Freesurfer

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30089 discussions

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.

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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

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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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Re: [Freesurfer] Using SPM transformation matrices as initial guess in talairach_avi
by Bruce Fischl 13 Jul '12

13 Jul '12

Hi Simon I'm also puzzled about your "quantitative T1 maps". Are these T1 values in ms? If so, the image won't have "T1-weighted contrast" as WM will be darker (shorter T1) than GM, in which case everything would fail. I assume that what you are going to FreeSurfer (and Avi's code) is instead the larger flip angle FLASH image. cheers Bruce On Thu, 12 Jul 2012, Snyder, Avi wrote: > I don't see that it is possible to avoid double resampling if you use > FreeSurfer to segment. As far as I can tell, the problem with your dataset > is that a substantial fraction of cases results a clearly poor Talarrach > atlas transform, e.g., too "fat" or too "thin" or distorted. There is no > provision, as far as I am aware, to, initialize the Talairach transform > module based on a prior computations. There are two main possibilities > that underly bad Talairach transforms (1) input images very displaced or > rotated from standard acquisitions (2) mismatch between contrast > mechanisms in the sample T1W and the atlas representative target. It is > possible to correct error mechanism 2. A dialog regarding this possibility > is ongoing with the FreeSurfer developers. > > Avi > ----------------------------------- > On 7/12/12 5:09 AM, "Baudrexel, Simon" <Simon.Baudrexel(a)kgu.de> wrote: > >> Dear Avi, >> >> thank you for your reply, probably I didn't make my point clear enough. >> Our high resolution quantitative T1-maps (derived from multispectral >> FLASH) have excellent GM-WM contrast and once autorecon1 (talairach-avi) >> gets over this tricky coregistration into standard space all other >> following steps look very fine (including the subcortical segmentation >> which I'm interested in). Since registration is often more robust when >> images are approximately realigned from the beginning, I thought to use >> SPM (or fsl) affine coregistration parameters (to MNI space) as a guess >> in talairach_avi would be worth a try (I think the problem lies in a >> somewhat different contrast of the neck and skull which appear brighter >> in our qT1 maps compared to MPRAGE). I could use SPM-coregistered T1 >> maps instead an put them into the freesurfer pipeline which, however, >> would mean an additional interpolation (which is not what I want). Is >> there another workaround? ( I read that in tkregister2 there is the >> option to apply fsl transformation matrices - something like that would >> be needed - but I'm no too familiar with the way freesurfer handels and >> stores those transformations). As my doctorate fellow sees himself >> manually segmenting all the subcortical structurs any help would be >> greatly appreciated -:) >> >> Thanks, >> >> Simon Baudrexel >> Brain Imaging Center >> Goethe University >> Frankfurt >> ________________________________ >> >> Von: Snyder, Avi [avi(a)npg.wustl.edu] >> Gesendet: Donnerstag, 12. Juli 2012 01:58 >> Bis: Baudrexel, Simon; Bruce Fischl >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Betreff: Re: AW: [Freesurfer] Using SPM transformation matrices as >> initial guess in talairach_avi >> >> Simon, >> >> The standard Talairach atlas transform module in FreeSurfer was designed >> for T1W high-resolution structural images (e.g., MP-RAGE or SPGR). This is >> a design choice partly driven by the fact that the FreeSurfer segmentation >> algorithm assumes high-resolution T1 weighting. Reliable atlas >> transformation with any other contrast mechanism would be highly >> uncertain. Atlas transformation modules theoretically could be produced >> for other contrast mechanisms, e.g., R1 or FA. However, it is not clear >> that, even if this were done, that the tissue classification part of >> FreeSurfer would work. If you have R1 and/or FA images that need to be >> analyzed using FreeSurfer segmentations, I would think that you should >> submit a minimally processed high-resolution T1W image to FreeSurfer and >> then use the generated results as ROIs in subsequent analyses. Of course, >> this strategy requires that the images containing the contrast to be >> evaluated are co-registered to the segmented MP-RAGE. >> >> I hope I have correctly understood your scientific objectives. >> >> Avi Snyder >> ------------ >> On 7/10/12 4:20 AM, "Baudrexel, Simon" <Simon.Baudrexel(a)kgu.de> wrote: >> >>> Hi Bruce, >>> >>> I'm using freesurfer version 5.1.0. I currently try to process >>> quantitative T1 (R1) maps derived from 4 and 18 deg. FLASH images and FA >>> maps. Interestingly, transformation appears to fail less often when using >>> single (16 deg.) FLASH images, only. SPM segmentation routine on the >>> other hand works pretty well on both T1 and FLASH images (probably >>> because of using header origin information - which was set to the >>> anterior commissure- as first guess in the registration). >>> >>> Thanks >>> Simon >>> ________________________________________ >>> Von: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >>> Gesendet: Montag, 9. Juli 2012 20:03 >>> Bis: Baudrexel, Simon >>> Cc: freesurfer(a)nmr.mgh.harvard.edu; Avi Snyder >>> Betreff: Re: [Freesurfer] Using SPM transformation matrices as initial >>> guess in talairach_avi >>> >>> Hi Simon >>> >>> what version are you using? Avi Snyder (ccd) has been tracking down some >>> interactions between his talairach code and our intensity normalization >>> that seem to have made it more fragilie, particularly in 5.1. He has some >>> suggested fixes that may improve things for you. >>> >>> cheers >>> Bruce >>> >>> On Mon, 9 Jul 2012, Baudrexel, Simon >>> wrote: >>> >>>> Hello, >>>> >>>> since I experienced a high rate of registration errors using >>>> talairach_avi >>>> in the conventional recon-all processing stream (more than 50% >>>> misregistration), I would like to incorporate SPM affine registration >>>> parameters (as provided in the seg_inv_sn.mat file obtained from the >>>> segmentation routine) as initial guess "to help" talairach-avi. Is >>>> there a >>>> possibility to do this? How do I have to adjust the transformation >>>> matrix >>>> that it can be handled by freesurfer? >>>> >>>> I also tried to circumvent the registration-problem using >>>> skull-stripped >>>> images, which unfortunately also did not improve the results (I think a >>>> template made from skull-stripped images has to be used in that case) >>>> >>>> Any help would be much appreciated >>>> >>>> Regards, >>>> Simon >> > > > >

2 1

Control Point Problem: CPs removing white matter from surface instead of adding it
by Peter McNally 12 Jul '12

12 Jul '12

Dear FreeSurfer, Hello, I am currently working on a project using FreeSurfer (version 5.1.0) at the Kable Labs at the University of Pennsylvania, and I have come across a problem when using control points to add incorporate more of the white matter into the white matter surface. After highlighting the parts of the white matter that have yet to be brought into the white matter surface with CPs, it will sometimes do what I intend it to but often will not. The strange part is that when it fails to incorporate more wm into the wm surfs it often actually removes a considerable amount the white matter both from the wm.mgz volume and from the white matter surface. Once it even did so on the opposite hemisphere as where I had put down control points. This problem seems to occur exclusively in the anterior end of the temporal lobe (everywhere else my use of control points has presented me with no problems), and it happens both when using control points sparingly and aggressively (I did a bit of experimenting, and the quantity of CPs that I used seemed to make no difference). Do you have any advice for how I might be able to get around this dilemma and/or why it likely is occurring? Thank you very much for your time. Best, Peter McNally

3 8

Hippocampus Doubt
by Gabriel Gonzalez Escamilla 12 Jul '12

12 Jul '12

2 1

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