Freesurfer

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30132 discussions

multiple correction
by Meng Li 16 Jul '12

16 Jul '12

Hi, freesurfer expert, I performed the statistical analysis between two groups first in left hemisphere, and got some regions which showed different. 1) so if I then do multiple correction, i don't need to run the mri_glmfit-sim command, and just press the button of the monte carlo null-z simulation in the qdec interface, am i right? 2) Whether mri_glmfit-sim --cache command line and the mc-z in qdec get the same results, or not? and as to the option --cwpvalthresh, should i choose 0.05 or 0.025? 3) And what is the difference between fdr and mc-z correction? Thanks, Meng

2 1

Error compiling FS with GPU
by Akio Yamamoto 16 Jul '12

16 Jul '12

Hi FS experts, My colleague is trying to compile FreeSurfer by configuring with a "--with-cuda" flag. The build process stopped with the error message: ===== em_register_cuda.cu(347): error: calling a host function("LinearGenerator::LinearGenerator") from a __device__/__global__ function("TransformLogps") is not allowed em_register_cuda.cu(350): error: calling a host function("LinearGenerator::LinearGenerator") from a __device__/__global__ function("TransformLogps") is not allowed em_register_cuda.cu(353): error: calling a host function("LinearGenerator::LinearGenerator") from a __device__/__global__ function("TransformLogps") is not allowed em_register_cuda.cu(357): error: calling a host function("TransformGenerator::TransformGenerator") from a __device__/__global__ function("TransformLogps") is not allowed 4 errors detected in the compilation of ... ===== FYI, the build environment is as follows: GeForce GTX 690 CUDA Toolkit 4.2 CentOS 6.2 Are there any specific requirements for building CUDA-enabled FreeSurfer? Any information/help would be appreciated. Thanks, Akio

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Cutting non-cortex
by Sourena Soheilinezhad 15 Jul '12

15 Jul '12

Hi experts, I have two (unrelated) issues. I am seeking a command-line method to remove non-cortex vertices and triangles from a surface. I have seen the manual method with tksurfer, but perhaps this is not suitable for larger datasets? I have tried to use surf2surf for downsampling of the meshes NOT generated by Freesurfer into icosahedron, to no avail, maybe because this command seeks to map the .sulc data which is absent in the alien mesh. Please let me have any advice for this goal if basically possible with available freesurfer tools. Thanks, Sourena Soheili

2 9

MPRAGE intensity variations
by Chris Watson 15 Jul '12

15 Jul '12

Hello, I ran a subject through recon-all both with and without the "-mprage" flag, and naturally got different results. I'm attaching a screenshot of the pial and main surfaces, along with the orig.mgz of the same slice. The image tends to be brighter in the frontal lobe, and there is an intensity change when going through the slices. The scanner is Siemens 3T (Trio, I think), using a 32-channel head coil. The imaging parameters are: (not sure which are most relevant) TR: 1410 TI: 800 TE: 2.2 Matrix: 256x256 FOV: 256 Flip angle: 9 deg ImagingFrequency: 123.259181 Pixel bandwidth: 199 Is there anything I can do to improve the results? Thanks, Chris PS When I didn't use the '-mprage' flag, I used the '-nuintensitycor-3T' flag. So I changed 2 separate things.

3 3

multiple comparisons correction
by Meng Li 14 Jul '12

14 Jul '12

Hi, freesurfer expert, I have three questions about the multiple comparisons correction in Qdec. I performed the statistical analysis between two groups first in left hemisphere, and got some regions which showed different. 1) so if I then do multiple correction, i don't need to run the mri_glmfit-sim command, and just press the button of the monte carlo null-z simulation in the qdec interface, am i right? 2) Whether mri_glmfit-sim --cache command line and the mc-z in qdec get the same results, or not? and as to the option --cwpvalthresh, should i choose 0.05 or 0.025? 3) And what is the difference between fdr and mc-z correction? I also want to find a solution about an ERROR. I tried to run a cortical thickness analysis to look for differences between two groups (patients and controls) with regressing out the gender factor, the patients group have 1 female and 17 male, after analysis, I got the results. But when I add another continuous variable as covariate, I received the message: "ERROR: matrix is ill-conditioned or badly scaled." Then I tried to change the gender composition the patients groups: 2 female/16 male, and the problem was solved. so is it right about what i did, or I need another way to solve this problem? Thanks, Meng

