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30135 discussions

QDEC error and analysis termination during 'concatenating volumes' and different results from Monte Carlo Simulation from QDEC & Command line
by Isotalus, Hanna 29 Jul '14

29 Jul '14

Dear Doug, Thanks for the quick response. I will try running the analyses on the command line. I've put the whole error message here if that is of any use and sheds any light to the problem? https://www.dropbox.com/s/1h1wzwidt3k1scu/ErrorMessage.txt Also, when I try to plot the stats tables using QDEC I get the following error: X Error of failed request: BadAlloc (insufficient resources for operation) I've a screenshot of this error here:https://www.dropbox.com/s/1jf9vd4bms0zv99/x%20error.pdf I get this when I try to plot stats tables for those subjects on whom the analysis works on QDEC. Could this be related to my initial problem? I haven't tried generating these stats tables on the command line yet. I also have an additional question. When I run the analysis on QDEC (for those subjects it works for) I get one cluster after correcting for multiple comparisons but when I correct for multiple comparisons using the same settings (?) on the command line I get three clusters. The settings I chose on QDEC were Monte Carlo Null Z at 1.3 (0.05) and with the abs setting. The first of these three clusters matches the one I get on QDEC. I used the following command: mri_glmfit-sim --glmdir directory --cache 1.3 abs --sim-sign abs Why am I getting different results? Thank you so much for your time and help. Best wishes, Hanna ------------------------------ Date: Mon, 28 Jul 2014 12:22:16 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] QDEC error and analysis termination during 'concatenating volumes' To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <53D678B8.7060904(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=UTF-8; format=flowed I can't make anything out of the error msg gif. Somewhere in there, there should be a mris_preproc command line. Can you try cutting and pasting that into a shell? Trying to do this in the context of qdec will be difficult doug On 07/25/2014 05:09 AM, Isotalus, Hanna wrote: > > Dear FreeSurfer gurus, > > > I am using QDEC to run my analyses on a large data set. The analysis > works fine with up to 1224 subjects but as soon as I add subject 1225 > I get an error and the analysis stops. The error displays during > 'concatenating volumes' and it just displays file names. When I try to > run the analysis on the remaining subjects (around 360 of them) the > analysis runs fine ? so I am inclined to think there's nothing wrong > with the data files. I've tried rotating the order of subjects and it > just doesn't seem to allow me to run the analysis on all of them. Do > you have any suggestions? > > > > Here's a link to a screenshot of the error I get: > > https://www.dropbox.com/s/08pqnmgep6crmr5/error%20message.gif > > I can't actually see all of the error message, here's it from the > beginning of what I can see and it continues like that ? displaying > all file names I think. > > > Thank you and best wishes, > > ? > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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apply transform matrix to coordinates
by Manuel Mercier 29 Jul '14

29 Jul '14

Dear Freesurfers I want to apply the transform matrix talairach.xfm, to a set of discrete points. (in order to get mni coordinate and use template brain). These are electrodes, with coordinates in the brain.mgz space. Here is what I did following the advices from the Coordinates systems page : get Norig and Torig using mri_info, then apply the transform: VOX_coor_tr = (tr_mat*Norig*inv(Torig)*VOX_coor)'; with tr_mat = [talairach.xfm;0 0 0 1]; and VOX_coor = [(n electrodes by 3 coordinates))' ; ones(1,length(VOX_coor))]; Looking at the result, it looks like something is wrong. Electrodes are few centimeters too lateral and anterior/frontal. I have been struggling with this problem for sometime and I am hoping that someone could help. Thanks, Manuel

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tkmedit doesn't show lines distinguishing grey and white matter
by Talia Raney 29 Jul '14

29 Jul '14

Hi, I'm having issues with tkmedit. I'm doing visual inspection and I checked tkregister to be sure that the white matter is outlined in the functional image. However, when I open tkmedit for surface and cortical segmentation, it doesn't show up the red and green lines that distinguish the boundaries of the grey and white matter. It had previously and I put a few control points but now it doesn't show up at all. Why might this be and how can it be fixed? Thanks! Talia

