >>> this: >>> >>> dyn1097-8:subjects cpellica$ tkmedit bert >>> orig.mgz >>> -bash: tkmedit: command not found >>> dyn1097-8:subjects cpellica$ tkmedit -s bert >>> orig.mgz >>> -bash: tkmedit: command not found >>> dyn1097-8:subjects cpellica$ tksurfer -s bert rh >>> pial >>> -bash: tksurfer: command not found >>> dyn1097-8:subjects cpellica$ qdec >>> -bash: qdec: command not found >>> dyn1097-8:subjects cpellica$ recon-all help >>> -bash: recon-all: command not found >>> dyn1097-8:subjects cpellica$ recon-all -s bert >>> -all >>> -bash: recon-all: command not found >>> >>> >>> I don't know how to do. Please, could you help >>> me? >>> >>> Thanks >>> >>> Clelia >>> >>> >>> >>> >>> The information in this e-mail is intended only for the >>> person to whom it is >>> addressed. If you believe this e-mail was sent to you in >>> error and the e-mail >>> contains patient information, please contact the Partners >>> Compliance HelpLine at >>> >>> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >>> If the e-mail was sent to you in error >>> but does not contain patient information, please contact the >>> sender and properly >>> dispose of the e-mail. >>> >>> >>> >>> >>> >>> >

3 3

ERRORS in Tracula Preprocessing
by Vivian Roger Steiger 25 May '13

25 May '13

Dear Freesurfer experts I am trying to process the data of a Longitudinal DTI Study with 2 Timepoints I have encountered the following error while running the tracula pre-processing: ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/ FSFAST_HOME /Applications/freesurfer//fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Users/zenso/Subjects/structural_23VPs FSL_DIR /Applications/fsl MNI_DIR /Applications/freesurfer//mni FSL_DIR /Applications/fsl [iMac:Subjects] zenso% trac-all -prep -c /Users/zenso/Subjects/Tracula/dmrirc.long.sad Too many )'s. INFO: SUBJECTS_DIR is /Users/zenso/Subjects/structural_23VPs INFO: Diffusion root is /Users/zenso/Subjects/Tracula Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Users/zenso/Subjects/Tracula/1Pre_VP3/scripts/dmrirc.local -log /Users/zenso/Subjects/Tracula/1Pre_VP3/scripts/trac-all.log -cmd /Users/zenso/Subjects/Tracula/2Post_VP3/scripts/trac-all.log -cmd /Users/zenso/Subjects/Tracula/2Post_VP3/scripts/trac-all.cmd ; trac-preproc -c /Users/zenso/Subjects/Tracula/VP3_Base/scripts/dmrirc.local -log /Users/zenso/Subjects/Tracula/VP3_Base/scripts/trac-all.log -cmd /Users/zenso/UZH/MSc/FS2013/Psychologie/Masterarbeit/Subjects/Tracula/VP3_Base/scripts/trac-all.cmd ; ERROR: flag ; unrecognized -c /Users/zenso/Subjects/Tracula/1Pre_VP3/scripts/dmrirc.local -log /Users/zenso/Subjects/Tracula/1Pre_VP3/scripts/trac-all.log -cmd /Users/zenso/Subjects/Tracula/1Pre_VP3/scripts/trac-all.cmd ; trac-preproc -c /Users/zenso/Subjects/Tracula/2Post_VP3/scripts/dmrirc.local -log /Users/zenso/Subjects/Tracula/2Post_VP3/scripts/trac-all.log -cmd /Users/zenso/Subjects/Tracula/2Post_VP3/scripts/trac-all.cmd ; trac-preproc -c /Users/zenso/Subjects/Tracula/VP3_Base/scripts/dmrirc.local -log /Users/zenso/Subjects/Tracula/VP3_Base/scripts/trac-all.log -cmd /Users/zenso/Subjects/Tracula/VP3_Base/scripts/trac-all.cmd ; Darwin iMac.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Sa 25 Mai 2013 11:28:57 CEST IsRunningFile: Undefined variable. ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Please let me know if this is not enough information. Thanks a lot for your support. Vivian

1 0

Peak coordinates & Paired t-test with QDEC
by Jaime Ide 24 May '13

24 May '13

Dear Freesurfer experts: I have two questions: 1) How can I obtain the *peak coordinates* and *the size* of the *clusters*(with uncorrected threshold) visualized in *tksurfer*? (like the tables generated with glmfit-sim) 2) *Is it possible to run paired t-test in QDEC*? I have run Paired Analysis as suggested by Doug Greve at https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis, and it worked perfectly. I wonder to know if there is an alternative way to run paired t-test using QDEC. (I apologize if these questions were previously answered. I did some search in the list, but I couldn't find the exact answer to my questions..) Any comment or help will be very welcome. Thanks in advance, Jaime

2 1

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