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Neuroimaging Postdoc opportunity Melbourne, Australia
by David Abbott 13 Jul '12

13 Jul '12

Research Scientist - Neuroimaging Analysis Level depending upon qualifications and experience: Research Officer / Senior Research Officer / Research Fellow / Senior Research Fellow. · 2 positions available - Structural & Functional Neuroimaging Analysis (both positions requiring methods development and application) · Medical research based at the Florey Neuroscience Institutes, Melbourne, Australia. The Florey Neuroscience Institutes employs more than 400 people who are passionately committed to researching the way the brain works. We are internationally renowned for our discoveries and research on the central nervous system and associated brain disorders. Key areas of interest include addiction, Alzheimer’s disease, cardiovascular disease, depression, epilepsy, Huntington’s disease, motor neuron disease, multiple sclerosis, Parkinson’s disease, schizophrenia, stroke and traumatic and spinal cord injury. An excellent opportunity is available for two Research Scientists to work on projects investigating brain disorders (in particular epilepsy) using brain imaging methods within the Brain Research Institute at our Austin facility in Melbourne, Australia. Successful applicants will assist in the implementation and development of MRI analysis techniques within the Institute. This includes development, implementation and advancement of structural and functional MRI techniques for use in research and clinical environments. - The first position has an initial requirement that the candidate performs analysis and solves problems related to the implementation of structural MRI analysis methods including quantitative morphometric methods such as voxel based morphometry and cortical thickness analyses. - The second position has an initial requirement that the candidate performs analysis and solves problems related to the implementation of functional MRI analysis methods including conventional functional MRI (fMRI), functional connectivity, and simultaneous electroencephalography (EEG) and fMRI. Each Research Scientist will also be expected to assist with aspects of MRI quality control, software development, and participate in general research activities of the Institute including submission of research grants, publication of peer reviewed papers, and publication of software. For more information or to obtain a position description please visit our web site at www.florey.edu.au/careers -- David Abbott, PhD Senior Research Fellow (Physics & Neuroinformatics), Brain Research Institute, Florey Neuroscience Institutes. Honorary Senior Fellow, Department of Medicine, The University of Melbourne. Address: Melbourne Brain Centre, 245 Burgundy Street Heidelberg, Victoria, 3084, Australia.

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Fwd: Register ROI5.nii to fsaverage in tutorial "Cortical Thickness of a Volume-defined ROI"?
by Garikoitz Lerma Usabiaga 13 Jul '12