2 1

localGI - results interpretation
by elisa veronese 29 Jul '14

29 Jul '14

Dear FS users, can anybody help me in understanding the results of the localGI pipeline? After calling the recon-all -s *subj *-localGI recon-all -s *subj* -qcache -measure pial_lgi mri_segstats --annot *subj *lh aparc --i $SUBJECTS_DIR/*subj*/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats what I obtain is a text file with 10 columns, i.e. # TableCol 1 ColHeader Index # TableCol 2 ColHeader SegId # TableCol 3 ColHeader NVertices # TableCol 4 ColHeader Area_mm2 # TableCol 5 ColHeader StructName # TableCol 6 ColHeader Mean # TableCol 7 ColHeader StdDev # TableCol 8 ColHeader Min # TableCol 9 ColHeader Max # TableCol 10 ColHeader Range and 34 rows (i.e. 34 ROIs). What I cannot understand is the meaning of the last five columns (*intensity mean, stdev, min, max, range*). Is this "intensity" measure linked to the gyrification index? If yes, how? And, if no, how can I obtain the actual gyrification index? Thank you. Best, Elisa -- Elisa Veronese - PhD *Research Unit on Brain Imaging and Neuropsychology (RUBIN)* *Inter-University Center for Behavioral Neurosciences (ICBN)University of Udine and University of Verona, ItalyICBN Website: http://icbn.uniud.it/tiki-index.php <http://icbn.uniud.it/tiki-index.php>*

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Re: [Freesurfer] missing anterior temporal lobe
by Xiaomin Yue 29 Jul '14

29 Jul '14

Hi, I had successfully reconstructed a primate brain using fs5.3. But one part of left anterior temporal lobe was not correct, even with the accurate wm.mgz. See attached image for what I mean. Are there parameters to be used to correct this problem? Thanks,Xiaomin

1 0

newbie questions - mri_convert+
by Krieger, Donald N. 29 Jul '14

29 Jul '14

I have an MPRAGE dicom file sequences on which I wish to run recon-all . Here is the command I am using: mri_convert DICOM_DIRECTORY SubjectName/mri/orig/001.mgz It returns immediately with the error message: corRead(): can't open file DICOM_DIRECTORY/COR-.info Your suggestions would be welcome. Here are 2 other simple questions: (1) Where do I find the list of which labels correspond to which structures? (2) Are there labels for the white matter volumes or only for the gray matter volumes? If they exist, where are they? Regards, Don

2 1

Determining problems for subjects using recon-all.log
by Vy Dinh 28 Jul '14

28 Jul '14

Dear Freesurfer develops, I'm having issues running recon-all -all on 2 of our subjects using the raw t1.nii file. According to their recon-all log, both subjects' recon-all -all command errs when encountering the mris_sphere step. I'm not sure how to address this problem, considering we have no known issues with these subject's data for our other data processing (VBM, etc). Any help will be much appreciated. Please not that I've attached recon-all.logs for both subjects. Thank you. Best, -- Vy Dinh MD Candidate, Class of 2017 University of Wisconsin School of Medicine and Public Health

2 1

preserve manual edits?
by Jason Tourville 28 Jul '14

28 Jul '14

Hi there, We have performed manual volume edits on a number of scans. Recently, we ran those scans through recon-all with a new Tal volume target. The seg and surfaces are improved using the new target but most of the manual edits performed on the earlier version would improve the surfaces. Is there an established means for porting the manually edited voxel values to the volumes of the new re-con? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

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Cerebellum white matter mask {Disarmed}
by Alshikho, Mohamad J. 28 Jul '14

28 Jul '14

Hi Fs expers, What is the best way in Freesurfer to create a mask for the cerebellum white matter from the output of T1 segmentation? Thanks mohamad

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QDEC error and analysis termination during 'concatenating volumes'
by Isotalus, Hanna 28 Jul '14

28 Jul '14

Dear FreeSurfer gurus, I am using QDEC to run my analyses on a large data set. The analysis works fine with up to 1224 subjects but as soon as I add subject 1225 I get an error and the analysis stops. The error displays during 'concatenating volumes' and it just displays file names. When I try to run the analysis on the remaining subjects (around 360 of them) the analysis runs fine - so I am inclined to think there's nothing wrong with the data files. I've tried rotating the order of subjects and it just doesn't seem to allow me to run the analysis on all of them. Do you have any suggestions? Here's a link to a screenshot of the error I get: https://www.dropbox.com/s/08pqnmgep6crmr5/error%20message.gif I can't actually see all of the error message, here's it from the beginning of what I can see and it continues like that - displaying all file names I think. Thank you and best wishes, ?

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