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30132 discussions

R: Re: R: R: Re: Mask from cortical parcellation
by stdp82＠virgilio.it 04 Sep '13

04 Sep '13

I'd like to perform probtrackx (FSL) from seed (subcortical) to target (cortical) masks. To this aim, I should trasform all cortical and subcortical masks obtained by FS on MNI space. Therefore, firstly, I'd like to overlay the masks that I obtained by mri_binarize on the structural image to check the masks. Next, I'd like to apply FLIRT to trasform all masks in a common MNI152_1mm space. My problem is " which is the T1.nii.gz that can I use to overlay the cortical masks created by mri_binarize?" Thanks, Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 4-set-2013 23.28 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: R: Re: Mask from cortical parcellation I don't understand your question. Can you elaborate? On 09/04/2013 05:27 PM, stdp82(a)virgilio.it wrote: > I mean anatomical.nii.gz with the same spatial features of the masks. > > Thanks, > > > Stefano > > ----Messaggio originale---- > Da: stdp82(a)virgilio.it > Data: 4-set-2013 23.02 > A: <greve(a)nmr.mgh.harvard.edu>, <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: [Freesurfer] R: Re: Mask from cortical parcellation > > Thank you very much. > > A last help, please. How is the anatomical file that I can use to > overlay the masks. I'm noting that masks are characterized by: > data_type INT32 > dim1 256 > dim2 256 > dim3 256 > dim4 1 > datatype 8 > pixdim1 1.0000000000 > pixdim2 1.0000000000 > pixdim3 1.0000000000 > pixdim4 0.0109999999 > cal_max 0.0000 > cal_min 0.0000 > file_type NIFTI-1+ > > Regards, > > > Stefano > > ----Messaggio originale---- > Da: greve(a)nmr.mgh.harvard.edu > Data: 4-set-2013 17.10 > A: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] Mask from cortical parcellation > > > > you can use mri_binarize on aparc+aseg, eg, something like > > mri_binarize --i aparc+aseg.mgz --match 1003 1012 1014 1032 --o > frontal.nii.gz > > those numbers come from $FREESURFER_HOME/FreeSurferColorLUT.txt > That table has a lot of ROIs in it, and not all will be in the > aparc+aseg. You'll be interested in the ones between 1000-1035 and > 2000-2035 > > doug > > > > > On 09/04/2013 08:46 AM, stdp82(a)virgilio.it wrote: > > Hi list, > > > > I need to create a mask of frontal, parietal, temporal and occipital > > lobes in a subject by using cortical parcellation output. > > > > Is it possible? Eventually, how can I transform these masks file to > > mii.gz (to import them in FSL analysis). > > > > Thank you very much. > > > > Regards, > > > > > > Stefano > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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. > > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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R: R: Re: Mask from cortical parcellation
by stdp82＠virgilio.it 04 Sep '13

04 Sep '13

I mean anatomical.nii.gz with the same spatial features of the masks. Thanks, Stefano ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 4-set-2013 23.02 A: <greve(a)nmr.mgh.harvard.edu>, <freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: Mask from cortical parcellation Thank you very much. A last help, please. How is the anatomical file that I can use to overlay the masks. I'm noting that masks are characterized by:data_type INT32dim1 256dim2 256dim3 256dim4 1datatype 8pixdim1 1.0000000000pixdim2 1.0000000000pixdim3 1.0000000000pixdim4 0.0109999999cal_max 0.0000cal_min 0.0000file_type NIFTI-1+ Regards, Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 4-set-2013 17.10 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Mask from cortical parcellation you can use mri_binarize on aparc+aseg, eg, something like mri_binarize --i aparc+aseg.mgz --match 1003 1012 1014 1032 --o frontal.nii.gz those numbers come from $FREESURFER_HOME/FreeSurferColorLUT.txt That table has a lot of ROIs in it, and not all will be in the aparc+aseg. You'll be interested in the ones between 1000-1035 and 2000-2035 doug On 09/04/2013 08:46 AM, stdp82(a)virgilio.it wrote: > Hi list, > > I need to create a mask of frontal, parietal, temporal and occipital > lobes in a subject by using cortical parcellation output. > > Is it possible? Eventually, how can I transform these masks file to > mii.gz (to import them in FSL analysis). > > Thank you very much. > > Regards, > > > Stefano > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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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R: Re: Mask from cortical parcellation
by stdp82＠virgilio.it 04 Sep '13

04 Sep '13

Thank you very much. A last help, please. How is the anatomical file that I can use to overlay the masks. I'm noting that masks are characterized by:data_type INT32dim1 256dim2 256dim3 256dim4 1datatype 8pixdim1 1.0000000000pixdim2 1.0000000000pixdim3 1.0000000000pixdim4 0.0109999999cal_max 0.0000cal_min 0.0000file_type NIFTI-1+ Regards, Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 4-set-2013 17.10 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Mask from cortical parcellation you can use mri_binarize on aparc+aseg, eg, something like mri_binarize --i aparc+aseg.mgz --match 1003 1012 1014 1032 --o frontal.nii.gz those numbers come from $FREESURFER_HOME/FreeSurferColorLUT.txt That table has a lot of ROIs in it, and not all will be in the aparc+aseg. You'll be interested in the ones between 1000-1035 and 2000-2035 doug On 09/04/2013 08:46 AM, stdp82(a)virgilio.it wrote: > Hi list, > > I need to create a mask of frontal, parietal, temporal and occipital > lobes in a subject by using cortical parcellation output. > > Is it possible? Eventually, how can I transform these masks file to > mii.gz (to import them in FSL analysis). > > Thank you very much. > > Regards, > > > Stefano > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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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Tracula threshold path
by celine＠nmr.mgh.harvard.edu 04 Sep '13