13 Jul '12

Begin forwarded message: *From:* Garikoitz Lerma Usabiaga <garikoitz(a)gmail.com> *To:* Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> *Subject:* *Re: [Freesurfer] Register ROI5.nii to fsaverage in tutorial "Cortical Thickness of a Volume-defined ROI"?* Thanks for your answer Louis, I think I'm using it, the steps were: 1- Correct visualization of ROI with: tkmedit -f TT_avg152T1.nii -overlay ROI45.nii -fthresh 0.5 2- I execute spmregister: spmregister --s fsaverage --mov ../../ROI2/TT_avg152T1.nii --reg TT_avg152T1_to_fsaverage.dat 3.-Incorrect visualization when I execute: tkmedit fsaverage T1.mgz -overlay ../../ROI2/ROI45.nii -overlay-reg TT_avg152T1_to_fsaverage.dat -fthresh 0.5 -surface lh.white -aux-surface rh.white What I understand is that the .dat is a transformation matrix between TT_avg152T1 and fsaverage, so when I am asking to overlay ROI45.nii, I am asking tkmedit to transform it to fsaverage by the .dat file. Is that correct? What do you think that could be the error? I am attaching the images just in case... Thanks again, Gari PS This is the TT_avg152T1_to_fsaverage.dat: fsaverage 2.000000 2.000000 0.150000 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0 0 0 1 round On 2012-07-12, at 17:56, Louis Nicholas Vinke wrote: Hi Gari, When you view the ROI5.nii on fsaverage make sure you include '-overlay-reg TT_avg152T1_to_fsaverage.dat'. TT_avg152T1_to_fsaverage.dat is the transformation computed in the previous step which you need to apply. Nothing was resampled in step 2. -Louis On Thu, 12 Jul 2012, Garikoitz Lerma Usabiaga wrote: Dear All, I am trying to automate ROI creation in freesurfer following the VolumeRoiCorticalThickness tutorial, based on the AAL defined ROI-s from MarsBar. QUESTION ROI5.nii was originally in the same space as TT_avg152T1.nii (see MORE INFO below). I understand that after Step 2 (when TT_avg152T1.nii is registered to fsaverage with spmregister), TT_avg152T1 will be in fsaverage space. But, we didn't transform or register ROI5.nii, so I understand that it will continue in the same original space. When I visualize ROI5 over the original TT_avg152T1 it is ok, but when I visualize it over the fsaveraged one, it is not. Shouldn't we need to register or normalize ROI5.nii to fsaverage as well prior to the mri_vol2surface mapping? MORE INFO: 1.- I created the ROI5.nii in MarsBar: "ROI definition" > "Export" > "Export ROI to image" (select: MNI_Frontal_Inf_Tri_L_roi.mat) > from image (select: avg152T1.nii) > Save it (name: ROI45.nii) 2.- I follow exactly the same steps as the tutorial, but in step 3) when I check the ROI in the inflated surface, it is clearly out of place... Thank you very much in advance, Gari Garikoitz Lerma Usabiaga Predoctoral Researcher www.bcbl.eu 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.

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mapping label to vol and aseg to vol
by Marie Schaer 13 Jul '12

13 Jul '12

Hi FreeSurfer team, I have two small questions related to exporting label or aseg into mgz volumes: 1) I want to save one label into a volume, I used mri_label2vol which works perfectly, but I am getting only a thin label. I saw that I can use the --proj option with mri_label2vol to increase the "thickness" of my label, but I was wondering if there is any way to obtain the whole cortical ribbon corresponding to the label (i.e. something looking like the volumetric counterpart of the parcellation as found in the aparc+aseg.mgz)? 2) Similarly, I wanted to export the 5 subregions of the corpus callosum as individual volumes (i.e. one mgz volume for each subregions). Is that any way to do that? Or to export the 5 CC subregions as labels that could be then loaded on the cortical surface? Many thanks for your help, Marie

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Re: [Freesurfer] Hippocampus Doubt
by Gabriel Gonzalez Escamilla 13 Jul '12

