Freesurfer July 2012

freesurfer@nmr.mgh.harvard.edu

128 participants
194 discussions

Re: [Freesurfer] Using SPM transformation matrices as initial guess in talairach_avi
by Baudrexel, Simon 12 Jul '12

12 Jul '12

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

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Using bet with Freesurfer
by Lugar, Heather 11 Jul '12

11 Jul '12

Hello, We're working with a pediatric data set and have found that Freesurfer's skullstripping process is inadequate for our purposes. We're interested in using FSL's bet, which we have found to do a better job of skullstripping, in combination with the other steps of Freesurfer. In a previous email, Bruce recommended that the best way to do this would be to replace the watershed step with bet. How would we go about doing that while still obtaining the brainmask.mgz necessary for the rest of the stream? We've unsuccessfully tried using bet at different points in the stream. When using bet prior to initiating the Freesurfer stream, we've found that the Talairach transform is irreparably bad (leading to a severely altered ICV). We have also encountered difficulties when using bet on the skullstripped brainmask.mgz. So, we think that replacing Freesurfer's skullstrip with bet is the option, but we are unsure about how to proceed. Thank you for your help, Heather

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Re: [Freesurfer] error message for recon-all
by Muriel Bruchhage 11 Jul '12

11 Jul '12

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 >>> >>> >>> >

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Re: [Freesurfer] Combining linear transformations
by Martin Reuter 11 Jul '12

11 Jul '12

Hi Usman , Try validating each step by applying each transform. I usually use mri_convert -at For it. Best MartinUsman Khan <usman(a)bwh.harvard.edu> wrote:Hi Martin, Thanks for the quick reply. I tried the following commands, but it looks like the volumes are still out of line. Is there something I am missing? to get from hc_subfield --> nu.mgz --> t1_cbv #register and create transforms 1) mri_vol2vol --mov hc_subfield.mgz --targ nu.mgz --reg-final xfm_hcsubfield_to_nu.dat --regheader 2) mri_robust_register --mov nu.mgz --dst t1_cbv.mgz --lta xfm_nu_to_t1.lta --satit #convert output from (1) from reg-final.dat to .lta 3) tkregister2 --noedit --mov hc_subfield.mgz --targ nu.mgz --reg xfm_hcsubfield_to_nu.dat --ltaout test.lta 4) mri_concatenate_lta test.lta xfm_nu_to_t1.lta final.lta #apply lta file, using t1_cbv as target and hc_subfield as --mov file 5) mri_vol2vol --mov subfield --targ t1_cbv.mgz --reg final.lta --out test.mgz On Tue, Jul 10, 2012 at 6:10 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: Hi Usman, you need to convert the reg to lta (using tkregister2) and then you can use mri_concatenate_lta . Cheers, Martin On Tue, 2012-07-10 at 17:36 -0400, Usman Khan wrote: > Hi FreeSurfer, > I have two images. One MPRAGE (1x1x1mm) and a T1-weighted > (0.682x0.682x3mm) image used for CBV mapping. We have run FS, with > hippocampal subfields on the MPRAGE and would now like to transform > the posterior probability maps to the T1-weighted CBV space. > > > I have been using > 1) mri_vol2vol with --regheader to map the posterior_* subfield files > to nu.mgz space > 2) mri_robust_register to coregister the nu.mgz file to the > T1-weighted CBV image > > > Is there any way to combine the .reg and .lta files from (1) and (2) > to transform the subfield posterior probability maps directly from > their 0.5mm^3 space to the T1-weighted CBV space? I have been > reluctant to create an intermediate volume between steps 1 and 2, as > resampling the subfield probability maps into 1x1x1mm nu.mgz space > will result in loss of resolution to the 0.68x0.68 (coronal) space in > the T1-weighted CBV scan. > > > Any help would be appreciated > > > Usman > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] error message for recon-all
by Muriel Bruchhage 11 Jul '12

11 Jul '12

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. >

2 3

slanted
by Borzello, Mia 11 Jul '12

11 Jul '12

Hi, I'm not exactly sure what the problem is, but for some reason, this brain is kind of sheered. I'm not sure if it's because of the CT, but on the right side of the picture i attached, it kind of wider on one side. It's alignment isn't right, and using "rotate" does help. How should I correct this? Thanks, Mia

