Freesurfer September 2013

freesurfer@nmr.mgh.harvard.edu

124 participants
243 discussions

Interpretation of red/blue clusters in group analysis
by Anita van Loenhoud 12 Sep '13

12 Sep '13

Hi FreeSurfers, I'm doing an analysis with two groups: patients and controls. When I look at "Does the average thickness differ between 1 (patients) and 2 (controls)?", I can see blue (negative) and red (positive) correlations. I know that it means that in some cases, the patients have a higher cortical thickness compared to the controls, and in others it's the other way around. But which is which? Since most of the clusters are blue, I assume that blue means: patients have a lower cortical thickness compared to controls, and red means: patients have a higher cortical thickness compared to controls. Is this correct? How does FreeSurfer decide which group to use as the 'reference group' (i.e. the group to which the other group is compared)? Thanks, Anita

2 1

talairach transforms
by swathy p.s 12 Sep '13

12 Sep '13

after motiioncor was runned sucessfully,getting error with talairach.comand was as given bellow [root@ml freesurfer]# recon-all -talairach -subjid Stress_v12 Terminal window display was as shown bellow Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r--. 1 root root 346264 Sep 10 23:10 /usr/local/freesurfer/subjects/Stress_v12/scripts/recon-all.log Linux ml 3.3.4-5.fc17.i686 #1 SMP Mon May 7 17:45:26 UTC 2012 i686 i686 i386 GNU/Linux nu_correct: Command not found. #-------------------------------------------- #@# Talairach Tue Sep 10 23:11:50 EDT 2013 /usr/local/freesurfer/subjects/Stress_v12/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux ml 3.3.4-5.fc17.i686 #1 SMP Mon May 7 17:45:26 UTC 2012 i686 i686 i386 GNU/Linux recon-all -s Stress_v12 exited with ERRORS at Tue Sep 10 23:11:55 EDT 2013

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R: Re: mris_calc erroe in recon-all
by stdp82＠virgilio.it 12 Sep '13

12 Sep '13

Thanks. These are the output[iMac-di-Stefano:Con28/SUBJECTS_DIR/surf] Stefano% mris_calc lh.area stats Size [ 126850 ] Min@(index) [ -0.322716 (56402) ] Max@(index) [ 12.367171 (123284) ] Mean [ 0.587518 ] Std [ 0.402374 ] Sum [ 74526.703125 ] Prod [ 0.000000 ][iMac-di-Stefano:Con28/SUBJECTS_DIR/surf] Stefano% mris_calc lh.area.pial stats Size [ 126355 ] Min@(index) [ 0.000000 (97676) ] Max@(index) [ 22.833410 (119901) ] Mean [ 0.785660 ] Std [ 0.738523 ] Sum [ 99272.054688 ] Prod [ 0.000000 ] but I do not understand what's happen. Stefano ----Messaggio originale---- Da: rudolph(a)nmr.mgh.harvard.edu Data: 12-set-2013 14.49 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] mris_calc erroe in recon-all The error would indicate that the number of elements in 'lh.area' and 'lh.area.pial' are not the same. You can check this also with mris_calc: mris_calc lh.area stats mris_calc lh.area.pial stats which will provide some basic statistical output, including the size (i.e. number of elements) of each. The sizes have to match in order to add. HTH -=R On 9/12/13 02:56 , stdp82(a)virgilio.it wrote: > Hi list, > > I have a problem during recon-all > > #@# Surf Volume lh Thu Sep 12 08:25:31 CEST 2013 > /Applications/freesurfer/subjects/subject_prova/Con28/SUBJECTS_DIR/surf > \n mris_calc -o lh.area.mid lh.area add lh.area.pial \n > > mris_calc: > Sorry, but I seem to have encountered an error. > While checking on input filetype sizes, > I found a size mismatch, i.e. len(input1)!=len(input2) > > Darwin iMac-di-Stefano.local 12.4.0 Darwin Kernel Version 12.4.0: Wed > May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 > > recon-all -s SUBJECTS_DIR exited with ERRORS at Thu Sep 12 08:25:31 > CEST 2013 > > For more details, see the log file > /Applications/freesurfer/subjects/subject_prova/Con28/SUBJECTS_DIR/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > Thanks, > > > > Stefano > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA 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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Watershed and Normalization Problem
by Erica Tatham 12 Sep '13

12 Sep '13

Hello Freesurfer People, Below is the error that I have been receiving after running a recon-all. There seems to be a problem in the normalization stage. I checked the orig.mgz and the transform.xfm, and both seem to be reasonable. I was hoping for some guidance/expert advice for how to precede from here. I have not tried to add control points as I am fairly novice to freesurfer and not quite sure how to complete this task. Thank you for any advise you are able to give, Cheers, Erica Error: *************************WATERSHED************************** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all.