04 Sep '13

Dear experts, I read some previous answers about the thresholding of the paths obtained after tracula process, but I am not completely sure I had the right answer. I will need to get an roi from a path for example the cortico-spinal tract that will be consistent amongst patients. I will further use this roi to calculate the lesion volume (my subjects are patients with MS) within a specific path. My question is: is the path.pd.nii.gz file already threshold or should I threshold it to a specific value? If I use the same threshold for each subject for example at 10% of the maximum value, will I obtain an ROI that is consistent among subjects or is is possible that I would get a very thin CST in some subjects, or a very wide cst for example? Thanks for your help Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129

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Improving the accuracy of average surfaces made from make_average_subject
by Miggy Chuapoco 04 Sep '13

04 Sep '13

Hi all, I'm trying to make a group average of a set of subjects that we've collected various functional data on and use anatomical landmarks of the group average surface to predict the locations of functional areas that we've found to be correlated to the anatomy of the ventral cortex. As such, we'd like to get as accurate of an average surface as possible. I've come up on two problems that I'd like to address and was wondering if anyone could help come up with a solution. I ran the recon-all command on all the subjects and created a segmentation, however we made edits to the segmentation using ITK-SNAP, and not tkmedit. Some of the changes were fairly drastic and we'd like to use the fixed segmentations in the averaging process. I've considered perhaps running the -autorecon2-wm flag, but unfortunately using ITK-SNAP essentially makes edits to ribbon.mgz, and not wm.mgz. I was wondering if there was a way to "extract" a new wm.mgz from an edited ribbon.mgz. My second problem involves trying to anchor a sulcus on the ventral surface during the averaging process (the mid-fusiform sulcus) in hopes of getting a more accurate representation of the sulcus on the average surface. As it stands there is a bit too much variability of the average MFS location when compared to the individual subjects' MFS location, and we'd like to reduce that if possible. Is there any way of using a label, or something similar, that can be considered as an "anchor" during the averaging process? Thanks and regards, Miggy Chuapoco

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Extracting LGI values
by Alan Francis 04 Sep '13

04 Sep '13

Hi Marie et al, I have run recon all on the data and calculated LGI for all the brains in my dataset. How does one go about extracting LGI values for each region (eg left Pars Triangularis). Is the Folding index given in the aparc stats sheet the same as LGI? thanks so much, Alan

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Recon checker - actual file order disagrees with common file order
by Sinead Kelly 04 Sep '13

04 Sep '13

Dear all, I have preprocessed my data using Freesurfer v5.2. I have checked the the recon-all.log for each subject to make sure that the process completed without error and that all the appropriate files were created. I have also visually inspected each image. However, when I run recon checker (from freesurfer QA tools) I receive the following error for all of my subjects: 'actual file order disagrees with common file order'. Is this a bug or do I need to re-run the preprocessing again from scratch? If I need to re-run, is there a way to ensure that this won't happen again? Kind regards, Sinead -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8

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Mask from cortical parcellation
by stdp82＠virgilio.it 04 Sep '13

04 Sep '13

Hi list, I need to create a mask of frontal, parietal, temporal and occipital lobes in a subject by using cortical parcellation output. Is it possible? Eventually, how can I transform these masks file to mii.gz (to import them in FSL analysis). Thank you very much. Regards, Stefano

3 2

questions regarding longitudinal processing
by Rongxiang Tang 04 Sep '13

04 Sep '13

Hi All, This may seem to be an easy question, I would just like to confirm... I have two groups that underwent different types of training and were measured at two time points (before and after training). My understanding is that I should use the longitudinal scheme in freesurfer to run recon-all? I have processed all data using normal recon-all command, and was wondering if I should rerun them all with the longitudinal command: recon-all -subjid <tpNid> -all Thanks in advance, Catherine

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nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280)
by Elena Molina 04 Sep '13

04 Sep '13

Hi Freesurfers, I am running recon-all -autorecon1 and I have an error like this: /libdisk/tmp_EMM/subj/mri /libdisk/freesurfer/bin/mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux neuron1 3.3.8-gcg-201303011431 #1 SMP Fri Mar 1 14:34:57 PST 2013 x86_64 x86_64 x86_64 GNU/Linux Wed Sep 4 14:45:46 UTC 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva(x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.28384 /libdisk/tmp_EMM/subj/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28384/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28384/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=10.02, TE=4.56, TI=600.00, flip angle=12.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.28384/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Sep 4 14:45:49 UTC 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.28384/nu0.mnc ./tmp.mri_nu_correct.mni.28384/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.28384/0/ -iterations 1000 -distance 50 [Elena@neuron1:/libdisk/tmp_EMM/subj/mri/] [2013-09-04 14:45:49] running: /libdisk/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.28384/0/ ./tmp.mri_nu_correct.mni.28384/nu0.mnc ./tmp.mri_nu_correct.mni.28384/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /libdisk/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done nu_estimate_np_and_em: crashed while running spline_smooth (termination status=11) nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) Does anyone have any idea how I can fix this? Thanks in advance Regards, Elena

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