Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

Re: [Freesurfer] rerun interrupted processes
by Bruce Fischl 28 May '13

28 May '13

Hi Valeria can you address this type of question to the list so that others can answer and learn from the answers? Yes, you can run recon-all -make all -s <subject id> and it should pick up from where it left off Bruce On Tue, 28 May 2013, Valeria Contarino wrote: > Dear Bruce, > I have a new question for you. > I was running 30 subjects when processes were interrupted because of no more space left on device. > Do I have the chance for starting again the processes from where they stopped? > > Thank you. > > Regards, > Valeria > >

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recon-all with FLAIR error no FSL installed
by Popescu, Veronica 28 May '13

28 May '13

Dear all, I am running FreeSurfer 5.3 with FLAIR refinement. I do not have FSL installed. I do get results but there's an error message in the log file (attached) about the FSL installation missing. How bad is it? Do I have to rerun everything with FSL installed? And if so, is there any version that is preferable? Thank you very much in advance! Best wishes, Veronica

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Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
by Salil Soman 27 May '13

27 May '13

Dear Doug, Thank you for your email. Following up on our previous discussions: 1) *bbregister fail *- this was happening because of error from fslregister. The variable fsvol was translating to "ERROR". In fslregister th value for fsvol is set to brainmask, along with numerous other parameters being initialized. By adding the line "set fsvol = brain mask" (without quotes) at the beginning of the section "#Convert reference to analyze" the CentOS 6 version I am running on ubuntu 12.04 (with SGE), now works. 2) when you suggested I run bbregister on the lowb.nii file, was it because I had suggested I wanted to register to a 2D ADC map? If I want to instead use a 3D volume (e.g. a 3D ASL), would I use the actual volume I want to get value from instead of lowb.nii? I ended up running 3) for the mri_vol2vol step - I had to change targ to fstarg, and I left out the interp flag so it would do its default trilinear: mri_vol2vol --mov Vol_906.nii --fstarg T1.mgz --o Vol_906_Reg_Bold.nii --no-save-reg --reg register_bold.dat --inv 4) I would like to get the segmentations from aparc+aseg.mgz as the areas where I get the values summed. So I entered mri_segstats --seg mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum Vol_aparc_aseg.stats but then I received this error: ERROR: dimension mismatch between input volume and seg input 224 224 170 seg 256 256 256 * * *So, in summary, while I've fixed bbregister to work on my system, I am still having trouble normalizing my 3D non T1 volume data into the FS space to be able to use the labels from aparc+aseg.mgz to get statistics for each anatomic area.* Any ideas on how to proceed? Thanks, Sal On Sat, May 25, 2013 at 11:51 AM, Douglas Greve <greve(a)nmr.mgh.harvard.edu>wrote: > > On 5/25/13 1:39 PM, Salil Soman wrote: > > Thank you Doug. > > Just so I am clear - is the anatomical the nifti T1.mgz or is it a > different file. From your email I gather should do the following: > > *1) Use bbregister to register the lowb image to the anatomical. This > creates a registration matrix.* > > bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat > > That is right, but add --t2 (since it is t2 weighted). > > > *2) Use mri_vol2vol and the registration to map the ADC map to the > anatomical* > > mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff --reg $outdir/register.dat --no-save-reg > > Use the ADC as the moveable (not lowb, but use the lowb for > bbregister). The target volume should be the T1.mgz (or any conformed > volume). The output will be the adc in the anatomical space (not sure why > you call it vol2diff). > > *3) use mri_segstats to extract the values* > > *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats > > The input would be the adc volume mapped the anatomical space. I would > use WMParcStatsLUT.txt or else you'll get a billion different areas not > represented in wmparc. You may also want to add "--seg-erode 1" to erode > the segmentations by a voxel. This helps to prevent partial voluming. > > doug > > > > Where lowb.nii is the other MRI tissue sequence I am analyzing (e.g. > ADC), $vol2diff is the output image of the registration, and fa.stats will > be my output stats table? > > I suspect there is part of the syntax for these tools I do not > understand. Also, what input would $vol be? > > Best wishes, > > Sal > > > On Sat, May 25, 2013 at 10:06 AM, Douglas Greve <greve(a)nmr.mgh.harvard.edu > > wrote: > >> >> Hi Sal, yes you can. Use bbregister to register the lowb image to the >> anatomical. This creates a registration matrix. Use mri_vol2vol and the >> registration to map the ADC map to the anatomical, then use mri_segstats to >> extract the values >> doug >> >> ps. Please post questions to the FS list instead of us directly so that >> others can benefit and it gets archived. thanks! >> >> >> >> On 5/25/13 1:03 PM, Salil Soman wrote: >> >>> Dear Dr. Greve, >>> >>> Is it possible to register a nonstructural MR sequences (e.g. an ADC >>> map) with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, using >>> the segmentation from the aseg (or aparc+aseg) file to output a mean ADC >>> value for each anatomic area segmented? >>> >>> Thank you for your time and consideration. >>> >>> Best wishes, >>> >>> Sal >>> >>> Salil Soman, MD, MS >>> >> >> >> >> 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. >> >> > >

2 6

white matter volume per lobe...
by Gonzalo Rojas Costa 27 May '13

27 May '13

Hi: I used the following commands to get the cortical volume per each lobe: mri_annotation2label --subject OAS1_0001_MR1 --hemi rh --lobesStrict lobulos --seg lobulos --stat lobulos mri_annotation2label --subject OAS1_0001_MR1 --hemi lh --lobesStrict lobulos --seg lobulos --stat lobulos mris_anatomical_stats -a lobulos -f OAS1_0001_MR1_lobulos_rh -b OAS1_0001_MR1 rh mris_anatomical_stats -a lobulos -f OAS1_0001_MR1_lobulos_lh -b OAS1_0001_MR1 lh Which commands (sintaxis) must I use to compute the white matter volume per each lobe ?... I tested the mri_aparc2aseg and mri_segstats commans with different options, but I couldn't get the volume that I need... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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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

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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

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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 >

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