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dicom -> nifti, diffusion data gradient problems
by P Taylor 12 Sep '13

12 Sep '13

Hello, I have a question about using mri_convert on diffusion *.dcm files. When extracted, the gradient table is different than that given by either MRIConvert (from the UCLA-LCNI webpage) or than dcm2nii of MRICron; NB: the latter give the *same* results. The differences in gradient are also not simply sign changes, unfortunately (though, there is that issue as well, since many x- and y- gradients of mri_convert are close to the others, but the z-gradient appears to be uniformly oppositely signed). This is coupled with the fact that often both the orientation is different (noted in previous entries), as well as the ORIGIN information being different. Is there any comment about this? And any suggestions about what can be done to resolve these differences? Thanks.

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mris_calc erroe in recon-all
by stdp82＠virgilio.it 12 Sep '13

12 Sep '13

Hi list, I have a problem during recon-all #@# Surf Volume lh Thu Sep 12 08:25:31 CEST 2013/Applications/freesurfer/subjects/subject_prova/Con28/SUBJECTS_DIR/surf\n mris_calc -o lh.area.mid lh.area add lh.area.pial \n mris_calc: Sorry, but I seem to have encountered an error. While checking on input filetype sizes, I found a size mismatch, i.e. len(input1)!=len(input2) Darwin iMac-di-Stefano.local 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 recon-all -s SUBJECTS_DIR exited with ERRORS at Thu Sep 12 08:25:31 CEST 2013 For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Con28/SUBJECTS_DIR/scripts/recon-all.logTo report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thanks, Stefano

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updating the tables and volumes associated with aseg.mgz
by silver47＠gmx.com 12 Sep '13

12 Sep '13

Hi, I'm seeking some advice on updating the tables and volumes associated with aseg.mgz. I have completed the cortical analysis on a number of subjects and now would like to review and edit (if needed) aseg.mgz My strategy is to not cause any changes to the surfaces already completed and involves running: recon-all -subjid subject -surfsegedit to fix the aseg, using info from the surfaces. Followed by manual editing (if needed) of aseg.mgz, then recon-all -subjid subject -aparc2aseg -segstats -wmparc to update stats/aseg.stats, aparc+aseg.mgz, aparc.a2009s+aseg.mgz wmparc.mgz, and stats/wmparc.stats Does this look right? Are there any other considerartions? Thanks, P.

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reconall question
by Rashmi Singh 11 Sep '13

11 Sep '13

Hello FreeSurfer experts, I am doing volumetrics study. During the scan we get 2-3 mprage per scan for a subject. While running the FreeSurfer, if I want to use the three mprages for that subject as an input file, may I just keep the three mgz files (001.mgz, 002.mgz and 003.mgz) in the orig folder and run the simple recon all command :Recon-all –s (subject file name) -all or do I need to have some additional flags so that recon all command will use the three T1 images to get one output file? Thanks, Rashmi

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Re: [Freesurfer] Could not find .mat
by Bruce Fischl 11 Sep '13

11 Sep '13

no, you'll need to figure out which series to give an a file from, but it will figure out the other files in the same series. Also, please cc the list so that others can answer Bruce On Wed, 11 Sep 2013, Pedro Rosa wrote: > Hi, > Thanks for your help. > Is freesurfer able to select T1-w dicoms among dicoms from other acquisitions (dwi, t2w)? I ask this because I have dicoms from all acquisitions in a single folder, and I believe that the process of sorting them may be leading to these problems. > > Pedro Rosa > > On 11 Sep 2013, at 03:17 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > >> Hi Pedro >> >> you are *far* better off avoiding the analyze format. If you must convert, try nifti, but in general we prefer starting with the dicoms directly. If you give recon-all a *single* image file in the correct (T1-weighted) dicom series we will figure out the other ones >> >> cheers >> Bruce >> On Wed, 11 Sep 2013, Pedro Rosa wrote: >> >>> Hi, >>> I am finding a warning at recon-all when creating the folders: >>> INFO: could not find /Path/subject.mat file for direction cosine info. >>> INFO: use Analyze 7.5 hdr->hist.orient value: 1, coronal unflipped. >>> INFO: if not valid, please provide the information in /Path/subject.mat file >>> >>> What are the consequences of this to image orientation or to registration in further steps? >>> I have sorted the DICOMs using MRIcron (generates .img and .hdr for T1 acquisition). >>> Regards, >>> Pedro. >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> >> 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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Could not find .mat
by Pedro Rosa 11 Sep '13

11 Sep '13

Hi, I am finding a warning at recon-all when creating the folders: INFO: could not find /Path/subject.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 1, coronal unflipped. INFO: if not valid, please provide the information in /Path/subject.mat file What are the consequences of this to image orientation or to registration in further steps? I have sorted the DICOMs using MRIcron (generates .img and .hdr for T1 acquisition). Regards, Pedro.

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Freesurfer September 2013