4 11

error message for recon-all
by Muriel Bruchhage 11 Jul '12

11 Jul '12

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/ and with $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

2 1

cortical thickness and ICA of resting state fMRI
by Mojdeh Zamyadi 11 Jul '12

11 Jul '12

Hi all, I was wondering if anyone knows about any articles that compare/relate cortical thickness analysis with resting state ICA results? More specifically, I'm looking for articles that study cortical thickness changes in different regions of brain and its possible relation to group clusters found using ICA analysis of resting state fMRI. Thanks, Mojdeh Zamyadi, MSc Clinical Research Project Assistant The Hospital for Sick Children 555 University Avenue Toronto ON M5G 1X8

1 0

annot 2 surf
by Arnaud Messé 11 Jul '12

11 Jul '12

Dear all, There is a way to convert annot file into surface? -- Arnaud Messé, PhD Laboratoire d'imagerie fonctionnelle (LIF) UMRS 678 Inserm/UPMC CHU Pitié-Salpêtrière 91 boulevard de l'Hôpital F-75634 Paris Cedex 13 +33(0)1538284 03 (fax: 48) Arnaud.Messe(a)imed.jussieu.fr http://www.imed.jussieu.fr

2 1

Fwd: pars triangular and BA44 segmentation bug?
by Gabor Perlaki 11 Jul '12

11 Jul '12

Dear Bruce, Did you also identified a strong rightward asymmetry (with pars triangular and BA44) in your data analyzed by freesurfer 5.1? Just, to be sure, that this is not an issue only with our data. I'd like to use the TRACULA as well, and because tracula uses the cortical parcellation of our subjects I'm not sure that it is worth to start TRACULA now, or waiting for your cortical parcellation fix. Sorry for disturbing you again with the same issue, but it is very important for us to know, that it is a real issue with the cortical parcellation or we messed up something, and if it is a real issue, which labels we shouldn't use for statistical analysis. Thank you in advance for your answer, Gabor 2012/6/25 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > sure. Thanks for pointing out the BA44 issue. We'll put together a fix in > the next couple of weeks > Bruce > > On Mon, 25 Jun 2012, Gabor Perlaki wrote: > > Dear Bruce, >> >> I've checked the pars triangularis. It was right-lateralized in 79 >> subjects >> and left-lateralized in only 19 subjects. >> >> Thanks, Gabor >> >> 2012/6/23 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> the structures don't need a threshold. Do you know that pars >> triangularis is left lateralized? For the BAs will get you a >> solution >> >> On Sat, 23 Jun 2012, Gabor Perlaki wrote: >> >> Dear Bruce, >> >> We don't used any thresholding by ourselves, we just >> took BA44 volumes out >> of the text-file in the stats directory. >> Should we use thresholded values instead of the >> volumes reported by the text >> files in the stats directory? >> Could we use the volumes reported by the aparc.stats >> and aseg.stats files >> for any statistical analyses, or do we need >> threshold that structures as >> well? >> >> >> Thanks, >> Gabor >> >> 2012/6/23 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi Gabor >> >> are you thresholding the BA4 label? In 5.2 we >> will distribute >> some tools to automatically threshold the >> labels so that the >> predicted area has the average area of the >> input labels. The >> right BA44 had more spatial spread than the >> left, so you might >> be including a lot of low probability vertices. >> >> cheers >> Bruce >> >> On Sat, 23 Jun 2012, Gabor Perlaki wrote: >> >> Dear Bruce, >> >> In the paper "Left-right asymmetry in >> volume and >> number of neurons in adult >> Broca's area." by Katrin Amunts, 10 >> subjects (5 men >> and 5 women) were >> studied, and the volume of BA44 was >> greater in the >> left hemisphere than in >> the right in all ten cases. So, it is >> very strange >> that the volume of BA44 >> was greater in the right hemisphere in >> all of the 80 >> subjects analyzed by >> Eniko. >> >> Thanks, >> Gabor >> >> >> >> >> 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. >> >> >> >> >> >> >>

2 1

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Freesurfer July 2012