13 Jul '12

2 1

Re: [Freesurfer] error message for recon-all
by Muriel Bruchhage 13 Jul '12

13 Jul '12

Thank you so much Bruce, it now works like a charm! Best, Muriel On Jul 12, 2012, at 2:30 AM, Bruce Fischl wrote: > Hi Muriel > > not sure what your second frame is, but you should be able to do this: > > cd $SUBJECTS_DIR/<subject id>/mri/orig > mv 001.mgz multiframe.mgz > mri_convert -nth 0 multiframe.mgz 001.mgz > recon-all -s <subject id> -all > > cheers > Bruce > > On Thu, 12 Jul 2012, Muriel Bruchhage wrote: > >> Maybe this is easiest: >> >> >> >> Best, >> Muriel >> >> >> On Jul 12, 2012, at 12:54 AM, Bruce Fischl wrote: >> >>> did it have 2 frames? If so, what is the difference between them? >>> >>> On Thu, 12 Jul 2012, Muriel Bruchhage wrote: >>> >>>> Hi Bruce, >>>> >>>> I tried to send the .mgz file to you, but it apparently exceeded the limit. Nevertheless, I thought that it looked fine (I compared it to the bert data freesurfer came with). >>>> >>>> Thank you very much again for all your efforts! >>>> >>>> Best, >>>> >>>> Muriel >>>> >>>> On Jul 11, 2012, at 11:51 PM, Bruce Fischl wrote: >>>> >>>>> you can run freeview on the 001.mgz and see what is in it. If it has more than one frame freeview will include a slider that lets you change from one to the other. Or you can email it to me and I'll take a look. >>>>> >>>>> On Wed, 11 Jul 2012, Muriel Bruchhage wrote: >>>>> >>>>>> Hi Bruce, >>>>>> >>>>>> To be quite honest, I am not sure, but I used the same data on a fsl segmentation task (using a nifti format though) and I never got any error messages back there. >>>>>> >>>>>> Best, >>>>>> Muriel >>>>>> >>>>>> On Jul 11, 2012, at 11:26 PM, Bruce Fischl wrote: >>>>>> >>>>>>> Hi Muriel >>>>>>> >>>>>>> what was the scan that you are trying to run FreeSurfer on? Did it have more than one echo? >>>>>>> >>>>>>> Bruce >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Wed, 11 Jul 2012, Muriel Bruchhage wrote: >>>>>>> >>>>>>>> >>>>>>>> On Jul 11, 2012, at 11:23 PM, Muriel Bruchhage wrote: >>>>>>>> >>>>>>>>> I added the -all at the end and skipped the -i flag, but I still get an error message: >>>>>>>>> >>>>>>>>> Checking for (invalid) multi-frame inputs... >>>>>>>>> ERROR: input(s) cannot have multiple frames! >>>>>>>>> /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz has 2 frames >>>>>>>>> >>>>>>>>> I am so sorry to bother you with these probably very amateur questions - but how can I have multiple frames when I just got one .mgz file and just one T1? >>>>>>>>> >>>>>>>>> Best, >>>>>>>>> Muriel >>>>>>>>> >>>>>>>>> On Jul 11, 2012, at 10:55 PM, Bruce Fischl wrote: >>>>>>>>> >>>>>>>>>> oh, you need to specify what you want it to do. Add -all at the end of the command line and it will do everything. Note that if you are rerunning, you can leave out the -i <path to dicom> >>>>>>>>>> >>>>>>>>>> cheers >>>>>>>>>> Bruce >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Wed, 11 Jul 2012, Muriel Bruchhage wrote: >>>>>>>>>> >>>>>>>>>>> Hei, >>>>>>>>>>> >>>>>>>>>>> Thanks you very much again for your help! >>>>>>>>>>> >>>>>>>>>>> Nevertheless, even though I got the message that the recon-all has been done without any errors, no talaraich transform, skull stripping or segmentation has been done. I placed my fsaverage folder in the same folder where all my participant-folders are - could that have been the problem? (this is also the same place where my $SUBJECTS_DIR is directed to) >>>>>>>>>>> >>>>>>>>>>> Best, >>>>>>>>>>> >>>>>>>>>>> Muriel >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Jul 11, 2012, at 10:39 PM, Bruce Fischl wrote: >>>>>>>>>>> >>>>>>>>>>>> sure, glad it worked out >>>>>>>>>>>> Bruce >>>>>>>>>>>> On Wed, 11 Jul 2012, Muriel Bruchhage wrote: >>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> It worked! >>>>>>>>>>>>> >>>>>>>>>>>>> Thank you so so much! >>>>>>>>>>>>> >>>>>>>>>>>>> Best, >>>>>>>>>>>>> Muriel >>>>>>>>>>>>> >>>>>>>>>>>>> On Jul 11, 2012, at 6:34 PM, Muriel Bruchhage wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Bruce, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thank you very much for your fast response. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Unfortunately though, I still get an error response when typing in "recon-all -i /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/ -subjid GID02" >>>>>>>>>>>>>> >>>>>>>>>>>>>> recon-all -i /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/ -subjid GID02 >>>>>>>>>>>>>> Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 >>>>>>>>>>>>>> Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 >>>>>>>>>>>>>> INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM >>>>>>>>>>>>>> Actual FREESURFER_HOME /Applications/freesurfer >>>>>>>>>>>>>> Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 >>>>>>>>>>>>>> /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02 >>>>>>>>>>>>>> \n mri_convert /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz \n >>>>>>>>>>>>>> mri_convert /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz >>>>>>>>>>>>>> corRead(): can't open file /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/COR-.info >>>>>>>>>>>>>> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >>>>>>>>>>>>>> reading from /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM... >>>>>>>>>>>>>> Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 >>>>>>>>>>>>>> >>>>>>>>>>>>>> recon-all -s GID02 exited with ERRORS at Wed Jul 11 18:32:26 CEST 2012 >>>>>>>>>>>>>> >>>>>>>>>>>>>> For more details, see the log file /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/scripts/recon-all.log >>>>>>>>>>>>>> To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thank you very much in advance for all your help! >>>>>>>>>>>>>> >>>>>>>>>>>>>> Best, >>>>>>>>>>>>>> Muriel >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Jul 11, 2012, at 6:20 PM, Bruce Fischl wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Muriel >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> the -s switch should be followed by a subject identifier (e.g. subject0001), not the 001.mgz file. Note that you don't need to convert your dicom to mgz either, just point recon-all at one slice in the correct (T1-weighted) dicom series with -i <path to dicom file>. And one acquisition is usually sufficient these days depending on the coil and field strength. We don't use T2s at the moment. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> cheers >>>>>>>>>>>>>>> Bruce >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Wed, 11 Jul 2012, Muriel Bruchhage wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>> I am new to freesurfer and tried to run recon-all on it (I am using a >>>>>>>>>>>>>>>> MacBook Pro with Lion if that is of any importance). >>>>>>>>>>>>>>>> What I have been done so far: >>>>>>>>>>>>>>>> 1) I set my Freesurfer environment in my .tcshrc file to: >>>>>>>>>>>>>>>> setenv FREESURFER_HOME /Applications/freesurfer/ >>>>>>>>>>>>>>>> source $FREESURFER_HOME/SetUpFreeSurfer.csh >>>>>>>>>>>>>>>> source $FREESURFER_HOME >>>>>>>>>>>>>>>> setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/ >>>>>>>>>>>>>>>> 2) I converted my original T1 DICOM files into one MGZ file using the >>>>>>>>>>>>>>>> mri_convert command (mri_convert <first dicom>.dcm 001.mgz). Both files can >>>>>>>>>>>>>>>> be found under $SUBJECTS_DIR/GID02/2_T1_3DSAG - the MGZ file under a MGZ >>>>>>>>>>>>>>>> folder and the DICOMs under a DICOM folder >>>>>>>>>>>>>>>> ($SUBJECTS_DIR/GID02/2_T1_3DSAG/MGZ or $SUBJECTS_DIR/GID02/2_T1_3DSAG/DICOM >>>>>>>>>>>>>>>> respectively). >>>>>>>>>>>>>>>> 3) I tried the recon-all command with both the setenv >>>>>>>>>>>>>>>> $SUBJECTS_DIR//Applications/freesurfer/subjects/MRI_04_2012/ andwith $SUBJECTS_DIR//Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1 >>>>>>>>>>>>>>>> _3DSAG/MGZ where the MGZ file actually lies. >>>>>>>>>>>>>>>> Does the fact that I only have one .mgz file have an influence on my data >>>>>>>>>>>>>>>> processing? Would a T2 scan count as a second structural scan? >>>>>>>>>>>>>>>> As I always get this error message: >>>>>>>>>>>>>>>> 1) for running it with recon-all -all -subjid GID02 on setenv SUBJECTS_DIR >>>>>>>>>>>>>>>> /Applications/freesurfer/subjects/MRI_04_2012/ >>>>>>>>>>>>>>>> [Muriels-MacBook-Pro:freesurfer/subjects/MRI_04_2012] mbruchhage% ls >>>>>>>>>>>>>>>> GID02 GID251 GID51_2 GID70 GID753 >>>>>>>>>>>>>>>> GID100 GID28 GID53 GID701 GID76 >>>>>>>>>>>>>>>> GID117 GID33 GID549 GID710 VBM >>>>>>>>>>>>>>>> GID12 GID47 GID61 GID72 fsaverage >>>>>>>>>>>>>>>> GID140 GID51 GID62 GID75 >>>>>>>>>>>>>>>> [Muriels-MacBook-Pro:freesurfer/subjects/MRI_04_2012] mbruchhage% cd >>>>>>>>>>>>>>>> GID02/2_T1_3DSAG/MGZ/ >>>>>>>>>>>>>>>> [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% ls >>>>>>>>>>>>>>>> 001.mgz >>>>>>>>>>>>>>>> [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all >>>>>>>>>>>>>>>> -subjid 001.mgz >>>>>>>>>>>>>>>> ERROR: cannot find /Applications/freesurfer/subjects/MRI_04_2012/001.mgz >>>>>>>>>>>>>>>> [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all >>>>>>>>>>>>>>>> -subjid GID02 >>>>>>>>>>>>>>>> Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 >>>>>>>>>>>>>>>> Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 >>>>>>>>>>>>>>>> INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/MRI_04_2012 >>>>>>>>>>>>>>>> Actual FREESURFER_HOME /Applications/freesurfer >>>>>>>>>>>>>>>> -rw-rw-r-- 1 mbruchhage wheel 33313 Jul 11 12:13 >>>>>>>>>>>>>>>> /Applications/freesurfer/subjects/MRI_04_2012/GID02/scripts/recon-all.log >>>>>>>>>>>>>>>> Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu >>>>>>>>>>>>>>>> Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 >>>>>>>>>>>>>>>> #-------------------------------------------- >>>>>>>>>>>>>>>> #@# MotionCor Wed Jul 11 17:54:17 CEST 2012 >>>>>>>>>>>>>>>> ERROR: no run data found in >>>>>>>>>>>>>>>> /Applications/freesurfer/subjects/MRI_04_2012/GID02/mri. Make sure to >>>>>>>>>>>>>>>> have a volume called 001.mgz in >>>>>>>>>>>>>>>> /Applications/freesurfer/subjects/MRI_04_2012/GID02/mri/orig. >>>>>>>>>>>>>>>> If you have a second run of data call it 002.mgz, etc. >>>>>>>>>>>>>>>> See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion >>>>>>>>>>>>>>>> Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu >>>>>>>>>>>>>>>> Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 >>>>>>>>>>>>>>>> recon-all -s GID02 exited with ERRORS at Wed Jul 11 17:54:17 CEST 2012 >>>>>>>>>>>>>>>> For more details, see the log file >>>>>>>>>>>>>>>> /Applications/freesurfer/subjects/MRI_04_2012/GID02/scripts/recon-all.log >>>>>>>>>>>>>>>> To report a problem, >>>>>>>>>>>>>>>> see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>>>>>>>>>> 2) for running it with recon-all -all -subjid 001.mgz on setenv SUBJECTS_DIR >>>>>>>>>>>>>>>> /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ >>>>>>>>>>>>>>>> [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all >>>>>>>>>>>>>>>> -subjid 001.mgz >>>>>>>>>>>>>>>> mkdir:/Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz: >>>>>>>>>>>>>>>> Not a directory >>>>>>>>>>>>>>>> cp:/Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz/ >>>>>>>>>>>>>>>> scripts/build-stamp.txt: Not a directory >>>>>>>>>>>>>>>> cat:/Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz/ >>>>>>>>>>>>>>>> scripts/build-stamp.txt: Not a directory >>>>>>>>>>>>>>>> INFO: FreeSurfer build stamps do not match >>>>>>>>>>>>>>>> Subject Stamp: >>>>>>>>>>>>>>>> Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 >>>>>>>>>>>>>>>> INFO: SUBJECTS_DIR is >>>>>>>>>>>>>>>> /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ >>>>>>>>>>>>>>>> Actual FREESURFER_HOME /Applications/freesurfer >>>>>>>>>>>>>>>> /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz: >>>>>>>>>>>>>>>> Not a directory. >>>>>>>>>>>>>>>> Thank you very much in advance and greetings from Oslo, >>>>>>>>>>>>>>>> Muriel Bruchhage >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> 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. >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> >>>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>> >>>> >>>> >>>> >> >>

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